1.6.5 release: Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.

* H5MultiBlock: added halo exchange routine: still needs debugging

.gitattributes

@@ -1,175 +1,93 @@
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+/COPYING -text
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.gitignore

@@ -0,0 +1,13 @@
+/Makefile.in
+/aclocal.m4
+/autom4te.cache
+/build
+/config.h.in
+/configure
+doc/Makefile.in
+/ltmain.sh
+/m4
+src/H5PartF.h
+src/Makefile.in
+test/Makefile.in
+tools/Makefile.in

AUTHORS

@@ -6,5 +6,6 @@ Benedikt Oswald (PSI)
 Wes Bethel (NERSC/LBNL)
 John Shalf (NERSC/LBNL)
 Cristina Siegerist (NERSC/LBNL)
+Mark Howison (NERSC/LBNL)
 
 Please use h5part@lists.psi.ch for communicaion.

COPYING

@@ -0,0 +1,71 @@
+*** Copyright Notice ***
+
+H5Part  Copyright (c) 2006-2009, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory (subject to receipt of any
+required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
+Institut (Switzerland).  All rights reserved.
+
+If you have questions about your rights to use or distribute this
+software, please contact Berkeley Lab's Technology Transfer Department
+at  TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
+
+NOTICE.  This software was developed under partial funding from the U.S.
+Department of Energy.  As such, the U.S. Government has been granted for
+itself and others acting on its behalf a paid-up, nonexclusive,
+irrevocable, worldwide license in the Software to reproduce, prepare
+derivative works, and perform publicly and display publicly.  Beginning
+five (5) years after the date permission to assert copyright is obtained
+from the U.S. Department of Energy, and subject to any subsequent five
+(5) year renewals, the U.S. Government is granted for itself and others
+acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide
+license in the Software to reproduce, prepare derivative works,
+distribute copies to the public, perform publicly and display publicly,
+and to permit others to do so.
+
+
+*** License agreement ***
+
+H5Part  Copyright (c) 2006-2009, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory (subject to receipt of any
+required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
+Institut (Switzerland).  All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+(1) Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence Berkeley
+National Laboratory, U.S. Dept. of Energy, Paul Scherrer Institut
+(Switzerland) nor the names of its contributors may be used to endorse
+or promote products derived from this software without specific prior
+written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes,
+patches, or upgrades to the features, functionality or performance of
+the source code ("Enhancements") to anyone; however, if you choose to
+make your Enhancements available either publicly, or directly to
+Lawrence Berkeley National Laboratory, without imposing a separate
+written license agreement for such Enhancements, then you hereby grant
+the following license: a  non-exclusive, royalty-free perpetual license
+to install, use, modify, prepare derivative works, incorporate into
+other computer software, distribute, and sublicense such enhancements or
+derivative works thereof, in binary and source code form.
+

COPYRIGHT

@@ -1,7 +0,0 @@
-*** Copyright Notice ***
-
-H5Part  Copyright (c) 2006, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and the Paul Scherrer Institut (Switzerland).  All rights reserved.
-
-If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at  TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
-
-NOTICE.  This software was developed under partial funding from the U.S. Department of Energy.  As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly.  Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

INSTALL

@@ -0,0 +1,437 @@
+==============================================================================
+README file for H5Part configure
+==============================================================================
+
++ 0. HDF5 library
+-----------------
+
+Make sure you have a working version of the HDF5 library installed. If you plan
+to use parallel I/O you need to use a parallel HDF5 version. Source files and
+installation instructions are available from the HDF5 website:
+
+http://www.hdfgroup.org/HDF5/
+
+
++ 1. Quick start (If you feel lucky...)
+----------------------------------------
+
+For many platforms, where compilers are installed in the "default" location
+and all the environment variables are set correctly, it should be sufficient 
+to type: 
+
+./configure [OPTIONS] && make [install]
+
+to have the libraries and test program compiled.
+
+
++ 2. Configure line options
+----------------------------
+
+To view a full list of configure option, use:
+
+./configure --help
+
+(1) Enable options
+--enable-fortran
+--enable-parallel
+--enable-tools
+--enable-python
+--enable-64 (only for AIX and Irix)
+
+(2) Setting compilers related variables manually
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE before running configure. For example, if you are using the bash
+shell, you might type:
+
+export CC=gcc
+
+to set the default C compiler. See below for descriptions of some useful
+variables.
+
+Compiler environment variables:
+  CC          C compiler command
+  CXX         C++ compiler command
+  FC          Fortran compiler command
+  MPICC       MPI-enabled C compiler command
+  MPICXX      MPI-enabled C++ compiler command
+  MPIFC       MPI-enabled Fortran compiler command
+  CFLAGS      flags to append when invoking the C compiler
+
+Library environment variables:
+  LDFLAGS     flags to append when invoking the linker
+
+(3) Setting prefix for installation manually (by default, the package will
+install itself in the 'build' subdirectory of your source directory)
+--prefix=PREFIX         install files in PREFIX
+
+
++ 3. Platform specific settings for compiling libraries & test programs
+------------------------------------------------------------------------
+
+Building
+        make  : builds the libraries and test programs
+	make install: builds and installs
+        make clean : removes extraneous object files
+        make distclean : returns configuration to unconfigured state
+
+As tested on hosts:
+
+(0) Franklin <franklin.nersc.gov> (CNL - Cray XT4)
+--------------------------------------------------
+
+module add hdf5_par
+module add zlib
+module add szip
+export CC=cc CXX=CC FC=ftn MPICC=cc MPICXX=CC MPIFC=ftn 
+export LDFLAGS=$HDF5
+./configure --enable-fortran --enable-parallel --with-hdf5path=$HDF5_PAR_DIR --with-mpiposix
+make install
+
+
+(1) Davinci <davinci.nersc.gov> (Linux"SUSE"-ia64)
+---------------------------------------------------
+FIRST THING FIRST!! Type:
+
+module load intel
+to have the proper compilers set up for use.
+
+module load hdf5_par
+
+[NOTE: module load hdf5 does not work at this moment. 
+Possible installation error of HDF5 on Davinci.]
+
+
+Brief profile:
+CC = icc
+CXX = icc
+FC = ifort
+MPICC = icc
+MPICXX = icc
+MPIFC = ifort
+
+If default doesn't work, try:
+
+For C shell: 
+env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
+
+For Korn or Bourne shell:
+CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
+
+And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
+
+
+On this host, executing:
+
+For C shell: 
+env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
+
+For Korn or Bourne shell:
+CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
+
+has functioned correctly.
+
+
+To run test program, go to test directory:
+
+(i) Serial test
+run:
+./H5testF
+./H5PartTest
+
+(ii) Parallel test
+run:
+mpirun 2 H5testFpar
+mpirun 2 H5PartTestP
+
+NOTE: Number 2 above is a arbitrary number that indicates the number of processes.
+
+
+
+
+
+(2) Jacquard <jacquard.nersc.gov> (Linux"SUSE"-x86_64)
+-------------------------------------------------------
+Brief profile:
+CC = pathcc
+CXX = pathCC
+FC = pathf90
+MPICC = mpicc
+MPICXX = mpicxx
+MPIFC = mpif90
+
+
+
+If default doesn't work, try:
+
+For C shell: 
+env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
+
+For Korn or Bourne shell:
+CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
+
+And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
+
+
+
+On this host, executing:
+
+For C shell: 
+env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
+
+For Korn or Bourne shell:
+CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
+
+has functioned correctly.
+
+
+
+To run test program, go to test directory:
+
+(i) Serial test
+run:
+./H5testF
+./H5PartTest
+
+(ii) Parallel test
+In Jacquard, we need a script to run parallel programs, since Jacquard does not support interactive parallel processing. Instead, we need to submit the task to a queue. A sample script (run_H5testFpar.scr) may look like below:
+
++++++++++++++++++++++++++++++++++++++++
+#!/bin/csh
+#PBS -l nodes=1:ppn=2,walltime=00:05:00
+#PBS -N  H5testFpar
+#PBS -o H5testFpar.out
+#PBS -e H5testFpar.err
+#PBS -q debug
+#PBS -A mpccc
+#PBS -V
+
+setenv PBS_OWORKDIR /home/H5Part/test
+
+cd $PBS_O_WORKDIR
+mpirun -np 2 ./H5testFpar
++++++++++++++++++++++++++++++++++++++++
+
+Then, we need to submit the task to a queue by running:
+
+qsub run_H5testFpar.scr
+
+After processed, the result will appear in H5testFpar.out, and error messages will appear in H5testFpar.err.
+
+
+
+
+
+(3) Bassi <bassi.nersc.ogv> (AIX5.3.0.0-Power 3)
+-------------------------------------------------
+FIRST THING FIRST!! Type:
+
+module load gcc
+
+to have the proper compilers set up for use.
+
+Brief profile:
+CC = cc_r
+CXX = cc_r
+FC = xlf_r
+MPICC = mpcc_r
+MPICXX = mpcc_r
+MPIFC = mpxlf_r
+
+
+
+If default doesn't work, try:
+
+For C shell: 
+env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
+
+For Korn or Bourne shell:
+CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
+
+And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
+
+
+
+On this host, executing:
+
+For C shell: 
+env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
+
+For Korn or Bourne shell:
+CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
+
+has functioned correctly.
+
+
+
+To run test program, go to test directory:
+
+(i) Serial test
+run:
+./H5testF
+./H5PartTest
+
+(ii) Parallel test
+run:
+unsetenv MP_SINGLE_THREAD
+poe ./H5PartTestP -procs 2 -nodes 1
+poe ./H5testFpar -procs 2 -nodes 1
+
+For more details on how to run parallel programs on Bassi, go to:
+
+http://www.nersc.gov/nusers/resources/bassi/running_jobs/
+
+
+
+
+
+(4) Starsky <starsky.lbl.gov> (Darwin8.5.0-PowerPC)
+----------------------------------------------------
+FIRST THING FIRST!! Set environment variables: (in tcsh)
+
+setenv LD_LIBRARY_PATH /usr/local/g95/lib/gcc-lib/powerpc-apple-darwin8.5.0/4.0.3/
+setenv PATH ${PATH}:/usr/local/g95/bin
+
+NOTE: This environment variable setting is specifit to Starsky. It is to make configure find the fortran compiler.
+
+Brief profile:
+CC = gcc
+CXX = g++
+FC = g95
+
+
+
+If default doesn't work, try:
+
+For C shell: 
+env CC=gcc CXX=g++ FC=g95 ./configure && make install
+
+For Korn or Bourne shell:
+CC=gcc CXX=g++ FC=g95 ./configure && make install
+
+And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
+
+
+
+On this host, executing:
+
+For C shell: 
+env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
+
+For Korn or Bourne shell:
+CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
+
+has functioned correctly.
+
+
+
+To run test program, go to test directory:
+
+(i) Serial test
+run:
+./H5testF
+./H5PartTest
+
+
+
+
+
+(5) Linux AMD64 Visualization group workstations (Linux"SUSE"-x86_64)
+---------------------------------------------------------
+Brief profile:
+CC = gcc
+CXX = g++
+FC = g95
+
+
+
+If default doesn't work, try:
+
+For C shell: 
+env CC=gcc CXX=g++ FC=g95 ./configure && make install
+
+For Korn or Bourne shell:
+CC=gcc CXX=g++ FC=g95 ./configure && make install
+
+And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
+
+
+
+On this host, executing:
+
+For C shell: 
+env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
+
+For Korn or Bourne shell:
+CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
+
+has functioned correctly.
+
+
+
+To run test program, go to test directory:
+
+(i) Serial test
+run:
+./H5testF
+./H5PartTest
+
+
+(6) Cray XT3 @ CSCS gele
+
+  1) modules/3.1.6         9) PrgEnv-pgi/1.4.26    17) xt-lustre-ss/1.4.26
+  2) MySQL/4.0.26         10) xt-pbs/5.3.4         18) Base-opts/1.4.26
+  3) acml/3.0             11) xt-service/1.4.26    19) subversion/1.3.2
+  4) pgi/6.1.4            12) xt-libc/1.4.26       20) zlib/1.2.3
+  5) totalview/7.2.0      13) xt-os/1.4.26         21) szip/2.0
+  6) xt-libsci/1.4.26     14) xt-catamount/1.4.26  22) hdf5/1.6.5
+  7) xt-mpt/1.4.26        15) xt-boot/1.4.26
+  8) xt-pe/1.4.26         16) xt-crms/1.4.26
+
+
+CFLAGS="-I$H5HOME/include -DF77_SINGLE_UNDERSCORE" LDFLAGS="-L$H5HOME/lib -L$ZHOME/lib" ./configure --enable-parallel --enable-fortran
+
+
+(7) merlin00 / merlin3 
+
+Currently Loaded Modulefiles:
+  1) hdf5/hdf5-1.6.5            2) root/root-5.10.00          3) mpi/mpich2-1.0.3-pgi-6.1   4) pgi/pgi_64-6.1
+
+FC=mpif90 ./configure --enable-parallel --enable-fortran
+
+
+
+
+==============================================================================
+
+
++ 4. Trouble shooting (Things to check for...)
+--------------------------------------------
+(0) Have you set the LD_LIBRARY_PATH?
+---Some systems require the user to manually set the environment variable, LD_LIBRARY_PATH. To do so:
+
+set the environment variable HDF5ROOT or PHDF5ROOT to point to your installation of HDF5 (serial and/or parallel respectively).
+
+For Korn or Bourne shell:
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HDF5ROOT}/lib;export LD_LIBRARY_PATH
+	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:{PHDF5ROOT}/lib;export LD_LIBRARY_PATH
+
+For C shell:
+	setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5ROOT}/lib
+	setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${PHDF5ROOT}/lib
+
+Note that the values of HDF5ROOT & PHDF5ROOT will be in the "summary" section when you run configure.
+
+Not properly set LD_LIBRARY_PATH value may result in a runtime error:
+
+./H5PartTest: error while loading shared libraries: libhdf5.so.0: cannot open shared object file: No such file or directory
+
+(1) Are the compilers set correctly? 
+---Check with: which COMPILER
+
+(2) Have you installed HDF5?
+---You can get it at: http://vis.lbl.gov/Research/AcceleratorSAPP/index.html
+
+(3) Have you loaded the proper modules? 
+---It is necessary in Davinci & Bassi, and configure && make install may not work without it.
+
+

Makefile.am

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-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:

NEWS

@@ -0,0 +1,358 @@
+#### H5PART 1.6.5 ############################################################
+
+Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
+
+#### H5PART 1.6.4 ############################################################
+
+Fixed bug where H5PartSetViewIndices was not setting an empty view when the
+number of elements is 0.
+
+Set a threshold on the HDF5 alignment parameter so that small metadata writes
+are not aligned, which causes large gaps in the file.
+
+#### H5PART 1.6.3 ############################################################
+
+New build system uses libtool and can build shared libraries.
+
+Fixed a bug that incorrectly identifies the number of selected points in a view
+when using H5PartSetViewIndices.
+
+Fixed bug in Fortran test reported by several people, as well as several
+incorrect views set in the C test that were causing segfaults.
+
+Fixed name mismatches in the Fortran interface, and an off-by-one indexing
+problem.
+
+#### H5PART 1.6.2 ############################################################
+
+Removed H5PartSetViewEmpty
+--------------------------
+
+An empty view can now be selected with:
+H5PartSetNumParticles(file, 0);
+
+Bug Fixes to Attribute Calls in Fortran API
+-------------------------------------------
+
+Fixed a problem where attribute values were reverting to zero.
+
+#### H5PART 1.6.1 ############################################################
+
+Chunking in the H5Part API
+--------------------------
+
+There is now an H5Part equivalent H5PartSetChunkSize to the existing
+H5BlockDefine3DChunkDims call. Both of these calls enable the chunking
+mechanism in the underlying HDF5 layer. Chunking is used in combination
+with the aligned open calls to pad datasets to alignment multiples
+on disk.
+
+All Steps Available on Write
+----------------------------
+
+Previously, existing steps in a file were only accessible in read-only mode.
+Now, all steps are available in all modes, including write-truncate and
+write-append. Thus, it is now possible to overwrite existing data in write
+mode. To help alert the user to this possibility, a warning is issued every
+time an existing dataset is written to. Warnings can be printed by setting
+the verbosity to H5PART_VERB_WARN or higher.
+
+New Throttling Routine
+----------------------
+
+Previously, a throttle factor of N meant that for P processors, the total
+number of P writes were divided into N batches of P/N writes.
+
+To better accommodate round-robin lustre striping, the new policy is to
+execute P/N batches of N writes. Thus, matching N to the number of stripes
+results in the desirable 1-1 matching of writers to stripes.
+
+Other Fixes
+-----------
+
+* The configure script should correctly detect PGI compilers now.
+* There was a small memory leak in the Fortran file open calls.
+* There was a compile error with HDF5 1.6.x due to a missing assignment.
+
+#### H5PART 1.6 ##############################################################
+
+Updated Documentation
+---------------------
+
+The Fortran API has been added to the doxygen documentation. Most entries have
+a reference to their respective C API call.
+
+Regression Test Suite
+---------------------
+
+The test subdirectory has been reorganized to include a systematic series
+of regression tests of common use cases for the API. The goal is to have both
+complete coverage of the API (every call is exercised) and testing of some
+unlikely or unsuspected values and cases.
+
+Currently, the C test covers the entire H5Part API and the Fortran test is
+still in development.
+
+Benchmark Utilities
+-------------------
+
+Two benchmarking utilities, H5PartBench and H5BlockBench, have been added to
+the tools collection. Both require the parallel library and have functionality
+and syntax similar to the IOR benchmark:
+
+  http://sourceforge.net/projects/ior-sio/
+
+File Mode Flags
+---------------
+
+Previously, the only flags used were H5PART_READ, H5PART_WRITE, and
+H5PART_APPEND, and these were mutually exclusive. Additional flags have been
+added to select the underlying virtual file driver (VFD) that HDF5 uses in
+parallel mode and to accommodate the lustre filesystem:
+
+H5PART_VFD_MPIPOSIX (use the MPI-POSIX driver, which bypasses MPI-IO)
+H5PART_VFD_MPIIO_IND (use MPI-IO in independent mode)
+H5PART_FS_LUSTRE (activate H5P tunings for the lustre stripe size)
+
+These flags can be specified using the typical bitwise OR method, e.g.
+
+  char flag = H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE;
+
+will select write mode with these two additional options.
+
+The parallel library now defaults to using the MPI-IO collective mode driver
+(previously it used independent mode). The collective buffering algorithm in
+the Cray XT4/5 environment has been substantially improved in the last year,
+and defaulting to collective mode allows us to take advantage of these
+improvements automatically.
+
+There are also new open calls H5PartOpenAlign and H5PartOpenParallelAlign that
+take an additional 'alignment' value. This value is passed to HDF5 and used to
+pad out objects so that they align to filesystem boundaries. For instance, it
+would make sense to use the stripe size as the alignment value when writing to
+a lustre filesystem.
+
+Unified 'View' Model
+--------------------
+
+Views are now supported in both read and write mode (previously only supported
+in read mode). It is possible to specify non-sensical views: you could for
+instance specify a read view that is larger than the dataset on disk. Or you
+could create a write view that is larger than the data in memory. In those
+cases, you will encounter an error when you try to perform a read or write
+operation on a dataset.
+
+There are two new methods for selecting views. H5PartSetNumParticlesStrided
+selects a view with $n$ particles per processor, but such that the data in
+memory is expected to have a 'stride' factor. For instance, if you have
+particle data with fields $x$ and $y$ and a single array with entries
+$x1,y1,x2,y2...$, then the stride factor is 2. Striding works for both reads
+and writes and only affects the view of memory: individual fields are still
+stored as individual arrays on disk.
+
+The second new method is H5PartSetViewIndices, which allows for point
+selections of datasets. You can pass a list of indices for the points you
+want to select. This is useful, for instance, when interfacing with FastBit
+to perform queries that select a small subset of non-contiguous particles.
+
+Because views are now supported on write, it is possible to write a dataset
+using multiple 'passes' or to leave some values unwritten.
+
+Also, all views are now *inclusive*, so that a view of (0,9) corresponds
+to the 10 items 0, 1, 2, ... 9.
+
+Internal Handling of Dataspaces
+-------------------------------
+
+H5PartSetNumParticles and H5PartSetNumParticlesStrided now share the same
+HDF5 dataspace state in the H5PartFile struct with the calls that modify
+the view (H5PartSetView etc.). Previously, the memory and disk dataspaces
+were regenerated from the view on every read access, which was unnecessary.
+
+Autogeneration of API Calls
+---------------------------
+
+Python scripts have been added to automatically generate read/write call
+variants for different data types.
+
+Renamed Fortran Include
+-----------------------
+
+The automake system no longer greps the *F90.inc files to generate an include
+called 'H5Part.inc'. Instead, the *F90.inc files have been renamed to *.f90,
+and awk is used to generate an 'H5PartF.h' file (the same naming convention
+as in MPI's 'mpif.h').
+
+The change to *.f90 was necessary to facilitate integration of the Fortran
+API into doxygen. Note that the *.f90 files will not compile, nor can they
+be included directly. Simply use
+
+  include 'H5PartF.h'
+
+in your Fortran code to include all the definitions for Fortran H5Part/H5Block
+calls.
+
+64 Char Limit on Dataset Names
+------------------------------
+
+Previously, a user could overrun internal buffers for dataset names. Now, a
+fixed limit of 64 chars is imposed. Dataset names that are longer than this are
+truncated and a warning is printed. We expect that most users are using
+short canonical names like x, px, id, etc.
+
+Changes to Existing API
+-----------------------
+
+The H5BlockGetFieldInfo and H5BlockGetFieldInfoByName calls now both include
+a parameter for the 'type' of the field.
+
+
+#### H5PART 1.4 ##############################################################
+
+Error Handling
+--------------
+ Now all functions, in which an error could occure, are returning a
+value. This value is either a 64bit integer or a pointer.
+
+ A negative 64bit integer as result indicates an error. Values >= 0
+indicates successfull execution.   This is similiar to the convention
+used in UNIX system calls, but we do not return -1 but the error
+number (which is always negative).
+
+ For functions returning a pointer the NULL-pointer is used to indicate
+an error. You can call the function H5PartGetErrno() to get the error
+number.  For the time being there is no strerror(3) or perror(3)
+equivalent. 
+
+
+API Changes
+-----------
+ There are several changes in the API of H5Part. The biggest change is
+a side-effect of the implementation of strict error handling.  The
+impact to the existing C/C++ code is very small.  But now you *can*
+and *should* implement some kind of error handling.  The simplest
+error handling is to set an error handler which aborts the program as
+soon as an error occured.
+
+ The next "biggest" change is the use of H5Part types instead of "long
+long" and "double". The replacement of "long long" is "h5part_int64_t"
+and for "double" "h5part_float64_t". This change has now effect in
+Fortran.  
+
+ In some functions the argument type changed from "int" to
+"h5part_int64_t". Since on most systems "int" is a 32bit integer,
+calls to these functions must be adapted to the new API. In C/C++ the
+compiler will complain about it. But in Fortran you will *not* get an
+error message.So, you must check your Fortran code carefully.
+
+ Changes in detail (not listed are functions where only the return
+type changed from any to "h5part_int64_t"):
+
+	New API					Changes to old API
+
+	h5part_int64_t				void
+	H5PartSetNumParticles (
+		H5PartFile *f,
+		h5part_int64_t nparticles	long long
+		);
+
+	h5part_int64_t				int
+	H5PartWriteDataFloat64 (
+		H5PartFile *f,
+		char *name, 
+		h5part_float64_t *dta		double
+		);
+
+	h5part_int64_t				int
+	H5PartWriteDataInt64 (
+		H5PartFile *f,
+		char *name,
+		h5part_int64_t *dta		long long
+		);
+
+	h5part_int64_t				void
+	H5PartSetStep (
+		H5PartFile *f,
+		h5part_int64_t step		int
+		);
+
+	h5part_int64_t				void
+	H5PartSetView (
+		H5PartFile *f,
+		h5part_int64_t start,		long long
+		h5part_int64_t end		long long
+		);
+
+	h5part_int64_t				int
+	H5PartGetView (
+		H5PartFile *f,
+		h5part_int64_t *start,		long long
+		h5part_int64_t *end		long long
+		);
+
+	h5part_int64_t				int
+	H5PartReadDataFloat64 (
+		H5PartFile *f,
+		char *name,
+		h5part_float64_t *dta		double
+		);
+
+	h5part_int64_t				int
+	H5PartReadDataInt64 (
+		H5PartFile *f,
+		char *name,
+		h5part_int64_t *dta		long long
+		);
+    
+	h5part_int64_t				void
+	H5PartReadParticleStep (		
+		H5PartFile *f,
+		h5part_int64_t step,		int
+		h5part_float64_t *x,		double
+		h5part_float64_t *y,		double
+		h5part_float64_t *z,		double
+		h5part_float64_t *px,		double
+		h5part_float64_t *py,		double
+		h5part_float64_t *pz,		double
+		h5part_int64_t *id		long long
+		);
+
+New functions:
+
+	h5part_int64_t
+	H5PartSetVerbosityLevel (
+		unsigned int
+		);
+
+	h5part_int64_t
+	H5PartSetErrorHandler ( 
+		h5part_error_handler handler
+		);
+
+	h5part_int64_t
+	H5PartGetErrno (
+		void
+		);
+
+	h5part_int64_t
+	H5PartDefaultErrorHandler (
+		const char *funcname,
+		const h5part_int64_t eno,
+		const char *fmt,
+		...
+		);
+
+	h5part_int64_t
+	H5PartAbortErrorHandler (
+		const char *funcname,
+		const h5part_int64_t eno,
+		const char *fmt,
+		...
+		);
+
+Removed functions:
+
+	int
+	H5PartFileIsValid (
+		H5PartFile *f
+		);

README

@@ -1,393 +1,29 @@
-==============================================================================
-README file for H5Part configure
-==============================================================================
-
-+ 0. HDF5 library
------------------
-
-Make sure you have a working version of the HDF5 library in your computer. If you plan
-to use parallel I/O you need to use a parallel HDF5 version. If you don't have the
-library download the sources from http://hdf.ncsa.uiuc.edu/HDF5/
-
-+ 1. Quick start (If you feel lucky...)
-----------------------------------------
-
-For many platforms, where compilers are installed in the "default" location
-and all the environment variables are set correctly, it should be sufficient 
-to type: 
-
-./configure [OPTIONS] && make [install]
-
-to have the libraries and test program compiled.
-
-
-==============================================================================
-
-
-+ 2. configure line options
-----------------------------
-
-(1) Enable options
---enable-fortran
---enable-parallel
---enable-tools
---enable-python
---enable-64 (only for AIX and Irix)
-
-(2) Setting compilers related variables manually
-To assign environment variables (e.g., CC, CFLAGS...), specify them as
-VAR=VALUE.  See below for descriptions of some of the useful variables.
-
-Compiler environment variables:
-  CC          C compiler command
-  CXX         C++ compiler command
-  FC          Fortran compiler command
-
-(3) Setting prefix for installation manually
---prefix=PREFIX         install files in PREFIX
-
-
-For more information, type:
-
-./configure --help
-
-
-==============================================================================
-
-
-+ 3. Platform specific settings for compiling libraries & test programs
-------------------------------------------------------------------------
-
-Building
-        make  : builds the libraries and test programs
-	make install: builds and installs
-        make clean : removes extraneous object files
-        make distclean : returns configuration to unconfigured state
-
-As tested on hosts:
-
-(1) Davinci <davinci.nersc.gov> (Linux"SUSE"-ia64)
----------------------------------------------------
-FIRST THING FIRST!! Type:
-
-module load intel
-to have the proper compilers set up for use.
-
-module load hdf5_par
-
-[NOTE: module load hdf5 does not work at this moment. 
-Possible installation error of HDF5 on Davinci.]
-
-
-Brief profile:
-CC = icc
-CXX = icc
-FC = ifort
-MPICC = icc
-MPICXX = icc
-MPIFC = ifort
-
-If default doesn't work, try:
-
-For C shell: 
-env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
-
-For Korn or Bourne shell:
-CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
-
-And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
-
-
-On this host, executing:
-
-For C shell: 
-env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
-
-For Korn or Bourne shell:
-CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
-
-has functioned correctly.
-
-
-To run test program, go to test directory:
-
-(i) Serial test
-run:
-./H5testF
-./H5PartTest
-
-(ii) Parallel test
-run:
-mpirun 2 H5testFpar
-mpirun 2 H5PartTestP
-
-NOTE: Number 2 above is a arbitrary number that indicates the number of processes.
-
-
-
-
-
-(2) Jacquard <jacquard.nersc.gov> (Linux"SUSE"-x86_64)
--------------------------------------------------------
-Brief profile:
-CC = pathcc
-CXX = pathCC
-FC = pathf90
-MPICC = mpicc
-MPICXX = mpicxx
-MPIFC = mpif90
-
-
-
-If default doesn't work, try:
-
-For C shell: 
-env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
-
-For Korn or Bourne shell:
-CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
-
-And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
-
-
-
-On this host, executing:
-
-For C shell: 
-env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
-
-For Korn or Bourne shell:
-CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
-
-has functioned correctly.
-
-
-
-To run test program, go to test directory:
-
-(i) Serial test
-run:
-./H5testF
-./H5PartTest
-
-(ii) Parallel test
-In Jacquard, we need a script to run parallel programs, since Jacquard does not support interactive parallel processing. Instead, we need to submit the task to a queue. A sample script (run_H5testFpar.scr) may look like below:
-
-+++++++++++++++++++++++++++++++++++++++
-#!/bin/csh
-#PBS -l nodes=1:ppn=2,walltime=00:05:00
-#PBS -N  H5testFpar
-#PBS -o H5testFpar.out
-#PBS -e H5testFpar.err
-#PBS -q debug
-#PBS -A mpccc
-#PBS -V
-
-setenv PBS_OWORKDIR /home/H5Part/test
-
-cd $PBS_O_WORKDIR
-mpirun -np 2 ./H5testFpar
-+++++++++++++++++++++++++++++++++++++++
-
-Then, we need to submit the task to a queue by running:
-
-qsub run_H5testFpar.scr
-
-After processed, the result will appear in H5testFpar.out, and error messages will appear in H5testFpar.err.
-
-
-
-
-
-(3) Bassi <bassi.nersc.ogv> (AIX5.3.0.0-Power 3)
--------------------------------------------------
-FIRST THING FIRST!! Type:
-
-module load gcc
-
-to have the proper compilers set up for use.
-
-Brief profile:
-CC = cc_r
-CXX = cc_r
-FC = xlf_r
-MPICC = mpcc_r
-MPICXX = mpcc_r
-MPIFC = mpxlf_r
-
-
-
-If default doesn't work, try:
-
-For C shell: 
-env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
-
-For Korn or Bourne shell:
-CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
-
-And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
-
-
-
-On this host, executing:
-
-For C shell: 
-env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
-
-For Korn or Bourne shell:
-CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
-
-has functioned correctly.
-
-
-
-To run test program, go to test directory:
-
-(i) Serial test
-run:
-./H5testF
-./H5PartTest
-
-(ii) Parallel test
-run:
-unsetenv MP_SINGLE_THREAD
-poe ./H5PartTestP -procs 2 -nodes 1
-poe ./H5testFpar -procs 2 -nodes 1
-
-For more details on how to run parallel programs on Bassi, go to:
-
-http://www.nersc.gov/nusers/resources/bassi/running_jobs/
-
-
-
-
-
-(4) Starsky <starsky.lbl.gov> (Darwin8.5.0-PowerPC)
-----------------------------------------------------
-FIRST THING FIRST!! Set environment variables: (in tcsh)
-
-setenv LD_LIBRARY_PATH /usr/local/g95/lib/gcc-lib/powerpc-apple-darwin8.5.0/4.0.3/
-setenv PATH ${PATH}:/usr/local/g95/bin
-
-NOTE: This environment variable setting is specifit to Starsky. It is to make configure find the fortran compiler.
-
-Brief profile:
-CC = gcc
-CXX = g++
-FC = g95
-
-
-
-If default doesn't work, try:
-
-For C shell: 
-env CC=gcc CXX=g++ FC=g95 ./configure && make install
-
-For Korn or Bourne shell:
-CC=gcc CXX=g++ FC=g95 ./configure && make install
-
-And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
-
-
-
-On this host, executing:
-
-For C shell: 
-env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
-
-For Korn or Bourne shell:
-CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
-
-has functioned correctly.
-
-
-
-To run test program, go to test directory:
-
-(i) Serial test
-run:
-./H5testF
-./H5PartTest
-
-
-
-
-
-(5) Linux AMD64 Visualization group workstations (Linux"SUSE"-x86_64)
----------------------------------------------------------
-Brief profile:
-CC = gcc
-CXX = g++
-FC = g95
-
-
-
-If default doesn't work, try:
-
-For C shell: 
-env CC=gcc CXX=g++ FC=g95 ./configure && make install
-
-For Korn or Bourne shell:
-CC=gcc CXX=g++ FC=g95 ./configure && make install
-
-And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
-
-
-
-On this host, executing:
-
-For C shell: 
-env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
-
-For Korn or Bourne shell:
-CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
-
-has functioned correctly.
-
-
-
-To run test program, go to test directory:
-
-(i) Serial test
-run:
-./H5testF
-./H5PartTest
-
-
-
-
-
-==============================================================================
-
-
-+ 4. Trouble shooting (Things to check for...)
---------------------------------------------
-(0) Have you set the LD_LIBRARY_PATH?
----Some systems require the user to manually set the environment variable, LD_LIBRARY_PATH. To do so:
-
-set the environment variable HDF5ROOT or PHDF5ROOT to point to your installation of HDF5 (serial and/or parallel respectively).
-
-For Korn or Bourne shell:
-	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HDF5ROOT}/lib;export LD_LIBRARY_PATH
-	LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:{PHDF5ROOT}/lib;export LD_LIBRARY_PATH
-
-For C shell:
-	setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5ROOT}/lib
-	setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${PHDF5ROOT}/lib
-
-Note that the values of HDF5ROOT & PHDF5ROOT will be in the "summary" section when you run configure.
-
-Not properly set LD_LIBRARY_PATH value may result in a runtime error:
-
-./H5PartTest: error while loading shared libraries: libhdf5.so.0: cannot open shared object file: No such file or directory
-
-(1) Are the compilers set correctly? 
----Check with: which COMPILER
-
-(2) Have you installed HDF5?
----You can get it at: http://vis.lbl.gov/Research/AcceleratorSAPP/index.html
-
-(3) Have you loaded the proper modules? 
----It is necessary in Davinci & Bassi, and configure && make install may not work without it.
-
+Website:
+
+http://vis.lbl.gov/Research/AcceleratorSAPP/
+
+Particle based simulations of accelerator beam-lines, especially in six
+dimensional phase space, generate vast amounts of data. Even though a subset of
+statistical information regarding phase space or analysis needs to be preserved,
+reading and writing such enormous restart files on massively parallel
+supercomputing systems remains challenging.
+
+H5Part is a very simple data storage schema and provides an API that simplifies
+the reading/writing of the data to the HDF5 file format. An important
+foundation for a stable visualization and data analysis environment is a stable
+and portable file storage format and its associated APIs. The presence of a
+"common file storage format," including associated APIs, will help foster a
+fundamental level of interoperability across the project's software
+infrastructure. It will also help ensure that key data analysis capabilities
+are present during the earliest phases of the software development effort.
+
+H5Part is built on top of the HDF5 (Hierarchical Data Format). HDF5 offers a
+self-describing machine-independent binary file format that supports scalable
+parallel I/O performance for MPI codes on a variety of supercomputing systems,
+and works equally well on laptop computers. The API is available for C, C++, and
+Fortran codes. The H5Part file format and APIs enable disparate research groups
+with different simulation implementations to transparently share datasets and
+data analysis tools. For instance, the common file format will enable groups
+that depend on completely different simulation implementations to share data
+analysis tools. 
 

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-# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2005
-# Free Software Foundation, Inc.
-#
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-

autogen.sh

@@ -1,46 +1,48 @@
 #!/bin/sh
 # Run this to generate all the initial makefiles, etc.
 
+ACLOCAL_FLAGS="-I m4 $ACLOCAL_FLAGS"
+LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
+AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
+
+LIBTOOLIZE=`which libtoolize`
+if [ "$LIBTOOLIZE" = "" ]; then
+        LIBTOOLIZE=`which glibtoolize`
+fi
+if [ "$LIBTOOLIZE" = "" ]; then
+        echo "libtoolize not found" 1>&2
+        exit 1
+fi
+
 echo "+ making misc files ..."
 touch NEWS README AUTHORS ChangeLog
 echo
-echo
+$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
+	echo "libtoolize failed"
+	exit 1
+}
 echo
 echo "+ running aclocal ..."
 aclocal $ACLOCAL_FLAGS || {
-  echo
-  echo "aclocal failed - check that all needed development files are present on system"
-  exit 1
+	echo "aclocal failed - check that all needed development files are present on system"
+	exit 1
 }
 echo
-echo
-echo
-echo
 echo "+ running autoheader ... "
 autoheader || {
-  echo
-  echo "autoheader failed"
-  exit 1
+	echo "autoheader failed"
+	exit 1
 }
 echo
-echo
-echo
 echo "+ running autoconf ... "
 autoconf || {
-  echo
-  echo "autoconf failed"
-  exit 1
+	echo "autoconf failed"
+	exit 1
 }
 echo
-echo
-echo
 echo "+ running automake ... "
-automake -a -c --foreign || {
-  echo
-  echo "automake failed"
-  exit 1
+automake $AUTOMAKE_FLAGS || {
+	echo "automake failed"
+	exit 1
 }
-echo
-echo
-echo
 

config.h.in

@@ -1,44 +0,0 @@
-/* config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* "" */
-#undef MY_BUILD_CPU
-
-/* "" */
-#undef MY_BUILD_OS
-
-/* "" */
-#undef MY_BUILD_VENDOR
-
-/* "" */
-#undef MY_GNUNAME
-
-/* "" */
-#undef MY_UNAME
-
-/* Name of package */
-#undef PACKAGE
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* Version number of package */
-#undef VERSION
-
-/* Define to 1 if on AIX 3.
-   System headers sometimes define this.
-   We just want to avoid a redefinition error message.  */
-#ifndef _ALL_SOURCE
-# undef _ALL_SOURCE
-#endif

configure-crayxt

@@ -0,0 +1,20 @@
+#!/bin/sh
+
+F90=gfortran
+
+ ./configure \
+        $@ \
+        --enable-parallel \
+        --enable-fortran \
+        --enable-tools \
+        CC=cc CXX=CC FC=$F90 \
+        MPICC=cc MPICXX=CC MPIFC=ftn
+sed -e 's/$F90/ftn/g' <Makefile > newMakefile
+mv newMakefile Makefile
+sed -e 's/$F90/ftn/g' <src/Makefile > newMakefile
+mv newMakefile src/Makefile
+sed -e 's/$F90/ftn/g' <test/Makefile > newMakefile
+mv newMakefile test/Makefile
+sed -e 's/$F90/ftn/g' <tools/Makefile > newMakefile
+mv newMakefile tools/Makefile
+

configure.ac

@@ -1,45 +1,62 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5Part], [Ver.1.0], [vis@hpcrdm.lbl.gov])
-
+AC_INIT([H5Part], [1.6.5], [h5part@lists.psi.ch], H5Part)
 
 # Ensure that a recent enough version of Autoconf is being used. 
 # If the version of Autoconf being used to create configure is earlier than version, 
 # print an error message to the standard error output and do not create configure.
 AC_PREREQ(2.59)
 
-
 # should be called right after AC_INIT.
 # configure scripts can create a C header file containing `#define' directives. 
 # The AC_CONFIG_HEADERS macro selects this kind of output.
-AC_CONFIG_HEADER(config.h)
+AC_CONFIG_HEADERS(config.h)
 
+AC_CONFIG_MACRO_DIR([m4])
 
-##################################################################################
-#################### A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-##################################################################################
+# AM_INIT_AUTOMAKE is required to use autoconf with automake
+AM_INIT_AUTOMAKE
 
+BUILD_LIBS='libH5Part'
+BUILD_TESTS='test'
 
-SAVE_CC=$CC
-SAVE_CXX=$CXX
-SAVE_FC=$FC
-SAVE_MPICC=$MPICC
-SAVE_MPICXX=$MPICXX
-SAVE_MPIFC=$MPIFC
-SAVE_MPILIB=$MPILIB
-SAVE_MPIINC=$MPIINC
-SAVE_CFLAGS=$CFLAGS
-SAVE_FFLAGS=$FFLAGS
-SAVE_MPIROOT=$MPIROOT
-SAVE_HDF5ROOT=$HDF5ROOT
-SAVE_PHDF5ROOT=$PHDF5ROOT
-SAVE_PYTHON_PATH=$PYTHON_PATH
-SAVE_LDFLAGS=$LDFLAGS
+###############################################################################
+################# --enable-xxx and --with-xxx Argument ########################
+###############################################################################
 
+AC_ARG_ENABLE(
+	[debug],
+	[AC_HELP_STRING([--enable-debug],
+	[Compile with debug flags [default=no]])],
+	[USE_DEBUG=$enableval])
 
-##################################################################################
-################## PATH SERACH FUNCTION - to be used later... ####################
-##################################################################################
+AC_ARG_ENABLE(
+	[fortran],
+	[AC_HELP_STRING([--enable-fortran],
+	[Compile the Fortran interface [default=no]])],
+	[USE_FORTRAN=$enableval])
+
+AC_ARG_ENABLE(
+	[parallel],
+	[AC_HELP_STRING([--enable-parallel],
+	[Compile the MPI/IO interface [default=no]])],
+	[USE_PARALLEL=$enableval])
+
+AC_ARG_ENABLE(
+	[tools],
+        [AC_HELP_STRING([--enable-tools],
+	[Compile h5part tools [default=no]])],
+        [USE_TOOLS=$enableval])
+
+AC_ARG_WITH(
+	[hdf5],
+	[AC_HELP_STRING([--with-hdf5],
+	[path to HDF5 installation [default=""]])],
+	[HDF5PATH=$withval], [HDF5PATH=""])
+
+###############################################################################
+############### PATH SERACH FUNCTION - to be used later... ####################
+###############################################################################
 # /*@@
 #   @routine    CCTK_Search
 #   @date       Wed Jul 21 11:16:35 1999
@@ -49,122 +66,64 @@ SAVE_LDFLAGS=$LDFLAGS
 #   @enddesc
 #@@*/
 
-PATH_Search()
-{
-  eval  $1=""
-  if test $# -lt 4 ; then
-    h5part_basedir=""
-  else
-    h5part_basedir="$4/"
-  fi
-  for h5part_place in $2
-    do
-      echo "Looking in $h5part_place ... $ac_c" #1>&6
-      if test -r "$h5part_basedir$h5part_place/$3" ; then
-        echo "$ac_t""... Found" #1>&6
-        eval $1="$h5part_place"
-        break
-      fi
-      if test -d "$h5part_basedir$h5part_place/$3" ; then
-        echo "$ac_t""... Found" #1>&6
-        eval $1="$h5part_place"
-        break
-      fi
-      echo "$ac_t"" No" #1>&6
-    done
-
-  return
+PATH_Search() {
+	eval  $1=""
+	if test $# -lt 4 ; then
+		h5part_basedir=""
+	else
+		h5part_basedir="$4/"
+	fi
+	for h5part_place in $2; do
+		AC_MSG_CHECKING([looking in $h5part_place ... ])
+		if test -r "$h5part_basedir$h5part_place/$3" ; then
+			AC_MSG_RESULT([found])
+			eval $1="$h5part_place"
+			break
+		fi
+		AC_MSG_RESULT([no])
+	done
+	return
 }
 
 
-
-##################################################################################
-################ MISC SETTINGS INCLUDING C & C++ COMPILER SETTING ################
-##################################################################################
-# Compute the canonical host-system type variable, host, and its three individual 
-# parts host_cpu, host_vendor, and host_os.
+###############################################################################
+############# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING ################
+###############################################################################
+# Compute the canonical host-system type variable, host, and its three
+# individual parts host_cpu, host_vendor, and host_os.
 AC_CANONICAL_HOST
 
+AC_PROG_MAKE_SET
 
-uname=`uname -s`
-if test $uname = "AIX"; then
-  # Notify the user that configure is checking for a particular feature. 
-  # This macro prints a message that starts with `checking ' and ends with `...' and no newline. 
-  # It must be (?) followed by a call to AC_MSG_RESULT to print the result of the check and the newline.
-  AC_MSG_CHECKING([if system is AIX])
-
-  # AC_MSG_RESULT (result-description)
-  # Notify the user of the results of a check
-  AC_MSG_RESULT([OK])
-
-  # If on AIX, define _ALL_SOURCE. Allows the use of some BSD functions. 
-  # Should be called before any macros that run the C compiler.
-  AC_AIX
-fi
-
-
-# DAVINCI SPECIFIC!!!
-if test `uname -n` = "davinci"; then
-   echo "DAVINCI SPECIFIC TESTING FOR STDC++ LIBRARY!"
-   PATH_Search STDCXX_CHECK '/usr/lib64 /usr/lib' libstdc++.a
-
-   # if STDCXX_CHECK is set...
-   if test "$STDCXX_CHECK" = "/usr/lib64"; then
-      echo "STDCXX setting ..."
-      echo "STDCXX_CHECK = $STDCXX_CHECK ..."
-      STDCXX="-L/usr/lib64 -lstdc++"
-      echo "STDCXX =  $STDCXX ..."
-   elif test "$STDCXX_CHECK" = "/usr/lib"; then
-      echo "STDCXX setting ..."
-      echo "STDCXX_CHECK = $STDCXX_CHECK ..."
-      STDCXX="-L/usr/lib -lstdc++"
-      echo "STDCXX =  $STDCXX ..."
-   fi 
-fi
-
-
-# Determine a C compiler to use. 
-# If CC is not already set in the environment, check for gcc and cc, then for other C compilers. 
+# Determine a C/C++ compiler to use. 
+# If CC is not already set in the environment, check for gcc and cc, then
+# for other C compilers. 
 # Set output variable CC to the name of the compiler found.
-# Look for mpicc first, then icc, mpcc_r
-AC_PROG_CC(pathcc icc cc_r gcc cc)
+if test "x$USE_PARALLEL" = "xyes"; then
+   	CCOMPILERS="mpicc cc"
+   	CXXCOMPILERS="mpic++ mpicxx CC"
+else
+	CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
+   	CXXCOMPILERS="pgCC pathCC icpc g++"
+fi
 
-# AC_PROG_CC doesn't pick up cc_r in Bassi. The following AC_PATH_PROGS is the fix.
-AC_PATH_PROGS([BAS_CC], [cc_r], [], [$PATH])
+AC_PROG_CC($CCOMPILERS)
 
-# if BAS_CC not empty
-if test -n "$BAS_CC"; then
-  echo "CC setting for Bassi ..."
-  CC=$BAS_CC
-  echo "CC =  $CC ..."
-fi 
+# Only need C++ for some of the tools
+#if test "x$USE_TOOLS" = "xyes"; then
+	AC_PROG_CXX($CXXCOMPILERS)
+#fi
 
-
-# Determine a C++ compiler to use. 
-# Check if the environment variable CXX or CCC (in that order) is set; 
-# if so, then set output variable CXX to its value.
-# Otherwise, if the macro is invoked without an argument, 
-# then search for a C++ compiler under the likely names (first g++ and c++ then other names). 
-# If none of those checks succeed, then as a last resort set CXX to g++.
-AC_PROG_CXX(pathCC icc cc_r g++ gcc cc)
-
-
-# Set output variable INSTALL to the path of a BSD-compatible install program, if one is 
-# found in the current PATH. 
+# Set output variable INSTALL to the path of a BSD-compatible install program,
+# if one is found in the current PATH. 
 # Otherwise, set INSTALL to `dir/install-sh -c`
 AC_PROG_INSTALL
 
-
-# AM_INIT_AUTOMAKE is required to use autoconf with automake
-AM_INIT_AUTOMAKE()
-
-
-AC_PROG_RANLIB
+AC_PROG_AWK
 
 # Default prefix for bindir, etc... (eg >> ./build/bin)
 AC_PREFIX_DEFAULT(`pwd`/build)
 
-
 # AC_DEFINE_UNQUOTED (variable, value, [description])
 # Define the C preprocessor variable variable to value
 # Use this macro instead of AC_DEFINE when variable or value is a shell variable. 
@@ -175,399 +134,227 @@ AC_DEFINE_UNQUOTED(MY_GNUNAME, "${host_cpu}-${host_vendor}-${host_os}", "")
 AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
 
 
+###############################################################################
+######################## CONFIGURE LINE OPTIONS ###############################
+###############################################################################
 
-##################################################################################
-########################### CONFIGURE LINE OPTIONS ###############################
-##################################################################################
+AC_MSG_CHECKING([if debug is enabled])
 
-######################### 64-bit compilation enabled #############################
-AC_MSG_CHECKING([if 64-bit compilation is enabled])
-
-# AC_ARG_ENABLE (feature, help-string, [action-if-given], [action-if-not-given])
-# If the user gave configure the option `--enable-feature' or `--disable-feature',
-# run shell commands action-if-given. 
-# You should format your help-string with the macro AC_HELP_STRING.
-AC_ARG_ENABLE([64],
-		[AC_HELP_STRING([--enable-64],[Compile using 64-bit flags [default=no]])],
-		[USE_64=$enableval])
-
-
-# If --enable-64 is set in the configure line
-if test "X$USE_64" = "Xyes"; then
-   echo "YES, 64-BIT ENABLED"
-   if test $uname = "AIX"; then
-      CFLAGS="$CFLAGS -q64"
-      FFLAGS="$FFLAGS -q64"
-   fi
-
-   if test $uname = "IRIX64"; then
-      CFLAGS="$CFLAGS -64"
-      FFLAGS="$FFLAGS -64 -fPIC -fno-second-underscore"
-   fi
+if test "X$USE_DEBUG" = "Xyes"; then
+    AC_MSG_RESULT([yes])
+    CFLAGS="$CFLAGS -g"
+    CXXFLAGS="$CXXFLAGS -g"
+    FFLAGS="$FFLAGS -g"
 else
-   echo "NO, 64-BIT NOT ENABLED"
+    AC_MSG_RESULT([no])
 fi
 
-
-############################### fortran enabled ##################################
+############################ fortran enabled ##################################
 AC_MSG_CHECKING([if fortran interface enabled])
-AC_MSG_RESULT([OK])
-AC_ARG_ENABLE([fortran],
-              [AC_HELP_STRING([--enable-fortran], [Compile the Fortran interface [default=no]])],
-              [USE_FORTRAN=$enableval])
-
-
 if test "X$USE_FORTRAN" = "Xyes"; then
-   echo "YES, FORTRAN ENABLED"
+	AC_MSG_RESULT([yes])
+	LIB_FORTRAN="libH5PartF.la"
+        BUILD_LIBS="$BUILD_LIBS libH5PartF"
+	BUILD_TESTS="$BUILD_TESTS testf"
 
-   # Start looking for ifort first
-   AC_PROG_FC(ifort xlf_r pathf90 g95 g90)
+	if test "X$USE_PARALLEL" = "Xyes"; then
+		AC_PROG_FC(mpif90 mpif77 ftn)
+	else
+		AC_PROG_FC(pgf90 pathf90 ifort ftn xlf_r g95 g90 gfortran)
+	fi
 
+	if test -z "$FC" ; then
+		AC_MSG_ERROR([Cannot find a Fortran compiler!])
+		exit 1
+	fi
 
-   if test -n $FC ; then
-      AC_MSG_CHECKING([Test Number of FC Underscores])
-      AC_MSG_RESULT([OK])
-      `cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
-      `cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
-      `cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
-      `cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o -lc`
+	if test $FC = "g90"; then
+		FFLAGS="${FFLAGS} -fno-second-underscore"
+	fi
+
+	if test $FC = "g95"; then
+		FFLAGS="${FFLAGS} -fno-second-underscore"
+	fi
+
+	AC_MSG_CHECKING([symbol convention in object files])
+	`cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
+	`cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
+	`cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
+	`cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
+
+	if test -f src/TestUnderscore ; then
+		UNDERSCORE_H=Underscore.h
+		`cd src && ./TestUnderscore > Underscore.h`
+		AC_MSG_RESULT([ok])
+	else
+		AC_MSG_RESULT([nok])
+		AC_MSG_ERROR([Cannot determine the symbon convention for Fortran object files!])
+		exit 1
+	fi
 
-      if test -f src/TestUnderscore ; then
-         UNDERSCORE_H=Underscore.h
-         `cd src && cat COPYRIGHT > Underscore.h`
-         `cd src && ./TestUnderscore >> Underscore.h`
-         echo "==== Underscore.h contains ============="
-         cat src/Underscore.h
-         echo "========================================"
-      else
-         AC_MSG_ERROR(could not build fortran executable)
-         USE_FORTRAN = "no"
-      fi
-   else
-      AC_MSG_ERROR(could not find a fortran compiler)
-      USE_FORTRAN = "no"
-   fi
 else
-   echo "NO, FORTRAN NOT ENABLED"
+	AC_MSG_RESULT([no])
 fi
 
 
-########################### parallel interface enabled ###########################
+# Disable shared libraries by default: can be enabled with --enable-shared
+LT_INIT([disable-shared])
+AC_PROG_LIBTOOL
+
+
+######################## parallel interface enabled ###########################
 AC_MSG_CHECKING([if parallel interface enabled])
-AC_ARG_ENABLE([parallel],
-              [AC_HELP_STRING([--enable-parallel], [Compile the MPI/IO interface [default=no]])],
-              [USE_PARALLEL=$enableval])
-
-
-# if parallel
 if test "X$USE_PARALLEL" = "Xyes"; then
-   echo "YES, PARALLEL ENABLED"
-   AC_MSG_CHECKING([ for location of MPI libs------------])
-   AC_MSG_RESULT([OK])
-   PATH_Search MPIROOT '/usr /usr/local /usr/local/mpi /usr/local/packages/mpi' include/mpi.h
+	AC_MSG_RESULT([yes])
 
-   # AC_PATH_PROGS (variable, progs-to-check-for, [value-if-not-found], [path])
-   # Like AC_CHECK_PROGS, but if any of progs-to-check-for are found, set variable to the 
-   # entire path of the program found.
-   AC_PATH_PROGS([MPICC], [mpicc mpcc_r], [], [$PATH])
-   AC_PATH_PROGS([MPICXX], [mpicxx mpcc_r], [], [$PATH])
+	CFLAGS="${CFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
+	CXXFLAGS="${CXXFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
+	FFLAGS="${FFLAGS} -DPARALLEL_IO"
 
-   # if MPICC empty
-   if test ! -n "$MPICC"; then
-      AC_MSG_CHECKING([ No MPICC detected. Setting MPICC to CC ------------])
-      MPICC=$CC
-      echo "MPICC =  $MPICC ..."
-   else
-      MPIINC = "-I${MPIROOT}/include"
-      MPILIB = "-L${MPIROOT}/lib -lmpi"
-   fi 
+	AC_MSG_CHECKING([if we can compile MPI code without setting flags])
+	AC_TRY_LINK([#include "mpi.h"], [
+		MPI_Comm comm;
+		int n;
+		MPI_Comm_size( comm, &n ); ], 
+		[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
 
-   # if MPICXX empty
-   if test ! -n "$MPICXX"; then
-      AC_MSG_CHECKING([ No MPICXX detected. Setting MPICXX to CXX ------------])
-      MPICXX=$CXX
-      echo "MPICXX =  $MPICXX ..."
-   fi 
+	if test "X$r" = "Xno"; then
+		AC_MSG_ERROR([MPI wrapper can't compile or link MPI program! Please set the INCLUDE and LIBS variables manually.])
+		exit 1
+	fi
 
-   # parallel + fortran
-   if test "X$USE_FORTRAN" = "Xyes"; then
-      echo "PARALLEL ENABLED WITH FORTRAN"
-
-      AC_PATH_PROGS([MPIFC], [mpxlf_r mpif90], [], [$PATH])
-
-      # if MPIFC empty
-      if test ! -n "$MPIFC"; then
-         AC_MSG_CHECKING([ No MPIFC detected. Setting MPIFC to FC ------------])
-         MPIFC=$FC
-         echo "MPIFC =  $MPIFC ..."
-      fi 
-
-      MTARGET="libpH5Part.a libpH5PartF.a"
-      TTARGET="H5PartTestP H5PartAndreasTest H5testFpar Bench"
-   else
-      echo "PARALLEL ENABLED WITHOUT FORTRAN"
-
-      MTARGET="libpH5Part.a"
-      TTARGET="H5PartTestP H5PartAndreasTest Bench"
-   fi
-
-#if not parallel
-else
-   echo "NO, PARALLEL NOT ENABLED"
-
-   if test "X$USE_FORTRAN" = "Xyes"; then
-      echo "PARALLEL NOT ENABLED WITH FORTRAN ENABLED"
-
-      MTARGET="libH5Part.a libH5PartF.a"
-      TTARGET="H5PartTest H5testF H5test"
-   else
-      echo "BOTH PARALLEL & FORTRAN NOT ENABLED"
-
-      MTARGET="libH5Part.a"
-      TTARGET="H5PartTest H5test"
-   fi
+else  # --enable-parallel=no
+	AC_MSG_RESULT([no])
 fi
 
-AC_MSG_CHECKING([ for h5pTools file ---------------])
-AC_MSG_RESULT([OK])
-AC_ARG_ENABLE([tools],
-              [AC_HELP_STRING([--enable-tools], [Compile h5part tools [default=no]])],
-              [USE_TOOLS=$enableval])
-
 
+######################## tools enabled ###########################
+AC_MSG_CHECKING([whether tools are enabled])
 if test "X$USE_TOOLS" = "Xyes"; then
-  BUILD_TOOLS="h5pAttrib h5pToGNUplot"
-fi
-
-##################################################################################
-############################ PATH CHECKING & SETTING #############################
-##################################################################################
-AC_MSG_CHECKING([ for HDF5 library location------------])
-AC_MSG_RESULT([OK])
-if test "X$USE_64" = "Xyes"; then
-############## FIRST ARG TEMPORARILY SET FOR BASSI!!! ##################
-PATH_Search HDF5ROOT '/scratch/scratchdirs/cristina/hdf5/hdf5_serial /usr /usr/local /usr/local/hdf5 /usr/local/packages/hdf5 /usr/common/usg/hdf5_64/1.6.4/serial /usr/common/usg/hdf5_64/1.6.1/serial /usr/local/hdf5/hdf5_serial' include/hdf5.h
+    AC_MSG_RESULT([yes])
+    BUILD_TOOLS="h5pAttrib h5pToGNUplot homdynToH5p"
+    # tools + parallel
+    if test "X$USE_PARALLEL" = "Xyes"; then
+        BUILD_TOOLS="${BUILD_TOOLS} H5PartBench H5BlockBench"
+    fi
 else
-PATH_Search HDF5ROOT '/scratch/scratchdirs/cristina/hdf5/hdf5_serial /usr /usr/local /usr/local/hdf5 /usr/local/packages/hdf5 /usr/common/usg/hdf5/1.6.4/serial /usr/common/usg/hdf5/1.6.1/serial /usr/local/hdf5/hdf5_serial' include/hdf5.h
+    AC_MSG_RESULT([no])
 fi
 
-AC_MSG_CHECKING([ for Parallel HDF5 root---------------])
-AC_MSG_RESULT([OK])
-if test "X$USE_64" = "Xyes"; then
-PATH_Search PHDF5ROOT '/scratch/scratchdirs/cristina/hdf5/hdf5_par /usr /usr/local /usr/local/hdf5 /usr/local/packages/hdf5 /usr/common/usg/hdf5_64/1.6.4/parallel /usr/common/usg/hdf5_64/1.6.1/parallel /usr/local/hdf5/hdf5_par' include/hdf5.h
+
+###############################################################################
+######################### PATH CHECKING & SETTING #############################
+###############################################################################
+
+AC_MSG_CHECKING([for HDF5 root ])
+AC_MSG_RESULT([])
+if test -n "${HDF5PATH}" ; then
+	P=${HDF5PATH}
+elif test -n "${HDF5ROOT}"; then
+	P=${HDF5ROOT}
+elif test -n "${HDF5HOME}" ; then
+	P=${HDF5HOME}
+elif test -n "${HDF5_DIR}" ; then
+	P=${HDF5_DIR}
 else
-PATH_Search PHDF5ROOT '/scratch/scratchdirs/cristina/hdf5/hdf5_par /usr /usr/local /usr/local/hdf5 /usr/local/packages/hdf5 /usr/common/usg/hdf5/1.6.4/parallel /usr/common/usg/hdf5/1.6.1/parallel /usr/local/hdf5/hdf5_par' include/hdf5.h
+	P=''
+	P="$P /usr"
+	P="$P /usr/local"
+	P="$P /usr/local/hdf5"
+	P="$P /usr/local/packages/hdf5"
+	P="$P /apps/hdf5"
+	P="$P /opt/hdf5"
+fi
+PATH_Search HDF5ROOT "$P" include/hdf5.h
+if test -z "$HDF5ROOT"; then
+	AC_MSG_ERROR([Cannot find an HDF5 library!])
+	exit 1
 fi
 
-AC_MSG_CHECKING([if we need to link to libsz])
-AC_MSG_RESULT([OK])
+INCLUDES="$INCLUDES -I$HDF5ROOT/include"
+LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
+LIBS="$LIBS -lhdf5"
 
-if test -n HDF5ROOT; then
-  if test -f $HDF5ROOT/lib/libsz.a; then
-    echo "yes"
-    SZLIB="-L$HDF5ROOT/lib/ -lsz"
-  else
-    echo "no"
-    SZLIB=""
-  fi
-else
-  if test -f $PHDF5ROOT/lib/libsz.a; then
-    echo "yes"
-    SZLIB="-L$PHDF5ROOT/lib/ -lsz"
-  else
-    echo "no"
-    SZLIB=""
-  fi
+AC_MSG_CHECKING([if we need to link to libsz ])
+if test -n "$HDF5ROOT"; then
+	if test -f $HDF5ROOT/lib/libsz.a; then
+		AC_MSG_RESULT([yes])
+		LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
+                LIBS="$LIBS -lsz"
+	else
+		AC_MSG_RESULT([no])
+	fi
 fi
 
-####################### FOR PYTHON WRAPPER ###########################
-
-AC_MSG_CHECKING([ for Python header file ---------------])
-AC_MSG_RESULT([OK])
-AC_ARG_ENABLE([python],
-              [AC_HELP_STRING([--enable-python], [Compile Python wrapper [default=no]])],
-              [USE_PYTHON=$enableval])
+LIBS="$LIBS -lz -lm"
 
 
-if test "X$USE_PYTHON" = "Xyes"; then
+# Checks for header files.
+AC_CHECK_HEADERS([fcntl.h stdlib.h string.h unistd.h])
 
-  #ADD PATH TO MATCH YOUR SPECIFICATION!!
-  PATH_Search PYTHON_PATH '/usr/local/include/python2.0 /d/visguests/kheehyon/PYTHON/include/python2.4 /usr/include/python2.3' Python.h
+# Checks for typedefs, structures, and compiler characteristics.
+AC_HEADER_STDBOOL
+AC_TYPE_INT64_T
+AC_TYPE_SIZE_T
+AC_TYPE_SSIZE_T
 
-  #if PYTHON_PATH found...
-  if test -n "$PYTHON_PATH"; then
-  PY_WRAPPER="_H5Part.so"
-  fi
-fi
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_CHECK_FUNCS([memset pow strchr strdup])
 
-
-
-
-##################################################################################
-####################### MISC SETTINGS - path, flags, etc #########################
-##################################################################################
-
-# if not AIX
-if test ! $uname = "AIX"; then
-# Additional flags
-echo "SETTING ADDITIONAL FLAGS"
-ADDFLAGS="-fPIC -fno-second-underscore"
-fi
-
-
-H5P_LIB_LOC=`pwd`/src
-
-##################################################################################
-#################### A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-##################################################################################
-
-#if there was an external input for the variable...
-if test -n "$SAVE_CC"; then
-CC=$SAVE_CC
-fi
-
-if test -n "$SAVE_CXX"; then
-CXX=$SAVE_CXX
-fi
-
-if test -n "$SAVE_FC"; then
-FC=$SAVE_FC
-fi
-
-if test -n "$SAVE_MPICC"; then
-MPICC=$SAVE_MPICC
-fi
-
-if test -n "$SAVE_MPICXX"; then
-MPICXX=$SAVE_MPICXX
-fi
-
-if test -n "$SAVE_MPIFC"; then
-MPIFC=$SAVE_MPIFC
-fi
-
-if test -n "$SAVE_MPILIB"; then
-MPILIB=$SAVE_MPILIB
-fi
-
-if test -n "$SAVE_MPIINC"; then
-MPIINC=$SAVE_MPIINC
-fi
-
-if test -n "$SAVE_CFLAGS"; then
-CFLAGS=$SAVE_CFLAGS
-fi
-
-if test -n "$SAVE_FFLAGS"; then
-FFLAGS=$SAVE_FFLAGS
-fi
-
-if test -n "$SAVE_MPIROOT"; then
-MPIROOT=$SAVE_MPIROOT
-fi
-
-if test -n "$SAVE_HDF5ROOT"; then
-HDF5ROOT=$SAVE_HDF5ROOT
-fi
-
-if test -n "$SAVE_PHDF5ROOT"; then
-PHDF5ROOT=$SAVE_PHDF5ROOT
-fi
-
-if test -n "$SAVE_PYTHON_PATH"; then
-PYTHON_PATH=$SAVE_PYTHON_PATH
-fi
-
-if test -n "$SAVE_LDFLAGS"; then
-LDFLAGS=$SAVE_LDFLAGS
-fi
-
-if test -n "$MPICXX"; then
-TOOLS_CXX=$MPICXX
-TOOLS_H5PART_LIB="-lpH5Part"
-TOOLS_HDFLIB="-L$PHDF5ROOT/lib -lhdf5"
-else
-TOOLS_CXX=$CXX
-TOOLS_H5PART_LIB="-lH5Part"
-TOOLS_HDFLIB="-L$HDF5ROOT/lib -lhdf5"
-fi
-
-##################################################################################
-############################# PRINTING SUMMARY ###################################
-##################################################################################
-echo "+++++++++++++++++++++++++++++++"
-echo "+++++++++ SUMMARY for `(hostname || uname -n) 2>/dev/null | sed 1q` +++++++++"
-echo "CC = $CC"
-echo "CXX = $CXX"
-echo "FC = $FC"
-echo "MPICC = $MPICC"
-echo "MPICXX = $MPICXX"
-echo "MPIFC = $MPIFC"
-echo "CFLAGS = $CFLAGS"
-echo "FFLAGS = $FFLAGS"
-echo "MPILIB = $MPILIB"
-echo "MPIINC = $MPIINC"
-echo "MPIROOT = $MPIROOT"
-echo "HDF5ROOT = $HDF5ROOT"
-echo "PHDF5ROOT = $PHDF5ROOT"
-echo "PYTHON_PATH = $PYTHON_PATH"
-echo "LDFLAGS = $LDFLAGS"
-echo "host_os = $host_os"
-echo "host_cpu = $host_cpu"
-echo "host_vendor = $host_vendor"
-echo "Will Be Building Libraries ... : $MTARGET"
-echo "Will Be Building Test Programs ... : $TTARGET"
-echo "TOOLS_CXX = $TOOLS_CXX"
-echo "TOOLS_H5PART_LIB = $TOOLS_H5PART_LIB"
-echo "TOOLS_HDFLIB = $TOOLS_HDFLIB"
-echo "PY_WRAPPER = $PY_WRAPPER"
-echo "BUILD_TOOLS = $BUILD_TOOLS"
-echo "+++++++++++++++++++++++++++++++"
-
-
-##################################################################################
-################# EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
-##################################################################################
+###############################################################################
+############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
+###############################################################################
 # AC_SUBST (variable, [value])
-# Create an output variable from a shell variable. 
-# Make AC_OUTPUT substitute the variable variable into output files (typically one or more `Makefile's). 
-# This means that AC_OUTPUT will replace instances of `@variable@' in input files with the value that 
-# the shell variable variable has when AC_OUTPUT is called. 
-# This value of variable should not contain literal newlines.
-# If value is given, in addition assign it to variable. 
-AC_SUBST(MPIROOT)
-AC_SUBST(HDF5ROOT)
-AC_SUBST(PHDF5ROOT)
-AC_SUBST(MPIINC)
-AC_SUBST(MPILIB)
-AC_SUBST(MPICC)
-AC_SUBST(MPICXX)
-AC_SUBST(MPIFC)
-AC_SUBST(MTARGET)
-AC_SUBST(TTARGET)
-AC_SUBST(SZLIB)
+# Create an output variable from a shell variable.  Make AC_OUTPUT substitute
+# the variable variable into output files (typically one or more `Makefile's).
+# This means that AC_OUTPUT will replace instances of `@variable@' in input
+# files with the value that the shell variable variable has when AC_OUTPUT is
+# called.  This value of variable should not contain literal newlines.  If
+# value is given, in addition assign it to variable. 
 AC_SUBST(CFLAGS)
+AC_SUBST(CXXFLAGS)
 AC_SUBST(FFLAGS)
-AC_SUBST(ADDFLAGS)
-AC_SUBST(STDCXX)
-AC_SUBST(H5P_LIB_LOC)
-AC_SUBST(UNDERSCORE_H)
-AC_SUBST(BUILD_TOOLS)
-AC_SUBST(PYTHON_PATH)
-AC_SUBST(PY_WRAPPER)
+AC_SUBST(INCLUDES)
 AC_SUBST(LDFLAGS)
-AC_SUBST(TOOLS_CXX)
-AC_SUBST(TOOLS_H5PART_LIB)
-AC_SUBST(TOOLS_HDFLIB)
+AC_SUBST(LIBS)
+AC_SUBST(UNDERSCORE_H)
+AC_SUBST(LIB_FORTRAN)
+AC_SUBST(BUILD_TESTS)
+AC_SUBST(BUILD_TOOLS)
 
 # Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'),
 # substituting the output variable values.
 AC_CONFIG_FILES([
-Makefile
-src/Makefile
-test/Makefile
-tools/Makefile
+	Makefile
+	src/Makefile
+	doc/Makefile
+	test/Makefile
+	tools/Makefile
 ])
 
-
 AC_OUTPUT
+
+###############################################################################
+########################## PRINTING SUMMARY ###################################
+###############################################################################
+AC_MSG_RESULT([ ])
+AC_MSG_RESULT([Summary:])
+AC_MSG_RESULT([ ])
+AC_MSG_RESULT([Host OS:             $host_os])
+AC_MSG_RESULT([Host CPU:            $host_cpu])
+AC_MSG_RESULT([Host vendor:         $host_vendor])
+AC_MSG_RESULT([Build libraries:     $BUILD_LIBS])
+AC_MSG_RESULT([Build test programs: $BUILD_TESTS])
+AC_MSG_RESULT([Build tools:         $BUILD_TOOLS])
+AC_MSG_RESULT([CC =                 $CC])
+AC_MSG_RESULT([CXX =                $CXX])
+AC_MSG_RESULT([FC =                 $FC])
+AC_MSG_RESULT([CFLAGS =             $CFLAGS])
+AC_MSG_RESULT([CXXFLAGS =           $CXXFLAGS])
+AC_MSG_RESULT([FFLAGS =             $FFLAGS])
+AC_MSG_RESULT([INCLUDES =           $INCLUDES])
+AC_MSG_RESULT([LDFLAGS =            $LDFLAGS])
+AC_MSG_RESULT([LIBS =               $LIBS])
+AC_MSG_RESULT([HDF5ROOT =           $HDF5ROOT])
+AC_MSG_RESULT([ ])

doc/2006-Berkeley-Visit/H5xxxVisIt.fig

@@ -1,294 +0,0 @@
-#FIG 3.2
-Landscape
-Center
-Inches
-Letter  
-100.00
-Single
--2
-1200 2
-0 32 #c6b797
-0 33 #eff8ff
-0 34 #dccba6
-0 35 #404040
-0 36 #808080
-0 37 #c0c0c0
-0 38 #e0e0e0
-0 39 #8e8f8e
-0 40 #aaaaaa
-0 41 #555555
-0 42 #bebebe
-0 43 #515151
-0 44 #e7e3e7
-0 45 #000049
-0 46 #797979
-0 47 #303430
-0 48 #414141
-0 49 #c7b696
-0 50 #8e8e8e
-0 51 #414541
-0 52 #8e8e8e
-0 53 #000079
-0 54 #ff8200
-0 55 #007d00
-0 56 #0000be
-# Desktop computer
-6 375 2400 2025 4050
-6 1575 3825 2025 4050
-2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 8
-	 1615 3916 1719 3874 1908 3874 1950 3853 1972 3853 1846 3937
-	 1615 3937 1615 3916
-2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 6
-	 1888 3853 1846 3874 1908 3874 1950 3853 1908 3853 1888 3853
-2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
-	 1846 3874 1888 3853 1846 3853 1803 3874 1846 3874
-2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
-	 1803 3874 1740 3874 1803 3853 1824 3853 1803 3874
-2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 6
-	 1846 3958 1866 3916 1972 3853 1992 3895 1846 3979 1846 3958
-2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 5
-	 1615 3937 1866 3937 1846 3958 1615 3958 1615 3937
-2 3 0 1 -1 7 2 0 20 0.000 0 0 -1 0 0 9
-	 1615 3958 1594 4000 1719 4000 1846 4000 1866 4000 1992 3916
-	 1992 3895 1846 3958 1615 3958
--6
-6 600 2400 1950 3675
-2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 6
-	 669 2530 648 3307 1594 3307 1615 2468 1594 2468 669 2530
-2 3 0 1 -1 7 0 0 10 0.000 0 0 -1 0 0 5
-	 1615 2468 1594 3307 1719 3307 1719 2509 1615 2468
-2 3 0 1 -1 7 0 0 15 0.000 0 0 -1 0 0 5
-	 1762 2677 1908 2719 1908 3139 1762 3203 1762 2677
-2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 6
-	 732 3349 732 3412 1594 3454 1594 3371 753 3349 732 3349
-2 3 0 1 -1 7 1 0 15 0.000 0 0 -1 0 0 5
-	 1594 3371 1846 3280 1846 3348 1594 3454 1594 3371
-2 3 0 1 -1 7 2 0 15 0.000 0 0 -1 0 0 5
-	 732 3433 732 3559 1594 3601 1594 3454 732 3433
-2 3 0 1 -1 0 2 0 20 0.000 0 0 -1 0 0 5
-	 1594 3454 732 3412 753 3433 1572 3454 1594 3454
-2 3 0 1 -1 7 2 0 8 0.000 0 0 -1 0 0 5
-	 1594 3454 1594 3601 1635 3580 1635 3433 1594 3454
-2 3 0 1 -1 7 2 0 8 0.000 0 0 -1 0 0 5
-	 1719 3538 1846 3475 1846 3349 1719 3391 1719 3538
-2 3 0 1 -1 7 2 0 10 0.000 0 0 -1 0 0 5
-	 1635 3496 1719 3454 1719 3391 1635 3433 1635 3496
-2 3 0 1 -1 7 2 0 10 0.000 0 0 -1 0 0 5
-	 1635 3580 1719 3538 1719 3475 1635 3517 1635 3580
-2 1 0 2 -1 7 2 0 8 0.000 0 0 -1 0 0 2
-	 1635 3496 1719 3454
-2 1 0 2 -1 7 2 0 8 0.000 0 0 -1 0 0 2
-	 1635 3517 1719 3475
-2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 7
-	 732 3559 732 3601 816 3601 963 3559 963 3538 816 3559
-	 732 3559
-2 3 0 1 -1 7 3 0 10 0.000 1 0 -1 0 0 5
-	 1490 3596 1490 3641 1594 3643 1594 3601 1490 3596
-2 3 0 1 -1 7 3 0 10 0.000 1 0 -1 0 0 5
-	 1594 3643 1635 3601 1635 3580 1594 3601 1594 3643
-2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 5
-	 1846 3475 1846 3496 1803 3517 1803 3496 1846 3475
-2 3 0 1 -1 7 3 0 10 0.000 0 0 -1 0 0 4
-	 1803 3517 1740 3517 1803 3496 1803 3517
-2 3 0 1 -1 7 4 0 15 0.000 1 0 -1 0 0 6
-	 879 3307 732 3349 1594 3371 1846 3279 1762 3265 879 3307
-2 3 0 1 -1 7 0 0 10 0.000 1 0 -1 0 0 5
-	 1719 2509 1719 3307 1762 3265 1762 2552 1719 2509
-3 1 0 1 -1 7 1 0 20 0.000 0 0 0 11
-	 774 2656 816 2614 1488 2572 1510 2593 1530 2636 1530 3139
-	 1510 3181 1467 3203 837 3203 795 3181 774 3160
-	 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
-	 1.000 1.000 1.000
--6
-6 375 3675 1650 4050
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
-	 1207 3935 1205 3897 1229 3888 1265 3890 1264 3922 1244 3937
-	 1212 3937 1207 3935
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
-	 1264 3939 1261 3900 1285 3892 1320 3893 1319 3925 1300 3940
-	 1268 3940 1264 3939
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
-	 1318 3950 1315 3912 1339 3904 1374 3905 1374 3937 1355 3953
-	 1322 3953 1318 3950
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 8
-	 1151 3935 1150 3897 1173 3888 1209 3890 1207 3922 1188 3937
-	 1157 3937 1151 3935
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 1169 3900 1166 3861 1190 3853 1226 3854 1224 3886 1205 3901
-	 1173 3901 1169 3900
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 1225 3904 1223 3865 1247 3857 1282 3858 1281 3891 1262 3906
-	 1230 3906 1225 3904
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 1281 3908 1279 3869 1303 3860 1338 3862 1337 3893 1318 3909
-	 1286 3909 1281 3908
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 1344 3909 1342 3870 1366 3862 1401 3863 1399 3895 1381 3911
-	 1349 3911 1344 3909
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1214 3854 1214 3835 1233 3822 1272 3825 1272 3831 1260 3839
-	 1258 3856 1211 3854 1214 3854
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1258 3855 1258 3836 1277 3823 1315 3826 1315 3831 1304 3839
-	 1302 3857 1255 3855 1258 3855
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1300 3862 1300 3843 1319 3830 1359 3833 1359 3838 1346 3846
-	 1344 3863 1297 3862 1300 3862
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1344 3863 1344 3845 1363 3831 1402 3835 1402 3839 1390 3848
-	 1389 3865 1341 3863 1344 3863
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1387 3869 1387 3850 1406 3836 1444 3839 1444 3845 1436 3871
-	 1417 3882 1383 3869 1387 3869
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 708 3798 708 3779 727 3766 766 3769 766 3774 755 3783
-	 752 3800 705 3798 708 3798
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 747 3803 747 3784 766 3771 805 3775 805 3780 793 3788
-	 791 3805 744 3803 747 3803
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 794 3805 794 3787 813 3773 852 3777 852 3781 840 3790
-	 839 3807 791 3805 794 3805
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 832 3810 832 3792 850 3778 889 3781 889 3787 878 3795
-	 876 3812 828 3810 832 3810
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 876 3812 876 3793 894 3780 934 3784 934 3788 921 3797
-	 919 3814 872 3812 876 3812
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 919 3816 919 3797 938 3784 977 3787 977 3792 965 3800
-	 964 3817 916 3816 919 3816
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 962 3816 962 3797 981 3784 1019 3787 1019 3792 1008 3800
-	 1006 3817 959 3816 962 3816
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1001 3819 1001 3800 1019 3787 1058 3790 1058 3795 1047 3803
-	 1045 3820 997 3819 1001 3819
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1049 3819 1049 3800 1067 3787 1106 3790 1106 3795 1094 3803
-	 1092 3820 1045 3819 1049 3819
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 661 3822 661 3803 679 3790 718 3793 718 3799 706 3807
-	 704 3824 658 3822 661 3822
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 704 3831 704 3812 724 3799 762 3802 762 3807 750 3816
-	 748 3832 702 3831 704 3831
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 748 3834 748 3816 768 3802 806 3805 806 3810 794 3819
-	 793 3835 746 3834 748 3834
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 789 3838 789 3819 808 3805 847 3808 847 3814 835 3822
-	 833 3839 786 3838 789 3838
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 832 3840 832 3822 850 3808 889 3812 889 3817 878 3825
-	 876 3842 828 3840 832 3840
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 874 3842 874 3824 893 3810 932 3814 932 3819 919 3827
-	 918 3844 871 3842 874 3842
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 916 3846 916 3827 934 3814 974 3817 974 3822 962 3831
-	 960 3847 913 3846 916 3846
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 961 3846 961 3828 980 3814 1018 3817 1018 3823 1007 3831
-	 1005 3847 957 3846 961 3846
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1005 3849 1005 3831 1023 3817 1062 3821 1062 3826 1050 3834
-	 1049 3851 1002 3849 1005 3849
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 1049 3851 1049 3832 1067 3819 1107 3823 1107 3828 1095 3836
-	 1093 3853 1045 3851 1049 3851
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 656 3866 655 3827 678 3819 714 3820 713 3853 693 3868
-	 662 3868 656 3866
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 700 3869 698 3831 722 3822 757 3824 755 3856 737 3871
-	 704 3871 700 3869
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 744 3876 741 3838 766 3829 801 3831 799 3862 781 3878
-	 748 3878 744 3876
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 792 3882 790 3842 814 3834 849 3835 848 3868 829 3883
-	 797 3883 792 3882
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 832 3884 830 3846 854 3837 889 3839 887 3870 869 3886
-	 836 3886 832 3884
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 880 3890 879 3851 902 3842 938 3844 936 3876 918 3892
-	 886 3892 880 3890
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 932 3893 930 3854 954 3846 989 3847 988 3879 969 3895
-	 936 3895 932 3893
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 982 3895 981 3856 1004 3847 1040 3849 1038 3882 1019 3897
-	 988 3897 982 3895
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 1025 3898 1023 3860 1047 3851 1082 3853 1080 3885 1062 3900
-	 1029 3900 1025 3898
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 618 3861 616 3822 640 3814 675 3816 674 3847 655 3862
-	 623 3862 618 3861
-2 3 0 1 -1 7 1 0 20 0.000 0 0 -1 0 0 8
-	 572 3888 571 3849 594 3840 630 3842 629 3875 609 3890
-	 578 3890 572 3888
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 609 3888 609 3869 629 3856 667 3860 667 3864 655 3873
-	 654 3890 607 3888 609 3888
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 7
-	 654 3893 984 3934 988 3898 664 3866 652 3882 652 3888
-	 654 3893
-2 3 0 1 -1 7 0 0 20 0.000 0 0 -1 0 0 9
-	 986 3931 986 3913 1004 3900 1043 3902 1043 3908 1032 3916
-	 1029 3933 982 3931 986 3931
-2 3 0 1 -1 7 5 0 15 0.000 0 0 -1 0 0 9
-	 429 3871 683 3743 1551 3816 1576 3831 1573 3840 1426 3990
-	 427 3883 427 3869 429 3871
-2 1 0 1 -1 7 0 0 -1 0.000 0 0 -1 0 0 3
-	 423 3910 1434 4014 1575 3875
-2 3 0 0 -1 7 5 0 10 0.000 0 0 -1 0 0 8
-	 429 3885 429 3928 1430 4050 1580 3895 1576 3831 1423 3990
-	 425 3882 429 3885
--6
--6
-6 4050 3000 7500 3750
-2 1 0 1 0 0 0 0 -1 0.000 0 0 -1 0 0 4
-	 7500 3000 5430 3000 6120 3690 4050 3690
--6
-# TB Data
-6 8025 6000 9000 7425
-5 1 0 1 -1 -1 0 0 -1 0.000 0 1 0 0 8490.000 5700.000 8040 6300 8490 6450 8940 6300
-5 1 0 1 -1 -1 0 0 -1 0.000 0 1 0 0 8490.000 6600.000 8040 7200 8490 7350 8940 7200
-1 2 0 1 -1 -1 0 0 -1 0.000 1 0.0000 8490 6150 450 150 8040 6000 8940 6300
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 0 0 0 2
-	 8940 6225 8940 7200
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 0 0 0 2
-	 8040 6225 8040 7200
-4 1 -1 0 0 2 12 0.0000 6 135 270 8490 6675 TB\001
-4 1 -1 0 0 2 12 0.0000 6 135 405 8490 7275 Data\001
--6
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 1 1 2
-	0 0 1.00 60.00 120.00
-	0 0 1.00 60.00 120.00
-	 2025 3075 2475 3075
-2 4 0 1 0 7 50 0 -1 0.000 0 0 7 0 0 5
-	 3750 4650 3750 2100 2550 2100 2550 4650 3750 4650
-2 4 0 1 0 7 50 0 -1 0.000 0 0 7 0 0 5
-	 9075 4650 9075 2100 7875 2100 7875 4650 9075 4650
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
-	0 0 3.00 60.00 120.00
-	 8400 4800 8400 6000
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
-	0 0 3.00 60.00 120.00
-	 8250 4800 8250 6000
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
-	0 0 3.00 60.00 120.00
-	 8100 4800 8100 6000
-2 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 1 2
-	0 0 3.00 60.00 120.00
-	 8850 4800 8850 6000
-2 4 0 1 0 7 50 -1 -1 0.000 0 0 7 0 0 5
-	 12000 4500 12000 3975 8175 3975 8175 4500 12000 4500
-4 0 0 50 0 2 15 0.0000 4 30 360 8475 5550 ......\001
-4 0 0 50 0 0 20 0.0000 4 195 570 2625 3375 VisIt\001
-4 0 0 50 0 0 20 0.0000 4 195 570 7950 3375 VisIt\001
-4 0 0 50 -1 2 16 0.0000 4 225 1410 9375 4275 H5xxx plugin\001
-4 0 0 50 0 0 20 0.0000 4 255 1650 6450 5550 n-way parallel\001

doc/Building.html

@@ -1,262 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>Put your title here!!</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-
-<div id="maincenter">
-
-
-  <head>
-    <title>Building H5Part</title>
-  </head>
-
-  <body bgcolor="#F0F0F0">
-    <font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
-    <UL>
-      <LI><a href="#Quickstart">Quickstart guide for the impatient.</a>
-      <LI><a href="#Details">Details of the Configuration Script</a>
-	<!-- <LI><a href="UsingC++.html">Using the C++ interface</a> -->
-      <LI><a href="#ConfigOptions">Important Configure Options</a>
-      <LI><a href="#EnvVariables">Important Environment Variables</a>
-    </UL>
-
-    <hr>
-    <a name="Quickstart">
-    <h2>Quickstart <i>for the impatient</i></h2>
-    </a>
-
-<OL>
-
-      <LI><b>Configure</b>:<br>
-    For the serial implementation
-<pre>
-    ./configure
-</pre>
-    For the parallel implementation configure with
-<pre>
-    ./configure --enable-parallel
-</pre>
-    If you also want to build fortran bindings, add the
-    <code>--enable-fortran</code> flag to the configure line.
-    </LI><p>
-
-      <LI><b>Make the Library</b>:<br>
-	Type <code>make</code> to build the library. The libraries are
-	named accordingly.
-	<UL>
-	  <LI>libH5Part.a: Serial C/C++ Library.</LI>
-	  <LI>libpH5Part.a: Parallel C/C++ library.</LI>
-	  <LI>libH5PartF.a: Serial F77/F90 library.</LI>
-	  <LI>libpH5PartF.a: Parallel F77/F90 library.</LI>
-	</UL>
-      </LI><p>
-      
-      <LI><b>Make Regression Tests and Examples</b>:<br>
-	Just type <code>make tests</code> to build regression tests
-	and/or example programs for H5Part.  These tests are
-	<UL>
-	  <LI>H5PartF: Fortran example (only build if --enable-fortran
-	    is specified).</LI>
-	  <LI>H5PartFpar: Parallel Fortran example (only built if both
-	    --enable-fortran and --enable-parallel are specified).</LI>
-	  <LI>H5PartTest: Serial C example.  This test writes a sample
-	    datafile and then reopens it for reading.  It demonstrates
-	    the most basic reading/writing capabilities.</LI>
-	  <LI>H5PartTestP: Parallel C example (only built if
-	    --enable-parallel is specified).  This program only works
-	    as an MPI/parallel program.</LI>
-	  <LI>Bench: This program will only be built if
-	    --enable-parallel is specified.  It compares the
-	    performance of raw binary
-	    I/O (one file per processor), raw binary MPI-IO based
-	    parallel I/O to a single file, and the parallel H5Part/HDF5 to
-	    a single file. Generally, H5Part should be very close to the
-	    MPI-IO implementation in terms of performance, but slower
-	    than one-file-per-processor.  If HDF5 is slower the
-	    MPI-IO, it would indicate that some performance tuning
-	    will be required for your platform (contact us, and we will
-	    see what we can do!).</LI>
-    </UL>
-	</LI><p>
-      <LI><b>Building Your Own Programs</b>:<br>
-	There are many different subtleties to linking on various
-	computer platforms, but typically one does the following.
-	<UL>
-	  <LI>C/C++ Serial:
-	    <br><code>#include
-	      &lt H5Part.h &gt </code> into your
-	    source file.
-	    <br><code>$CC -I<i>path_to_H5Part.h</i> 
-	      -I<i>path_to_hdf5.h</i> -o outfile
-	      MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
-	      -L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
-	  </LI>
-	  <LI>C/C++ Parallel:
-	    <br><code>#include
-	      &lt H5Part.h &gt </code> into your
-	    source file.
-	    <br><code>$MPICC -I<i>path_to_H5Part.h</i> 
-	      -I<i>path_to_hdf5.h</i> -DPARALLEL_IO
-	      -DH5_HAVE_PARALLEL -o outfile
-	      MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
-	      -L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
-	  </LI>
-	  
-	  <LI>Fortran Serial:
-	    <br><code>include
-	      'H5Part.inc'</code> into your
-	    source file.
-	    <br><code>$FC -I<i>path_to_H5Part.h</i> 
-	      -I<i>path_to_hdf5.h</i> -o outfile
-	      MyFile.cc -L<i>path_to_libH5PartF.a</i> -lH5PartF
-	      -L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
-	  </LI>
-	  <LI>Fortran Parallel:
-	    <br><code>include
-	      'H5Part.inc'</code> into your
-	    source file.
-	    <br><code>$MPIF90 -I<i>path_to_H5Part.h</i> 
-	      -o outfile
-	      MyFile.cc -L<i>path_to_libpH5PartF.a</i> -lpH5PartF
-	      -L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
-	  </LI><p>
-	</UL>
-	  
-</OL>
-
-    <hr>
-
-    <a name="Details">
-    <h1>Details for H5Part Configure and Build</h1>
-  </a>
-    
-    
-    <a name="ConfigOptions">
-    <h2>Configure Options</h2>
-    </a>
-    H5Part uses GNU Autoconf to generate a Makefile from the makefile
-    template called <code>Makefile.in</code>.
-    The configure script pays attention to the following 
-    configure options;<p>
-
-<UL>
-<LI><b>--prefix=PREFIX</b> Install files in PREFIX</LI>
-<LI><b>--enable-fortran</b> By default H5part will make no attempt to
-	build Fortran bindings.  If you add the
-	<code>--enable-fortran</code> flag to the ./configure line, it
-	will create a small test program to determine how to generate
-	the fortran bindings and then create a library that includes
-	those bindings.  You may need to set the fortran compiler by
-	setting the <code>FC</code> environment variable in your shell.</LI>
-<LI><b>--enable-parallel</b> The version of HDF5 that you build for
-	Parallel I/O differs from the library you would build for
-	serial I/O.  Consequently, the H5Part libraries must be built
-	specifically for the kind of I/O you have in mind (parallel or
-	serial). The configure script will attempt to find an
-	<code>mpicc</code> if it is available.  If no
-	<code>mpicc</code> is available it will use the regular
-	C-compiler and will try to locate the location of the MPI
-	include files and libraries.  You can assist the configure
-	program in its search by setting the <code>MPIROOT</code>
-	environment variable.</LI>
-<LI><b>--enable-tools</b> Builds the currently available tools
-	<br>
-	<b>h5pAttrib</b>, an inspection tool that prints the number of timesteps in a file
-	the file attributes, the step attributes, the dataset names and their values. 
-	<br>
-	<b>h5pToGNUplot</b>, a converter to two column ASCII format to load in GNUplot.
-</LI>
-<LI><b>--enable-python</b><font color=red> Under construction</font> Option to build python bindings. It has not been tested.
-</LI>
-<LI><b>--help</b> Prints configure options.
-</LI>
-</UL>
-    <p>
-
-<a name="MakeOptions">
-<h2>Make Options</h2>
-</a>
-
-<UL>
-        <LI>make</LI>builds the libraries and test programs
-       <LI>make install</LI>builds and installs
-        <LI>make clean</LI>removes extraneous object files
-        <LI>make distclean</LI>returns configuration to unconfigured state
-</UL>
-
-      <a name="EnvVariables">
-    <h2>Environment Variables for Configure</h2>
-  </a>
-      The
-      configuration script is of limited intelligence.  Sometimes, you
-      have to define the following environment variables in order to
-      help it on its way. You will often only need to tell it where to
-      find the HDF5 libraries (<code>H5ROOT</code> for serial or
-      <code>PHDF5ROOT</code> for parallel builds). All of these
-      environment variables can also be overidden in the Makefile that
-      is generated by the autoconfigure script.
-      The configure script pays attention to the following 
-      environment variables;
-    <p>
-
-<UL>
-<LI><b>CC</b>: Use the <code>CC</code> environment variable to tell the
-	configure script where to find the C compiler.  You can
-	also directly modify this variable in the
-	<code>Makefile</code> that is generated by the autoconfigure</LI>
-<LI><b>CXX</b>: Use the <code>CXX</code> environment variable to tell the
-	configure script where to find the C++ compiler.  You can
-	also directly modify this variable in the
-	<code>Makefile</code> that is generated by the autoconfigure</LI>
-<LI><b>FC</b>: Use the <code>FC</code> environment variable to tell the
-	configure script where to find the fortran compiler.  You can
-	also directly modify this variable in the
-	<code>Makefile</code> that is generated by the autoconfigure</LI>
-<LI><b>MPICC</b>: If you are building for parallel C I/O, then it is
-	useful to tell the configure script where to find the
-	<code>mpicc</code> script.  Normally, <code>mpicc</code> is
-	merely a wrapper script for a build using a regular C-compiler.
-	If no <code>mpicc</code> is available, then the
-	<code>configure</code> script will attempt to locate the mpi
-	header files and libraries. In that case, it may be useful to
-	define the <code>MPI_HOME</code> environment variable.</LI>
-<LI><b>MPICXX</b>If you are building for parallel C++</LI>
-<LI><b>MPIFC</b>: If you are building for parallel Fortran I/O, then it is
-	useful to tell the configure script where to find the parallel fortran compiler.
-<LI><b>MPIROOT</b>: Set this environment variable to help the
-	configure script to locate the MPI libraries that should be
-	used to build the parallel version of the libraries.  This
-	variable will be ignored if configured only to build the
-	serial implementation of the library.</LI>
-<LI><b>HDF5ROOT</b>: Find the path to your serial HDF5 installation.  If you
-	are building the serial version of H5part, then you should set
-      the <code>PHDF5ROOT</code> environment variable.</LI>
-</UL><p>
-
-<h3>Common compiler environemt variables for NERSC platforms</h3>
-<UL>
-<LI><b>DaVinci</b>: Linux ia64 </LI>
-	CC=icc CXX=icc F90=ifort MPICC=icc  MPIFC=ifort MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include
-<LI><b>Bassi</b>: AIX</LI> 
-	CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r
-<LI><b>Jacquard</b>: Linux x86_64</LI>
-	CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90
-<LI><b>Starsky.lbl.gov:</b> (Darwin) PowerPC</LI>
-	CC=gcc CXX=g++ FC=g95
-</UL>
-<br> 
-NOTE: You might need to set the MPI library path (MPILIB) and MPI includes (MPIIINC) if they are in non standard places. For example: <br>
-MPILIB=-L/usr/lpp/ppe.poe/lib -lmpi_r  MPIINC=-I/usr/lpp/ppe.poe/include/thread 
-<h3>How to set the variables for configure:</h3>
-It is very simple just call env with the variables together with configure. Notice the quotes in MPILIB.
-<pre>
-% env CC=icc CXX=icc F90=ifort MPICC=icc  MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include ./configure (configure options follow here)
-</pre>
-In the worst case, you can edit the <code>src/Makefile.am</code> and <code>test/Makefile.am</code> as
-      needed to perform the proper build.
-</div>
-

doc/BuildingHDF5.html

@@ -1,68 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>Put your title here!!</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-<!--#include virtual="/include/topIncludes.html"-->
-
-<div id="maincenter">
-
-
-  <head>
-    <title>Building HDF5</title>
-  </head>
-
-  <body bgcolor="#F0F0F0">
-    <font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
-    <UL>
-      <LI><a href="#ConfigOptions">Configure Options</a>
-      <LI><a href="#EnvVariables">Important Environment Variables</a>
-    </UL>
-
-    <hr>
-    <a name="ConfigOptions">
-    <h2>Configure options</h2></a>
-    </a>
-To set the installation path configure with
-<pre>
-	./configure --prefix=your hdf5 installation full path, e.g.--prefix=/usr/local/hdf5 
-</pre>
-    For the serial implementation configure with
-<pre>
-	./configure
-</pre>
-    For the parallel implementation configure with
-<pre>
-	./configure --enable-parallel
-</pre>
-To enable shared objects configure with	
-<pre>
-	./configure --enable-shared 
-</pre>
-<a name="EnvVariables">
-    <h2>Environment Variables</h2></a>
-    </a>
-To add HDF5 to your PATH and LD_LIBRARY_PATH edit your
-.tcshr, or .cshrc depending on the shell you are using and add
-<pre>
-setenv HDF5 "your hdf5 installation full path"
-setenv PATH ${PATH}:${HDF5}/bin
-setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5}/lib
-</pre>
-if you are using bash, add to your .bashrc
-<pre>
-export HDF5="your hdf5 installation full path"
-export  PATH=$PATH:${HDF5}/bin
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF5}/lib
-</pre>
-
-Open a new terminal or do a 
-source .tcshr (.cshrc, .bashrc) in the one that you are using.
-
-You can <a href="http://vis.lbl.gov/Research/AcceleratorSAPP/Downloading.html">continue <a/>downloading and installing H5Part.
-</div>
-
-<!--#include virtual="/include/dateFooter.html"-->

doc/Downloading.html

@@ -1,48 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>Put your title here!!</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-<!--#include virtual="/include/topIncludes.html"-->
-
-<div id="maincenter">
-  <head>
-    <title>Downloading H5Part</title>
-  </head>
-
-  <body bgcolor="#F0F0F0">
-    <font face="arial,helvetica" size="+2" color="#555588"><h2>Downloading H5Part</h2></font>
-    <UL>
-      <LI><a href="#svnano">Subversion access.</a>
-    </UL>
-    <hr>
-    <a name="svnano">
-    <h2>Subversion access</h2>
-    </a>
-
-      <LI><b>Anonymous via. Savannah</b>:<br>
-    Use svn from <a href="http://subversion.tigris.org"> tigris </a>	
-<pre>
-    svn checkout svn+ssh://svn@savannah.psi.ch/afs/psi.ch/project/amas/svn/root/amas/H5Part/ .
-</pre>
-    Password is svn.
-      <LI><b>Using AFS</b>:<br>
-	You need AFS (openAFS) and must have an AFS-Account at PSI which in consequence gives you
-        the needed access right.
-      </LI><p>
-<pre>
-    svn checkout file:///afs/psi.ch/project/amas/svn/root/amas/H5Part/ .
-</pre>
-In case of trouble please contact the person mentioned at the bottom of this page. 
-<hr>
-       	<address><a href="mailto:andreas.adelmann@psi.ch">Andreas Adelmann</a></address>
-    <!-- Created: March 7 12:52:52 PST 2005 -->
-	<!-- hhmts start -->
-Last modified: Mon Jan  9 22:18:55 CET 2006
-<!-- hhmts end -->
-</div>
-
-<!--#include virtual="/include/dateFooter.html"-->

doc/Doxyfile

@@ -4,8 +4,8 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 PROJECT_NAME           = H5Part
-PROJECT_NUMBER         = V1.0
-OUTPUT_DIRECTORY       = ./doxydoc
+PROJECT_NUMBER         = 1.6.1
+OUTPUT_DIRECTORY       = ./ReferencePages
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English
 USE_WINDOWS_ENCODING   = NO
@@ -43,10 +43,10 @@ SUBGROUPING            = YES
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
-EXTRACT_ALL            = YES
+EXTRACT_ALL            = NO
 EXTRACT_PRIVATE        = NO
 EXTRACT_STATIC         = NO
-EXTRACT_LOCAL_CLASSES  = YES
+EXTRACT_LOCAL_CLASSES  = NO
 EXTRACT_LOCAL_METHODS  = NO
 HIDE_UNDOC_MEMBERS     = YES
 HIDE_UNDOC_CLASSES     = YES
@@ -55,18 +55,18 @@ HIDE_IN_BODY_DOCS      = NO
 INTERNAL_DOCS          = NO
 CASE_SENSE_NAMES       = YES
 HIDE_SCOPE_NAMES       = NO
-SHOW_INCLUDE_FILES     = YES
+SHOW_INCLUDE_FILES     = NO
 INLINE_INFO            = YES
 SORT_MEMBER_DOCS       = YES
-SORT_BRIEF_DOCS        = NO
-SORT_BY_SCOPE_NAME     = NO
+SORT_BRIEF_DOCS        = YES
+SORT_BY_SCOPE_NAME     = YES
 GENERATE_TODOLIST      = YES
 GENERATE_TESTLIST      = YES
 GENERATE_BUGLIST       = YES
 GENERATE_DEPRECATEDLIST= YES
 ENABLED_SECTIONS       = 
 MAX_INITIALIZER_LINES  = 30
-SHOW_USED_FILES        = YES
+SHOW_USED_FILES        = NO
 SHOW_DIRECTORIES       = YES
 FILE_VERSION_FILTER    = 
 #---------------------------------------------------------------------------
@@ -82,21 +82,19 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = ../src
-FILE_PATTERNS          = *.c \
-                         *.cc \
-                         *.cxx \
-                         *.cpp \
-                         *.c++ \
-                         *.h \
-                         *.hh \
-                         *.C \
-                         *.CC \
-                         *.C++ \
-                         *.H \
-                         *.HH
+INPUT                  += ../src/H5Part.c
+INPUT                  += ../src/H5PartAttrib.c
+INPUT		       += ../src/H5Block.c
+INPUT		       += ../src/H5BlockReadWrite.c
+INPUT		       += ../src/H5MultiBlock.c
+INPUT		       += ../src/H5MultiBlockReadWrite.c
+INPUT		       += ../src/H5Part.f90
+INPUT		       += ../src/H5PartAttrib.f90
+INPUT		       += ../src/H5Block.f90
+INPUT		       += ../src/H5BlockReadWrite.f90
+FILE_PATTERNS          = 
 RECURSIVE              = YES
-EXCLUDE                = 
+EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = 
 EXAMPLE_PATH           = 
@@ -109,13 +107,13 @@ FILTER_SOURCE_FILES    = NO
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
-SOURCE_BROWSER         = YES
+SOURCE_BROWSER         = NO
 INLINE_SOURCES         = NO
 STRIP_CODE_COMMENTS    = YES
-REFERENCED_BY_RELATION = YES
-REFERENCES_RELATION    = YES
+REFERENCED_BY_RELATION = NO
+REFERENCES_RELATION    = NO
 USE_HTAGS              = NO
-VERBATIM_HEADERS       = YES
+VERBATIM_HEADERS       = NO
 #---------------------------------------------------------------------------
 # configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -126,10 +124,10 @@ IGNORE_PREFIX          =
 # configuration options related to the HTML output
 #---------------------------------------------------------------------------
 GENERATE_HTML          = YES
-HTML_OUTPUT            = html
+HTML_OUTPUT            = .
 HTML_FILE_EXTENSION    = .html
 HTML_HEADER            = 
-HTML_FOOTER            = 
+HTML_FOOTER            = doxyfooter 
 HTML_STYLESHEET        = 
 HTML_ALIGN_MEMBERS     = YES
 GENERATE_HTMLHELP      = NO
@@ -145,7 +143,7 @@ TREEVIEW_WIDTH         = 250
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = no
 LATEX_OUTPUT           = latex
 LATEX_CMD_NAME         = latex
 MAKEINDEX_CMD_NAME     = makeindex
@@ -201,13 +199,13 @@ EXPAND_ONLY_PREDEF     = NO
 SEARCH_INCLUDES        = YES
 INCLUDE_PATH           = 
 INCLUDE_FILE_PATTERNS  = 
-PREDEFINED             = 
+PREDEFINED             = PARALLEL_IO
 EXPAND_AS_DEFINED      = 
 SKIP_FUNCTION_MACROS   = YES
 #---------------------------------------------------------------------------
 # Configuration::additions related to external references   
 #---------------------------------------------------------------------------
-TAGFILES               = YES
+TAGFILES               = 
 GENERATE_TAGFILE       = 
 ALLEXTERNALS           = NO
 EXTERNAL_GROUPS        = YES
@@ -215,21 +213,21 @@ PERL_PATH              = /usr/bin/perl
 #---------------------------------------------------------------------------
 # Configuration options related to the dot tool   
 #---------------------------------------------------------------------------
-CLASS_DIAGRAMS         = YES
-HIDE_UNDOC_RELATIONS   = YES
-HAVE_DOT               = YES
-CLASS_GRAPH            = YES
-COLLABORATION_GRAPH    = YES
-GROUP_GRAPHS           = YES
+CLASS_DIAGRAMS         = NO
+HIDE_UNDOC_RELATIONS   = NO
+HAVE_DOT               = NO
+CLASS_GRAPH            = NO
+COLLABORATION_GRAPH    = NO
+GROUP_GRAPHS           = NO
 UML_LOOK               = NO
 TEMPLATE_RELATIONS     = NO
-INCLUDE_GRAPH          = YES
-INCLUDED_BY_GRAPH      = YES
-CALL_GRAPH             = YES
+INCLUDE_GRAPH          = NO
+INCLUDED_BY_GRAPH      = NO
+CALL_GRAPH             = NO
 GRAPHICAL_HIERARCHY    = YES
 DIRECTORY_GRAPH        = YES
 DOT_IMAGE_FORMAT       = png
-DOT_PATH               = /Applications/Graphviz.app/Contents/MacOS
+DOT_PATH               = 
 DOTFILE_DIRS           = 
 MAX_DOT_GRAPH_WIDTH    = 1024
 MAX_DOT_GRAPH_HEIGHT   = 1024

doc/H5PartExpress.html

@@ -1,14 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>Put your title here!!</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-
-<div id="maincenter">
-
-Under construction, will be here soon.
-</div>
-

doc/H5PartIDL.html

@@ -1,15 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>Put your title here!!</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-
-<div id="maincenter">
-
-Under construction, will be here soon.
-
-</div>
-

doc/H5PartParaview.html

@@ -1,15 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>Put your title here!!</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-
-<div id="maincenter">
-
-Under construction, will be here soon.
-
-</div>
-

doc/H5PartTools.html

@@ -1,99 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>Put your title here!!</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-<!--#include virtual="/include/topIncludes.html"-->
-
-<div id="maincenter">
-
-
-<head>
-	<title>H5Part Utility Tools</title>
-</head>
-
-  <body bgcolor="#F0F0F0">
-    <font face="arial,helvetica" size="+2" color="#555588"><h2>H5Part Utility Tools</h2></font>
-    <UL>
-      <LI><a href="h5pAttrib">h5pAttrib</a>
-      <LI><a href="h5pToGNUplot">h5pToGNUplot</a>
-    </UL>
-
-<hr>
-
-<a name="h5pAttrib">
-<h2>h5pAttrib</h2>
-</a>
-
-<b>h5pAttrib</b> is an inspection tool that prints to stdout the number of timesteps in a file
-        the file attributes, the step attributes, the dataset names and their values. It's simpler to use than h5dump.
-	Usage options are given by typing:
-<br><br>
-<PRE>
-% ./h5pAttrib -h
-usage: h5pAttrib [OPTIONS] file
-
-  OPTIONS
-   -h, --help           Print help page
-   -n, --nstep          Print number of steps
-   -A, --fileA          Print file attributes
-   -a, --stepA          Print step attributes & values for time step n
-   -d, --dataset        Print data sets names & values for time step n
-   -H, --header         Print shorter version without the values
-</PRE>
-
-<h3>Examples</h3>
-<OL>
-  <LI>
-  Show file attribute names & values of sample.h5part
-  </LI>
-        h5pAttrib -A sample.h5part
-  <LI>
-  Show step attribute names for time step 5 of sample.h5part
-  </LI>
-        h5pAttrib -a 5 -H sample.h5part
-</OL>
-
-<a name="h5pToGNUplot">
-<h2>h5pToGNUplot</h2>
-</a>
-
-<b>h5pToGNUplot</b> is a converter from H5Part to two column ASCII text format for loading into GNUplot. Usage options are given by typing:
-<br><br>
-<PRE>
-% ./h5pToGNUplot -h
-
-usage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]
-
-  FLAGS
-   -h, --help           Print help page
-   -1, --1var           (REQUIRED) Takes first variable parameter
-   -2, --2var           (REQUIRED) Takes second variable parameter
-   -i, --input          (REQUIRED) Takes input file name
-   -t, --timestep       (REQUIRED) Sets the timestep (Value -1 will result in dumping values of all timesteps.)
-   -o, --output         (OPTIONAL) Takes output file name (without this flag, the program will print to stdout)
-   -n, --number         (OPTIONAL) Sets number of output points
-   -s, --start          (OPTIONAL) Sets the starting particle index
-</PRE>
-
-<h3>Examples</h3>
-<OL>
-	<LI>	
-  Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
-	</LI>
-        h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt
-	<LI>	
-  Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
-     using 1200 points from particle index 76
-	</LI>	
-        h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt -s 76 -n 1200
-</OL>
-
-</div>
-
-<!--#include virtual="/include/dateFooter.html"-->
-
-

doc/H5PartVisIt.html

@@ -1,75 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>H5Part: VisIt Plugins</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-
-<div id="maincenter">
-<font face="arial,helvetica"><h1>H5Part: VisIt Plugins</h1></font>
-<font face="arial,helvetica" color="#555588"><h2>Introduction</h2></font>
-<P>
-<a href="http://www.llnl.gov/visit">VisIt</a> is an open source point-and-click 3D scientific visualization application that supports most of the common visualization techniques on structured and unstructured grids. One of its advantages is that it employs a distributed and parallel architecture in order to handle extremely large data sets interactively. VisIt's rendering and data processing capabilities are split into viewer and engine components that may be distributed across multiple machines.  See this link for <a href="http://vis.lbl.gov/NERSC/Software/visit/">details</a> on how to run VisIt in NERSC.
-</P>
-<P>
-VisIt achieves extensibility through the use of dynamically loaded plugins. All of VisIt's plots, operators, and database readers are implemented as plugins and are loaded at run-time from the plugin directory. New plugins can be added simply by installing them in this directory. VisIt comes with a graphical plugin creation tool, which greatly simplifies the process of creating new plugins. The user describes the properties of the plugin and then the tool generates most of the code necessary to implement the plugin. For example, in the case of an operator, the plugin creation tool creates the code necessary for the graphical user interface attribute window; the C++, Python, and Java interfaces; and the code necessary to interface to VisIt. The only code you need to write is the C++ code that actually performs the operation.
-</P>
-<font face="arial,helvetica" color="#555588"><h2>H5Part in VisIt</h2></font>
-<font face="arial,helvetica" color="#555588"><h3>Database Reader Plugin</h3></font>
-<P>
-We wrote a Multiple Time Step Multiple Domain database reader to read H5Part data into VisIt. H5Part datasets should be named with the extension <font color=red>".h5part"</font> to be recognized by the reader since VisIt does not have a format selection mechanism at the time of reading.  Figure 1 shows a Pseudocolor plot of a data set and Figure 2 shows a Scatter plot x-y (any combination of x, px, y, py, z, pz, id are possible).
-</P>
-<P>
-<TABLE>
-<TR>
-<TD>
-<a href="H5PartVisIt/cloud_visit.png"><img src="H5PartVisIt/cloud_visit.s.png" width=400 height=300></a>
-</TD
-></TR>
-<TR>
-<TD width=300>
-Figure 1. VisIt User interface showing an H5Part particle file rendered as spheres using the Pseudocolor plot.
-</TD>
-</TR>
-<TR>
-<TD>
-<a href="H5PartVisIt/cloud_visit_2D.png"><img src="H5PartVisIt/cloud_visit_2D.s.png" width=300 height=300></a>
-</TD>
-</TR>
-<TR>
-<TD>
-Figure 2. A Scatter plot of the x-y projection of the particles.
-</TD>
-</TR>
-</TABLE>
-</P>
-
-<P>
-VisIt provides a Query interface, for single time steps and for time series. Figure 3 shows the query interace over time for the sum of the x position and the z position of the particoes.
-</P>
-<P>
-<TABLE>
-<TR>
-<TD>
-<a href="H5PartVisIt/visit_query1.png"><img src="H5PartVisIt/visit_query1.s.png" width=400 height=300></a>
-</TD
-></TR>
-<TR>
-<TD width=300>
-Figure 3. VisIt's Time Query Output.
-</TD>
-</TR>
-</TABLE>
-</p>
-<font face="arial,helvetica" color="#555588"><h2>Operator Plugins</h2></font>
-<P>
-<font face="arial,helvetica" color="#555588"><h3>Particle Random Sampler</h3></font>
-
-
-</P>
-<P>
-<font face="arial,helvetica" color="#555588"><h3>Particle Binner</h3></font>
-</P>
-</div>

doc/H5X_File_Format.txt

@@ -0,0 +1,170 @@
+Proposal for a more general file format used by H5Part/H5Block
+
+                                                 Authors: Achim Gsell
+                                                 Status:  Draft
+
+1. Introduction
+
+H5X is the file format used by H5Part and H5Block.  H5X is designed on
+top of HDF5: A H5X file is a very special HDF5 file.
+
+	+--------------------+
+	|   Application      |
+	+--------------------+
+	| H5Part/H5Block API |
+	+--------------------+
+	|      H5X API       |
+	+--------------------+
+	|     HDF5 API       |
+	+--------------------+
+	|  Filesystem of OS  |
+	+--------------------+
+
+
+2. H5X file format specification
+
+2.1 The root group
+
+2.1.1 File attributes
+
+Attributes of the HDF5 root group are called "file attributes". There
+are no restrictions on file attribute names.  Names with "__" as prefix and
+postfix are intended for internal use. Supported values for file attributes
+are scalars and arrays of 64bit integer and 64bit floating point number as
+well as string values. Arrays of strings are not supported.
+
+2.1.1.1 Predefined file attributes
+
+__stepname__ (optional)
+	See below.
+
+__stepnumwidth__ (optional)
+	See below.
+
+2.1.2 Members of the root group
+
+Members of the root group are special formated HDF5 groups called
+"step groups".  The name of a step group is "<name>#<number>". 
+Whereby <name> is either defined by the optional file attribute
+__stepname__ or set to "Step" by default. <number> is an 
+unsigned integer less than 2^63. 
+
+/
++- Step#0
++- Step#1
+...
++- Step#n
++- StepProperties [NEW]
++- Mesh [NEW]
+
+The optional file attribute __stepnumwidth__ defines the minimum width
+of <number> in the name of the step group. The number is padded with
+'0'. The minimum width defaults to zero, so that no paddings occurs. 
+Example: With __stepnumwidth__ := 5 the name of the step group with
+number 42 is "Step#00042", with __stepnumwidth__ := 0 the name is
+"Step#42". 
+
+Step groups may be unsorted in the HDF5 file und needn't be number
+consecutively. 
+
+2.1.3 Other members of the root group
+
+Other sub-groups of the root group are allowed, but the group names are restricted
+to names not matching "Step#.*".
+
+2.2    Format of a step group
+
+2.2.1  Step attributes
+
+Step attributes are HDF5 attributes asigned to a step group.  There
+are no restrictions on step attribute names. As with file attributes names
+enclosed in "__" are intended for internal use. Supported values are the same
+as for file attributes:
+	* 64bit integer value
+	* arrays of 64bit integer values
+	* 64bit floating point number
+	* array of 64bit floating point number
+	* strings
+Note that array of strings are not supported! 
+
+2.2.2  Predefined step attributes
+
+No predefined step attributes exists.
+
+
+2.2.3  Members of a step group
+
+Members of a step group are HDF5 datasets and optional one HDF5 group
+with the name "Block". HDF5 datasets in a step group are called "step
+datasets". The optional block group is called "block data". 
+
+Mesh?!
+
+2.2.4  Step datasets
+
+Step datasets are arrays of rank 1.  The dataset size must be the same
+for all datasets inside a step.  The size of the dataset may vary
+from step to step.  Array values are 64bit integer or 64bit floating
+point numbers. No limitations (other than given by HDF5) are given on
+step dataset names.
+
+
+2.2.5  Block Data
+
+The block data group is a container for an arbitrary number of field
+data. A field is a data structure to store arrays of rank m with
+n-dimensional vector values. Fields are represented within HDF5
+groups. The HDF5 group name is the unique identifier for a field in
+the current step.
+
+2.2.5.1 m-rank fields with n-dimensional-vector values
+
+Values are stored per dimension in separate datasets. Thus we have n
+datasets for a field with n-dimensional vector values.  Each dataset
+corresponse to one dimension. The datasets are numbered from '0' to
+'n-1'. Arrays are stored in column major order (Fortran indexing
+scheme).
+
+/				# HDF5 root group
+...
++- Step#<i>			# HDF5 group
+   |
+   +- Block			# HDF5 group
+      |
+      +- <field name>		# HDF5 group
+         |
+         +- 0			# HDF5 dataset, first dim of vector
+	 +- 1			# HDF5 dataset, second dim of vector
+         ...
+        +- n-1			# HDF5 dataset, last dim of vector
+...
+
+2.2.5.2 m-rank fields with scalar values
+
+Fields with scalar values are stored as special case of fields with
+n-dimensional vector values with n := 1.
+
+/				# HDF5 root group
+...
++- Step#<i>			# HDF5 group
+   |
+   +- Block			# HDF5 group
+      |
+      +- <field name>		# HDF5 group
+         |
+         +- 0			# HDF5 dataset, scalar value
+...
+
+
+2.3    Step properties [NEW]
+
+Why? Much faster than step attributes if you need to access consecutive values
+
+Group of root group with name "StepProperties"
+
+Members are datasets
+
+Supported values are the same as for step attributes
+
+Mapping of value to step via object index of step group
+

doc/H5tools/H5tools.htm

@@ -1,417 +0,0 @@
-<html><head><title>H5Part Tools How-to</title>
-
-<meta http-equiv="Content-Type" content="text/html; charset=euc-kr"></head>
-<body bgcolor="#ffffff" text="#000000">
-
-<table border="0" cellpadding="0" cellspacing="0" width="987">
-  <tbody><tr> 
-    <td height="6050" width="27"></td>
-    <td colspan="3" valign="top"> 
-      <div id="body"> 
-        <div id="mainleft"><font face="Arial, Helvetica, sans-serif"><a name="TOP"></a> 
-          </font></div>
-        <div id="maincenter"> <font face="arial,helvetica"> 
-          <h1 align="center"><font face="Arial, Helvetica, sans-serif"><b><font color="#666699">H5Part 
-            Tools How-to</font></b></font></h1>
-          </font><font color="#555588" face="arial,helvetica"> 
-          <h2><font color="#666699" face="Arial, Helvetica, sans-serif">Table 
-            of Contents</font></h2>
-          </font> 
-          <p><font face="Arial, Helvetica, sans-serif"><b><a href="#Quick%20Guide"> 
-            [1] Quick Guide</a></b> </font></p>
-          <p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">--- 
-            For h5pAttrib</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
-            <b><br>
-            <a href="#timesteps">[2] To see number of timesteps in a h5part file</a><br>
-            <br>
-            <a href="#file%20attributes">[3] To see file attributes in a h5part 
-            file</a><br>
-            <br>
-            <a href="#step%20attributes"> [4] To see step attributes in a h5part 
-            file</a><br>
-            <br>
-            <a href="#dataset">[5] To see dataset in a h5part file</a><br>
-            <br>
-            <a href="#flags">[6] Providing more than one flag at once for h5pAttrib</a></b></font></p>
-          <p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">--- 
-            For h5pToGNUplot</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
-            <br>
-            <b><a href="#parameters">[7] What parameters to provide</a><br>
-            <br>
-            <a href="#input%20file">[8] How to create an input file to GNUplot</a></b></font></p>
-          <p>&nbsp;</p>
-          <p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back 
-            to top&gt;</a></font></p>
-          <p>&nbsp;</p>
-          <h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="Quick Guide">[1] 
-            Quick Guide</a></font></h2>
-          <p><font face="Arial, Helvetica, sans-serif">Executing the program with 
-            -h option will display a concise help page.</font></p>
-          <p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">./h5pAttrib 
-            -h</font></font></p>
-          <p><font face="Courier New, Courier, mono">usage: h5pAttrib [OPTIONS] 
-            file</font></p>
-          <p><font face="Courier New, Courier, mono"> OPTIONS<br>
-            -h, --help Print help page<br>
-            -n, --nstep Print number of steps<br>
-            -A, --fileA Print file attributes<br>
-            -a n, --stepA n Print step attributes &amp; values for time step n<br>
-            -d n, --dataset n Print data sets names &amp; values for time step 
-            n<br>
-            -H, --header Print shorter version without the values</font></p>
-          <p><font face="Courier New, Courier, mono"> Examples:</font></p>
-          <p><font face="Courier New, Courier, mono"> 1) Show file attribute names 
-            &amp; values of sample.h5part</font></p>
-          <p><font face="Courier New, Courier, mono"> h5pAttrib -A sample.h5part<br>
-            OR<br>
-            h5pAttrib --fileA sample.h5part</font></p>
-          <p><font face="Courier New, Courier, mono"> 2) Show step attribute names 
-            for time step 5 of sample.h5part</font></p>
-          <p><font face="Courier New, Courier, mono"> h5pAttrib -a 5 -H sample.h5part<br>
-            OR<br>
-            h5pAttrib --stepA 5 -H sample.h5part</font></p>
-          <p><font face="Courier New, Courier, mono"><br>
-            <b><font size="+1">$&gt;</font></b> ./h5pToGNUplot -h</font></p>
-          <p><font face="Courier New, Courier, mono">usage: h5pToGNUplot -t TIMESTEP 
-            -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]</font></p>
-          <p><font face="Courier New, Courier, mono"> FLAGS<br>
-            -h, --help Print help page</font><br>
-            <font face="Courier New, Courier, mono">-1 par, --1var par (REQUIRED) 
-            Takes first variable parameter to "par"<br>
-            -2 par, --2var par (REQUIRED) Takes second variable parameter to "par"<br>
-            -i file, --input file (REQUIRED) Takes input file name to "file"<br>
-            </font><font face="Courier New, Courier, mono">-t step, --timestep 
-            step (REQUIRED) Sets the timestep to "step" (Value -1 will 
-            result in dumping values of all timesteps.)<br>
-            -o file, --output file (OPTIONAL) Takes output file name to "file" 
-            (without this flag, the program will print to stdout)<br>
-            -n num, --number num (OPTIONAL) Sets number of output points to "num"<br>
-            -s idx, --start idx (OPTIONAL) Sets the starting particle index to 
-            "idx"</font></p>
-          <p><font face="Courier New, Courier, mono"><br>
-            Examples:</font></p>
-          <p><font face="Courier New, Courier, mono"> 1) Create GNU plot file 
-            output.txt from sample.h5part by ploting x vs px for timestep 54</font></p>
-          <p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x 
-            -2 px -i sample.h5part -o output.txt</font></p>
-          <p><font face="Courier New, Courier, mono"> 2) Create GNU plot file 
-            output.txt from sample.h5part by ploting x vs px for timestep 54<br>
-            using 1200 points from particle index 76</font></p>
-          <p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x 
-            -2 px -i sample.h5part -o output.txt -s 76 -n 1200</font></p>
-          <p>&nbsp;</p>
-    <p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back 
-            to top&gt;</a></font></p>
-          <p>&nbsp;</p>
-          <p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">--- 
-            For h5pAttrib</font></b></font></p>
-          <p>&nbsp;</p>
-          <h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="timesteps">[2] 
-            To see number of timesteps in a h5part file</a></font></h2>
-          <p>Executing the program h5pAttrib with -n flag will display the number 
-            of timesteps in the file.</p>
-          <p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
-          <p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono"> 
-            ./h5pAttrib -n sample.h5part</font></p>
-          <p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">Printing number of timesteps 
-            for: sample.h5part ...</font></p>
-          <p><font face="Courier New, Courier, mono">There are total 252 number 
-            of timesteps.<br>
-            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">done</font><font face="Arial, Helvetica, sans-serif"><br>
-            </font></p>
-          <p>&nbsp; </p>
-          <p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back 
-            to top&gt;</a></font></p>
-          <h2><font color="#666699" face="Arial, Helvetica, sans-serif"><br>
-            <font color="#555588"><a name="file attributes">[3] To see file attributes 
-            in a h5part file</a></font></font></h2>
-          <p>File attribute contains information about the file. (file description 
-            etc...) Executing the program h5pAttrib with -A flag will display 
-            the file attributes in the file.</p>
-          <p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
-          <p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono"> 
-            ./h5pAttrib -A sample.h5part</font></p>
-          <p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">Printing file attributes 
-            for: sample.h5part ...</font></p>
-          <p><font face="Courier New, Courier, mono">The number of file attributes 
-            for file sample.h5part is 0 ...<br>
-            There are no file attributes.<br>
-            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">done</font></p>
-          <p><font face="Arial, Helvetica, sans-serif"><br>
-            <i>NOTE: -H option will omit the list of values of file attributes.</i></font></p>
-          <p>&nbsp; </p>
-          <p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back 
-            to top&gt;</a></font></p>
-          <p align="center">&nbsp;</p>
-          <h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="step attributes">[4] 
-            To see step attributes in a h5part file</a></font></h2>
-          <p>Step attribute contains information that belongs to a specific step. 
-            (step name, timestep number, etc...) Executing the program h5pAttrib 
-            with -a flag will display the step attributes in the file.<br>
-            Note that the timestep index should follow -a flag.</p>
-          <p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
-          <p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono"> 
-            ./h5pAttrib -a 2 sample.h5part</font></font></p>
-          <p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">Printing step attributes 
-            for: sample.h5part ...</font></p>
-          <p><font face="Courier New, Courier, mono">The number of step attributes 
-            for timestep #2 is 10 ...</font></p>
-          <p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
-            There are 1 elements in the attribute<br>
-            Attribute Type is H5T_NATIVE_INT64<br>
-            Printing 1 element value(s):<br>
-            COUNT[0]: 2</font></p>
-          <p><font face="Courier New, Courier, mono">Attribute #1 = Spos<br>
-            There are 1 elements in the attribute<br>
-            Attribute Type is H5T_NATIVE_DOUBLE<br>
-            Printing 1 element value(s):<br>
-            COUNT[0]: 0.143580</font></p>
-          <p><font face="Courier New, Courier, mono">Attribute #2 = structLen<br>
-            There are 1 elements in the attribute<br>
-            Attribute Type is H5T_NATIVE_DOUBLE<br>
-            Printing 1 element value(s):<br>
-            COUNT[0]: 2.393000</font></p>
-          <p><font face="Courier New, Courier, mono">.<br>
-            .<br>
-            .</font></p>
-          <p><font face="Courier New, Courier, mono"><br>
-            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">done</font></p>
-          <p><font face="Arial, Helvetica, sans-serif"><br>
-            <i>NOTE: -H option will omit the list of values of step attributes.</i></font></p>
-          <p>&nbsp; </p>
-          <p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back 
-            to top&gt;</a></font></p>
-          <h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
-            <a name="dataset">[5] To see dataset in a h5part file</a></font></h2>
-          <p>Executing the program h5pAttrib with -d flag will display the datasets 
-            information in the file. (dataset name, type, number of elements, 
-            etc...) Executing the program h5pAttrib with -d flag will display 
-            the datasets information in the file.<br>
-            Note that the timestep index should follow -d flag.</p>
-          <p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
-          <p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono"> 
-            ./h5pAttrib -d 2 -H sample.h5part</font></p>
-          <p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">Printing names of datasets 
-            for: sample.h5part ...</font></p>
-          <p><font face="Courier New, Courier, mono">The number of datasets for 
-            timestep #2 is 7 ...</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
-            Dataset Type is H5T_NATIVE_INT64<br>
-            Number of elements: 67587</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 67587</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 67587</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 67587</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 67587</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 67587</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 67587</font></p>
-          <p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">done</font></p>
-          <p><font face="Arial, Helvetica, sans-serif"><br>
-            <i>NOTE: -H option will omit the list of values of datasets.</i></font></p>
-          <p>&nbsp; </p>
-          <p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back 
-            to top&gt;</a></font></p>
-          <p>&nbsp;</p>
-          <h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="flags">[6] 
-            Providing more than one flag at once</a></font></h2>
-          <p><font face="Arial, Helvetica, sans-serif">When more than one flags 
-            are provided, one result after another will be displayed.</font></p>
-          <p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
-          <p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono"> 
-            ./h5pAttrib -H -a 1 -d 1 sample.h5part</font></p>
-          <p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">Printing step attributes 
-            for: sample.h5part ...</font></p>
-          <p><font face="Courier New, Courier, mono">The number of step attributes 
-            for timestep #1 is 10 ...</font></p>
-          <p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
-            Attribute #1 = Spos<br>
-            Attribute #2 = structLen<br>
-            Attribute #3 = org<br>
-            Attribute #4 = maxX<br>
-            Attribute #5 = minX<br>
-            Attribute #6 = maxP<br>
-            Attribute #7 = minP<br>
-            Attribute #8 = centroid<br>
-            Attribute #9 = nloc<br>
-            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono"><br>
-            ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">Printing names of datasets 
-            for: sample.h5part ...</font></p>
-          <p><font face="Courier New, Courier, mono">The number of datasets for 
-            timestep #1 is 7 ...</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
-            Dataset Type is H5T_NATIVE_INT64<br>
-            Number of elements: 60214</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 60214</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 60214</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 60214</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 60214</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 60214</font></p>
-          <p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
-            Dataset Type is H5T_NATIVE_DOUBLE<br>
-            Number of elements: 60214</font></p>
-          <p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
-          <p><font face="Courier New, Courier, mono">done</font></p>
-          <p>&nbsp;</p>
-          <div align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back 
-            to top&gt;</a></font></div>
-        </div>
-      </div>
-    </td>
-  </tr>
-  <tr> 
-    <td height="80"></td>
-    <td colspan="3" valign="top"> 
-      <h2><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">--- 
-        For h5pToGNUplot</font></b></font></h2>
-      <h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="parameters">[7] 
-        What parameters to provide</a></font></h2>
-      <p><font face="Arial, Helvetica, sans-serif">When you execute the program 
-        with -h option, it displays what flags are necessary and what flags are 
-        optional.</font></p>
-    </td>
-  </tr>
-  <tr> 
-    <td height="200"></td>
-    <td valign="top" width="137"> 
-      <p align="left"><b><font face="Arial, Helvetica, sans-serif">Short Version</font></b></p>
-      <p><font face="Arial, Helvetica, sans-serif">-h<br>
-        -1<br>
-        -2<br>
-        -i<br>
-        -t<br>
-        -o<br>
-        -n<br>
-        -s </font></p>
-    </td>
-    <td valign="top" width="144"> 
-      <p align="left"><b><font face="Arial, Helvetica, sans-serif">Long Version</font></b></p>
-      <p><font face="Arial, Helvetica, sans-serif">--help<br>
-        --1var<br>
-        --2var<br>
-        --input<br>
-        --timestep<br>
-        --output<br>
-        --number<br>
-        --start </font></p>
-    </td>
-    <td valign="top" width="679"> 
-      <p align="left"><b><font face="Arial, Helvetica, sans-serif">Meanings</font></b></p>
-      <p><font face="Arial, Helvetica, sans-serif">Print help page<br>
-        (REQUIRED) Takes first variable parameter<br>
-        (REQUIRED) Takes second variable parameter<br>
-        (REQUIRED) Takes input file name<br>
-        (REQUIRED) Sets the timestep (Value -1 will result in dumping values of 
-        all timesteps.)<br>
-        (OPTIONAL) Takes output file name (without this flag, the program will 
-        print to stdout)<br>
-        (OPTIONAL) Sets number of output points<br>
-        (OPTIONAL) Sets the starting particle index</font> </p>
-    </td>
-  </tr>
-  <tr> 
-    <td height="1786"></td>
-    <td colspan="3" valign="top"> 
-      <p>&nbsp;</p>
-      <p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back 
-        to top&gt;</a></font></p>
-      <h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
-        <a name="input file">[8] How to create an input file to GNUplot</a></font></h2>
-      <p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b><br>
-        <i>Create input file to GNUplot that plots x vs. y.</i></font></p>
-      <p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono"> 
-        ./h5pToGNUplot -1 x -2 y -t 1 -i sample.h5part -o output.txt<br>
-        <b><font size="+1">$&gt;</font></b> cat output.txt<br>
-        -0.390779 -0.254793<br>
-        -0.396527 -0.252781<br>
-        -0.375362 -0.285137<br>
-        -0.396527 -0.252781<br>
-        -0.379917 -0.283147<br>
-        -0.390779 -0.254793<br>
-        -0.387536 -0.287346<br>
-        -0.371787 -0.319797<br>
-        -0.379917 -0.283147<br>
-        -0.378967 -0.326058<br>
-        -0.378976 -0.326078<br>
-        -0.387536 -0.287346<br>
-        -0.378957 -0.326069<br>
-        -0.379917 -0.283147<br>
-        -0.388762 -0.265390<br>
-        -0.371787 -0.319797<br>
-        -0.390779 -0.254793<br>
-        -0.376825 -0.266804<br>
-        -0.379917 -0.283147<br>
-        -0.375362 -0.285137<br>
-        ...</font></font></p>
-      <p><font face="Courier New, Courier, mono"><i>Then run GNUplot...</i></font></p>
-      <p><font face="Courier New, Courier, mono"><b><font size="+1">$&gt;</font></b> 
-        gnuplot</font></p>
-      <p><font face="Courier New, Courier, mono"> G N U P L O T<br>
-        Version 4.0 patchlevel 0<br>
-        last modified Thu Apr 15 14:44:22 CEST 2004<br>
-        System: Linux 2.6.11.4-21.11-smp</font></p>
-      <p><font face="Courier New, Courier, mono"> Copyright (C) 1986 - 1993, 1998, 
-        2004<br>
-        Thomas Williams, Colin Kelley and many others</font></p>
-      <p><font face="Courier New, Courier, mono"> This is gnuplot version 4.0. 
-        Please refer to the documentation<br>
-        for command syntax changes. The old syntax will be accepted<br>
-        throughout the 4.0 series, but all save files use the new syntax.</font></p>
-      <p><font face="Courier New, Courier, mono"> Type `help` to access the on-line 
-        reference manual.<br>
-        The gnuplot FAQ is available from<br>
-        http://www.gnuplot.info/faq/</font></p>
-      <p><font face="Courier New, Courier, mono"> Send comments and requests for 
-        help to<br>
-        &lt;gnuplot-info@lists.sourceforge.net&gt;<br>
-        Send bugs, suggestions and mods to<br>
-        &lt;gnuplot-bugs@lists.sourceforge.net&gt;</font></p>
-      <p><font face="Courier New, Courier, mono"><br>
-        Terminal type set to 'x11'<br>
-        <font size="+1"><b>gnuplot&gt;</b></font> plot "output.txt"</font></p>
-      <p><font face="Arial, Helvetica, sans-serif"><i>This will open a GNUplot 
-        window that plots output.txt.</i></font></p>
-      <p align="center"><img src="H5tools_files/snapshot1.jpg" height="541" width="672"><br>
-        <font face="Arial, Helvetica, sans-serif">&lt;Sample screen shot of GNUplot 
-        with input datafile generated by h5pToGNUplot&gt;</font></p>
-    </td>
-  </tr>
-  <tr> 
-    <td height="44"></td>
-    <td></td>
-    <td></td>
-    <td></td>
-  </tr>
-</tbody></table>
-</body></html>

doc/H5xxx/H5xxx.tex

@@ -1,345 +0,0 @@
-\documentclass[acus]{JAC2003}
-
-%%
-%%  Use \documentclass[boxit]{JAC2003}
-%%  to draw a frame with the correct margins on the output.
-%%
-%%  Use \documentclass[acus]{JAC2003}
-%%  for US letter paper layout
-%%
-
-\usepackage{graphicx}
-
-%%
-%%   VARIABLE HEIGHT FOR THE TITLE BOX (default 35mm)
-%%
-
-\setlength{\titleblockheight}{40mm}
-
-\begin{document}
-\title{H5Pie: A Portable High Performance Parallel Data Interface for Electromagnetics Simulations Including Particles\thanks{
-This work (LBNL-57607) was supported by the Director, Office of Science, Office of Advanced Scientific Computing Research, of the U.S. Department of Energy under Contract No. DE-AC03-76SF00098 and the DOE SciDAC project on ``Advanced Computing for 21st Century Accelerator Science and Technology.''.
-}}
-
-\author{A. Adelmann, A. Gsell, B. Oswald, PSI, Villigen, Switzerland \\ 
-        R.D. Ryne, LBNL/AFR, Berkeley, California, USA\\
-        W. Bethel, J.M. Shalf, C. Siegerist, LBNL/NERSC, Berkeley, California, USA}
-
-\maketitle
-\begin{abstract}
-The very largest parallel particle simulations, for problems 
-involving six dimensional phase space,
-generate vast quantities of data. It is desirable to 
-store such enormous datasets efficiently and also to share data 
-effortlessly between data analysis tools 
-such as VisIt or ParaView
-among other groups who are working on particle-based accelerator
-simulations. We define a very simple file schema built on top of HDF5~\cite{hdf5hp}
-(Hierarchical Data Format version 5) as well as an API that simplifies
-the reading/writing of the data to the HDF5 file format. HDF5 offers a
-self-describing machine-independent binary file format that supports
-scalable parallel I/O performance for MPI codes on computer systems
-ranging from laptops to supercomputers. 
-
-H5Pie is actually a composition of three parts. On a very abstract view we have,
-H5Part  which handles the macro particles of a simulation. H5Mesh defines the (spatial) geometry of the
-computational domain and H5Fields represents scalar and vector filds. (H5Pie = H5{\bf P} art + H5F{\bf i}eld+ H5M{\bf e}sh)
-
-
-The sample H5Pie
-API will be available for C, C++, and Fortran codes. 
-The common file format will enable groups that
-use completely different simulation implementations to transparently share
-datasets.
-\end{abstract}
-
-\section{Motivation}
-The motivation for this undertaking is to create a file format that is
-suitable for large-scale parallel simulation codes.   
-A suitable data format must have the following properties: 
-it must be a machine-independent binary representation that is 
-self-describing, easily extensible, language independent, efficient
-(both for serial and parallel), and produces files that are seamlessly sharable
-between different programs.  In the following sections we describe 
-the motivation for these features and how they can be accomplished
-using the proposed implementation.
-
-\subsection{Machine Independence}
-Processor architectures use different binary representations
-for data.  While the IEEE 754 standard has decreased the number of
-differing floating point number represenations, byte-order still remains
-a source of incompatibility.  While it is trivial to byte-swap a file from
-a programming standpoint, it creates a number of long-term file management
-difficulties for groups that are sharing or maintaining a repository of simulation
-data.  Given files that store data structures with differently sized elements,
-one must know the storage format precisely in order to apply byte-swapping
-properly. 
-HDF5 does not suffer from these problems because the file format is completely
-self-describing and the internal binary structures are all machine independent.
-The HDF5 library is able to convert data that is stored in any native machine 
-represenation in the data file into a native binary representation in memory 
-as part of the reading process with little performance penalty.
-
-\subsection{Language Independence}
-The three most common languages used for implementing applications 
-in the arena of computational sciences are
-Fortran, C and C++. The file format and associated API must hide
-differences in the binary file-storage conventions of these languages
-as well as offering native API bindings for each of these 
-programming languages.
-
-For instance, Fortran unformatted binary files contain integer fields
-at the beginning and the end of each record that describe the length
-of the record.  The size of these integer tags is usually 32-bits, but some
-fortran compiler implementations will use larger tags in order to represent
-larger record sizes. C and C++ binary files have no such convention for 
-record-oriented storage.  The language-dependent differences in 
-binary storage layout conventions
-can cause difficulties for scientists who wish to share data files between 
-Fortran and C/C++ implementations of a code, or with visualization tools
-that are primarily written in C/C++.  The API bindings and underlying file format
-provided by the H5Part API and the underlying HDF5 file format are able to
-hide these differences in order to provide symmetric access via all languages.
-
-\subsection{Self-Describing}
-The data is accessed by names, for example, one might ask for `the
-column of data called $p_x$' -- affording a layer of file-layout independence.
-In other words, self-describing data is
-not accessed by a position in a file but by name of the datasets.  Various attributes
-of the data that may be necessary to using it are available. For
-example, one can ask ``what are the units of column $p_x$?'. 
-
-There are a number of examples of self-describing file formats.  Examples include HDF earlier HDF implementations leading up to HDF version 5 and the Unidata NetCDF format.  Another
-very popular approach is the Self Describing Data Sets (SDDS) \cite{SDDS} although it 
-is only serial in nature. HDF5 is a complete rewrite of the HDF file format that supports
-parallel I/O and offers a much leaner, more flexible interface.
-Because it is self-describing, the entire contents of an HDF5 file can be
-browsed and even converted to ASCII text, including XML syntax text files,
-using the built-in 'h5ls' and 'h5dump' 
-tools without specific knowledge of the internal file format.
-
-\begin{figure}[htb]
-\begin{minipage}[b]{0.5\textwidth}
-%\includegraphics[scale=0.095]{./partview1.eps}
-%\includegraphics[scale=0.097]{./density70.eps}
-\end{minipage}
-\caption{color: A common self-describing file format allows different codes to share a common set of visualization and data analysis tools.  PartView and AVS/Express, pictured above, are able to read and display contents of  an H5Part/HDF5 file written on any machine in any language, regardless of how many processors are used.}
-\label{fig:vis}
-\end{figure}
-
-The primary advantage of accessing data and its attributes is that one
-can then construct more flexible data manipulation tools that are capable
-of surviving the natural evolution of file formats.  Data formats can be extended
-to include additional information without breaking older file readers. 
-Self-describing data contains all the information
-that analysis tools need to manipulate various types of data
-correctly. Two examples of such tools using the proposed file format
-are shown in Figure ~\ref{fig:vis} As a result, data exchange between different simulations tools is
-much simpler, robust  and better defined by using self-describing data sets. 
-
-\subsection{High Performance}  
-The HDF5 file format allows data elements to be written to disk in the
-native binary representation.  The file format stores a description of
-the native data representation of the machine that wrote the data so
-that it can be automatically translated to the native binary
-representation of the machine that reading the data (eg. if the byte
-order differs). In contrast to XDR, where the data always gets
-translated to/from an intermediate machine-neutral format, the HDF5
-data conversion only occurs if the stored data represenation is
-different from the native binary representation of the machine that is
-reading the file, so there is no performance penalty if the machines
-have the compatible binary data formats. [ada: need work] In general, HDF5 offers
-performance that is very close to what can be achieved by writing an
-ad-hoc machine-dependent binary for F77 unformatted data file.
-
-\subsection{Parallel I/O}
-HDF5 also supports parallel I/O capabilities for MPI programs. 
-The naive approach to writing data from a parallel program is to
-write one file per processor.  While this is simple to implement and
-very efficient on most cluster filesystems, it leads to file management 
-headaches when it comes the time to analyze the data.  One must either
-recombine these separate files into a single file or create ponderous
-user-interfaces that allow a data analysis application to read from a
-directory full of files instead of just one file.
-
-Parallel I/O methods, allow you to write data into a single file from all
-of the tasks of a parallel program.  The performance is typically lower
-than that of writing one-file-per-processor, but it makes data management
-much simpler after the program has finished.  No additional recombining
-steps are required to make the file accessible by vis-tools or for
-restarting a simulation using a different number of processors.
-
-Parallel HDF5 uses MPI-I/O for its low-level implementation.  The 
-mechanics of using MPI-I/O are all hidden from the user by our
-H5Part file API (the code looks nearly identical to reading/writing the data
-from a serial program).  While the performance is not as good as
-writing one-file-per-processor, we demonstrate that writing files
-with Parallel HDF5 is consistently faster than writing the data
-in raw/native binary using the MPI-I/O library.  This efficiency is
-made possible through sophisticated HDF5 tuning directives that
-control data alignment and caching within the HDF5 layer.  
-Therefore, we argue that it would be difficult to match
-HDF5 performance even using a home-grown binary file format.
-
-\section{H5Mesh File Organization and API}
- 
-\section{H5Field File Organization and API}
-
-\section{H5Part File Organization and API}
-The proposed file storage format uses HDF5 for the low-level file
-storage and a simple API to provide a high-level interface to that
-file format.  A programmer can either use the H5Part API to access
-the data files or write directly to the file format using some simple
-conventions for organizing and naming the objects stored in the
-file.
-
-The HDF5 format, its benefits, and its file organization is decribed
-at \cite{hdf5hp}.  The file format was also adopted by the DOE
-ASCI-VIEWS effort, so the library has been tuned and adapted to read
-and write data efficiently on large-scale parallel computing
-systems. We adopted HDF5 for our file storage needs because it offers
-all that is needed as stipulated in the motivation section.
-
-We describe now the H5Part conventions for storing
-objects in the HDF5 file as well as some examples of the API.
-\subsection{H5Part File Organization}
-In order to store Particle Data in the HDF5 file format, we have
-formalized the hierarchical arrangement of the datasets and naming 
-conventions for the groups and associated datasets.  The sample H5Part API formally 
-encodes these conventions in order to provide a simple and uniform
-way to access these files from C, C++, and Fortran codes.  The API makes
-it easier to write very portable data adaptors for visualization tools in order to
-expand the number of tools available to access the data.  Even so,
-anyone can use the HDF5 $h5ls$ utility to examine the organization 
-of the H5Part files and even write their own HDF5-based interface for reading and writing the
-file format. The standards offered by the sample API are completely independent of the
-standard for organizing data within the file.
-
-The file format supports the storage of multiple timesteps of
-datasets that contain multiple fields. The fields correspond to different properties of
-the particles at that particular time step -- for instance, 
-the 3-dimensional cartesian position of the particles 
-$(X,Y,Z)$ as well as the 3-dimensional phase of each 
-particle $(PX,PY,PZ)$. These two degrees of freedom
-are organized such that the timesteps are groups (time groups) that are added sequentially
-to the root group (``/'').  The fields are datasets that are nested within the 
-time groups.  The convention for naming the time group is $Particles<integer>$ where $<integer>$ is a monotonically increasing counter for the number of timesteps stored in the file.  
-
-The fields contained within a given time group are simply named for the property of the particle they represent.   For instance, the phase of the particle stored in a simulation variable called 'px' is simply named $``px''$. The field names are user-defined and 
-can be understood automatically by the visualization 
-tools that read the file. The only other convention is that each time group must contain the same set of fields -- the contents of the fields will change, but the set of names for these fields must remain the same for all timesteps.
-
-The fields can be either integer or real data types.  Initially, the file format supports double precision float and 64-bit integers in order to simplify the requirements for file readers, but HDF5 is capable of automatically down-converting to 32-bit data types upon request.  The API will be extended accordingly to support these conversions.
-
-Finally, the file, the individual timesteps, and the individual data arrays can contain {\em attributes} that provide additional information about the data.  For instance, the datasets can be annotated with attributes containing {\em units} for a given data field, simulation parameters, or code revision information.  The {\em attributes} are key-value pairs where the $key$ is a string that is associated with the file, group, or dataset, and the $value$ is either a string, a real value, or an integer associated with that key.  
-
-%Visualization and data analysis tools can take advantage of this additional information if they are programmed to recognize it, but less-sophisticated tools can safely ignore it without compromising their ability to read the file format.
-
-% ada: to philosophic for a 3 page paper, although it is very important and of course right!
-%The ability to ignore such information is arguably one of the most powerful capabilities of the HDF5 file format.  Whereas changes to headers or data layout in conventional, non-self-describing file formats can render an older reader interface useless, one can continuously add new descriptive information to the HDF5 file without having any detrimental effect on readers that were designed to work with older versions of the file format.  This provides enormous benefits for the long term maintenance and evolution of the file format.
-
-\section{GENERAL FORM IN PSEUDOCODE}
-In Figure \ref{fig:usage} we show the very simple API for writing
-data. The API for reading is almost symmetric. It is also worth to
-note that there are minimal differences whether one read/write serial
-or in parallel. The API consists of a small number of C, C++ and
-Fortran functions and will be described elsewhere.
-In the parallel case the original domain decomposition can be used or
-the data can be decomposed according to the new number of processor
-nodes available.
-The resulting HDF5 file will contains a simple directory structure that can be navigated using the generic 'h5ls' utility;
-\begin{figure}[h!] \label{fig:sbendVect}
-\newsavebox{\gogo}
-        \setbox\gogo=\hbox{%
-        \begin{minipage}{0.4\textwidth}
-        \small
-        \begin{tabbing}
-        111111\=aaaa\=aaaa\=aaaa\=\kill
-\texttt{if(not parallel);}\\ 
-\quad\texttt{filehandle=OpenFile(filename,mode)} \\
-\texttt{else}\\ 
-\quad\texttt{filehandle=OpenFile(filename,mode,mpicomm)} \\
-\texttt{SetNumberOfParticles(filehandle);}\\
-\texttt{loop(step=1,NSteps);}\\ 
-\quad\texttt{SetStep(filehandle,step);}\\
-\quad\texttt{WriteData(filehandle,fieldname1,data1);}\\
-\centerline{\texttt{{\bf write more data}}}\\
-\quad\texttt{WriteData(filehandle,fieldname<n>,data<n>);}\\
-\texttt{CloseFile(filehandle);}
-\end{tabbing}
-\end{minipage}
-}
-\fbox{\usebox{\gogo}}
-\caption{Usage of H5Part in pseudo-code}
-\label{fig:usage}
-\end{figure}
-
-% \begin{figure}[h!] \label{fig:sbendVect}
-% \newsavebox{\gugu}
-%        \setbox\gugu=\hbox{%
-%        \begin{minipage}{0.4\textwidth}
-%        \small
-%        \begin{tabbing}
-%        111111\=aaaa\=aaaa\=aaaa\=\kill
-%\texttt{/Particles1/fieldname1 } \\
-%\texttt{/Particles1/fieldname2} \\
-%\texttt{ . . . } \\
-%\texttt{/Particles1/fieldname<n> } \\
-%\texttt{/Particles2/fieldname1} \\
-%\texttt{ . . .}\\
-%\texttt{ /Particles<nsteps>/fieldname<n>}
-%\end{tabbing}
-%\end{minipage}
-%}
-%\fbox{\usebox{\gugu}}
-%\end{figure}
-\vspace{-5mm}
-\section{PERFORMANCE}
-% [ada] We also have data for 4 procs
-% [ada] name for one file per proc
-Preliminary performance estimations, looking at global (GD) and local data (LD)
-rates, suggests that our HDF5 writing has a very good performance even
-with respect to raw mpi, as shown in Table \ref{tab:perf}.
-\begin{table}[h!]
-\begin{flushleft} \footnotesize
- \begin{tabular}{|l|l|l|}
-\hline
-\bf Mode & \bf GD [MB/s]  & \bf LD [MB/s]\\
-\hline
-mpi-io (one file) & 241 & 3.7 \\
-\hline
-one file per proc & 1288 & 20 \\
-\hline
-H5Part/pHDFf5 (one file) & 773 & 12 \\
-\hline
-\end{tabular}
-\end{flushleft}
-\caption{\label{tab:perf}{64 IBM SP-3 nodes writing $51e6$ particles (6D). }}
-%, each having 6 double-precision floating point fields for 64 timesteps over 3 trials.}}			  
-\end{table}
-\vspace{-4mm}
-\section{Conclusions and Future Work}
-The file format will be extended in the near future to integrate fast bitmap indexing 
-technology~\cite{DEX} in order to provide accelerated queries of data
-stored in the file. With fastbit technolgy, a user can efficiently extract subsets of data
-using compound query expressions such
-as {\it $(velocity > 1e6)$ AND $(0.4 < phase < 1.0)$}. 
-%Such a query-driven approach offers advantages over scalable technologies aimed at visualizing ever-larger datasets.
-
-We are also constantly tuning the performance of the parallel data
-file format implementation.  We will also be porting the H5Part reader
-to a wider variety of visualization tools. 
-%in order to expand the arena
-%of tools available for analyzing the stored particle data.
-\begin{thebibliography}{9}   % Use for  1-9  references
-\bibitem{FPAT082}
-A. Adelmann, R.D Ryne, C. Siegerist, J. Shalf, "From Visualization to Data Mining With Large Datasets," PAC, 2005.
-\bibitem{hdf5hp}
-HDF5 Home Page, http://hdf.ncsa.uiuc.edu/HDF5.
-\bibitem{SDDS}
-Definitions and libraries for SDDS implementation may be found at the link http://www.aps.anl.gov/asd/oag/oagPackages.shtml.
-\bibitem{DEX}
-K. Stockinger, J. Shalf, W. Bethel, K. Wu. "DEX: Increasing the Capability of Scientific Data Analysis Pipelines by Using Efficient Bitmap Indices to Accelerate Scientific Visualization." Scientific and Statistical Database Management Conference (SDDBM), 2005.
-\end{thebibliography}
-
-\end{document}

doc/H5xxx/JAC2003.cls

@@ -1,217 +0,0 @@
-%%
-%% This file has been developed as a common template for papers
-%% destined for electronic production using Adobe Acrobat
-%% software for Accelerator Conferences
-%%
-%% See the JACo Website for more information
-%% 
-%%       http://www.cern.ch/accelconf/
-%%
-
-%  Special thanks to John Jowett and Michel Goossens from CERN and
-%  Martin Comyn at TRIUMF for their significant contributions to 
-%  this class file over the period 1996 to 2000.
-%                                                 John Poole
-%                                                 March 2000
-
-
-%  JAC2001.cls is a modified version of JAC2000.cls to produce indented
-%  first paragraphs after section, subsection and subsubsection headings.
-%
-%                                                 Martin Comyn  April 2001
-
-\def\fileversion{1.2}
-\def\filedate{2003/03/10}
-\def\docdate {2003/03/10}
-
-\newlength{\dsep}
-\newlength{\dwid}
-\newlength{\dht}
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesClass{JAC2003}[\filedate\space Version \fileversion]
-\DeclareOption{acus}
-   {\setlength{\dwid}{6mm}%
-    \setlength{\dht}{-18mm}
-    \setlength{\paperheight}{11in}
-    \setlength{\paperwidth}{8.5in}
-    \typeout{Setup for US LETTER PAPER}}
-\DeclareOption{aca4}
-   {\setlength{\dwid}{0mm}%
-    \setlength{\dht}{0mm}}
-\DeclareOption{boxit}
-%%
-%%  This option draws a box on the output text with the correct margins
-%%
-   {\special{!userdict begin /bop-hook{
-         gsave
-         newpath
-         58 55 moveto
-         58 737 lineto
-         539 737 lineto
-         539 55 lineto
-         closepath
-         stroke
-         grestore
-         }def end}}
-\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
-
-\ExecuteOptions{aca4}
-\ProcessOptions
-
-\LoadClass[10pt]{article}
-%%
-%%  Using Times fonts produces a Uniform, compact document
-%%  suitable for the Acrobat Software and printable anywhere.
-%%
-%%  In a 'modern' TeX installation 
-%%  e.g TeXLive Version 3 or later (more information on the JACo Website)
-%%  one can use the following command
-%%
-
-\renewcommand{\rmdefault}{ptm}
-
-%%
-%%  Older installations may require
-%%              \RequirePackage{times}
-%%
-\typeout{------------------------------------------------------------------------}
-\typeout{LaTeX2e Class file for Accelerator Conference publication for LaTeX2e users}
-\typeout{ }
-\typeout{Use the boxit option to draw a box on page showing the correct margins}
-\typeout{ }
-\typeout{Itemize, Enumerate and Description environments are compact versions}
-\typeout{------------------------------------------------------------------------}
-\typeout{ }
- 
-%
-% DIMENSION OF TEXT:
- 
-\setlength{\textheight}{241mm}
-\setlength{\textwidth}{170mm}
-\setlength{\topmargin}{23mm}
-\addtolength{\topmargin}{\dht}
-\setlength{\oddsidemargin}{20mm}
-\setlength{\evensidemargin}{20mm}
-\setlength{\columnsep}{5mm}
-
- 
-\hoffset -25.4mm
-\voffset -25.4mm
- 
-\columnseprule 0pt      %    Width of rule between columns.
- 
-% Use Michel Goossens' dense lists
-% Prevent infinite loops
-
-\let\Otemize =\itemize
-\let\Onumerate =\enumerate
-\let\Oescription =\description
-% Zero the vertical spacing parameters
-\def\Nospacing{\itemsep=0pt\topsep=0pt\partopsep=0pt\parskip=0pt\parsep=0pt}
-% Redefine the environments in terms of the original values
-\newenvironment{Itemize}{\Otemize\Nospacing}{\endlist}
-\newenvironment{Enumerate}{\Onumerate\Nospacing}{\endlist}
-\newenvironment{Description}{\Oescription\Nospacing}{\endlist}
-
-\renewcommand{\topfraction}{.95}
-\renewcommand{\bottomfraction}{.95}
-\renewcommand{\textfraction}{0.1}
-\renewcommand{\floatpagefraction}{0.8}
- 
-\def\@oddhead{}\def\@evenhead{}
-\def\@oddfoot{}
-\def\@evenfoot{\@oddfoot}
- 
-%-----------------------------------------------------------------------
-% We acknowledge the borrowing of the clever part of
-% Steven Gildea's definition of \section
-% from geophysi.sty.
-%
-% \section is tricky because we want to both support \section* and have
-% the section title uppercased.
- 
-\def\section{\secdef\@sectionb\@sections}
-\def\@sectionb[#1]#2{\@sections{#2}}
-\def\@sections#1{\@startsection {section}{1}{\z@}
-                {2.8ex plus 0.8ex minus .1ex}{1.5ex plus .2ex}
-                {\large\bf\boldmath\centering}{\uppercase{#1}}}
-% Should there be any problem with this, we can revert to the following
-% but then the onus is on the user to type the argument of \section in
-% uppercase in the input file.
-%
-%\def\section{\@startsection {section}{1}{\z@}{2.8ex plus 0.8ex minus.1ex}
-%                          {1.5ex plus .2ex}{\large\bf\boldmath\centering}}
- 
-\def\subsection{\@startsection{subsection}{2}{\z@}{2.6ex plus .8ex minus
-   .17ex}{1.2ex plus .17ex}{\large\it}}
-\def\subsubsection{\@startsection{subsubsection}{3}{\parindent}
- {2.5ex plus .7ex minus .17ex}{-1em}{\normalsize\bf}}
-\def\paragraph{\@startsection
-     {paragraph}{4}{\z@}{2.5ex plus .7ex minus .17ex}{-1em}{\normalsize\it}}
-\def\subparagraph{\@startsection
-     {subparagraph}{4}{\parindent}{2.25ex plus .7ex minus
-     .17ex}{-1em}{\normalsize\bf}}
- 
-\setcounter{secnumdepth}{0}
- 
-% This definition of \maketitle taken from article.sty, and has been
-% somewhat modified.
- 
-\def\maketitle{\par
- \begingroup
-   \def\thefootnote{\fnsymbol{footnote}}
-   \def\@makefnmark{\hbox
-       to 5pt{$^{\@thefnmark}$\hss}}
-   \twocolumn[\@maketitle]
-   \@thanks
- \endgroup
- \setcounter{footnote}{0}
- \let\maketitle\relax
- \let\@maketitle\relax
- \gdef\@thanks{}\gdef\@author{}\gdef\@title{}\let\thanks\relax}
- 
-\newlength{\titleblockheight}       % so user can change it if need be
-\setlength{\titleblockheight}{3.5cm}
- 
- 
-\def\@maketitle{\vbox to \titleblockheight {\hsize\textwidth
-  \linewidth\hsize \vskip 3pt \centering
-  {\Large\bf \@title \par}
-  \vskip 2em                % Vertical space after title.
-  {\large\begin{tabular}[t]{@{}c@{}}\@author \end{tabular}\par}
-  \vfil}}
- 
- 
-% The \copyrightspace command is used to produce a blank space in the first
-% column where a copyright notice may go.  It works by producing a
-% blank footnote of the appropriate size.  Note that it should appear
-% after any \footnote commands that produce footnotes for the first
-% column.   Adjusted to leave just 1cm.
- 
-\def\copyrightspace{\footnotetext[0]{\mbox{}\vrule height 1cm width 0pt}}
- 
-\def\abstract{\subsection*{Abstract}}
-\def\endabstract{\par}
- 
-% Redefine to use smaller fonts
-\def\thebibliography#1{\setlength{\itemsep}{0pt}\setlength{\parsep}{0pt}
-  \section*{REFERENCES\@mkboth
-  {REFERENCES}{REFERENCES}}\small\list
-  {[\arabic{enumi}]}{\settowidth\labelwidth{[#1]}\leftmargin\labelwidth
-    \advance\leftmargin\labelsep
-    \usecounter{enumi}}
-    \def\newblock{\hskip .11em plus .33em minus .07em}
-    \sloppy\clubpenalty4000\widowpenalty4000
-    \sfcode`\.=1000\relax}
- 
-\let\endthebibliography=\endlist
- 
-\twocolumn
-\sloppy
-\parindent 1em
-\leftmargini 2em
-\leftmargin\leftmargini
-\leftmarginv .5em
-\leftmarginvi .5em
-\flushbottom
-%-----------------------------------------------------------------------

doc/H5xxx/makefile

@@ -1,14 +0,0 @@
-#################################################                             
-##BEGIN OF makefile "makefile" - using the gnu-compiler g++                    
-##This file is used by the Make command.                                       
-###################################################                           
-
-FILE=H5xxx
-
-all:	$(FILE).tex 
-	latex $(FILE).tex
-#bibtex $(FILE)
-	dvips -j0 $(FILE).dvi -o $(FILE).ps 
-#	dvips $(FILE).dvi -o $(FILE).ps -x 1200 -O 10mm,15mm
-clean:		
-	rm *~ *.bbl *.aux *.blg *.log *.dvi *.ps 

doc/InternalLayout.html

@@ -1,54 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>H5Part, Logical Internal HDF5 File Layout</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-
-<div id="maincenter">
-<font face="arial,helvetica"><h1>H5Part: Logical Internal HDF5 File Layout</h1></font>
-<P>
-HDF5 is extremely flexible in the sense that it allows the user to define a higher level data model to describe domain-specific data relationships. This flexibility however makes it necessary to develop an agreement on the logical layout of the data.  The H5Part data model consists of Particle groups corresponding to the simulation time steps, each with seven datasets corresponding to x, px, y, py, z, pz, id for each particle. Attributes can be added to the file and to the datasets.
-</P>
-<center><img src="layout.png"></center>
-<PRE>
-HDF5 "parttest.h5" {
-GROUP "/" {
-   GROUP "Particles#0" {
-      DATASET "id" {
-         DATATYPE  H5T_STD_I64LE
-         DATASPACE  SIMPLE { ( 10 ) / ( 10 ) }
-      }
-      DATASET "px" {
-         DATATYPE  H5T_IEEE_F64LE
-         DATASPACE  SIMPLE { ( 10 ) / ( 10 ) }
-      }
-      DATASET "py" {
-         DATATYPE  H5T_IEEE_F64LE
-         DATASPACE  SIMPLE { ( 10 ) / ( 10 ) }
-      }
-      DATASET "pz" {
-         DATATYPE  H5T_IEEE_F64LE
-         DATASPACE  SIMPLE { ( 10 ) / ( 10 ) }
-      }
-      DATASET "x" {
-         DATATYPE  H5T_IEEE_F64LE
-         DATASPACE  SIMPLE { ( 10 ) / ( 10 ) }
-      }
-      DATASET "y" {
-         DATATYPE  H5T_IEEE_F64LE
-         DATASPACE  SIMPLE { ( 10 ) / ( 10 ) }
-      }
-      DATASET "z" {
-         DATATYPE  H5T_IEEE_F64LE
-         DATASPACE  SIMPLE { ( 10 ) / ( 10 ) }
-      }
-   }
-</PRE>
-<P>
-See <a href="http://www-vis.lbl.gov/Publications/2002/hdf5.pdf">hdf5.pdf</a> for an introduction on the use of HDF5.
-</P>
-</div>
-

doc/Makefile.am

@@ -0,0 +1,2 @@
+EXTRA_DIST = \
+	Doxyfile doxyfooter

doc/ReferencePages/H5Part_8h-source.html

@@ -1,146 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
-<title>H5Part: H5Part.h Source File</title>
-<link href="doxygen.css" rel="stylesheet" type="text/css">
-</head><body>
-<!-- Generated by Doxygen 1.4.4 -->
-<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
-<h1>H5Part.h</h1><a href="H5Part_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#ifndef _H5Part_H_</span>
-<a name="l00002"></a>00002 <span class="preprocessor"></span><span class="preprocessor">#define _H5Part_H_</span>
-<a name="l00003"></a>00003 <span class="preprocessor"></span>
-<a name="l00004"></a>00004 <span class="preprocessor">#include &lt;hdf5.h&gt;</span>
-<a name="l00005"></a>00005 <span class="preprocessor">#ifdef PARALLEL_IO</span>
-<a name="l00006"></a>00006 <span class="preprocessor"></span><span class="preprocessor">#include &lt;mpi.h&gt;</span>
-<a name="l00007"></a>00007 <span class="preprocessor">#endif</span>
-<a name="l00008"></a>00008 <span class="preprocessor"></span>
-<a name="l00016"></a><a class="code" href="structH5PartFile.html">00016</a> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structH5PartFile.html">H5PartFile</a> {
-<a name="l00017"></a><a class="code" href="structH5PartFile.html#o0">00017</a>   hid_t <a class="code" href="structH5PartFile.html#o0">file</a>;
-<a name="l00018"></a><a class="code" href="structH5PartFile.html#o1">00018</a>   <span class="keywordtype">int</span> <a class="code" href="structH5PartFile.html#o1">timestep</a>;
-<a name="l00019"></a>00019 
-<a name="l00020"></a><a class="code" href="structH5PartFile.html#o2">00020</a>   hid_t <a class="code" href="structH5PartFile.html#o2">timegroup</a>;
-<a name="l00021"></a><a class="code" href="structH5PartFile.html#o3">00021</a>   hid_t <a class="code" href="structH5PartFile.html#o3">properties</a>;
-<a name="l00022"></a><a class="code" href="structH5PartFile.html#o4">00022</a>   hsize_t <a class="code" href="structH5PartFile.html#o4">nparticles</a>;
-<a name="l00023"></a><a class="code" href="structH5PartFile.html#o5">00023</a>   hid_t <a class="code" href="structH5PartFile.html#o5">shape</a>;
-<a name="l00024"></a><a class="code" href="structH5PartFile.html#o6">00024</a>   <span class="keywordtype">unsigned</span> <a class="code" href="structH5PartFile.html#o6">mode</a>;
-<a name="l00025"></a><a class="code" href="structH5PartFile.html#o7">00025</a>   <span class="keywordtype">int</span> <a class="code" href="structH5PartFile.html#o7">maxstep</a>;
-<a name="l00026"></a><a class="code" href="structH5PartFile.html#o8">00026</a>   hid_t <a class="code" href="structH5PartFile.html#o8">xfer_prop</a>,<a class="code" href="structH5PartFile.html#o9">create_prop</a>,<a class="code" href="structH5PartFile.html#o10">access_prop</a>;
-<a name="l00027"></a><a class="code" href="structH5PartFile.html#o12">00027</a>   hid_t <a class="code" href="structH5PartFile.html#o11">diskshape</a>,<a class="code" href="structH5PartFile.html#o12">memshape</a>; <span class="comment">/* for parallel I/O (this is on-disk) H5S_ALL </span>
-<a name="l00028"></a>00028 <span class="comment">                    if serial I/O */</span>
-<a name="l00029"></a><a class="code" href="structH5PartFile.html#o13">00029</a>   <span class="keywordtype">long</span> <span class="keywordtype">long</span> <a class="code" href="structH5PartFile.html#o13">viewstart</a>,<a class="code" href="structH5PartFile.html#o14">viewend</a>; <span class="comment">/* -1 if no view is available: A "view" looks at a subset of the data. */</span>
-<a name="l00030"></a>00030   
-<a name="l00031"></a>00031 <span class="preprocessor">#ifdef PARALLEL_IO</span>
-<a name="l00032"></a>00032 <span class="preprocessor"></span>  <span class="keywordtype">long</span> <span class="keywordtype">long</span> *pnparticles; <span class="comment">/* the number of particles in each processor.</span>
-<a name="l00033"></a>00033 <span class="comment">                             With respect to the "VIEW", these numbers</span>
-<a name="l00034"></a>00034 <span class="comment">                             can be regarded as non-overlapping subsections</span>
-<a name="l00035"></a>00035 <span class="comment">                             of the particle array stored in the file.</span>
-<a name="l00036"></a>00036 <span class="comment">                             So they can be used to compute the offset of</span>
-<a name="l00037"></a>00037 <span class="comment">                             the view for each processor */</span>
-<a name="l00038"></a>00038   MPI_Comm comm;
-<a name="l00039"></a>00039   <span class="keywordtype">int</span> nprocs,myproc;
-<a name="l00040"></a>00040 <span class="preprocessor">#endif</span>
-<a name="l00041"></a>00041 <span class="preprocessor"></span>}<a class="code" href="structH5PartFile.html">H5PartFile</a>;
-<a name="l00042"></a>00042 
-<a name="l00043"></a><a class="code" href="H5Part_8h.html#a0">00043</a> <span class="preprocessor">#define H5PART_READ 0x01</span>
-<a name="l00044"></a><a class="code" href="H5Part_8h.html#a1">00044</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PART_WRITE 0x02</span>
-<a name="l00045"></a>00045 <span class="preprocessor"></span>
-<a name="l00046"></a>00046 <span class="comment">/*========== File Opening/Closing ===============*/</span>
-<a name="l00047"></a>00047 <span class="preprocessor">#ifdef PARALLEL_IO</span>
-<a name="l00048"></a>00048 <span class="preprocessor"></span><span class="preprocessor">#include &lt;mpi.h&gt;</span>
-<a name="l00049"></a>00049 <a class="code" href="structH5PartFile.html">H5PartFile</a> *<a class="code" href="H5Part_8c.html#a3">H5PartOpenFileParallel</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename,
-<a name="l00050"></a>00050                                    <span class="keywordtype">unsigned</span> flags,
-<a name="l00051"></a>00051                                    MPI_Comm communicator);
-<a name="l00052"></a>00052 <span class="preprocessor">#endif</span>
-<a name="l00053"></a><a class="code" href="H5Part_8h.html#a2">00053</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PartOpenFileSerial(x,y) H5PartOpenFile(x,y)</span>
-<a name="l00054"></a>00054 <span class="preprocessor"></span>
-<a name="l00055"></a>00055 <a class="code" href="structH5PartFile.html">H5PartFile</a> *<a class="code" href="H5Part_8c.html#a4">H5PartOpenFile</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename, <span class="comment">/* name of datafile */</span>
-<a name="l00056"></a>00056                                  <span class="keywordtype">unsigned</span> flags); <span class="comment">/* H5PART_READ | H5PART_WRITE */</span>
-<a name="l00057"></a>00057 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a5">H5PartFileIsValid</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
-<a name="l00058"></a>00058 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a6">H5PartCloseFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
-<a name="l00059"></a>00059 
-<a name="l00060"></a>00060 
-<a name="l00061"></a>00061 <span class="comment">/*============== File Writing Functions ==================== */</span>
-<a name="l00062"></a>00062 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a7">H5PartSetNumParticles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> nparticles);
-<a name="l00063"></a>00063 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a8">H5PartWriteDataFloat64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">double</span> *array);
-<a name="l00064"></a>00064 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a9">H5PartWriteDataInt64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *array);
-<a name="l00065"></a>00065 
-<a name="l00066"></a>00066 <span class="comment">/*================== File Reading Routines =================*/</span>
-<a name="l00067"></a>00067 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a24">H5PartSetStep</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="comment">/* file handle */</span>
-<a name="l00068"></a>00068                    <span class="keywordtype">int</span> step); <span class="comment">/* current timestep to select (0 to n-1) */</span>
-<a name="l00069"></a>00069 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a27">H5PartGetNumSteps</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
-<a name="l00070"></a>00070 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a28">H5PartGetNumDatasets</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
-<a name="l00071"></a>00071 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a29">H5PartGetDatasetName</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> index,<span class="keywordtype">char</span> *name,<span class="keywordtype">int</span> maxlen);
-<a name="l00072"></a>00072 <span class="keywordtype">long</span> <span class="keywordtype">long</span> <a class="code" href="H5Part_8c.html#a33">H5PartGetNumParticles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
-<a name="l00073"></a>00073 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a34">H5PartSetView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> start,<span class="keywordtype">long</span> <span class="keywordtype">long</span> end);
-<a name="l00074"></a><a class="code" href="H5Part_8h.html#a3">00074</a> <span class="preprocessor">#define H5PartResetView(f) H5PartSetView(f,-1,-1)</span>
-<a name="l00075"></a><a class="code" href="H5Part_8h.html#a4">00075</a> <span class="preprocessor"></span><span class="preprocessor">#define H5PartHasView(f) ((f-&gt;viewstart&lt;0||f-&gt;viewend&lt;0)?0:1)</span>
-<a name="l00076"></a>00076 <span class="preprocessor"></span><span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a35">H5PartGetView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *start,<span class="keywordtype">long</span> <span class="keywordtype">long</span> *end);
-<a name="l00077"></a>00077 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a36">H5PartSetCanonicalView</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
-<a name="l00078"></a>00078 
-<a name="l00079"></a>00079 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a37">H5PartReadDataFloat64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,
-<a name="l00080"></a>00080                           <span class="keywordtype">char</span> *name, <span class="comment">/* name of the array to read</span>
-<a name="l00081"></a>00081 <span class="comment">                                         "x"=position in x direction (y,z)</span>
-<a name="l00082"></a>00082 <span class="comment">                                         "vx"=velocity in x directio (y,z)</span>
-<a name="l00083"></a>00083 <span class="comment">                                         "px"=position in x dir (y,z) */</span>
-<a name="l00084"></a>00084                           <span class="keywordtype">double</span> *array); <span class="comment">/* array to read data into */</span>
-<a name="l00085"></a>00085 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a38">H5PartReadDataInt64</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,
-<a name="l00086"></a>00086                           <span class="keywordtype">char</span> *name, <span class="comment">/* name of the array to read</span>
-<a name="l00087"></a>00087 <span class="comment">                                         "x"=position in x direction (y,z)</span>
-<a name="l00088"></a>00088 <span class="comment">                                         "vx"=velocity in x directio (y,z)</span>
-<a name="l00089"></a>00089 <span class="comment">                                         "px"=position in x dir (y,z) */</span>
-<a name="l00090"></a>00090                           <span class="keywordtype">long</span> <span class="keywordtype">long</span> *array); <span class="comment">/* array to read data into */</span>
-<a name="l00091"></a>00091 
-<a name="l00092"></a>00092 <span class="comment">/* the following is a back-door for extensions to the data writing */</span>
-<a name="l00093"></a>00093 <span class="preprocessor">#if 0</span>
-<a name="l00094"></a>00094 <span class="preprocessor"></span><span class="keywordtype">int</span> H5PartReadData(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *array,hid_t type);
-<a name="l00095"></a>00095 <span class="keywordtype">int</span> H5PartWriteData(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *array,hid_t type);
-<a name="l00096"></a>00096 <span class="preprocessor">#endif</span>
-<a name="l00097"></a>00097 <span class="preprocessor"></span><span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a39">H5PartReadParticleStep</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="comment">/* filehandle */</span>
-<a name="l00098"></a>00098                            <span class="keywordtype">int</span> step, <span class="comment">/* selects timestep to read from*/</span>
-<a name="l00099"></a>00099                            <span class="keywordtype">double</span> *x,<span class="keywordtype">double</span> *y,<span class="keywordtype">double</span> *z, <span class="comment">/* particle positions */</span>
-<a name="l00100"></a>00100                            <span class="keywordtype">double</span> *px,<span class="keywordtype">double</span> *py,<span class="keywordtype">double</span> *pz, <span class="comment">/* particle momenta */</span>
-<a name="l00101"></a>00101                            <span class="keywordtype">long</span> <span class="keywordtype">long</span> *<span class="keywordtype">id</span>); <span class="comment">/* and phase */</span>
-<a name="l00102"></a>00102 <span class="comment">/**********==============Attributes Interface============***************/</span>
-<a name="l00103"></a>00103 <span class="comment">/* currently there is file attributes:  Attributes bound to the file</span>
-<a name="l00104"></a>00104 <span class="comment">   and step attributes which are bound to the current timestep.  You </span>
-<a name="l00105"></a>00105 <span class="comment">   must set the timestep explicitly before writing the attributes (just</span>
-<a name="l00106"></a>00106 <span class="comment">   as you must do when you write a new dataset.  Currently there are no</span>
-<a name="l00107"></a>00107 <span class="comment">   attributes that are bound to a particular data array, but this could</span>
-<a name="l00108"></a>00108 <span class="comment">   easily be done if required.</span>
-<a name="l00109"></a>00109 <span class="comment">*/</span>
-<a name="l00110"></a>00110 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a12">H5PartWriteStepAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
-<a name="l00111"></a>00111     hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem);
-<a name="l00112"></a>00112 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a14">H5PartWriteFileAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
-<a name="l00113"></a>00113     hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem);
-<a name="l00114"></a>00114 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a13">H5PartWriteAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
-<a name="l00115"></a>00115                       hid_t type,<span class="keywordtype">void</span> *attrib,<span class="keywordtype">int</span> nelem); <span class="comment">/* this should be deprecated */</span>
-<a name="l00116"></a>00116 
-<a name="l00117"></a>00117 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a10">H5PartWriteFileAttribString</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
-<a name="l00118"></a>00118     <span class="keywordtype">char</span> *attrib);
-<a name="l00119"></a>00119 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a11">H5PartWriteStepAttribString</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,
-<a name="l00120"></a>00120     <span class="keywordtype">char</span> *attrib);
-<a name="l00121"></a>00121 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a16">H5PartGetNumStepAttribs</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f); <span class="comment">/* for current filestep */</span>
-<a name="l00122"></a>00122 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a17">H5PartGetNumFileAttribs</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
-<a name="l00123"></a>00123 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a19">H5PartGetStepAttribInfo</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> idx,
-<a name="l00124"></a>00124     <span class="keywordtype">char</span> *name,size_t maxnamelen,
-<a name="l00125"></a>00125                          hid_t *type,<span class="keywordtype">int</span> *nelem);
-<a name="l00126"></a>00126 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a20">H5PartGetFileAttribInfo</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> idx,
-<a name="l00127"></a>00127     <span class="keywordtype">char</span> *name,size_t maxnamelen,
-<a name="l00128"></a>00128     hid_t *type,<span class="keywordtype">int</span> *nelem);
-<a name="l00129"></a>00129 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a21">H5PartReadStepAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
-<a name="l00130"></a>00130 <span class="keywordtype">void</span> <a class="code" href="H5Part_8c.html#a22">H5PartReadAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
-<a name="l00131"></a>00131 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a23">H5PartReadFileAttrib</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *name,<span class="keywordtype">void</span> *data);
-<a name="l00132"></a>00132 
-<a name="l00133"></a>00133 
-<a name="l00134"></a>00134 <span class="comment">/**************** File Stashing Interfaces *************************/</span>
-<a name="l00135"></a>00135 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a42">H5PartStashFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">char</span> *filename);
-<a name="l00136"></a>00136 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a43">H5PartUnstashFile</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f, <span class="keywordtype">char</span> *filename, <span class="keywordtype">char</span> *outputpath); <span class="comment">/* outputpath can be null for cwd */</span>
-<a name="l00137"></a>00137 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a44">H5PartGetNumStashFiles</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f);
-<a name="l00138"></a>00138 <span class="keywordtype">int</span> <a class="code" href="H5Part_8c.html#a45">H5PartFileGetStashFileName</a>(<a class="code" href="structH5PartFile.html">H5PartFile</a> *f,<span class="keywordtype">int</span> nameindex,<span class="keywordtype">char</span> *filename,<span class="keywordtype">int</span> maxnamelen);
-<a name="l00139"></a>00139 
-<a name="l00140"></a>00140 
-<a name="l00141"></a>00141 <span class="preprocessor">#endif</span>
-</pre></div><hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
-<a href="http://www.doxygen.org/index.html">
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-<!-- Generated by Doxygen 1.4.4 -->
-<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindexHL" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
-<h1>H5Part Class List</h1>Here are the classes, structs, unions and interfaces with brief descriptions:<table>
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doc/ReferencePages/files.html

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doc/ReferencePages/functions.html

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doc/ReferencePages/functions_vars.html

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doc/ReferencePages/globals.html

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-: <a class="el" href="H5Part_8h.html#a11">H5Part.h</a>, <a class="el" href="H5Part_8c.html#a9">H5Part.c</a><li>H5PartWriteFileAttrib()
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-<hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
-<a href="http://www.doxygen.org/index.html">
-<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
-</body>
-</html>

doc/ReferencePages/globals_defs.html

@@ -1,59 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
-<title>H5Part: Class Members</title>
-<link href="doxygen.css" rel="stylesheet" type="text/css">
-</head><body>
-<!-- Generated by Doxygen 1.4.4 -->
-<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindexHL" href="globals.html">File&nbsp;Members</a></div>
-<div class="qindex"><a class="qindex" href="globals.html">All</a> | <a class="qindex" href="globals_func.html">Functions</a> | <a class="qindex" href="globals_type.html">Typedefs</a> | <a class="qindexHL" href="globals_defs.html">Defines</a></div>
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-<p>
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-<p>
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-<h3><a class="anchor" name="index_h">- h -</a></h3><ul>
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-<hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
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doc/ReferencePages/globals_func.html

@@ -1,97 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
-<title>H5Part: Class Members</title>
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-<div class="qindex"><a class="qindex" href="globals.html">All</a> | <a class="qindexHL" href="globals_func.html">Functions</a> | <a class="qindex" href="globals_type.html">Typedefs</a> | <a class="qindex" href="globals_defs.html">Defines</a></div>
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-<h3><a class="anchor" name="index_h">- h -</a></h3><ul>
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-<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
-</body>
-</html>

doc/ReferencePages/globals_type.html

@@ -1,19 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
-<title>H5Part: Class Members</title>
-<link href="doxygen.css" rel="stylesheet" type="text/css">
-</head><body>
-<!-- Generated by Doxygen 1.4.4 -->
-<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindexHL" href="globals.html">File&nbsp;Members</a></div>
-<div class="qindex"><a class="qindex" href="globals.html">All</a> | <a class="qindex" href="globals_func.html">Functions</a> | <a class="qindexHL" href="globals_type.html">Typedefs</a> | <a class="qindex" href="globals_defs.html">Defines</a></div>
-
-<p>
-<ul>
-<li>H5IO_getname_t
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-<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
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-</html>

doc/ReferencePages/index.html

@@ -1,14 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
-<title>H5Part: Main Page</title>
-<link href="doxygen.css" rel="stylesheet" type="text/css">
-</head><body>
-<!-- Generated by Doxygen 1.4.4 -->
-<div class="qindex"><a class="qindexHL" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
-<h1>H5Part Documentation</h1>
-<p>
-<hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
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doc/ReferencePages/structH5IO__getname__t-members.html

@@ -1,16 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
-<title>H5Part: Member List</title>
-<link href="doxygen.css" rel="stylesheet" type="text/css">
-</head><body>
-<!-- Generated by Doxygen 1.4.4 -->
-<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
-<h1>H5IO_getname_t Member List</h1>This is the complete list of members for <a class="el" href="structH5IO__getname__t.html">H5IO_getname_t</a>, including all inherited members.<p><table>
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-<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
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doc/ReferencePages/structH5IO__getname__t.html

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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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-<title>H5Part: H5IO_getname_t Struct Reference</title>
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-<!-- Generated by Doxygen 1.4.4 -->
-<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
-<h1>H5IO_getname_t Struct Reference</h1><!-- doxytag: class="H5IO_getname_t" --><a href="structH5IO__getname__t-members.html">List of all members.</a><table border="0" cellpadding="0" cellspacing="0">
-<tr><td></td></tr>
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-
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-H5IO_getname_t: Private
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-<hr><h2>Member Data Documentation</h2>
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-
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-<hr>The documentation for this struct was generated from the following file:<ul>
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doc/ReferencePages/structH5PartFile-members.html

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-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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-<title>H5Part: Member List</title>
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-<!-- Generated by Doxygen 1.4.4 -->
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doc/ReferencePages/structH5PartFile.html

@@ -1,399 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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-<title>H5Part: H5PartFile Struct Reference</title>
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-<!-- Generated by Doxygen 1.4.4 -->
-<div class="qindex"><a class="qindex" href="index.html">Main&nbsp;Page</a> | <a class="qindex" href="annotated.html">Class&nbsp;List</a> | <a class="qindex" href="files.html">File&nbsp;List</a> | <a class="qindex" href="functions.html">Class&nbsp;Members</a> | <a class="qindex" href="globals.html">File&nbsp;Members</a></div>
-<h1>H5PartFile Struct Reference</h1><!-- doxytag: class="H5PartFile" --><code>#include &lt;<a class="el" href="H5Part_8h-source.html">H5Part.h</a>&gt;</code>
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-  </tr>
-</table>
-<a class="anchor" name="o11"></a><!-- doxytag: member="H5PartFile::diskshape" ref="o11" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">hid_t <a class="el" href="structH5PartFile.html#o11">H5PartFile::diskshape</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o0"></a><!-- doxytag: member="H5PartFile::file" ref="o0" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">hid_t <a class="el" href="structH5PartFile.html#o0">H5PartFile::file</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o7"></a><!-- doxytag: member="H5PartFile::maxstep" ref="o7" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">int <a class="el" href="structH5PartFile.html#o7">H5PartFile::maxstep</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o12"></a><!-- doxytag: member="H5PartFile::memshape" ref="o12" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">hid_t <a class="el" href="structH5PartFile.html#o12">H5PartFile::memshape</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o6"></a><!-- doxytag: member="H5PartFile::mode" ref="o6" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">unsigned <a class="el" href="structH5PartFile.html#o6">H5PartFile::mode</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o4"></a><!-- doxytag: member="H5PartFile::nparticles" ref="o4" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">hsize_t <a class="el" href="structH5PartFile.html#o4">H5PartFile::nparticles</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o3"></a><!-- doxytag: member="H5PartFile::properties" ref="o3" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">hid_t <a class="el" href="structH5PartFile.html#o3">H5PartFile::properties</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o5"></a><!-- doxytag: member="H5PartFile::shape" ref="o5" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">hid_t <a class="el" href="structH5PartFile.html#o5">H5PartFile::shape</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o2"></a><!-- doxytag: member="H5PartFile::timegroup" ref="o2" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">hid_t <a class="el" href="structH5PartFile.html#o2">H5PartFile::timegroup</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o1"></a><!-- doxytag: member="H5PartFile::timestep" ref="o1" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">int <a class="el" href="structH5PartFile.html#o1">H5PartFile::timestep</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o14"></a><!-- doxytag: member="H5PartFile::viewend" ref="o14" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">long long <a class="el" href="structH5PartFile.html#o14">H5PartFile::viewend</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o13"></a><!-- doxytag: member="H5PartFile::viewstart" ref="o13" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">long long <a class="el" href="structH5PartFile.html#o13">H5PartFile::viewstart</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<a class="anchor" name="o8"></a><!-- doxytag: member="H5PartFile::xfer_prop" ref="o8" args="" --><p>
-<table class="mdTable" cellpadding="2" cellspacing="0">
-  <tr>
-    <td class="mdRow">
-      <table cellpadding="0" cellspacing="0" border="0">
-        <tr>
-          <td class="md" nowrap valign="top">hid_t <a class="el" href="structH5PartFile.html#o8">H5PartFile::xfer_prop</a>          </td>
-        </tr>
-      </table>
-    </td>
-  </tr>
-</table>
-<table cellspacing="5" cellpadding="0" border="0">
-  <tr>
-    <td>
-      &nbsp;
-    </td>
-    <td>
-
-<p>
-    </td>
-  </tr>
-</table>
-<hr>The documentation for this struct was generated from the following file:<ul>
-<li><a class="el" href="H5Part_8h-source.html">H5Part.h</a></ul>
-<hr size="1"><address style="align: right;"><small>Generated on Tue Jan 31 11:52:45 2006 for H5Part by&nbsp;
-<a href="http://www.doxygen.org/index.html">
-<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.4.4 </small></address>
-</body>
-</html>

doc/UsingC.html

@@ -1,606 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>H5Part, the C/C++ API</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-<!--#include virtual="/include/topIncludes.html"-->
-
-<div id="maincenter">
-
-<h1>The C/C++ Application Programming Interface (API)</h1>
-<UL>
-<LI><a href="#Opening">Opening, Closing, and Validating Datafiles</a>
-<LI><a href="#SetStep">Setting the Simulation Timestep</a>
-<LI><a href="#SetNumParticles">Setting the Number of Particles</a>
-<LI><a href="#Writing">Writing Datasets</a>
-<LI><a href="#ReadingNumTimeSteps">Reading the Number of Time Steps</a>
-<LI><a href="#ReadingNumParticles">Reading the Number of Particles</a>
-<LI><a href="#Reading">Reading Datasets</a>
-<LI><a href="#DatasetsInfo">Reading the Number and the Names of Datasets</a>
-<LI><a href="#AttributesInfo">Attributes Interface</a>
-<LI><a href="#WriteAttribs">Writing Additional Attributes</a>
-<LI><a href="#ReadAttribs">Reading Attributes</a>
-</UL>
-<br>
-<a href="ReferencePages/index.html">Reference Manual (Doxygen)</a>
-<br>
-<hr>
-<a name="Opening"><h2>Opening Datafiles</h2></a>
-<P>
-Just like the familiar <code>FILE*</code> type for C stdio operations, all
-H5Part file operations require a file handle.  The type of this handle is
-<code>(H5PartFile*)</code>.
-<br>
-<code>H5PartOpenFile()</code> is
-used to open a serial file and
-<code>HDFPartOpenFileParallel()</code> is used to open a file for
-Parallel I/O (in an MPI program).
-After you open the file handle you can use the same set of 
-subroutines for operations on the file regardless of whether the
-file is a parallel or serial I/O file.  
-The libraries manage all of this internally.<p>
-</P>
-<b>C Prototypes</b><br>
-<P>
-<b>Serial File</b><br>
-<code>H5PartFile *H5PartOpenFile(const char *filename, unsigned
-accessmode);</code><br>
-<b>Parallel File</b><br>
-<code>H5PartFile *H5PartOpenFileParallel(char *filename,int
-accessmode,MPI_Comm communicator);</code><br>
-<DT><i>filename</i>: </DT><DD>The name of the IEEEIO data file to
-open.  The typical extension for these files is <i>.h5</i></DD>
-<DT><i>accessmode</i>: </DT><DD>The accessmode for the file.  This is
-one of 2 different access modes<br>
-<code>H5PART_READ</code> : Opens a file in read-only mode.</DT><br>
-<code>H5PART_WRITE</code> : Opens a file in write-only mode.
-If the
-file does not exist, it will be created.  If it does
-exist, it will be
-truncated. 
-<DT><i>communicator</i>: </DT>
-<DD>This argument is only available if the program has been
-compiled with the <code>PARALLEL_IO</code> C-preprocessor flag
-defined. It is used to pass in the communicator that will be
-used for all collective I/O operations that target the same
-file on disk.</DD>
-<DT><i>Returns</i>:</DT><DD>A new filehandle with an open file or NULL if error.</DD>	
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-. . . code . . .
-    /* Open an HDF5 file for writing */
-    H5PartFile *writer = H5PartOpenFile("datafileout.h5",H5PART_WRITE);
-    /* Open an HDF5 file for Parallel I/O */
-    H5PartFile *writer = H5PartOpenFileParallel("datafileout.h5",H5PART_WRITE,MPI_COMM_WORLD);
-    /* open HDF5 file for reading */ 
-    H5PartFile *reader = H5PartOpenFile("datafilein.h5",H5PART_READ); 
-    /* open HDF5 file for parallel reads */ 
-    H5PartFile *reader = H5PartOpenFileParallel("datafilein.h5",H5PART_READ,MPI_COMM_WORLD);
-. . . more code . . .
-</pre> <br>
-
-
-<hr>
-
-
-<h2>Closing Datafiles</h2>
-<P>
-To close the file, you simply use H5PartCloseFile() for both
-parallel and serial files. You must call H5PartCloseFile() on any
-file descriptor created by H5PartFileOpen() regardless of
-whether the file turns out to be valid or not.
-</P>
-<b>C Prototypes</b><br>
-<P>
-<code>void H5PartCloseFile(H5PartFile *fileID);</code>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-H5PartOpenFile() or H5PartOpenFileParallel().</DD>
-<DT><i>Returns</i>:</DT><DD>void.</DD>	
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *file;
-... code ...
-file=H5PartOpenFileParallel("parttest.h5",H5PART_WRITE,comm);
-... more code ...
-H5PartCloseFile(file);
-</pre>
-<br>
-<hr>
-
-
-<h2>Validating Datafiles</h2>
-<P>
-You can test if the file was opened successfully using the
-H5PartFileIsValid() function. It returns 1 if valid, 0 if invalid.<p>
-</P>
-<b>C Prototype</b><br>
-<P>
-<code>int H5PartFileIsValid(H5PartFile *fileID);</code>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-H5PartOpenFile() or H5PartOpenFileParallel().</DD>
-<DT><i>Returns</i>:</DT><DD>1 if valid, 0 if invalid.</DD>	
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<P>
-Here is an example of validating a newly opened file.  Even if
-the file is invalid, you must use H5PartCloseFile() to reclaim
-the file handle.
-</P>
-<pre>
-#include &lt H5Part.h &gt
-. . . code . . .
-    H5PartFile *fileID = H5PartOpenFile("datafileout.h5",H5PART_WRITE);
-    if(!H5PartFileIsValid(fileID)){ 
-       puts("The file you specified does not exist or is not in a
-readable format");
-       H5PartClose(fileID); /* must reclaim fileID even if file is invalid */
-       . . . do other cleanup . . .
-    }
-. . . more code . . .
-</pre><br>
-
-<hr>
-
-<a name="SetStep">
-<h2>Setting the Timestep</h2>
-</a>
-<P>
-When writing data to a file the current time step must be set (even if there is only one). In a file with N time steps, the steps are numbered from 0 to N-1.
-</P>
-<b>C Prototype</b><br>
-<P>
-<code>void H5PartSetStep((H5PartFile *fileID,int step);</code>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-H5PartOpenFile() or H5PartOpenFileParallel().</DD>
-<DT><i>step</i>: </DT><DD>An integer time step.
-</DD>
-<DT><i>Returns</i>: </DT><DD>void.</DD>
-</DL>
-<br><b>Example Use</b><br>
-</P>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-int timeStep;
-....
-H5PartSetStep(fileID,timeStep);
-....
-</pre>
-
-<hr>
-	
-
-<a name="SetNumParticles">
-</a>
-<h2>Setting the Number of Particles</h2>
-<P>
-H5PartSetNumParticles:  This function's sole purpose is to 
-prevent needless creation of new HDF5 DataSpace handles if
-the number of particles is invariant throughout the sim.
-That's its only reason for existence.  After you call this
-subroutine, all subsequent operations will assume this 
-number of particles will be written.
-</P>
-<b>C Prototype</b><br>
-<P>
-<code>void H5PartSetNumParticles(H5PartFile *fileID,long long nparticles);</code>
-
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-H5PartOpenFile() or H5PartOpenFileParallel().</DD>
-<DT><i>nparticles</i>: </DT><DD>A long long integer specifying  the number of particles.
-</DD>
-<DT><i>Returns</i>: </DT><DD>void.</DD>
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-long long nparticles;
-....
-H5PartSetStep(fileID,nparticles);
-....
-</pre>
-
-<hr>
-
-<a name="Writing">
-<h2>Writing Datasets</h2>
-</a>
-<P>
-After setting the number of particles with 
-<a  href="#SetNumParticles">H5PartSetNumParticles()</a>
-and the current timestep using 
-<a href="#SetStep">H5PartSetStep()</a>, you can start
-writing datasets into the file.  Each dataset has a name
-associated with it (chosen by the user) in order to facilitate
-later retrieval.  The writing routines also implicitly store
-the datatype of the array so that the array can be
-reconstructed properly on other systems with incompatible type
-representations. The data is committed to disk before the
-routine returns. All data that is written after setting the
-timestep is associated with that timestep. While the number of
-particles can change for each timestep, you cannot change the
-number of particles in the middle of a given timestep.
-</P>
-<b>C Prototypes</b><br>
-<P>
-<code>int H5PartWriteDataFloat64(H5PartFile *fileID,char
-  *name,double *array);</code></br>
-<code>int H5PartWriteDataInt64(H5PartFile *fileID,char
-  *name,double *array);</code>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or 
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>name</i>: </DT><DD>A null-terminated string for the
-name of the array.  When retrieving datasets from disk,
-you ask for them by name.  There are no restrictions on
-naming of arrays, but it is useful to arrive at some common
-naming convention when sharing data with other groups.</DD>
-<DT><i>array</i>: </DT><DD>A buffer containing an array of
-particle data to commit to disk.  The datatype for
-elements in the buffer is implicit in the name of the
-subroutine call.</DD>
-<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-double *x,*y,*z;
-int timeStep;
-long long nparticles;
-
-...
-
-H5PartSetStep(fileID,timeStep); /* must set the current timestep in file */
-H5PartSetNumParticles(fileID,nparticles); /* then set number of particles to store */
-
-/* now write different tuples of data into this timestep of the file */
-H5PartWriteDataFloat64(fileID,"x",x);
-H5PartWriteDataFloat64(fileID,"y",y);
-H5PartWriteDataFloat64(file,"z",z);
-..
-</pre>
-
-<hr>
-<a name="ReadingNumTimeSteps">
-<h2>Reading the Number of Time Steps</h2>
-</a>
-<P>
-This reads the number of datasteps that are 
-  currently stored in the datafile.
-  It works for both reading and writing of files, but is probably
-  only typically used when you are reading.
-
-</P>
-<b>C Prototype</b><br>
-<P>
-<code>int H5PartGetNumSteps  	(H5PartFile *fileID);</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by <a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD> 
-<DT><i>Returns</i>: </DT><DD>The number of timesteps currently stored in the file.
-</DL>
-</P>
-<hr>
-
-<a name="ReadingNumParticles">
-<h2>Reading the Number of Particles</h2>
-</a>
-<P>
-This reads the number of particles that are
-currently stored in the current time step.
-It will arbitrarily select a timestep if you haven't 
-already set the timestep with H5PartSetStep().
-
-</P>
-<b>C Prototype</b><br>
-<P>
-<code>long long H5PartGetNumParticles     (H5PartFile *fileID);</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by <a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>Returns</i>: </DT><DD>The number of particles in current timestep.
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-int timeStep;
-long long nparticles;
-
-H5PartSetStep(fileID,0);
-nparticles=H5PartGetNumParticles(fileID);
-...
-</pre>
-
-<hr>
-
-
-
-<a name="Reading">
-<h2>Reading Datasets</h2>
-</a>
-<P>
-After setting the time step and getting the number of particles to allocate the data arrays, you can start to read the data.
-</P>
-<b>C Prototypes</b><br>
-<P>
-<code>int H5PartReadDataFloat64(H5PartFile *fileID,char *name,double *array);</code><br>
-<code>int H5PartReadDataInt64(H5PartFile *fileID,char *name,long long *array);</code><br>
-
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>name</i>: </DT><DD>A null-terminated string for the
-name of the array.  When retrieving datasets from disk,
-you ask for them by name.  There are no restrictions on
-naming of arrays, but it is useful to arrive at some common
-naming convention when sharing data with other groups.</DD>
-<DT><i>array</i>: </DT><DD>A buffer to which the particle data will be read.i
-The datatype for
-elements in the buffer is implicit in the name of the
-subroutine call.</DD>
-<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-double *x,*y,*z;
-int timeStep;
-long long nparticles;
-
-H5PartSetStep(fileID,0);
-nparticles=H5PartGetNumParticles(fileID);
-... 
-
-H5PartReadDataFloat64(file,"x",x);
-H5PartReadDataFloat64(file,"y",y);
-H5PartReadDataFloat64(file,"z",z);
-...
-</pre>
-<hr>
-<a name="DatasetsInfo"><h2>Reading the Number and Names of Datasets</h2></a>
-<P>
-H5Part provides funtions to find out how many datasets are stored at a particular timestep
-and what their names are if you don't know what they are a-priori.
-</P>
-<b>C Prototypes</b><br>
-<P>
-<code>int H5PartGetNumDatasets(H5PartFile *fileID);</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>Returns</i>: </DT><DD>The number of datasets.</DD>
-</DL>
-</P>
-<P>
-<code>int H5PartGetDatasetName(H5PartFile *fileID,int index,char *name,int maxlen);</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>index</i>:</DT><DD> integer specifying the index of the dataset. If the number of datasets is
-nds, the range of index is  0 to nds-1.</DD>
-<DT><i>name</i>:</DT><DD> A null-terminated string for the name of the dataset.</DD>
-<DT><i>maxlen</i>:</DT><DD> An integer specifying the maximum length of the name array.</DD>
-<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-char name[64];
-int index, nds;
-
-...
-nds=H5PartGetNumDatasets(fileID);
-  for(index=0;index&lt nds;index++){
-    H5PartGetDatasetName(fileID,index,name,64);
-    printf("\tDataset[%u] name=[%s]\n", index,name);
-  }
-...
-</pre>
-
-<hr>
-
-<a name="AttributesInfo">
-<h2>Attributes Interface</h2></a>
-<P>
-In the current H5Part implemtation there are two types of attributes: file attributes which are bound to the file
-   and step attributes which are bound to the current timestep.  You 
-   must set the timestep explicitly before writing the attributes (just
-   as you must do when you write a new dataset.  Currently there are no
-   attributes that are bound to a particular data array, but this could
-   easily be done if required.
-</P>
-<P>H5PartGetNumStepAttribs and H5PartGetNumFileAttribs return the number of attributes bound to a step and to a file respectively. H5PartGetStepAttribInfo and H5PartGetFileAttribInfo return the name, type and number of elements of type "type" bound to a step and a file respectively.
-</P>
-<b>C Prototypes:</b><br>
-<code>int H5PartGetNumStepAttribs(H5PartFile *fileID);
-</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>Returns</i> </DT><DD> The number of step attributes for the current step.</DD>
-</DL>
-<code>int H5PartGetNumFileAttribs(H5PartFile *fileID);
-</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>Returns</i> </DT><DD> The number of file attributes.</DD>
-</DL>
-<code>void H5PartGetStepAttribInfo(H5PartFile *fileID,int idx, char *name,size_t maxnamelen,hid_t *type,int *nelem);
-</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>idx</i>: </DT><DD>Index of the attribute.</DD>
-<DT><i>name</i>: </DT><DD>A null-terminated string with the name of the attribute.</DD>
-<DT><i>maxnamelen</i></DT><DD>the length of the name of the attribute.</DD>
-<DT><i>type</i>: </DT><DD>One of the following: H5T_NATIVE_DOUBLE H5T_NATIVE_INT64 H5T_NATIVE_CHAR.</DD>
-<DT><i>nelem</i>: </DT><DD>Number of elements of type "type".</DD>
-<DT><i>Returns</i> </DT><DD> void.</DD>
-</DL>
-
-<code>void H5PartGetFileAttribInfo(H5PartFile *fileID,int idx, char *name,size_t maxnamelen, hid_t *type,int *nelem);
-</code><br>
-
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>idx</i>: </DT><DD>Index of the attribute.</DD>
-<DT><i>name</i>: </DT><DD>A null-terminated string with the name of the attribute.</DD>
-<DT><i>maxnamelen</i></DT><DD>the length of the name of the attribute.</DD>
-<DT><i>type</i>: </DT><DD>One of the following: H5T_NATIVE_DOUBLE H5T_NATIVE_INT64 H5T_NATIVE_CHAR.</DD>
-<DT><i>nelem</i>: </DT><DD>Number of elements of type "type".</DD>
-<DT><i>Returns</i> </DT><DD> void.</DD>
-</DL>
-
-
-<a name="WriteAttribs">
-<h2>Writing Attributes</h2>
-</a>
-<P>
-An attribute can be bound to the file or after setting the time step to this time step.
-</P>
-
-<b>C Prototypes: Generic Attributes</b><br>
-<P>
-<code>int H5PartWriteFileAttrib(H5PartFile *fileID,char *name,  hid_t type,void *value,int nelem);</code><br>
-<code>int H5PartWriteStepAttrib(H5PartFile *fileID,char *name,  hid_t type,void *value,int nelem);</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>name</i>: </DT><DD>A null-terminated string for the
-name of the array.  When retrieving datasets from disk,
-you ask for them by name.  There are no restrictions on
-naming of arrays, but it is useful to arrive at some common
-naming convention when sharing data with other groups.</DD>
-<DT><i>type</i>: One of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64, H5T_NATIVE_CHAR.</DD>
-<DT><i>value</i>: value of the attribute.</DD>
-<DT><i>nelem</i>: number of elements of type "type".</DD>
-<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-double actPos;
-
-...
-H5PartWriteStepAttrib(file_m,"Spos",H5T_NATIVE_DOUBLE,&actPos,1);
-...
-</pre>
-
-
-<b>C Prototypes: String Attributes</b><br>
-<P>
-<code>int H5PartWriteStepAttribString(H5PartFile *fileID,char *name, char *attrib);</code><br>
-<code>int H5PartWriteFileAttribString(H5PartFile *fileID,char *name, char *attrib);</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>name</i>: </DT><DD>A null-terminated string for the
-name of the array.  When retrieving datasets from disk,
-you ask for them by name.  There are no restrictions on
-naming of arrays, but it is useful to arrive at some common
-naming convention when sharing data with other groups.</DD>
-<DT><i>attrib</i>: the attribute character string.</DD>
-<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
-</DL>
-</P>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-char *newattrib;
-char *newname;
-
-...
-H5PartWriteFileAttribString(fileID, newname,newattrib);
-...
-</pre>
-<hr>
-
-<a name="ReadAttribs">
-<h2>Reading Attributes</h2>
-</a>
-<P>
-<P>
-As with the writing of attributes, there are two basic reading interfaces one that reads file bound attributes and one that reads
-step bound attributes. If the step is not set the current one will be used.
-</P>
-</P>
-<b>C Prototypes</b><br>
-<P>
-<code>void H5PartReadStepAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
-<code>void H5PartReadAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
-<code>int H5PartReadFileAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
-<DL>
-<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
-<a href="#Opening">H5PartOpenFile()</a> or
-<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
-<DT><i>name</i>: </DT><DD>A null-terminated string for the
-name of the array.  When retrieving datasets from disk,
-you ask for them by name.  There are no restrictions on
-naming of arrays, but it is useful to arrive at some common
-naming convention when sharing data with other groups.</DD>
-<DT><i>value</i>: value of the attribute.</DD>
-<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
-</DL>
-</P>
-<br>
-NOTE: H5PartReadAttrib has been superseeded by H5PartSetStep.
-<br>
-<br><b>Example Use</b><br>
-<pre>
-#include &lt H5Part.h &gt
-H5PartFile *fileID;
-int step;
-char name[MAXNAME];
-
-...
-
-H5PartSetStep(fileID, step);
-if (H5PartReadStepAttrib(file, "filename", &name[0]) == 1){
-	printf("Read step from file: %s\n", name);
-}
-
-...
-</pre>
-
-</div>
-
-<!--#include virtual="/include/dateFooter.html"-->

doc/UsingF.html

@@ -1,504 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>H5part, the Fortran API</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-<!--#include virtual="/include/topIncludes.html"-->
-
-<div id="maincenter">
-
-
-<h1>The FORTRAN Application Programming Interface (API)</h1>
-<P>
-These references contain the information on how to access the H5Part API using FORTRAN bindings. All pointers are cast to haddr_t (a unint64_t) within the C/C++ code. In fortran, these pointers (handles) are carried as INTEGER*8
-</P>
-<UL>
-<LI><a href="#Opening">Opening, Closing, and Validating Datafiles</a>
-<LI><a href="#SetStep">Setting the Simulation Timestep</a>
-<LI><a href="#SetNumParticles">Setting the Number of Particles</a>
-<LI><a href="#Writing">Writing Datasets</a>
-<LI><a href="#ReadingNumTimeSteps">Reading the Number of Time Steps</a>
-<LI><a href="#ReadingNumTimeSteps">Reading the Number of Particles</a>
-<LI><a href="#Reading">Reading Datasets</a>
-<LI><a href="#DatasetsInfo">Reading the Number and the Names of Datasets</a>
-<LI><a href="#AttributesInfo">Attributes Interface</a>
-<LI><a href="#WriteAttribs">Writing Additional Attributes</a>
-<LI><a href="#ReadAttribs">Reading Attributes</a>
-</UL>
-<hr>
-<a name="Opening"><h2>Opening Datafiles</h2></a>
-<P>
-Like the familiar OPEN in FORTRAN files can be opened to read and write. Different functions are used for the serial and parallel case.
-</P>
-<b>FORTRAN Prototypes</b><br>
-<P>
-<b>Serial File</b><br>
-<code>INTEGER*8 h5pt_openr</code><br>
-<code>FUNCTION h5pt_openw(file)<br>
-in CHARACTER file(*) : the filename to open for writing </code><br>
-returns INTEGER*8 : and open filehandle for serial reads</code><br>
-<br>
-<code>INTEGER*8 h5pt_openw</code><br>
-<code>FUNCTION h5pt_openw(file)<br>
-in CHARACTER file(*) : the filename to open for writing<br>
-returns INTEGER*8 : and open filehandle for serial writes</code><br>
-<br>
-<b>Parallel File</b><br>
-<code>INTEGER*8 h5pt_openr_par</code><br>
-<code>FUNCTION h5pt_openr_par(file,mpi_communicator)<br>
-in CHARACTER file(*) : the filename to open for writing<br>
-in INTEGER mpi_communicator : the MPI_Communicator used by the program<br>
-	returns INTEGER*8 : and open filehandle for parallel reads</code><br>
-<br>
-<code>INTEGER*8 h5pt_openw_par</code><br>
-<code>FUNCTION h5pt_openw_par(file,mpi_communicator)<br>
-	in CHARACTER file(*) : the filename to open for writing<br>
-	in INTEGER mpi_communicator : the MPI_Communicator used by the program<br>
-	returns INTEGER*8 : and open filehandle for parallel reads</code><br>
-</P>
-<P>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-...
-file = h5pt_openw("testfilef.h5")
-...
-</pre>
-</P>
-<hr>
-<h2>Closing Datafiles</h2>
-<P>
-To close the file, you simply use h5pt_close() for both parallel and serial files. You must call h5pt_close() on any file descriptor created by h5pt_open*() regardless of whether the file turns out to be valid or not.</P>
-<b>FORTRAN Prototype</b><br>
-<code>EXTERNAL h5pt_close</code><br>
-<code>SUBROUTINE h5pt_close(filehandle)<br>
-	in INTEGER*8 filehandle : close this open filehandle</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-...
-call h5pt_close(file)
-...
-</pre>
-</P>
-<hr>
-<h2> Validating Datafiles</h2>
-<P>
-You can test if the file was opened successfully using the
-h5p_isvalid() function. It returns 1 if valid, 0 if invalid.
-</P>
-<b>FORTRAN Prototype</b><br>
-<code>INTEGER h5pt_isvalid</code><br>
-<code>FUNCTION h5pt_isvalid(filehandle)<br>
-	in INTEGER*8 filehandle: an open filehandle <br>
-	returns INTEGER : 1 if the file is valid, 0 if it is not</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER status 
-...
-status = h5pt_isvalid(file)
-...
-</pre>
-</P>
-<hr>
-<a name="SetStep">
-<h2>Setting the Timestep</h2>
-</a>
-<P>
-When writing data to a file the current time step must be set (even if there is only one). In a file with N time steps, the steps are numbered from 0 to N-1.
-</P>
-<b>FORTRAN Prototype</b><br>
-<code>EXTERNAL h5pt_setstep</code><br>
-<code>SUBROUTINE h5pt_setstep(filehandle,step)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in INTEGER step  : Set the current timestep in the file to this
-</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER I
-INTEGER nstep
-...
-do I=1,nstep
-	call h5pt_setstep(file,I)
-... more code ...
-enddo
-</pre>
-</P>
-<hr>
-
-<a name="SetNumParticles">
-</a>
-<h2>Setting the Number of Particles</h2>
-<P>
-This function's sole purpose is to
-prevent needless creation of new HDF5 DataSpace handles if
-the number of particles is invariant throughout the sim.
-That's its only reason for existence.  After you call this
-subroutine, all subsequent operations will assume this
-number of particles will be written.
-</P>
-<b>FORTRAN Prototype</b><br>
-<code>EXTERNAL h5pt_setnpoints</code><br>
-<code>SUBROUTINE h5pt_setnpoints(filehandle,npoints)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in INTEGER*8 npoints : The number of particles on *this* processor</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER*8 npoints
-
-...
-call h5pt_setnpoints(file,npoints)
-...
-</pre>
-
-<hr>
-<a name="Writing">
-<h2>Writing Datasets</h2>
-</a>
-<P>
-After setting the number of particles with
-<a  href="#SetNumParticles">h5pt_setnpoints()</a>
-and the current timestep using
-<a href="#SetStep">h5pt_setstep()</a>, you can start
-writing datasets into the file.  Each dataset has a name
-associated with it (chosen by the user) in order to facilitate
-later retrieval.  The writing routines also implicitly store
-the datatype of the array so that the array can be
-reconstructed properly on other systems with incompatible type
-representations. The data is committed to disk before the
-routine returns. All data that is written after setting the
-timestep is associated with that timestep. While the number of
-particles can change for each timestep, you cannot change the
-number of particles in the middle of a given timestep.
-</P>
-<b>FORTRAN Prototypes</b><br>
-<P>
-The two data types supported for the moment are REAL*8 and INTEGER*8 (float64 and int64).
-</P>
-<code>EXTERNAL h5pt_writedata_r8</code><br>
-<code>SUBROUTINE h5pt_writedata_r8(filehandle,name,data)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in CHARACTER name(*) : The name of the data we are writing eg. "X" or "Y" or "PX" etc...<br>
-	in REAL*8 data(*) : The dataarray to write</code><br>
-<br>
-<code>EXTERNAL h5pt_writedata_i8</code><br>
-<code>SUBROUTINE h5pt_writedata_i8(filehandle,name,data)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in CHARACTER name(*) : The name of the data we are writing eg. "X" or "Y" or "PX" etc...<br>
-	in INTEGER*8 data(*) : The dataarray to write</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER nstep
-INTEGER I
-REAL*8,ALLOCATABLE:: X(:)
-
-...
-do I=1,nstep
-	call h5pt_setstep(file,I)
-	call h5pt_writedata_r8(file,"x",X)
-enddo
-...
-</pre>
-<hr>
-<a name="ReadingNumTimeSteps">
-<h2>Reading the Number of Time Steps</h2>
-</a>
-<P>
-This reads the number of datasteps that are
-  currently stored in the datafile.
-  It works for both reading and writing of files, but is probably
-  only typically used when you are reading.
-
-</P>
-<b>FORTRAN Prototypes</b><br>
-<code>INTEGER h5pt_getnsteps</code><br>
-<code>FUNCTION h5pt_getnsteps(filehandle)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	returns INTEGER : number of timesteps stored in the file</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER nstep
-
-file = h5pt_openr("testfilef.h5")
-nstep = h5pt_getnsteps(file)
-</pre>
-<hr>
-
-<a name="ReadingNumParticles">
-<h2>Reading the Number of Particles</h2>
-</a>
-<P>
-This reads the number of particles that are currently stored in the current time step. It will arbitrarily select a timestep if you haven't already set the timestep with H5PartSetStep().
-
-</P>
-<b>FORTRAN Prototypes</b><br>
-<code>INTEGER h5pt_getnpointss</code><br>
-<code>FUNCTION h5pt_getnpoints(filehandle)<br>
-        in INTEGER*8 filehandle : an open filehandle<br>
-        returns INTEGER : number of particles in the current time step</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER*8 npoints
-INTEGET step;
-
-file = h5pt_openr("testfilef.h5")
-call h5pt_setstep(file,0)
-npoints = h5pt_getnpoints(file)
-...
-</pre>
-<hr>
-
-
-
-
-<a name="Reading">
-<h2>Reading Datasets</h2>
-</a>
-<P>
-After setting the time step and getting the number of particles to allocate the data arrays, you can start to read the data.
-</P>
-<b>FORTRAN Prototypes</b><br>
-<code>INTEGER h5pt_readdata_r8</code><br>
-<code>FUNCTION h5pt_readdata_r8(filehandle,name,data)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in CHARACTER name(*) : The name of the data we are writing, eg. "X" or "Y" or "PX" etc...<br>
-	out REAL*8 data(*) : The data array to read. The number of points to read is either the number within 
-	the view setby h5pt_setview() or the default (the total number of particles in the file).<br>
-
-
-
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER err
-INTEGER*8,ALLOCATABLE:: ID(:)
-
-...
-call h5pt_setstep(file,step)
-err=h5pt_readdata_i8(file,"id",ID)
-...
-</pre>
-<hr>
-<a name="DatasetsInfo"><h2>Reading the Number and Names of Datasets</h2></a>
-<P>
-H5Part provides funtions to find out how many datasets are stored at a particular timestep
-and what their names are if you don't know what they are a-priori.
-</P>
-<b>FORTRAN Prototypes</b><br>
-<code>INTEGER  h5pt_getndatasets</code><br>
-<code>FUNCTION h5pt_getndatasets(filehandle)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	returns INTEGER*8 : number of datasets stored per timestep</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER ndata
-
-...
-call h5pt_setstep(file,1)
-ndata = h5pt_getndatasets(file)
-...
-
-</pre>
-<b>FORTRAN Prototypes</b><br>
-<code>INTEGER h5pt_getdatasetname</code><br>
-<code>FUNCTION h5pt_getdatasetname(filehandle,index,name)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in INTEGER index : Index for a given dataset name<br>
-	out CHARACTER name(*) returns the name of the dataset at that index<br>
-	returns INTEGER, 1 on success 0 on failure.</code><br>
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-INTEGER err
-CHARACTER,ALLOCATABLE:: name(:)
-
-...
-err=h5pt_getdatasetname(file, 1, name)
-...
-</pre>
-<hr>
-
-<a name="AttributesInfo">
-<h2>Attributes Interface</h2></a>
-<P>
-In the current H5Part implemtation there are two types of attributes: file attributes which are bound to the file
-   and step attributes which are bound to the current timestep.  You
-   must set the timestep explicitly before writing the attributes (just
-   as you must do when you write a new dataset.  Currently there are no
-   attributes that are bound to a particular data array, but this could
-   easily be done if required.
-</P>
-<b>FORTRAN Prototypes</b><br>
-<code>INTEGER h5pt_getnstepattribs</code><br>
-<code>FUNCTION h5pt_getnstepattribs(filehandle)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	returns INTEGER : number of attributes bound to this particular step<br>
-</code>
-<br>
-<code>INTEGER h5pt_getnfileattribs</code><br>
-<code>FUNCTION h5pt_getnfileattribs(filehandle)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	returns INTEGER : number of attributes bound to the file<br>
-</code>
-<br>
-<code>INTEGER h5pt_getstepattribinfo</code><br>
-<code>FUNCTION h5pt_getstepattribinfo(filehandle,idx,attribname,nelem)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in INTEGER idx : index of the attribute being queried<br>
-	out CHARACTER name(*) : The name of the attribute<br>
-	out INTEGER nelem : Number of elements in the attrib array<br>
-	returns INTEGER, 1 on success 0 on failure.<br>
-</code>
-<br>
-<code>INTEGER h5pt_getfileattribinfo</code><br>
-<code>FUNCTION h5pt_getfileattribinfo(filehandle,idx,attribname,nelem)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in INTEGER idx : index of the attribute being queried<br>
-	out CHARACTER name(*) : The name of the attribute<br>
-	out INTEGER nelem : Number of elements in the attrib array<br>
-	returns INTEGER, 1 on success 0 on failure.
-</code>
-<br>
-	
-
-
-
-
-<hr>	
-<a name="WriteAttribs">
-<h2>Writing Attributes</h2>
-</a>
-<P>
-An attribute can be bound to the file or after setting the time step to this time step.
-</P>
-<b>FORTRAN Prototypes</b><br>
-<code>INTEGER h5pt_writefileattrib_r8</code><br>
-<code>
-FUNCTION h5pt_writefileattrib_r8(filehandle,name,attrib,nelem)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in CHARACTER name(*) : The name of the attribute<br>
-	in REAL*8 attrib(*) : The array of data to write into the attribute<br>
-	in INTEGER nelem : Number of elements in the attrib array<br>
-	returns INTEGER, 1 on success 0 on failure<br>
-</code>	
-<br>
-<code>INTEGER h5pt_writefileattrib_i8</code><br>
-<code>FUNCTION h5pt_writefileattrib_i8(filehandle,name,attrib,nelem)<br>
-	in INTEGER*8 filehandle : The filehandle<br>
-	in CHARACTER name(*) : The name of the attribute<br>
-	in INTEGER*8 attrib(*) : The array of data to write into the attribute<br>
-	in INTEGER nelem : Number of elements in the attrib array<br>
-	returns INTEGER, 1 on success 0 on failure<br>
-</code>
-<br>
-<code>INTEGER h5pt_writefileattrib_string</code><br>
-<code>FUNCTION h5pt_writefileattrib_string(filehandle,name,string)<br>
-       in INTEGER*8 filehandle : an open filehandle<br>
-       in CHARACTER name(*) : The name of the attribute<br>
-       in CHARACTER*8 attrib(*) : The array of data to write into the attribute<br>
-	returns INTEGER, 1 on success 0 on failure<br>
-</code>
-<br>
-<code>INTEGER h5pt_writestepattrib_r8</code><br>
-<code>FUNCTION h5pt_writestepattrib_r8(filehandle,name,attrib,nelem)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in CHARACTER name(*) : The name of the attribute<br>
-	in REAL*8 attrib(*) : The array of data to write into the attribute<br>
-	in INTEGER nelem : Number of elements in the attrib array
-	returns INTEGER, 1 on success 0 on failure<br>
-</code>
-<br>
-<code>INTEGER h5pt_writestepattrib_i8</code><br>
-<code>FUNCTION h5pt_writestepattrib_i8(filehandle,name,attrib,nelem)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in CHARACTER name(*) : The name of the attribute<br>
-	in INTEGER*8 attrib(*) : The array of data to write into the attribute<br>
-	in INTEGER nelem : Number of elements in the attrib array<br>
-	returns INTEGER, 1 on success 0 on failure<br>
-</code>
-<br>
-<code>INTEGER h5pt_writestepattrib_string</code><br>
-<code>FUNCTION h5pt_writestepattrib_string(filehandle,name,string)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in CHARACTER name(*) : The name of the attribute<br>
-	in CHARACTER*8 attrib(*) : The array of data to write into the attribute<br>
-	returns INTEGER, 1 on success 0 on failure<br>
-</code>
-
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-REAL*8 REALTIME
-INTEGER err
-
-...
-err=h5pt_writefileattrib_string(file,"Annotation","Testing 1 2 3")
-err=h5pt_writestepattrib_r8(file,"RealTime",REALTIME,1)
-...
-
-</pre>
-
-<hr>
-<a name="ReadAttribs">
-<h2>Reading Attributes</h2>
-</a>
-<P>
-As with the writing of attributes, there are two basic reading interfaces one that reads file bound attributes and one that reads
-step bound attributes. If the step is not set the current one will be used.
-</P>
-<b>FORTRAN Prototypes</b><br>
-
-<code>INTEGER h5pt_readstepattrib</code><br>
-<code>FUNCTION h5pt_readstepattrib(filehandle,name,data)<br>
-	in INTEGER*8 filehandle : an open filehandle<br>
-	in CHARACTER attributename(*) : name of the attribute to read<br>
-	out <anytype> data(*) : the attribute data will be read into this array<br>
-	returns INTEGER, 1 on success 0 on failure<br>
-</code>
-<br>
-<code>INTEGER h5pt_readfileattrib</code><br>
-<code>FUNCTION h5pt_readfileattrib(filehandle,name,data)<br>
-	in INTEGER*8 filehandle an open filehandle<br>
-	in CHARACTER attributename(*) : name of the attribute to read<br>
-	out <anytype> data(*) : the attribute data will be read into this array<br>
-	returns INTEGER, 1 on success 0 on failure<br>
-</code>
-
-<b>Example Use</b><br>
-<pre>
-include 'H5Part.inc'
-INTEGER*8 file
-REAL*8 REALTIME
-
-...
-call h5pt_setstep(file,0)
-err=h5pt_readstepattrib(file,"RealTime",data)
-...
-</pre>
-
-
-</div>
-
-<!--#include virtual="/include/dateFooter.html"-->

doc/doxyfooter

@@ -0,0 +1,2 @@
+</BODY>
+</HTML>

doc/h5part.html

@@ -1,121 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-<title>H5Part: a Portable High Performance Parallel Data Interface to HDF5</title>
-<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
-<meta name="keywords" content="scientific visualization">
-<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
-
-
-<div id="maincenter">
-<font face="arial,helvetica"><h1>H5Part: a Portable High Performance Parallel Data Interface to HDF5</h1></font>
-<h2><font color="red"> THESE PAGES ARE UNDER CONSTRUCTION, July 2006</h2></font>
-<font face="arial,helvetica" color="#555588"><h2>Motivation</h2></font>
-<P>
-<TABLE>
-<TR>
-<TD>
-<a href="collision_6.png"><img src="collision_6.s.png" width=300 height=300></a>
-</TD
-></TR>
-<TR>
-<TD>
-Beam-beam collision simulation.
-</TD>
-</TR>
-</TABLE>
-</P>
-<P>
-Particle based simulations of accelerator beam-lines, especially in
-six dimensional phase space, generate vast amounts of data. Even
-though a subset of statistical information regarding phase space
-or analysis needs to be preserved, reading and writing such
-enormous restart files on massively parallel supercomputing
-systems remains challenging.<p>
-</P>
-
-<P>
-H5Part is a very simple data storage schema and provides an
-API that simplifies the reading/writing of the data to the HDF5
-file format. An important foundation for a stable visualization and data
-analysis environment is a stable and portable file storage format and
-its associated APIs. The presence of a "common file storage format,"
-including associated APIs, will help foster a fundamental level of
-interoperability across the project's software infrastructure. It will
-also help ensure that key data analysis capabilities are present
-during the earliest phases of the software development effort.
-</P>
-<P>
-H5Part is built on top of the <a href="http://hdf.ncsa.uiuc.edu/HDF5">HDF5 (Hierarchical Data Format).</a>
-HDF5 offers a self-describing machine-independent
-binary file format that supports scalable parallel I/O
-performance for MPI codes on a variety of supercomputing
-systems, and works equally well on laptop computers. The API is
-available for C, C++, and Fortran codes. The H5Part file format and APIs
-enable disparate research groups with different simulation
-implementations to transparently share datasets and data
-analysis tools. For instance, the common file format will enable
-groups that depend on completely different simulation
-implementations to share data analysis tools.
-</P>
-<font face="arial,helvetica" color="#555588"><h2>H5Part file organization and API</h2></font>
-<P>
-The proposed file storage format uses HDF5 for the lowlevel
-file storage and a simple API to provide a high-level
-interface to that file format. A programmer can either use
-the H5Part API to access the data files or write directly to
-the file format using some simple conventions for organizing
-and naming the objects stored in the file.
-</P>
-<P>
-In order to store Particle Data in the HDF5 file format,
-we have formalized the hierarchical arrangement of the
-datasets and naming conventions for the groups and associated
-datasets. The sample H5Part API formally encodes
-these conventions in order to provide a simple and uniform
-way to access these files from C, C++, and Fortran codes.
-The API makes it easier to write very portable data adaptors
-for visualization tools in order to expand the number of
-tools available to access the data. Even so, anyone can use
-the HDF5 h5ls utility to examine the organization of the
-H5Part files and even write their own HDF5-based interface
-for reading and writing the file format. The standards
-offered by the sample API are completely independent of
-the standard for organizing data within the file.The file
-format supports the storage of multiple timesteps
-of datasets that contain multiple fields.
-</P>
-<!-- 
-<font face="arial,helvetica" color="#555588"><h2>Requirements Specification</h2></font>
-<UL>
-<LI><a href="H5PartSpecs.html">H5Part API specifications
-</UL>
-</a>
--->
-
-<font face="arial,helvetica" color="#555588"><h2>Downloading and Installing H5Part</h2></font>
-<UL>
-<LI><a href="Downloading.html">Downloading HDF5 and H5Part
-<LI><a href="BuildingHDF5.html">Building the HDF5 Library</a>
-<LI><a href="Building.html">Building the H5Part Library</a>
-</UL>
-<font face="arial,helvetica" color="#555588"><h2>Bindings</h2></font>
-<UL>
-<LI><a href="UsingC.html">Using the C/C++ interface</a>
-<LI><a href="UsingF.html">Using the F77/F90 interface</a>
-<LI><a href="InternalLayout.html">Logical Internal HDF5 File</a>
-<LI><a href="H5PartTools.html">H5Part Utility Tools</a>
-<LI><a href="ReferencePages/index.html">Reference Manual</a>
-</UL>
-
-<font face="arial,helvetica" color="#555588"><h2>H5Part Visualization Tools</h2></font>
-<UL>
-<LI><a href="H5PartExpress.html">H5Part Express Reader</a>
-<LI><a href="H5PartVisIt.html">H5Part VisIt Reader</a>
-<LI><a href="H5PartIDL.html">H5Part IDL Reader</a>
-<LI><a href="http://www.cscs.ch/a-display.php?id=170">H5Part sparticles Reader: developed at CSCS, Switzerland</a>
-
-<LI><a href="H5PartPartView.html">PartView Visualization Application</a>
-</UL>
-</div>
-

examples/core_vfd.c

@@ -0,0 +1,51 @@
+#include <stdlib.h>
+#include <assert.h>
+#include <mpi.h>
+#include <H5Part.h>
+
+#define DATASIZE 32
+
+int main(int argc, char** argv)
+{
+    int i, rank, nprocs;
+    h5part_int32_t data[DATASIZE];
+    h5part_int64_t stat;
+    H5PartFile *file;
+
+    // initialize MPI
+    MPI_Init (&argc, &argv);
+    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
+
+    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
+
+    char filename[8];
+    sprintf (filename, "%d.h5", rank);
+
+    file = H5PartOpenFileParallel(
+            filename,
+            H5PART_WRITE | H5PART_VFD_CORE,
+            MPI_COMM_SELF);
+    assert (file != NULL);
+
+    stat = H5PartSetStep(file, 0);
+    assert (stat == H5PART_SUCCESS);
+
+    stat = H5PartSetNumParticles(file, DATASIZE);
+    assert (stat == H5PART_SUCCESS);
+
+    // create fake data
+    for (i=0; i<DATASIZE; i++) {
+        data[i] = i + rank * DATASIZE;
+    }
+
+    // write the data
+    stat = H5PartWriteDataInt32(file, "data", data);
+    assert (stat == H5PART_SUCCESS);
+
+    H5PartCloseFile(file);
+
+    MPI_Finalize();
+    return EXIT_SUCCESS;
+}
+

examples/fields.c

@@ -0,0 +1,45 @@
+#include <stdlib.h>
+#include <assert.h>
+#include <mpi.h>
+#include <H5Part.h>
+
+#define XSIZE 8
+#define YSIZE 8
+#define ZSIZE 8
+#define DATASIZE XSIZE*YSIZE*ZSIZE
+#define H5OpenFileParallel H5PartOpenFileParallel
+#define H5SetStep H5PartSetStep
+#define H5Block3dSetLayout H5BlockDefine3DFieldLayout
+#define H5CloseFile H5PartCloseFile
+
+int main(int argc, char** argv)
+{
+    int rank, nprocs;
+    h5part_float64_t ex[DATASIZE];
+    h5part_float64_t ey[DATASIZE];
+    h5part_float64_t ez[DATASIZE];
+    h5part_float64_t q[DATASIZE];
+    h5part_int64_t nparticles = DATASIZE;
+    H5PartFile *file;
+
+    // initialize MPI
+    MPI_Init (&argc, &argv);
+    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
+
+    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
+
+    file = H5OpenFileParallel("fields.h5", H5PART_WRITE, MPI_COMM_WORLD);
+    H5SetStep(file, 0);
+    H5Block3dSetLayout(file,
+            rank*XSIZE, (rank+1)*XSIZE - 1,
+            0, YSIZE - 1,
+            0, ZSIZE - 1);
+    H5Block3dWriteScalarFieldFloat64(file, "Q", q);
+    H5Block3dWrite3dVectorFieldFloat64(file, "E", ex, ez, ey);
+    H5CloseFile(file);
+
+    MPI_Finalize();
+    return EXIT_SUCCESS;
+}
+

examples/particles.c

@@ -0,0 +1,41 @@
+#include <stdlib.h>
+#include <assert.h>
+#include <mpi.h>
+#include <H5Part.h>
+
+#define DATASIZE 32
+
+int main(int argc, char** argv)
+{
+    int rank, nprocs;
+    h5part_float64_t x[DATASIZE];
+    h5part_float64_t y[DATASIZE];
+    h5part_float64_t z[DATASIZE];
+    h5part_float64_t px[DATASIZE];
+    h5part_float64_t py[DATASIZE];
+    h5part_float64_t pz[DATASIZE];
+    h5part_int64_t nparticles = DATASIZE;
+    H5PartFile *file;
+
+    // initialize MPI
+    MPI_Init (&argc, &argv);
+    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
+
+    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
+
+    file = H5PartOpenFileParallel("particles.h5", H5PART_WRITE, MPI_COMM_WORLD);
+    H5PartSetStep(file, 0);
+    H5PartSetNumParticles(file, nparticles);
+    H5PartWriteDataFloat64(file, "x", x);
+    H5PartWriteDataFloat64(file, "y", y);
+    H5PartWriteDataFloat64(file, "z", z);
+    H5PartWriteDataFloat64(file, "px", px);
+    H5PartWriteDataFloat64(file, "py", py);
+    H5PartWriteDataFloat64(file, "pz", pz);
+    H5PartCloseFile(file);
+
+    MPI_Finalize();
+    return EXIT_SUCCESS;
+}
+

examples/simplef.F90

@@ -0,0 +1,56 @@
+program H5PartTest
+  implicit none
+
+  include 'mpif.h'
+  include 'H5PartF.h'
+
+  integer :: comm, rank, ierr
+  integer*8 :: file_id, status, npoints, i
+  real*8, allocatable :: particles(:)
+  integer*8, allocatable :: id(:)
+  real*8 :: r8val
+  integer*8 :: i8val
+
+  comm = MPI_COMM_WORLD
+  call mpi_init(ierr)
+  call mpi_comm_rank(comm, rank, ierr)
+
+  ! open the a file for parallel writing
+  file_id = h5pt_set_verbosity_level(5)
+  file_id = h5pt_openw_par('test.h5', comm)
+
+  ! in the Fortran API, time steps start at 1
+  status = h5pt_setstep(file_id, 1_8)
+
+  ! write an attribute to the file
+  status = h5pt_writefileattrib_string(file_id, 'desc', 'This is a test.')
+
+  r8val = 0.5
+  i8val = 1
+  status = h5pt_writefileattrib_r8(file_id, 'double', r8val, i8val)
+
+  ! create fake data
+  npoints = 99
+  allocate(particles(npoints), id(npoints))
+  do i=1,npoints
+    particles(i) = real(i+npoints*rank)
+    id(i) = i+npoints*rank
+  enddo
+
+  ! set the size of the 1D array
+  status = h5pt_setnpoints(file_id, npoints)
+
+  ! write the particles
+  status = h5pt_writedata_r8(file_id, "x",  particles)
+
+  ! write the ids
+  status = h5pt_writedata_i8(file_id, "id", id)
+
+  ! close the file
+  status = h5pt_close(file_id)
+
+  deallocate(particles, id)
+
+  call mpi_finalize(ierr)
+
+end program H5PartTest

examples/stridedf.F90

@@ -0,0 +1,61 @@
+program H5PartTest
+  implicit none
+
+  include 'mpif.h'
+  include 'H5PartF.h'
+
+  integer :: comm, rank, ierr
+  integer*8 :: file_id, status, npoints, i
+  real*8, allocatable :: particles(:)
+  integer*8, allocatable :: id(:)
+
+  comm = MPI_COMM_WORLD
+  call mpi_init(ierr)
+  call mpi_comm_rank(comm, rank, ierr)
+
+  ! open the a file for parallel writing
+  file_id = h5pt_openw_par('test.h5', comm)
+
+  ! in the Fortran API, steps start at 1
+  status = h5pt_setstep(file_id, 1_8)
+
+  ! write an attribute to the file
+  status = h5pt_writefileattrib_string(file_id, 'desc', 'This is a test.')
+
+  ! create fake data
+  npoints = 99
+  allocate(particles(6*npoints), id(npoints))
+  do i=0,npoints-1
+    particles(6*i+1) = 0.0 + real(i+npoints*rank)
+    particles(6*i+2) = 0.1 + real(i+npoints*rank)
+    particles(6*i+3) = 0.2 + real(i+npoints*rank)
+    particles(6*i+4) = 0.3 + real(i+npoints*rank)
+    particles(6*i+5) = 0.4 + real(i+npoints*rank)
+    particles(6*i+6) = 0.5 + real(i+npoints*rank)
+    id(i+1) = i+npoints*rank
+  enddo
+
+  ! set the striding to 6
+  status = h5pt_setnpoints_strided(file_id, npoints, 6_8)
+
+  ! write the particles
+  status = h5pt_writedata_r8(file_id, "x",  particles(1))
+  status = h5pt_writedata_r8(file_id, "y",  particles(2))
+  status = h5pt_writedata_r8(file_id, "z",  particles(3))
+  status = h5pt_writedata_r8(file_id, "px", particles(4))
+  status = h5pt_writedata_r8(file_id, "py", particles(5))
+  status = h5pt_writedata_r8(file_id, "pz", particles(6))
+
+  ! disable the striding to write the ids
+  status = h5pt_setnpoints(file_id, npoints)
+  status = h5pt_writedata_i8(file_id, "id", id)
+
+  ! close the file
+  status = h5pt_close(file_id)
+
+  deallocate(particles, id)
+
+  call mpi_finalize(ierr)
+
+end program H5PartTest
+

examples/write_setview.c

@@ -0,0 +1,57 @@
+#include <stdlib.h>
+#include <assert.h>
+#include <mpi.h>
+#include <H5Part.h>
+
+#define DATASIZE 32
+#define ITERS 4
+
+int main(int argc, char** argv)
+{
+    int i, rank, nprocs;
+    h5part_int32_t data[ITERS*DATASIZE];
+    h5part_int64_t stat;
+    h5part_int64_t offset;
+    H5PartFile *file;
+
+    // initialize MPI
+    MPI_Init (&argc, &argv);
+    MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+    MPI_Comm_size (MPI_COMM_WORLD, &nprocs);
+
+    H5PartSetVerbosityLevel(H5PART_VERB_DEBUG);
+
+    file = H5PartOpenFileParallel("test.h5", H5PART_WRITE, MPI_COMM_WORLD);
+    assert (file != NULL);
+
+    stat = H5PartSetStep(file, 0);
+    assert (stat == H5PART_SUCCESS);
+
+    stat = H5PartSetNumParticles(file, ITERS*DATASIZE);
+    assert (stat == H5PART_SUCCESS);
+
+    // create fake data
+    for (i=0; i<ITERS*DATASIZE; i++) {
+        data[i] = i + rank * ITERS * DATASIZE;
+    }
+
+    offset = rank * ITERS * DATASIZE;
+
+    // iterate over arrays
+    for (i=0; i<ITERS; i++) {
+        // set the "view" to select a subset of the dataset
+        stat = H5PartSetView(file,
+                offset + i*DATASIZE,
+                offset + (i+1)*DATASIZE - 1);
+        assert (stat == H5PART_SUCCESS);
+        // write the data
+        stat = H5PartWriteDataInt32(file, "data", data + i*DATASIZE);
+        assert (stat == H5PART_SUCCESS);
+    }
+
+    H5PartCloseFile(file);
+
+    MPI_Finalize();
+    return EXIT_SUCCESS;
+}
+

src/H5Block.f90

@@ -0,0 +1,235 @@
+! Declaration of subroutines for Fortran Bindings
+
+!> \defgroup h5block_f90_api H5Block F90 API
+
+!> \ingroup h5block_f90_api
+!! \defgroup h5blockf_model      Setting up the Data Model
+!<
+
+!> \ingroup h5block_f90_api
+!! \defgroup h5blockf_data       Reading and Writing Datasets
+!<
+
+!> \ingroup h5block_f90_api
+!! \defgroup h5blockf_attrib     Reading and Writing Attributes
+!<
+
+
+!!!!!!!! Setting up the Data Model !!!!!!!!
+
+!> \ingroup h5blockf_model
+!! See \ref H5BlockDefine3DFieldLayout
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_define3dlayout ( filehandle, i_start, i_end, j_start, j_end, k_start, k_end )
+    INTEGER*8, INTENT(IN) :: filehandle
+    INTEGER*8, INTENT(IN) :: i_start
+    INTEGER*8, INTENT(IN) :: i_end
+    INTEGER*8, INTENT(IN) :: j_start
+    INTEGER*8, INTENT(IN) :: j_end
+    INTEGER*8, INTENT(IN) :: k_start
+    INTEGER*8, INTENT(IN) :: k_end
+END FUNCTION
+  
+!> \ingroup h5blockf_model
+!! See \ref H5BlockDefine3DChunkDims
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_define3dchunkdims ( filehandle, i, j, k )
+    INTEGER*8, INTENT(IN) :: filehandle
+    INTEGER*8, INTENT(IN) :: i
+    INTEGER*8, INTENT(IN) :: j
+    INTEGER*8, INTENT(IN) :: k
+END FUNCTION
+ 
+!> \ingroup h5blockf_model
+!! See \ref H5Block3dGetPartitionOfProc
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_get_partition_of_proc ( filehandle, proc, i_start, i_end, j_start, j_end, k_start, k_end )
+    INTEGER*8, INTENT(IN) :: filehandle
+    INTEGER*8, INTENT(OUT) :: proc
+    INTEGER*8, INTENT(OUT) :: i_start
+    INTEGER*8, INTENT(OUT) :: i_end
+    INTEGER*8, INTENT(OUT) :: j_start
+    INTEGER*8, INTENT(OUT) :: j_end
+    INTEGER*8, INTENT(OUT) :: k_start
+    INTEGER*8, INTENT(OUT) :: k_end
+ END FUNCTION
+  
+!> \ingroup h5blockf_model
+!! See \ref H5Block3dGetReducedPartitionOfProc
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_get_reduced_partition_of_proc ( filehandle, proc, i_start, i_end, j_start, j_end, k_start, k_end )
+    INTEGER*8, INTENT(IN) :: filehandle
+    INTEGER*8, INTENT(OUT) :: proc
+    INTEGER*8, INTENT(OUT) :: i_start
+    INTEGER*8, INTENT(OUT) :: i_end
+    INTEGER*8, INTENT(OUT) :: j_start
+    INTEGER*8, INTENT(OUT) :: j_end
+    INTEGER*8, INTENT(OUT) :: k_start
+    INTEGER*8, INTENT(OUT) :: k_end
+END FUNCTION
+  
+!> \ingroup h5blockf_model
+!! See \ref H5Block3dGetProcOf
+!! \return rank of processor error code
+!<
+INTEGER*8 FUNCTION h5bl_get_proc_of ( filehandle, i, j, k )
+    INTEGER*8, INTENT(IN) :: filehandle
+    INTEGER*8, INTENT(IN) :: i
+    INTEGER*8, INTENT(IN) :: j
+    INTEGER*8, INTENT(IN) :: k
+END FUNCTION
+  
+!> \ingroup h5blockf_model
+!! See \ref H5BlockGetNumFields
+!! \return number of fields or error code
+!<
+INTEGER*8 FUNCTION h5bl_getnumfields ( filehandle )
+    INTEGER*8, INTENT(IN) :: filehandle
+END FUNCTION
+  
+!> \ingroup h5blockf_model
+!! See \ref H5BlockGetFieldInfo
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_getfieldinfo ( filehandle, idx, field_name, grid_rank, grid_dims, field_dims )
+    INTEGER*8, INTENT(IN) :: filehandle
+    INTEGER*8, INTENT(IN) :: idx
+    CHARACTER(LEN=*), INTENT(OUT) :: field_name
+    INTEGER*8, INTENT(OUT) :: grid_rank
+    INTEGER*8, INTENT(OUT) :: grid_dims(*)
+    INTEGER*8, INTENT(OUT) :: field_dims
+    INTEGER*8, INTENT(OUT) :: type
+END FUNCTION
+
+!> \ingroup h5blockf_model
+!! See \ref H5BlockHasFieldData
+!! \return 0 if false, 1 if true, or error code
+!<
+INTEGER*8 FUNCTION h5bl_has_fielddata ( filehandle )
+    INTEGER*8, INTENT(IN) :: filehandle
+END FUNCTION
+  
+
+!!!!!!!! Reading and Writing Attributes !!!!!!!!
+ 
+!> \ingroup h5blockf_attrib
+!! See \ref H5BlockWriteFieldAttribString
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_writefieldattrib_string ( filehandle, field_name, attrib_name, attrib_value )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: field_name    ! The name of the field
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_name   ! The name of the attribute
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_value  ! The array of data to write into the attribute
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5BlockGetNumFieldAttribs
+!! \return number of attributes or error code
+!<
+INTEGER*8 FUNCTION h5bl_getnfieldattribs ( filehandle, field_name )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: field_name    ! The name of the field
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! See \ref H5BlockGetFieldAttribInfo
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_getfieldattribinfo ( filehandle, field_name, idx, attrib_name, attrib_nelem)
+    INTEGER*8,INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: field_name   ! The name of the field
+    INTEGER*8,INTENT(IN) :: idx  ! index of the attribute being queried
+    CHARACTER(LEN=*), INTENT(OUT):: attrib_name  ! The name of the attribute
+    INTEGER*8,INTENT(OUT):: attrib_nelem ! Number of elements in the attrib array
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! Read the attribute \c attrib_name from the field \c field_name at the
+!! current timestep, and store the int64 value in \c attrib_value.
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_readfieldattrib_i8 ( filehandle, field_name, attrib_name, attrib_value )
+    INTEGER*8,INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: field_name    ! The name of the field
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_name   ! name of the attribute to read
+    INTEGER*8,INTENT(OUT):: attrib_value(*)! the attribute data will be read into this array
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! Read the attribute \c attrib_name from the field \c field_name at the
+!! current timestep, and store the float64 value in \c attrib_value.
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_readfieldattrib_r8 ( filehandle, field_name, attrib_name, attrib_value )
+    INTEGER*8,INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: field_name    ! The name of the field
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_name   ! name of the attribute to read
+    REAL*8,   INTENT(OUT):: attrib_value(*)! the attribute data will be read into this array
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! Read the attribute \c attrib_name from the field \c field_name at the
+!! current timestep, and store the string value in \c attrib_value.
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_readfieldattrib_string ( filehandle, field_name, attrib_name, attrib_value )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: field_name    ! The name of the field
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_name   ! name of the attribute to read
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_value  ! The array of data to write into the attribute
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dGetFieldSpacing
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_get_field_spacing ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(OUT) :: x
+    REAL*8, INTENT(OUT) :: y
+    REAL*8, INTENT(OUT) :: z
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dSetFieldSpacing
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_set_field_spacing ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(IN) :: x
+    REAL*8, INTENT(IN) :: y
+    REAL*8, INTENT(IN) :: z
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dGetFieldOrigin
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_get_field_origin ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(OUT) :: x
+    REAL*8, INTENT(OUT) :: y
+    REAL*8, INTENT(OUT) :: z
+END FUNCTION
+  
+!> \ingroup h5blockf_attrib
+!! See \ref H5Block3dSetFieldOrigin
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_set_field_origin ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle
+    CHARACTER(LEN=*), INTENT(IN) :: name
+    REAL*8, INTENT(IN) :: x
+    REAL*8, INTENT(IN) :: y
+    REAL*8, INTENT(IN) :: z
+END FUNCTION
+  
+  

src/H5Block.h

@@ -1,185 +1,194 @@
-#ifndef H5BLOCK_H
-#define H5BLOCK_H
+#ifndef _H5BLOCK_H_
+#define _H5BLOCK_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*!
+  Include read/write call variants for different data types and
+  field dimensions.
+*/
+#include "H5BlockReadWrite.h"
+
+#define H5BLOCK_FIELD_ORIGIN_NAME	"__Origin__"
+#define H5BLOCK_FIELD_SPACING_NAME	"__Spacing__"
 
 /*! 
-
-    Interface for block structured field data
-
-    This  is used to store and retrieve scalar or vector valued field data.
-    With \f$  \Omega\ \f$  .... 
-
-    Basic items are blocks (\f$ \Omaga_i \f$ ), cartesian subdomains of \f$ \Omega \f$ . If a  \f$ \Omega_i \f$ 
-    is refined we view this \f$ \Omaga_i \f$  as a patch.
-   
-    \note My note  
-   
-
-	This is to discuss the HDF5 architecture:
-	
-    \timestep#k
-	            \particles
-				\topo
-	            \block
-	                 \patch1
-							\block 	
-
-	Idea: because we have more than one block per timestep
-	in case of AMR, the activity of a block could help.
-
-
+  Interface for block structured field data.
 */
+h5part_int64_t
+H5BlockDefine3DFieldLayout (
+	H5PartFile *f,
+	const h5part_int64_t i_start,
+	const h5part_int64_t i_end,
+	const h5part_int64_t j_start,
+	const h5part_int64_t j_end,
+	const h5part_int64_t k_start,
+	const h5part_int64_t k_end
+	);
+
+h5part_int64_t
+H5BlockDefine3DChunkDims (
+	H5PartFile *f,
+	const h5part_int64_t i,
+	const h5part_int64_t j,
+	const h5part_int64_t k
+	);
+
+h5part_int64_t
+H5BlockGet3DChunkDims(
+	H5PartFile *f,
+        const char *field_name,
+	h5part_int64_t *dims
+	);
+
+h5part_int64_t
+H5Block3dGetPartitionOfProc (
+	H5PartFile *f,
+	const h5part_int64_t proc,
+	h5part_int64_t *i_start,
+	h5part_int64_t *i_end,
+	h5part_int64_t *j_start,
+	h5part_int64_t *j_end,
+	h5part_int64_t *k_start,
+	h5part_int64_t *k_end
+	);
+
+h5part_int64_t
+H5Block3dGetReducedPartitionOfProc (
+	H5PartFile *f,
+	h5part_int64_t proc,
+	h5part_int64_t *i_start, 
+	h5part_int64_t *i_end,
+	h5part_int64_t *j_start,
+	h5part_int64_t *j_end,
+	h5part_int64_t *k_start,
+	h5part_int64_t *k_end
+	);
+
+h5part_int64_t
+H5Block3dGetProcOf (
+	H5PartFile *f,
+	h5part_int64_t i,
+	h5part_int64_t j,
+	h5part_int64_t k
+	);
+
+h5part_int64_t
+H5BlockGetNumFields (
+	H5PartFile *f
+	);
+
+h5part_int64_t
+H5BlockGetFieldInfo (
+	H5PartFile *f,
+	const h5part_int64_t idx,
+	char *name,
+	const h5part_int64_t len_name,
+	h5part_int64_t *grid_rank,
+	h5part_int64_t *grid_dims,
+	h5part_int64_t *field_rank,
+	h5part_int64_t *type
+	);
+
+h5part_int64_t
+H5BlockGetFieldInfoByName (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_int64_t *grid_rank,
+	h5part_int64_t *grid_dims,
+	h5part_int64_t *field_rank,
+	h5part_int64_t *type
+	);
+
+h5part_int64_t
+H5Block3dGetFieldOrigin (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_float64_t *x_origin,
+	h5part_float64_t *y_origin,
+	h5part_float64_t *z_origin
+	);
+
+h5part_int64_t
+H5Block3dSetFieldOrigin (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_float64_t x_origin,
+	const h5part_float64_t y_origin,
+	const h5part_float64_t z_origin
+	);
+
+h5part_int64_t
+H5Block3dGetFieldSpacing (
+	H5PartFile *f,
+	const char *field_name,
+	h5part_float64_t *x_spacing,
+	h5part_float64_t *y_spacing,
+	h5part_float64_t *z_spacing
+	);
+
+h5part_int64_t
+H5Block3dSetFieldSpacing (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_float64_t x_spacing,
+	const h5part_float64_t y_spacing,
+	const h5part_float64_t z_spacing
+	);
+
+h5part_int64_t
+H5BlockWriteFieldAttrib (
+	H5PartFile *f,
+	const char *field_name,
+	const char *attrib_name,
+	const h5part_int64_t attrib_type,
+	const void *attrib_value,
+	const h5part_int64_t attrib_nelem
+	);
+
+h5part_int64_t
+H5BlockWriteFieldAttribString (
+	H5PartFile *f,
+	const char *field_name,
+	const char *attrib_name,
+	const char *attrib_value
+	);
+
+h5part_int64_t
+H5BlockGetNumFieldAttribs (
+	H5PartFile *f,
+	const char *field_name
+	);
+
+h5part_int64_t
+H5BlockGetFieldAttribInfo (
+	H5PartFile *f,
+	const char *field_name,
+	const h5part_int64_t attrib_idx,
+	char *attrib_name,
+	const h5part_int64_t len_of_attrib_name,
+	h5part_int64_t *attrib_type,
+	h5part_int64_t *attrib_nelem
+	);
+
+h5part_int64_t
+H5BlockReadFieldAttrib (
+	H5PartFile *f,
+	const char *field_name,
+	const char *attrib_name,
+	void *attrib_value
+	);
+
+h5part_int64_t
+H5BlockHasFieldData (
+	H5PartFile *f
+	);
 
 
-//! Checks if the block of the actual time step is refined i.e. if we have a patch
-/*!
-      \param H5PartFile *f : file handle
-      \param char *name    : name of the data set
-*/
-bool H5BlockIsPatch(H5PartFile *f, char *name);
+#ifdef __cplusplus
+}
+#endif
 
-
-//! return the maximum level refinement of refinement at the current time step
-/*!
-      \param H5PartFile *f : file handle
-      \param char *name    : name of the data set
-*/
-int H5BlockGetMaxRefinementLevel(H5PartFile *f, char *name);
-
-
-
-//! Define the field layout (FL) given the dense index space at the actual time step
-/*!
-	  \param H5PartFile *f : file handle
-      \param char *name    : name of the data set
-      \param unsigned int Istart : start of index I
-      \param unsigned int Jstart : start of index J
-      \param unsigned int Kstart : start of index K
-      \param unsigned int Istart : end of index I
-      \param unsigned int Jstart : end of index J
-      \param unsigned int Kstart : end of index K
-      \note this defines  \f$ \Omega \f$ and the view for HDF5	
-	  
-	  \note we have to make a 1D and 2D version
-	  \note Q: what about a dimension independent version probably hard for the FOR-People?
-
-*/
-void H5BlockDefine3DFieldLayout(H5PartFile *f, 
-	char *name, 	unsigned int Istart, unsigned int Iend,	
- 	                        unsigned int Jstart, unsigned int Jend,	
-	                        unsigned int Kstart, unsigned int Kend);	
-
-
-//! Write the mesh spacing for the active (current) block 
-/*!
-	  \param H5PartFile *f : file handle
-      \param char *name    : name of teh data set
-      \param double dx: mesh spacing in x 
-      \param double dy: mesh spacing in y 
-      \param double dz: mesh spacing in z 
-	  
-*/
-void H5BlockSetMeshSpacing(H5PartFile *f, char *name, double dx, double dy, double dz,);
-
-//! Write a 3D real valued vector field using the defined FL for this block
-/*!
-      \param H5PartFile *f : file handle
-      \param char *name    : name of teh data set
-      \param double *xval : array of x component data
-      \param double *yval : array of y component data
-      \param double *zval : array of z component data
-
-	  \note we have to make a 1D and 2D version
-	  \note Q: what about a dimension independent version?
-	  
-*/
-void H5BlockWrite3DVField(H5PartFile *f, 
-	char *name, 	
-	double *xval,	
-	double *yval,	
-	double *zval);	
-
-// ===========================================================================================
-/*
-The following reflects the fact that we have fields which are decomposed into modes.
-
-Augment the field name with the mode number and use this name to store the field.
-For the mode freqency use the same procedure.
-
-*/
-
-	
-	//! Read the number of stored modes at actual timestep 
-	/*!
-      \param H5PartFile *f : file handle
-      \param char *name    : name of teh data set
-	  
-	*/
-	int  H5BlockGetNumberOfModes(H5PartFile *f, char *name); 
-	
-	//! Set the number of stored modes at actual timestep 
-	/*!
-      \param H5PartFile *f : file handle
-      \param char *name    : name of teh data set
-	  \param int modes: the number of modes
-	*/
-	void H5BlockSetNumberOfModes(H5PartFile *f, char *name, int modes); 
-
-
-	//! Write a 3D real valued vector field using the defined FL for this block
-	/*!
-      \param H5PartFile *f : file handle
-      \param char *name : name of teh data set
-	  \param int modeNumber : the mode number of the field
-	  \param double omega :  the eingenmode of the field
-      \param double *xval : array of x component data
-      \param double *yval : array of y component data
-      \param double *zval : array of z component data
-
-	  \note we have to make a 1D and 2D version
-	  \note Q: what about a dimension independent version?
-	  
-	*/
-	void H5BlockWrite3DVField(H5PartFile *f, 
-		char *name, int modeNumber, double omega, 	
-		double *xval,	
-		double *yval,	
-		double *zval);	
-
-
-	//! Write the quality factor for a given mode
-	/*!
-      \param H5PartFile *f : file handle
-      \param char *name : name of the data set
-	  \param int modeNumber : the mode number of the field
-	  \param double Q: the quality factor	
-	*/
-	void H5BlockSetQFactor(H5PartFile *f, char *name, int mode, double Q);
-
-	//! Write the S-parameters for a given mode
-	/*!
-      \param H5PartFile *f : file handle
-      \param char *name : name of the data set
-	  \param int modeNumber : the mode number of the field
-	  \param double **S: the quality factor	
-	*/	
-	void H5BlockSetSParams(H5PartFile *f, char *name, int mode, double **s);
-
-	//! Read the quality factor for a given mode
-	/*!
-      \param H5PartFile *f : file handle
-      \param char *name : name of the data set
-	  \param int modeNumber : the mode number of the field
-	  \param double *Q: the quality factor	
-	*/
-	void H5BlockGetQFactor(H5PartFile *f, char *name, int mode, double *Q);
-
-	//! Read the S-parameters for a given mode
-	/*!
-      \param H5PartFile *f : file handle
-      \param char *name : name of the data set
-	  \param int modeNumber : the mode number of the field
-	  \param double **S: the quality factor	
-	*/	
-	void H5BlockGetSParams(H5PartFile *f, char *name, int mode, double **s);
-
-#endif // H5BLOCK_H
+#endif

src/H5BlockErrors.h

@@ -0,0 +1,52 @@
+#ifndef _H5BLOCK_ERRORS_H_
+#define _H5BLOCK_ERRORS_H_
+
+extern h5part_error_handler _err_handler;
+
+#define CHECK_LAYOUT( f ) \
+	if ( ! f->block->have_layout ) \
+		return (*_err_handler) ( \
+			_H5Part_get_funcname(), \
+			H5PART_ERR_LAYOUT, \
+			"No layout defined." )
+
+#define HANDLE_H5PART_LAYOUT_ERR \
+		(*_err_handler) ( \
+			_H5Part_get_funcname(), \
+			H5PART_ERR_LAYOUT, \
+			"Bad layout." );
+
+#define HANDLE_H5PART_NOENT_ERR( name ) \
+		(*_err_handler) ( \
+			_H5Part_get_funcname(), \
+			H5PART_ERR_NOENT, \
+			"Object \"%s\" doesn't exists.", name );
+
+#define HANDLE_H5PART_DATASET_RANK_ERR( m, n ) \
+		(*_err_handler) ( \
+			_H5Part_get_funcname(), \
+			H5PART_ERR_INVAL, \
+			"Wrong rank of dataset: Is %d, but should be %d", \
+			m, n );
+
+#define HANDLE_H5PART_GROUP_EXISTS_ERR( name ) \
+		(*_err_handler) ( \
+			_H5Part_get_funcname(), \
+			H5PART_ERR_INVAL, \
+			"Group \"%s\" already exists", name )
+
+#define HANDLE_H5S_CREATE_SIMPLE_3D_ERR( dims ) \
+	 (*_err_handler) ( \
+		_H5Part_get_funcname(), \
+		H5PART_ERR_HDF5, \
+		"Cannot create 3d dataspace with dimension sizes " \
+		"\"(%lld,%lld,%lld)\".", \
+		 (long long)dims[0], (long long)dims[1], (long long)dims[2] );
+
+#define HANDLE_H5S_GET_SIMPLE_EXTENT_DIMS_ERR \
+	 (*_err_handler) ( \
+		_H5Part_get_funcname(), \
+		H5PART_ERR_HDF5, \
+		"Cannot get dimension sizes of dataset" );
+
+#endif

src/H5BlockF.c

@@ -0,0 +1,449 @@
+#include "H5Part.h"
+#include "H5PartPrivate.h"
+#include "H5Block.h"
+#include "Underscore.h"
+
+#if defined(F77_SINGLE_UNDERSCORE)
+#define F77NAME(a,b) a
+#elif defined(F77_CRAY_UNDERSCORE)
+#define F77NAME(a,b) b
+#elif defined(F77_NO_UNDERSCORE)
+#else
+#error Error, no way to determine how to construct fortran bindings
+#endif
+
+#if ! defined(F77_NO_UNDERSCORE)
+
+#define h5bl_define3dlayout F77NAME (					\
+					h5bl_define3dlayout_,		\
+					H5BL_DEFINE3DLAYOUT )
+#define h5bl_define3dchunkdims F77NAME (				\
+					h5bl_define3dchunkdims_,	\
+					H5BL_DEFINE3DCHUNKDIMS )
+#define h5bl_get_partition_of_proc F77NAME (				\
+					h5bl_get_partition_of_proc_,	\
+					H5BL_GET_PARTITION_OF_PROC )
+#define h5bl_get_reduced_partition_of_proc F77NAME (			\
+					h5bl_get_reduced_partition_of_proc_,\
+					H5BL_GET_REDUCED_PARTITION_OF_PROC )
+#define h5bl_get_proc_of F77NAME (					\
+					h5bl_get_proc_of_,		\
+					H5BL_GET_PROC_OF )
+#define h5bl_getnumfields F77NAME (					\
+					h5bl_getnumfields_,		\
+					H5BL_GETNUMFIELDS )
+#define h5bl_getfieldinfo F77NAME (					\
+					h5bl_getfieldinfo_,		\
+					H5BL_GETFIELDINFO )
+#define h5bl_writefieldattrib_string F77NAME (			\
+					h5bl_writefieldattrib_string_,	\
+					H5BL_WRITEFIELDATTRIB_STRING )
+#define h5bl_getnfieldattribs F77NAME (				\
+					h5bl_getnfieldattribs_,		\
+					H5BL_GETNFIELDATTRIBS )
+#define h5bl_getfieldattribinfo F77NAME (				\
+					h5bl_getfieldattribinfo_,	\
+					h5bl_getfieldattribinfo )
+#define h5bl_readfieldattrib_i8 F77NAME (				\
+					h5bl_readfieldattrib_i8_,	\
+					H5BL_READFIELDATTRIB_I8 )
+#define h5bl_readfieldattrib_r8 F77NAME (				\
+					h5bl_readfieldattrib_r8_,	\
+					H5BL_READFIELDATTRIB_R8 )
+#define h5bl_readfieldattrib_string F77NAME (				\
+					h5bl_readfieldattrib_string_,	\
+					H5BL_READFIELDATTRIB_STRING )
+#define h5bl_has_fielddata F77NAME (					\
+					h5bl_has_fielddata_,		\
+					H5BL_HAS_FIELDDATA )
+#define h5bl_3d_set_field_spacing F77NAME (				\
+					h5bl_3d_set_field_spacing_,	\
+					H5BL_3D_SET_FIELD_SPACING )
+#define h5bl_3d_get_field_spacing F77NAME (				\
+					h5bl_3d_get_field_spacing_,	\
+					H5BL_3D_GET_FIELD_SPACING )
+#define h5bl_3d_set_field_origin F77NAME (				\
+					h5bl_3d_set_field_origin_,	\
+					H5BL_3D_SET_FIELD_ORIGIN )
+#define h5bl_3d_get_field_origin F77NAME (				\
+					h5bl_3d_get_field_origin_,	\
+					H5BL_3D_GET_FIELD_origin )
+#endif
+
+h5part_int64_t
+h5bl_define3dlayout (
+	h5part_int64_t *f,
+	const h5part_int64_t *i_start,	/*!< start index of i */
+	const h5part_int64_t *i_end,	/*!< end index of i */
+	const h5part_int64_t *j_start,	/*!< start index of j */
+	const h5part_int64_t *j_end,	/*!< end index of j */
+	const h5part_int64_t *k_start,	/*!< start index of k */
+	const h5part_int64_t *k_end	/*!< end index of k */
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	return H5BlockDefine3DFieldLayout (
+		filehandle,
+		*i_start-1, *i_end-1,
+		*j_start-1, *j_end-1,
+		*k_start-1, *k_end-1 );
+}
+
+h5part_int64_t
+h5bl_define3dchunkdims (
+	h5part_int64_t *f,
+	const h5part_int64_t *i,
+	const h5part_int64_t *j,
+	const h5part_int64_t *k
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	return H5BlockDefine3DChunkDims ( filehandle, *i, *j, *k );
+}
+
+h5part_int64_t
+h5bl_get_partition_of_proc (
+	h5part_int64_t *f,		/*!< file handle */
+	const h5part_int64_t *proc,
+	h5part_int64_t *i_start,	/*!< start index of i */
+	h5part_int64_t *i_end,		/*!< end index of i */
+	h5part_int64_t *j_start,	/*!< start index of j */
+	h5part_int64_t *j_end,		/*!< end index of j */
+	h5part_int64_t *k_start,	/*!< start index of k */
+	h5part_int64_t *k_end		/*!< end index of k */
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	h5part_int64_t herr = H5Block3dGetPartitionOfProc (
+		filehandle,
+		*proc,
+		i_start, i_end, j_start, j_end, k_start, k_end );
+	if ( herr < 0 ) return herr;
+
+	(*i_start)++;
+	(*i_end)++;
+	(*j_start)++;
+	(*j_end)++;
+	(*k_start)++;
+	(*k_end)++;
+
+	return H5PART_SUCCESS;
+}
+
+h5part_int64_t
+h5bl_get_reduced_partition_of_proc (
+	h5part_int64_t *f,
+	const h5part_int64_t *proc,
+	h5part_int64_t *i_start, 
+	h5part_int64_t *i_end,
+	h5part_int64_t *j_start,
+	h5part_int64_t *j_end,
+	h5part_int64_t *k_start,
+	h5part_int64_t *k_end
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	h5part_int64_t herr = H5Block3dGetReducedPartitionOfProc (
+		filehandle,
+		*proc,
+		i_start, i_end, j_start, j_end, k_start, k_end );
+	if ( herr < 0 ) return herr;
+
+	(*i_start)++;
+	(*i_end)++;
+	(*j_start)++;
+	(*j_end)++;
+	(*k_start)++;
+	(*k_end)++;
+
+	return H5PART_SUCCESS;
+}
+
+h5part_int64_t
+h5bl_get_proc_of (
+	h5part_int64_t *f,
+	const h5part_int64_t *i,
+	const h5part_int64_t *j,
+	const h5part_int64_t *k
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	return H5Block3dGetProcOf ( filehandle, (*i)-1, (*j)-1, (*k)-1 );
+}
+
+h5part_int64_t
+h5bl_getnumfields (
+	h5part_int64_t *f			/*!< file handle */
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	return H5BlockGetNumFields ( filehandle );
+}
+
+h5part_int64_t
+h5bl_getfieldinfo (
+	h5part_int64_t *f,
+	const h5part_int64_t *idx,
+	char *field_name,
+	h5part_int64_t *grid_rank,
+	h5part_int64_t *grid_dims,
+	h5part_int64_t *field_dims,
+	h5part_int64_t *type,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	h5part_int64_t herr = H5BlockGetFieldInfo (
+		filehandle, *idx, field_name, l_field_name,
+		grid_rank, grid_dims, field_dims, type );
+	_H5Part_strc2for ( field_name, l_field_name );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_writefieldattrib_string (
+	h5part_int64_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	const char *attrib_value,
+	const int l_field_name,
+	const int l_attrib_name,
+	const int l_attrib_value
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =_H5Part_strdupfor2c ( field_name,  l_field_name );
+	char *attrib_name2=_H5Part_strdupfor2c ( attrib_name, l_attrib_name );
+	char *attrib_value2=_H5Part_strdupfor2c( attrib_value,l_attrib_value );
+
+	h5part_int64_t herr = H5BlockWriteFieldAttribString (
+		filehandle, field_name2, attrib_name2, attrib_value2 );
+
+	free ( field_name2 );
+	free ( attrib_name2 );
+	free ( attrib_value2 );
+	return herr;
+}
+
+
+h5part_int64_t
+h5bl_getnfieldattribs (
+	h5part_int64_t *f,
+	const char *field_name,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 = _H5Part_strdupfor2c ( field_name,   l_field_name );
+
+	h5part_int64_t herr = H5BlockGetNumFieldAttribs (
+		filehandle, field_name2 );
+	
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_getfieldattribinfo (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_int64_t *attrib_idx,
+	char *attrib_name,
+	h5part_int64_t *attrib_nelem,
+	const int l_field_name,
+	const int l_attrib_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	h5part_int64_t	attrib_type;
+
+	char *field_name2 = _H5Part_strdupfor2c ( field_name,   l_field_name );
+
+	h5part_int64_t herr = H5BlockGetFieldAttribInfo (
+		filehandle, field_name2, *attrib_idx,
+		attrib_name, l_attrib_name,
+		&attrib_type,
+		attrib_nelem );
+
+	_H5Part_strc2for ( attrib_name, l_attrib_name );
+
+	free ( field_name2 );
+	return herr;
+}
+
+
+h5part_int64_t
+h5bl_readfieldattrib_i8 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	h5part_int64_t *attrib_value,
+	const int l_field_name,
+	const int l_attrib_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =_H5Part_strdupfor2c ( field_name,   l_field_name );
+	char *attrib_name2=_H5Part_strdupfor2c ( attrib_name,  l_attrib_name );
+
+	h5part_int64_t herr = H5BlockReadFieldAttrib (
+		filehandle, field_name2, attrib_name2, attrib_value );
+
+	free ( field_name2 );
+	free ( attrib_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_readfieldattrib_r8 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	h5part_float64_t *attrib_value,
+	const int l_field_name,
+	const int l_attrib_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =_H5Part_strdupfor2c ( field_name,   l_field_name );
+	char *attrib_name2=_H5Part_strdupfor2c ( attrib_name,  l_attrib_name );
+
+	h5part_int64_t herr = H5BlockReadFieldAttrib (
+		filehandle, field_name2, attrib_name2, attrib_value );
+
+	free ( field_name2 );
+	free ( attrib_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_readfieldattrib_string (
+	h5part_int64_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	char *attrib_value,
+	const int l_field_name,
+	const int l_attrib_name,
+	const int l_attrib_value
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =_H5Part_strdupfor2c ( field_name,   l_field_name );
+	char *attrib_name2=_H5Part_strdupfor2c ( attrib_name,  l_attrib_name );
+
+	h5part_int64_t herr = H5BlockReadFieldAttrib (
+		filehandle, field_name2, attrib_name2, attrib_value );
+
+	_H5Part_strc2for ( attrib_value, l_attrib_value );
+
+	free ( field_name2 );
+	free ( attrib_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_has_fielddata (
+	h5part_int64_t *f
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	return H5BlockHasFieldData ( filehandle );
+}
+
+h5part_int64_t
+h5bl_3d_get_field_spacing (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *x,
+	h5part_float64_t *y,
+	h5part_float64_t *z,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dGetFieldSpacing (
+		filehandle, field_name2, x, y, z );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_set_field_spacing (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *x,
+	const h5part_float64_t *y,
+	const h5part_float64_t *z,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dSetFieldSpacing (
+		filehandle, field_name2, *x, *y, *z );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_get_field_origin (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *x,
+	h5part_float64_t *y,
+	h5part_float64_t *z,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dGetFieldOrigin (
+		filehandle, field_name2, x, y, z );
+
+	free ( field_name2 );
+	return herr;
+}
+
+h5part_int64_t
+h5bl_3d_set_field_origin (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *x,
+	const h5part_float64_t *y,
+	const h5part_float64_t *z,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name, l_field_name );
+
+	h5part_int64_t herr = H5Block3dSetFieldOrigin (
+		filehandle, field_name2, *x, *y, *z );
+
+	free ( field_name2 );
+	return herr;
+}

src/H5BlockPrivate.h

@@ -0,0 +1,70 @@
+#ifndef _H5BLOCK_PRIVATE_H_
+#define _H5BLOCK_PRIVATE_H_
+
+#define H5BLOCK_GROUPNAME_BLOCK	"Block"
+
+#define BLOCK_INIT( f ) { \
+	h5part_int64_t herr = _H5Block_init ( f ); \
+	if ( herr < 0 ) return herr; \
+}
+
+h5part_int64_t
+_H5Block_init (
+	H5PartFile *f
+	);
+
+h5part_int64_t
+_H5Block_close (
+	H5PartFile *f
+	);
+
+h5part_int64_t
+_H5Block_open_field_group (
+	H5PartFile *f,
+	const char *name
+	);
+
+h5part_int64_t
+_H5Block_close_field_group (
+	H5PartFile *f
+	);
+
+h5part_int64_t
+_H5Block_create_field_group (
+	H5PartFile *f,
+	const char *name
+	);
+ 
+h5part_int64_t
+_H5Block_select_hyperslab_for_reading (
+	H5PartFile *f,
+	hid_t dataset
+	);
+
+h5part_int64_t
+_H5Block_write_data (
+	H5PartFile *f,
+	const char *name,
+	const void *data,
+	const hid_t type
+	);
+
+h5part_int64_t
+_H5Block_read_data (
+	H5PartFile *f,
+	const char *name,
+	void *data,
+	hid_t type
+	);
+
+h5part_int64_t
+_write_field_attrib (
+	H5PartFile *f,
+	const char *field_name,
+	const char *attrib_name,
+	const hid_t attrib_type,
+	const void *attrib_value,
+	const h5part_int64_t attrib_nelem
+	);
+
+#endif

src/H5BlockReadWrite.c

@@ -0,0 +1,769 @@
+
+#include <stdlib.h>
+#include <string.h>
+
+#include <hdf5.h>
+#include "H5Part.h"
+#include "H5PartErrors.h"
+#include "H5PartPrivate.h"
+
+#include "H5BlockTypes.h"
+#include "H5Block.h"
+#include "H5BlockPrivate.h"
+#include "H5BlockErrors.h"
+
+/*!
+  \ingroup h5block_data
+
+  Write a 3-dimensional field \c name from the buffer starting at \c data
+  to the current time-step using the defined field layout. Values are
+  floating points (64-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dWriteScalarFieldFloat64 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	const h5part_float64_t *data      /*!< IN: scalar data to write */
+	) {
+
+	SET_FNAME ( "H5Block3dWriteScalarFieldFloat64" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_create_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_write_data ( f, "0", data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+
+  Read a 3-dimensional field \c name into the buffer starting at \c data from
+  the current time-step using the defined field layout. Values are
+  floating points (64-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dReadScalarFieldFloat64 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to read */
+	h5part_float64_t *data	  /*!< OUT: ptr to read buffer */
+	) {
+
+	SET_FNAME ( "H5Block3dReadScalarFieldFloat64" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_open_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_read_data ( f, "0", data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+*/
+/*!
+  Write a 3-dimensional field \c name with 3-dimensional vectors as values
+  from the buffers starting at \c x_data, \c y_data and \c z_data to the
+  current time-step using the defined field layout. Values are 3-dimensional
+  vectors with floating points (64-bit) values.
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dWrite3dVectorFieldFloat64 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	const h5part_float64_t *x_data, /*!< IN: X axis data */
+	const h5part_float64_t *y_data, /*!< IN: Y axis data */
+	const h5part_float64_t *z_data  /*!< IN: Z axis data */
+	) {
+
+	SET_FNAME ( "H5Block3dWrite3dVectorFieldFloat64" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_create_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_write_data ( f, "0", x_data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_write_data ( f, "1", y_data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_write_data ( f, "2", z_data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+*/
+/*!
+  Read a 3-dimensional field \c name with 3-dimensional vectors as values
+  from the buffers starting at \c x_data, \c y_data and \c z_data to the
+  current time-step using the defined field layout. Values are 3-dimensional
+  vectors with floating points (64-bit) values.
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dRead3dVectorFieldFloat64 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	h5part_float64_t *x_data, /*!< OUT: X axis data */
+	h5part_float64_t *y_data, /*!< OUT: Y axis data */
+	h5part_float64_t *z_data  /*!< OUT: Z axis data */
+	) {
+
+	SET_FNAME ( "H5Block3dRead3dVectorFieldFloat64" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_open_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_read_data ( f, "0", x_data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_read_data ( f, "1", y_data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_read_data ( f, "2", z_data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+
+  Write a 3-dimensional field \c name from the buffer starting at \c data
+  to the current time-step using the defined field layout. Values are
+  floating points (32-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dWriteScalarFieldFloat32 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	const h5part_float32_t *data      /*!< IN: scalar data to write */
+	) {
+
+	SET_FNAME ( "H5Block3dWriteScalarFieldFloat32" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_create_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_write_data ( f, "0", data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+
+  Read a 3-dimensional field \c name into the buffer starting at \c data from
+  the current time-step using the defined field layout. Values are
+  floating points (32-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dReadScalarFieldFloat32 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to read */
+	h5part_float32_t *data	  /*!< OUT: ptr to read buffer */
+	) {
+
+	SET_FNAME ( "H5Block3dReadScalarFieldFloat32" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_open_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_read_data ( f, "0", data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+*/
+/*!
+  Write a 3-dimensional field \c name with 3-dimensional vectors as values
+  from the buffers starting at \c x_data, \c y_data and \c z_data to the
+  current time-step using the defined field layout. Values are 3-dimensional
+  vectors with floating points (32-bit) values.
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dWrite3dVectorFieldFloat32 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	const h5part_float32_t *x_data, /*!< IN: X axis data */
+	const h5part_float32_t *y_data, /*!< IN: Y axis data */
+	const h5part_float32_t *z_data  /*!< IN: Z axis data */
+	) {
+
+	SET_FNAME ( "H5Block3dWrite3dVectorFieldFloat32" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_create_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_write_data ( f, "0", x_data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_write_data ( f, "1", y_data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_write_data ( f, "2", z_data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+*/
+/*!
+  Read a 3-dimensional field \c name with 3-dimensional vectors as values
+  from the buffers starting at \c x_data, \c y_data and \c z_data to the
+  current time-step using the defined field layout. Values are 3-dimensional
+  vectors with floating points (32-bit) values.
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dRead3dVectorFieldFloat32 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	h5part_float32_t *x_data, /*!< OUT: X axis data */
+	h5part_float32_t *y_data, /*!< OUT: Y axis data */
+	h5part_float32_t *z_data  /*!< OUT: Z axis data */
+	) {
+
+	SET_FNAME ( "H5Block3dRead3dVectorFieldFloat32" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_open_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_read_data ( f, "0", x_data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_read_data ( f, "1", y_data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_read_data ( f, "2", z_data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+
+  Write a 3-dimensional field \c name from the buffer starting at \c data
+  to the current time-step using the defined field layout. Values are
+  integers (64-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dWriteScalarFieldInt64 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	const h5part_int64_t *data      /*!< IN: scalar data to write */
+	) {
+
+	SET_FNAME ( "H5Block3dWriteScalarFieldInt64" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_create_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_write_data ( f, "0", data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+
+  Read a 3-dimensional field \c name into the buffer starting at \c data from
+  the current time-step using the defined field layout. Values are
+  integers (64-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dReadScalarFieldInt64 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to read */
+	h5part_int64_t *data	  /*!< OUT: ptr to read buffer */
+	) {
+
+	SET_FNAME ( "H5Block3dReadScalarFieldInt64" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_open_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_read_data ( f, "0", data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+*/
+/*!
+  Write a 3-dimensional field \c name with 3-dimensional vectors as values
+  from the buffers starting at \c x_data, \c y_data and \c z_data to the
+  current time-step using the defined field layout. Values are 3-dimensional
+  vectors with integers (64-bit) values.
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dWrite3dVectorFieldInt64 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	const h5part_int64_t *x_data, /*!< IN: X axis data */
+	const h5part_int64_t *y_data, /*!< IN: Y axis data */
+	const h5part_int64_t *z_data  /*!< IN: Z axis data */
+	) {
+
+	SET_FNAME ( "H5Block3dWrite3dVectorFieldInt64" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_create_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_write_data ( f, "0", x_data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_write_data ( f, "1", y_data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_write_data ( f, "2", z_data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+*/
+/*!
+  Read a 3-dimensional field \c name with 3-dimensional vectors as values
+  from the buffers starting at \c x_data, \c y_data and \c z_data to the
+  current time-step using the defined field layout. Values are 3-dimensional
+  vectors with integers (64-bit) values.
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dRead3dVectorFieldInt64 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	h5part_int64_t *x_data, /*!< OUT: X axis data */
+	h5part_int64_t *y_data, /*!< OUT: Y axis data */
+	h5part_int64_t *z_data  /*!< OUT: Z axis data */
+	) {
+
+	SET_FNAME ( "H5Block3dRead3dVectorFieldInt64" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_open_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_read_data ( f, "0", x_data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_read_data ( f, "1", y_data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_read_data ( f, "2", z_data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+
+  Write a 3-dimensional field \c name from the buffer starting at \c data
+  to the current time-step using the defined field layout. Values are
+  integers (32-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dWriteScalarFieldInt32 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	const h5part_int32_t *data      /*!< IN: scalar data to write */
+	) {
+
+	SET_FNAME ( "H5Block3dWriteScalarFieldInt32" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_create_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_write_data ( f, "0", data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+
+  Read a 3-dimensional field \c name into the buffer starting at \c data from
+  the current time-step using the defined field layout. Values are
+  integers (32-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dReadScalarFieldInt32 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to read */
+	h5part_int32_t *data	  /*!< OUT: ptr to read buffer */
+	) {
+
+	SET_FNAME ( "H5Block3dReadScalarFieldInt32" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_open_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_read_data ( f, "0", data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+*/
+/*!
+  Write a 3-dimensional field \c name with 3-dimensional vectors as values
+  from the buffers starting at \c x_data, \c y_data and \c z_data to the
+  current time-step using the defined field layout. Values are 3-dimensional
+  vectors with integers (32-bit) values.
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dWrite3dVectorFieldInt32 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	const h5part_int32_t *x_data, /*!< IN: X axis data */
+	const h5part_int32_t *y_data, /*!< IN: Y axis data */
+	const h5part_int32_t *z_data  /*!< IN: Z axis data */
+	) {
+
+	SET_FNAME ( "H5Block3dWrite3dVectorFieldInt32" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_create_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_write_data ( f, "0", x_data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_write_data ( f, "1", y_data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_write_data ( f, "2", z_data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_data
+*/
+/*!
+  Read a 3-dimensional field \c name with 3-dimensional vectors as values
+  from the buffers starting at \c x_data, \c y_data and \c z_data to the
+  current time-step using the defined field layout. Values are 3-dimensional
+  vectors with integers (32-bit) values.
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5Block3dRead3dVectorFieldInt32 (
+	H5PartFile *f,		  /*!< IN: file handle */
+	const char *name,	       /*!< IN: name of dataset to write */
+	h5part_int32_t *x_data, /*!< OUT: X axis data */
+	h5part_int32_t *y_data, /*!< OUT: Y axis data */
+	h5part_int32_t *z_data  /*!< OUT: Z axis data */
+	) {
+
+	SET_FNAME ( "H5Block3dRead3dVectorFieldInt32" );
+	BLOCK_INIT ( f );
+	CHECK_TIMEGROUP ( f );
+	CHECK_LAYOUT ( f );
+
+	h5part_int64_t herr = _H5Block_open_field_group ( f, name );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_read_data ( f, "0", x_data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_read_data ( f, "1", y_data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+	herr = _H5Block_read_data ( f, "2", z_data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+
+	herr = _H5Block_close_field_group ( f );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Write \c attrib_value with type floating points (64-bit) as attribute \c attrib_name
+  to field \c field_name.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5BlockWriteFieldAttribFloat64 (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const char *attrib_name,		/*!< IN: attribute name */
+	const h5part_float64_t *attrib_value,		/*!< IN: attribute value */
+	const h5part_int64_t attrib_nelem	/*!< IN: number of elements */
+	) {
+
+	SET_FNAME ( "H5BlockWriteFieldAttribFloat64" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		attrib_name,
+                H5T_NATIVE_DOUBLE,
+                attrib_value,
+		attrib_nelem );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Write \c attrib_value with type floating points (32-bit) as attribute \c attrib_name
+  to field \c field_name.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5BlockWriteFieldAttribFloat32 (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const char *attrib_name,		/*!< IN: attribute name */
+	const h5part_float32_t *attrib_value,		/*!< IN: attribute value */
+	const h5part_int64_t attrib_nelem	/*!< IN: number of elements */
+	) {
+
+	SET_FNAME ( "H5BlockWriteFieldAttribFloat32" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		attrib_name,
+                H5T_NATIVE_FLOAT,
+                attrib_value,
+		attrib_nelem );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Write \c attrib_value with type integers (64-bit) as attribute \c attrib_name
+  to field \c field_name.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5BlockWriteFieldAttribInt64 (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const char *attrib_name,		/*!< IN: attribute name */
+	const h5part_int64_t *attrib_value,		/*!< IN: attribute value */
+	const h5part_int64_t attrib_nelem	/*!< IN: number of elements */
+	) {
+
+	SET_FNAME ( "H5BlockWriteFieldAttribInt64" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		attrib_name,
+                H5T_NATIVE_INT64,
+                attrib_value,
+		attrib_nelem );
+}
+
+/*!
+  \ingroup h5block_attrib
+
+  Write \c attrib_value with type integers (32-bit) as attribute \c attrib_name
+  to field \c field_name.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5BlockWriteFieldAttribInt32 (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const char *attrib_name,		/*!< IN: attribute name */
+	const h5part_int32_t *attrib_value,		/*!< IN: attribute value */
+	const h5part_int64_t attrib_nelem	/*!< IN: number of elements */
+	) {
+
+	SET_FNAME ( "H5BlockWriteFieldAttribInt32" );
+	BLOCK_INIT ( f );
+	CHECK_WRITABLE_MODE( f );
+	CHECK_TIMEGROUP( f );
+
+	return _write_field_attrib (
+		f,
+		field_name,
+		attrib_name,
+                H5T_NATIVE_INT32,
+                attrib_value,
+		attrib_nelem );
+}

src/H5BlockReadWrite.f90

@@ -0,0 +1,224 @@
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dWriteScalarFieldFloat64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_r8 ( filehandle, name, data )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    REAL*8, INTENT(IN) :: data(*)    !< the array of data
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dReadScalarFieldFloat64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_r8 ( filehandle, name, data )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    REAL*8, INTENT(OUT) :: data(*)   !< buffer to read the data into
+END FUNCTION
+ 
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dWrite3dVectorFieldFloat64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_r8 ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    REAL*8, INTENT(IN) :: x(*)       !< the array of x data to write
+    REAL*8, INTENT(IN) :: y(*)       !< the array of y data to write
+    REAL*8, INTENT(IN) :: z(*)       !< the array of z data to write
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dRead3dVectorFieldFloat64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_r8 ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    REAL*8, INTENT(OUT) :: x(*)      !< buffer to read the x data into
+    REAL*8, INTENT(OUT) :: y(*)      !< buffer to read the y data into
+    REAL*8, INTENT(OUT) :: z(*)      !< buffer to read the z data into
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dWriteScalarFieldFloat32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_r4 ( filehandle, name, data )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    REAL*4, INTENT(IN) :: data(*)    !< the array of data
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dReadScalarFieldFloat32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_r4 ( filehandle, name, data )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    REAL*4, INTENT(OUT) :: data(*)   !< buffer to read the data into
+END FUNCTION
+ 
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dWrite3dVectorFieldFloat32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_r4 ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    REAL*4, INTENT(IN) :: x(*)       !< the array of x data to write
+    REAL*4, INTENT(IN) :: y(*)       !< the array of y data to write
+    REAL*4, INTENT(IN) :: z(*)       !< the array of z data to write
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dRead3dVectorFieldFloat32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_r4 ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    REAL*4, INTENT(OUT) :: x(*)      !< buffer to read the x data into
+    REAL*4, INTENT(OUT) :: y(*)      !< buffer to read the y data into
+    REAL*4, INTENT(OUT) :: z(*)      !< buffer to read the z data into
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dWriteScalarFieldInt64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_i8 ( filehandle, name, data )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    INTEGER*8, INTENT(IN) :: data(*)    !< the array of data
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dReadScalarFieldInt64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_i8 ( filehandle, name, data )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    INTEGER*8, INTENT(OUT) :: data(*)   !< buffer to read the data into
+END FUNCTION
+ 
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dWrite3dVectorFieldInt64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_i8 ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    INTEGER*8, INTENT(IN) :: x(*)       !< the array of x data to write
+    INTEGER*8, INTENT(IN) :: y(*)       !< the array of y data to write
+    INTEGER*8, INTENT(IN) :: z(*)       !< the array of z data to write
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dRead3dVectorFieldInt64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_i8 ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    INTEGER*8, INTENT(OUT) :: x(*)      !< buffer to read the x data into
+    INTEGER*8, INTENT(OUT) :: y(*)      !< buffer to read the y data into
+    INTEGER*8, INTENT(OUT) :: z(*)      !< buffer to read the z data into
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dWriteScalarFieldInt32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_write_scalar_field_i4 ( filehandle, name, data )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    INTEGER*4, INTENT(IN) :: data(*)    !< the array of data
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dReadScalarFieldInt32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_read_scalar_field_i4 ( filehandle, name, data )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    INTEGER*4, INTENT(OUT) :: data(*)   !< buffer to read the data into
+END FUNCTION
+ 
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dWrite3dVectorFieldInt32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_write_3dvector_field_i4 ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    INTEGER*4, INTENT(IN) :: x(*)       !< the array of x data to write
+    INTEGER*4, INTENT(IN) :: y(*)       !< the array of y data to write
+    INTEGER*4, INTENT(IN) :: z(*)       !< the array of z data to write
+END FUNCTION
+
+!> \ingroup h5blockf_data
+!! See \ref H5Block3dRead3dVectorFieldInt32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_3d_read_3dvector_field_i4 ( filehandle, name, x, y, z )
+    INTEGER*8, INTENT(IN) :: filehandle  !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
+    INTEGER*4, INTENT(OUT) :: x(*)      !< buffer to read the x data into
+    INTEGER*4, INTENT(OUT) :: y(*)      !< buffer to read the y data into
+    INTEGER*4, INTENT(OUT) :: z(*)      !< buffer to read the z data into
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5BlockWriteFieldAttribFloat64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_writefieldattrib_r8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem)
+    INTEGER*8, INTENT(IN) :: filehandle         !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: field_name  !< the name of the field
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute
+    REAL*8, INTENT(IN) :: attrib_value(*)   !< the array of data to write into the attribute
+    INTEGER*8, INTENT(IN) :: attrib_nelem       !< the number of elements in the array
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5BlockWriteFieldAttribFloat32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_writefieldattrib_r4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem)
+    INTEGER*8, INTENT(IN) :: filehandle         !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: field_name  !< the name of the field
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute
+    REAL*4, INTENT(IN) :: attrib_value(*)   !< the array of data to write into the attribute
+    INTEGER*8, INTENT(IN) :: attrib_nelem       !< the number of elements in the array
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5BlockWriteFieldAttribInt64
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_writefieldattrib_i8 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem)
+    INTEGER*8, INTENT(IN) :: filehandle         !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: field_name  !< the name of the field
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute
+    INTEGER*8, INTENT(IN) :: attrib_value(*)   !< the array of data to write into the attribute
+    INTEGER*8, INTENT(IN) :: attrib_nelem       !< the number of elements in the array
+END FUNCTION
+
+!> \ingroup h5blockf_attrib
+!! See \ref H5BlockWriteFieldAttribInt32
+!! \return 0 on success or error code
+!<
+INTEGER*8 FUNCTION h5bl_writefieldattrib_i4 ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem)
+    INTEGER*8, INTENT(IN) :: filehandle         !< the handle returned at file open
+    CHARACTER(LEN=*), INTENT(IN) :: field_name  !< the name of the field
+    CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute
+    INTEGER*4, INTENT(IN) :: attrib_value(*)   !< the array of data to write into the attribute
+    INTEGER*8, INTENT(IN) :: attrib_nelem       !< the number of elements in the array
+END FUNCTION

src/H5BlockReadWrite.h

@@ -0,0 +1,179 @@
+
+#ifndef _H5BLOCK_READWRITE_H_
+#define _H5BLOCK_READWRITE_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+h5part_int64_t
+H5Block3dWriteScalarFieldFloat64 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_float64_t *data
+	);
+
+h5part_int64_t
+H5Block3dReadScalarFieldFloat64 (
+	H5PartFile *f,
+	const char *name,
+	h5part_float64_t *data
+	);
+
+h5part_int64_t
+H5Block3dWrite3dVectorFieldFloat64 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_float64_t *xval,
+	const h5part_float64_t *yval,
+	const h5part_float64_t *zval
+	);
+
+h5part_int64_t
+H5Block3dRead3dVectorFieldFloat64 (
+	H5PartFile *f,
+	const char *name,
+	h5part_float64_t *xval,
+	h5part_float64_t *yval,
+	h5part_float64_t *zval
+	);
+
+h5part_int64_t
+H5Block3dWriteScalarFieldFloat32 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_float32_t *data
+	);
+
+h5part_int64_t
+H5Block3dReadScalarFieldFloat32 (
+	H5PartFile *f,
+	const char *name,
+	h5part_float32_t *data
+	);
+
+h5part_int64_t
+H5Block3dWrite3dVectorFieldFloat32 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_float32_t *xval,
+	const h5part_float32_t *yval,
+	const h5part_float32_t *zval
+	);
+
+h5part_int64_t
+H5Block3dRead3dVectorFieldFloat32 (
+	H5PartFile *f,
+	const char *name,
+	h5part_float32_t *xval,
+	h5part_float32_t *yval,
+	h5part_float32_t *zval
+	);
+
+h5part_int64_t
+H5Block3dWriteScalarFieldInt64 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_int64_t *data
+	);
+
+h5part_int64_t
+H5Block3dReadScalarFieldInt64 (
+	H5PartFile *f,
+	const char *name,
+	h5part_int64_t *data
+	);
+
+h5part_int64_t
+H5Block3dWrite3dVectorFieldInt64 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_int64_t *xval,
+	const h5part_int64_t *yval,
+	const h5part_int64_t *zval
+	);
+
+h5part_int64_t
+H5Block3dRead3dVectorFieldInt64 (
+	H5PartFile *f,
+	const char *name,
+	h5part_int64_t *xval,
+	h5part_int64_t *yval,
+	h5part_int64_t *zval
+	);
+
+h5part_int64_t
+H5Block3dWriteScalarFieldInt32 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_int32_t *data
+	);
+
+h5part_int64_t
+H5Block3dReadScalarFieldInt32 (
+	H5PartFile *f,
+	const char *name,
+	h5part_int32_t *data
+	);
+
+h5part_int64_t
+H5Block3dWrite3dVectorFieldInt32 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_int32_t *xval,
+	const h5part_int32_t *yval,
+	const h5part_int32_t *zval
+	);
+
+h5part_int64_t
+H5Block3dRead3dVectorFieldInt32 (
+	H5PartFile *f,
+	const char *name,
+	h5part_int32_t *xval,
+	h5part_int32_t *yval,
+	h5part_int32_t *zval
+	);
+
+h5part_int64_t
+H5BlockWriteFieldAttribFloat64 (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const char *attrib_name,		/*!< IN: attribute name */
+	const h5part_float64_t *attrib_value,		/*!< IN: attribute value */
+	const h5part_int64_t attrib_nelem	/*!< IN: number of elements */
+	);
+
+h5part_int64_t
+H5BlockWriteFieldAttribFloat32 (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const char *attrib_name,		/*!< IN: attribute name */
+	const h5part_float32_t *attrib_value,		/*!< IN: attribute value */
+	const h5part_int64_t attrib_nelem	/*!< IN: number of elements */
+	);
+
+h5part_int64_t
+H5BlockWriteFieldAttribInt64 (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const char *attrib_name,		/*!< IN: attribute name */
+	const h5part_int64_t *attrib_value,		/*!< IN: attribute value */
+	const h5part_int64_t attrib_nelem	/*!< IN: number of elements */
+	);
+
+h5part_int64_t
+H5BlockWriteFieldAttribInt32 (
+	H5PartFile *f,				/*!< IN: file handle */
+	const char *field_name,			/*!< IN: field name */
+	const char *attrib_name,		/*!< IN: attribute name */
+	const h5part_int32_t *attrib_value,		/*!< IN: attribute value */
+	const h5part_int64_t attrib_nelem	/*!< IN: number of elements */
+	);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

src/H5BlockReadWriteF.c

@@ -0,0 +1,555 @@
+
+#include "H5Part.h"
+#include "H5PartPrivate.h"
+#include "H5Block.h"
+#include "H5BlockReadWrite.h"
+#include "Underscore.h"
+
+#if defined(F77_SINGLE_UNDERSCORE)
+#define F77NAME(a,b) a
+#elif defined(F77_CRAY_UNDERSCORE)
+#define F77NAME(a,b) b
+#elif defined(F77_NO_UNDERSCORE)
+#else
+#error Error, no way to determine how to construct fortran bindings
+#endif
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_write_scalar_field_r8 F77NAME ( \
+	h5bl_3d_write_scalar_field_r8_, \
+	H5BL_3D_WRITE_SCALAR_FIELD_R8 )
+#endif
+
+h5part_int64_t
+h5bl_3d_write_scalar_field_r8 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float64_t *data,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWriteScalarFieldFloat64 (
+		filehandle, field_name2, data );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_read_scalar_field_r8 F77NAME ( \
+	h5bl_3d_read_scalar_field_r8_, \
+	H5BL_3D_READ_SCALAR_FIELD_R8 )
+#endif
+
+h5part_int64_t
+h5bl_3d_read_scalar_field_r8 (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float64_t *data,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWriteScalarFieldFloat64 (
+		filehandle, field_name2, data );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_write_3dvector_field_r8 F77NAME ( \
+	h5bl_3d_write_3dvector_field_r8_, \
+	H5BL_3D_WRITE_3DVECTOR_FIELD_R8 )
+#endif
+
+h5part_int64_t
+h5bl_3d_write_3dvector_field_r8 (
+	h5part_int64_t *f,	      /*!< file handle */
+	const char *field_name,	 /*!< name of the data set */
+	const h5part_float64_t *xval,   /*!< array of x component data */
+	const h5part_float64_t *yval,   /*!< array of y component data */
+	const h5part_float64_t *zval,   /*!< array of z component data */
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWrite3dVectorFieldFloat64 (
+		filehandle, field_name2, xval, yval, zval );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_read_3dvector_field_r8 F77NAME ( \
+	h5bl_3d_read_3dvector_field_r8_, \
+	H5BL_3D_READ_3DVECTOR_FIELD_R8 )
+#endif
+
+h5part_int64_t
+h5bl_3d_read_3dvector_field_r8 (
+	h5part_int64_t *f,	      /*!< file handle */
+	const char *field_name,	 /*!< name of the data set */
+	h5part_float64_t *xval,	 /*!< array of x component data */
+	h5part_float64_t *yval,	 /*!< array of y component data */
+	h5part_float64_t *zval,	 /*!< array of z component data */
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dRead3dVectorFieldFloat64 (
+		filehandle, field_name2, xval, yval, zval );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_write_scalar_field_r4 F77NAME ( \
+	h5bl_3d_write_scalar_field_r4_, \
+	H5BL_3D_WRITE_SCALAR_FIELD_R4 )
+#endif
+
+h5part_int64_t
+h5bl_3d_write_scalar_field_r4 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_float32_t *data,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWriteScalarFieldFloat32 (
+		filehandle, field_name2, data );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_read_scalar_field_r4 F77NAME ( \
+	h5bl_3d_read_scalar_field_r4_, \
+	H5BL_3D_READ_SCALAR_FIELD_R4 )
+#endif
+
+h5part_int64_t
+h5bl_3d_read_scalar_field_r4 (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_float32_t *data,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWriteScalarFieldFloat32 (
+		filehandle, field_name2, data );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_write_3dvector_field_r4 F77NAME ( \
+	h5bl_3d_write_3dvector_field_r4_, \
+	H5BL_3D_WRITE_3DVECTOR_FIELD_R4 )
+#endif
+
+h5part_int64_t
+h5bl_3d_write_3dvector_field_r4 (
+	h5part_int64_t *f,	      /*!< file handle */
+	const char *field_name,	 /*!< name of the data set */
+	const h5part_float32_t *xval,   /*!< array of x component data */
+	const h5part_float32_t *yval,   /*!< array of y component data */
+	const h5part_float32_t *zval,   /*!< array of z component data */
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWrite3dVectorFieldFloat32 (
+		filehandle, field_name2, xval, yval, zval );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_read_3dvector_field_r4 F77NAME ( \
+	h5bl_3d_read_3dvector_field_r4_, \
+	H5BL_3D_READ_3DVECTOR_FIELD_R4 )
+#endif
+
+h5part_int64_t
+h5bl_3d_read_3dvector_field_r4 (
+	h5part_int64_t *f,	      /*!< file handle */
+	const char *field_name,	 /*!< name of the data set */
+	h5part_float32_t *xval,	 /*!< array of x component data */
+	h5part_float32_t *yval,	 /*!< array of y component data */
+	h5part_float32_t *zval,	 /*!< array of z component data */
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dRead3dVectorFieldFloat32 (
+		filehandle, field_name2, xval, yval, zval );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_write_scalar_field_i8 F77NAME ( \
+	h5bl_3d_write_scalar_field_i8_, \
+	H5BL_3D_WRITE_SCALAR_FIELD_I8 )
+#endif
+
+h5part_int64_t
+h5bl_3d_write_scalar_field_i8 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_int64_t *data,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWriteScalarFieldInt64 (
+		filehandle, field_name2, data );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_read_scalar_field_i8 F77NAME ( \
+	h5bl_3d_read_scalar_field_i8_, \
+	H5BL_3D_READ_SCALAR_FIELD_I8 )
+#endif
+
+h5part_int64_t
+h5bl_3d_read_scalar_field_i8 (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_int64_t *data,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWriteScalarFieldInt64 (
+		filehandle, field_name2, data );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_write_3dvector_field_i8 F77NAME ( \
+	h5bl_3d_write_3dvector_field_i8_, \
+	H5BL_3D_WRITE_3DVECTOR_FIELD_I8 )
+#endif
+
+h5part_int64_t
+h5bl_3d_write_3dvector_field_i8 (
+	h5part_int64_t *f,	      /*!< file handle */
+	const char *field_name,	 /*!< name of the data set */
+	const h5part_int64_t *xval,   /*!< array of x component data */
+	const h5part_int64_t *yval,   /*!< array of y component data */
+	const h5part_int64_t *zval,   /*!< array of z component data */
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWrite3dVectorFieldInt64 (
+		filehandle, field_name2, xval, yval, zval );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_read_3dvector_field_i8 F77NAME ( \
+	h5bl_3d_read_3dvector_field_i8_, \
+	H5BL_3D_READ_3DVECTOR_FIELD_I8 )
+#endif
+
+h5part_int64_t
+h5bl_3d_read_3dvector_field_i8 (
+	h5part_int64_t *f,	      /*!< file handle */
+	const char *field_name,	 /*!< name of the data set */
+	h5part_int64_t *xval,	 /*!< array of x component data */
+	h5part_int64_t *yval,	 /*!< array of y component data */
+	h5part_int64_t *zval,	 /*!< array of z component data */
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dRead3dVectorFieldInt64 (
+		filehandle, field_name2, xval, yval, zval );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_write_scalar_field_i4 F77NAME ( \
+	h5bl_3d_write_scalar_field_i4_, \
+	H5BL_3D_WRITE_SCALAR_FIELD_I4 )
+#endif
+
+h5part_int64_t
+h5bl_3d_write_scalar_field_i4 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const h5part_int32_t *data,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWriteScalarFieldInt32 (
+		filehandle, field_name2, data );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_read_scalar_field_i4 F77NAME ( \
+	h5bl_3d_read_scalar_field_i4_, \
+	H5BL_3D_READ_SCALAR_FIELD_I4 )
+#endif
+
+h5part_int64_t
+h5bl_3d_read_scalar_field_i4 (
+	h5part_int64_t *f,
+	const char *field_name,
+	h5part_int32_t *data,
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWriteScalarFieldInt32 (
+		filehandle, field_name2, data );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_write_3dvector_field_i4 F77NAME ( \
+	h5bl_3d_write_3dvector_field_i4_, \
+	H5BL_3D_WRITE_3DVECTOR_FIELD_I4 )
+#endif
+
+h5part_int64_t
+h5bl_3d_write_3dvector_field_i4 (
+	h5part_int64_t *f,	      /*!< file handle */
+	const char *field_name,	 /*!< name of the data set */
+	const h5part_int32_t *xval,   /*!< array of x component data */
+	const h5part_int32_t *yval,   /*!< array of y component data */
+	const h5part_int32_t *zval,   /*!< array of z component data */
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dWrite3dVectorFieldInt32 (
+		filehandle, field_name2, xval, yval, zval );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_3d_read_3dvector_field_i4 F77NAME ( \
+	h5bl_3d_read_3dvector_field_i4_, \
+	H5BL_3D_READ_3DVECTOR_FIELD_I4 )
+#endif
+
+h5part_int64_t
+h5bl_3d_read_3dvector_field_i4 (
+	h5part_int64_t *f,	      /*!< file handle */
+	const char *field_name,	 /*!< name of the data set */
+	h5part_int32_t *xval,	 /*!< array of x component data */
+	h5part_int32_t *yval,	 /*!< array of y component data */
+	h5part_int32_t *zval,	 /*!< array of z component data */
+	const int l_field_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 =  _H5Part_strdupfor2c ( field_name,  l_field_name );
+
+	h5part_int64_t herr = H5Block3dRead3dVectorFieldInt32 (
+		filehandle, field_name2, xval, yval, zval );
+
+	free ( field_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_writefieldattrib_r8 F77NAME ( \
+	h5bl_writefieldattrib_r8_, \
+	H5BL_WRITEFIELDATTRIB_R8 )
+#endif
+
+h5part_int64_t
+h5bl_writefieldattrib_r8 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	const h5part_float64_t *attrib_value,
+	const h5part_int64_t *attrib_nelem,
+	const int l_field_name,
+	const int l_attrib_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 = _H5Part_strdupfor2c ( field_name,  l_field_name );
+	char *attrib_name2 =_H5Part_strdupfor2c ( attrib_name, l_attrib_name );
+
+	h5part_int64_t herr = H5BlockWriteFieldAttribFloat64 (
+		filehandle, field_name2, attrib_name2,
+		attrib_value, *attrib_nelem );
+
+	free ( field_name2 );
+	free ( attrib_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_writefieldattrib_r4 F77NAME ( \
+	h5bl_writefieldattrib_r4_, \
+	H5BL_WRITEFIELDATTRIB_R4 )
+#endif
+
+h5part_int64_t
+h5bl_writefieldattrib_r4 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	const h5part_float32_t *attrib_value,
+	const h5part_int64_t *attrib_nelem,
+	const int l_field_name,
+	const int l_attrib_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 = _H5Part_strdupfor2c ( field_name,  l_field_name );
+	char *attrib_name2 =_H5Part_strdupfor2c ( attrib_name, l_attrib_name );
+
+	h5part_int64_t herr = H5BlockWriteFieldAttribFloat32 (
+		filehandle, field_name2, attrib_name2,
+		attrib_value, *attrib_nelem );
+
+	free ( field_name2 );
+	free ( attrib_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_writefieldattrib_i8 F77NAME ( \
+	h5bl_writefieldattrib_i8_, \
+	H5BL_WRITEFIELDATTRIB_I8 )
+#endif
+
+h5part_int64_t
+h5bl_writefieldattrib_i8 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	const h5part_int64_t *attrib_value,
+	const h5part_int64_t *attrib_nelem,
+	const int l_field_name,
+	const int l_attrib_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 = _H5Part_strdupfor2c ( field_name,  l_field_name );
+	char *attrib_name2 =_H5Part_strdupfor2c ( attrib_name, l_attrib_name );
+
+	h5part_int64_t herr = H5BlockWriteFieldAttribInt64 (
+		filehandle, field_name2, attrib_name2,
+		attrib_value, *attrib_nelem );
+
+	free ( field_name2 );
+	free ( attrib_name2 );
+	return herr;
+}
+
+#if ! defined(F77_NO_UNDERSCORE)
+#define h5bl_writefieldattrib_i4 F77NAME ( \
+	h5bl_writefieldattrib_i4_, \
+	H5BL_WRITEFIELDATTRIB_I4 )
+#endif
+
+h5part_int64_t
+h5bl_writefieldattrib_i4 (
+	h5part_int64_t *f,
+	const char *field_name,
+	const char *attrib_name,
+	const h5part_int32_t *attrib_value,
+	const h5part_int64_t *attrib_nelem,
+	const int l_field_name,
+	const int l_attrib_name
+	) {
+
+	H5PartFile *filehandle = (H5PartFile*)(size_t)*f;
+
+	char *field_name2 = _H5Part_strdupfor2c ( field_name,  l_field_name );
+	char *attrib_name2 =_H5Part_strdupfor2c ( attrib_name, l_attrib_name );
+
+	h5part_int64_t herr = H5BlockWriteFieldAttribInt32 (
+		filehandle, field_name2, attrib_name2,
+		attrib_value, *attrib_nelem );
+
+	free ( field_name2 );
+	free ( attrib_name2 );
+	return herr;
+}

src/H5BlockTypes.h

@@ -0,0 +1,34 @@
+#ifndef _H5BLOCK_TYPES_H
+#define _H5BLOCK_TYPES_H
+
+struct H5BlockPartition {
+	h5part_int64_t	i_start;
+	h5part_int64_t	i_end;
+	h5part_int64_t	j_start;
+	h5part_int64_t	j_end;
+	h5part_int64_t	k_start;
+	h5part_int64_t	k_end;
+};
+
+struct H5BlockStruct {
+	h5part_int64_t timestep;
+	h5part_int64_t i_max;
+	h5part_int64_t j_max;
+	h5part_int64_t k_max;
+	struct H5BlockPartition *user_layout;
+	struct H5BlockPartition *write_layout;
+	int have_layout;
+	hsize_t chunk[3];
+
+	hid_t shape;
+	hid_t memshape;
+	hid_t diskshape;
+	hid_t blockgroup;
+	hid_t field_group_id;
+	hid_t create_prop;
+};
+
+#define H5PART_ERR_LAYOUT	-100
+#define H5PART_ERR_NOENT	-101
+
+#endif

src/H5MultiBlock.h

@@ -0,0 +1,78 @@
+#ifndef _H5MULTIBLOCK_H_
+#define _H5MULTIBLOCK_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*!
+  Include read/write call variants for different data types and
+  field dimensions.
+*/
+#include "H5MultiBlockReadWrite.h"
+
+#define H5MULTIBLOCK_ATTR_NAME "__BlockDims__"
+
+h5part_int64_t
+H5MultiBlock3dDefineRadius (
+	H5PartFile *f,
+	const h5part_int64_t r
+	);
+
+h5part_int64_t
+H5MultiBlock3dDefineRadii (
+	H5PartFile *f,
+	const h5part_int64_t ri,
+	const h5part_int64_t rj,
+	const h5part_int64_t rk
+	);
+
+h5part_int64_t
+H5MultiBlock3dDefineDims (
+	H5PartFile *f,
+	const h5part_int64_t *field_dims,
+	const h5part_int64_t *block_dims
+	);
+
+h5part_int64_t
+H5MultiBlock3dGetFieldDims(
+	H5PartFile *f,
+	h5part_int64_t *dims
+	);
+
+h5part_int64_t
+H5MultiBlock3dGetBlockDims(
+	H5PartFile *f,
+	const char *field_name,
+	h5part_int64_t *dims
+	);
+
+h5part_int64_t
+H5MultiBlock3dGetOffsetsOfProc (
+	H5PartFile *f,
+	const h5part_int64_t proc,
+	h5part_int64_t *offsets
+	);
+
+h5part_int64_t
+H5MultiBlock3dCalculateDecomp (
+	const int nprocs,
+	h5part_int64_t *decomp
+	);
+
+h5part_int64_t
+H5MultiBlockFree (
+	void *block
+	);
+
+h5part_int64_t
+H5MultiBlockShiftProcs (
+	H5PartFile *f,
+	const int shift
+	);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

src/H5MultiBlockErrors.h

@@ -0,0 +1,33 @@
+#ifndef _H5MULTIBLOCK_ERRORS_H_
+#define _H5MULTIBLOCK_ERRORS_H_
+
+extern h5part_error_handler _err_handler;
+
+#define CHECK_DECOMP( f ) \
+	if ( ! f->multiblock->have_decomp ) \
+		return (*_err_handler) ( \
+			_H5Part_get_funcname(), \
+			H5PART_ERR_DECOMP, \
+			"No dimensions defined." )
+
+#define HANDLE_H5PART_BLOCK_DECOMP_ERR \
+	 (*_err_handler) ( \
+		_H5Part_get_funcname(), \
+		H5PART_ERR_DECOMP, \
+		"Number of blocks does not equal number of procs" );
+
+#define HANDLE_MPI_TYPE_ERR \
+	 (*_err_handler) ( \
+		_H5Part_get_funcname(), \
+		H5PART_ERR_MPI, \
+		"Cannot create/commit/free strided vector MPI datatype." );
+
+#define HANDLE_MPI_INT64_ERR \
+	 (*_err_handler) ( \
+		_H5Part_get_funcname(), \
+		H5PART_ERR_MPI, \
+		"Integer overslow error! An offset/count/stride/etc. value " \
+		"passed to an MPI function exceeds the 32-bit limit imposed " \
+		"by the MPI standard." );
+
+#endif

src/H5MultiBlockPrivate.h

@@ -0,0 +1,35 @@
+#ifndef _H5MULTIBLOCK_PRIVATE_H_
+#define _H5MULTIBLOCK_PRIVATE_H_
+
+#define MULTIBLOCK_INIT( f ) { \
+	h5part_int64_t herr = _H5MultiBlock_init ( f ); \
+	if ( herr < 0 ) return herr; \
+}
+
+h5part_int64_t
+_H5MultiBlock_init (
+	H5PartFile *f
+	);
+
+h5part_int64_t
+_H5MultiBlock_close (
+	H5PartFile *f
+	);
+
+h5part_int64_t
+_H5MultiBlock_write_data (
+	H5PartFile *f,
+	const char *field_name,
+	const void *data,
+	const hid_t type
+	);
+
+h5part_int64_t
+_H5MultiBlock_read_data (
+	H5PartFile *f,
+	const char *field_name,
+	char **data,
+	hid_t type
+	);
+
+#endif

src/H5MultiBlockReadWrite.c

@@ -0,0 +1,244 @@
+
+#include <stdlib.h>
+#include <string.h>
+
+#include <hdf5.h>
+#include "H5Part.h"
+#include "H5PartErrors.h"
+#include "H5PartPrivate.h"
+
+#include "H5MultiBlockErrors.h"
+#include "H5MultiBlockPrivate.h"
+
+#ifdef PARALLEL_IO
+
+
+/*!
+  \ingroup h5multiblock_data
+
+  Write a multiblock field \c name from the buffer starting at \c data
+  to the current time-step using the defined block decomposition and dimensions.
+  Values are floating points (64-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5MultiBlock3dWriteFieldFloat64 (
+	H5PartFile *f,		/*!< IN: file handle */
+	const char *name,       /*!< IN: name of dataset to write */
+	const h5part_float64_t *data      /*!< IN: data to write */
+	) {
+
+	SET_FNAME( "H5MultiBlock3dWriteFieldFloat64" );
+
+	h5part_int64_t herr;
+
+	herr = _H5MultiBlock_write_data ( f, name, data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5multiblock_data
+
+  Allocate a buffer to hold a block from a multiblock field and place the
+  pointer in \c data, then read the block into the buffer. Uses the block
+  decomposition specified in the file and the defined halo radius.
+  Values are floating points (64-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5MultiBlock3dReadFieldFloat64 (
+	H5PartFile *f,		/*!< IN: file handle */
+	const char *name,	/*!< IN: name of dataset to read */
+	h5part_float64_t **data	/*!< OUT: ptr to read buffer */
+	) {
+
+	SET_FNAME( "H5MultiBlock3dReadFieldFloat64" );
+
+	h5part_int64_t herr;
+
+	herr = _H5MultiBlock_read_data ( f, name, (char**) data, H5T_NATIVE_DOUBLE );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5multiblock_data
+
+  Write a multiblock field \c name from the buffer starting at \c data
+  to the current time-step using the defined block decomposition and dimensions.
+  Values are floating points (32-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5MultiBlock3dWriteFieldFloat32 (
+	H5PartFile *f,		/*!< IN: file handle */
+	const char *name,       /*!< IN: name of dataset to write */
+	const h5part_float32_t *data      /*!< IN: data to write */
+	) {
+
+	SET_FNAME( "H5MultiBlock3dWriteFieldFloat32" );
+
+	h5part_int64_t herr;
+
+	herr = _H5MultiBlock_write_data ( f, name, data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5multiblock_data
+
+  Allocate a buffer to hold a block from a multiblock field and place the
+  pointer in \c data, then read the block into the buffer. Uses the block
+  decomposition specified in the file and the defined halo radius.
+  Values are floating points (32-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5MultiBlock3dReadFieldFloat32 (
+	H5PartFile *f,		/*!< IN: file handle */
+	const char *name,	/*!< IN: name of dataset to read */
+	h5part_float32_t **data	/*!< OUT: ptr to read buffer */
+	) {
+
+	SET_FNAME( "H5MultiBlock3dReadFieldFloat32" );
+
+	h5part_int64_t herr;
+
+	herr = _H5MultiBlock_read_data ( f, name, (char**) data, H5T_NATIVE_FLOAT );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5multiblock_data
+
+  Write a multiblock field \c name from the buffer starting at \c data
+  to the current time-step using the defined block decomposition and dimensions.
+  Values are integers (64-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5MultiBlock3dWriteFieldInt64 (
+	H5PartFile *f,		/*!< IN: file handle */
+	const char *name,       /*!< IN: name of dataset to write */
+	const h5part_int64_t *data      /*!< IN: data to write */
+	) {
+
+	SET_FNAME( "H5MultiBlock3dWriteFieldInt64" );
+
+	h5part_int64_t herr;
+
+	herr = _H5MultiBlock_write_data ( f, name, data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5multiblock_data
+
+  Allocate a buffer to hold a block from a multiblock field and place the
+  pointer in \c data, then read the block into the buffer. Uses the block
+  decomposition specified in the file and the defined halo radius.
+  Values are integers (64-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5MultiBlock3dReadFieldInt64 (
+	H5PartFile *f,		/*!< IN: file handle */
+	const char *name,	/*!< IN: name of dataset to read */
+	h5part_int64_t **data	/*!< OUT: ptr to read buffer */
+	) {
+
+	SET_FNAME( "H5MultiBlock3dReadFieldInt64" );
+
+	h5part_int64_t herr;
+
+	herr = _H5MultiBlock_read_data ( f, name, (char**) data, H5T_NATIVE_INT64 );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5multiblock_data
+
+  Write a multiblock field \c name from the buffer starting at \c data
+  to the current time-step using the defined block decomposition and dimensions.
+  Values are integers (32-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5MultiBlock3dWriteFieldInt32 (
+	H5PartFile *f,		/*!< IN: file handle */
+	const char *name,       /*!< IN: name of dataset to write */
+	const h5part_int32_t *data      /*!< IN: data to write */
+	) {
+
+	SET_FNAME( "H5MultiBlock3dWriteFieldInt32" );
+
+	h5part_int64_t herr;
+
+	herr = _H5MultiBlock_write_data ( f, name, data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+/*!
+  \ingroup h5multiblock_data
+
+  Allocate a buffer to hold a block from a multiblock field and place the
+  pointer in \c data, then read the block into the buffer. Uses the block
+  decomposition specified in the file and the defined halo radius.
+  Values are integers (32-bit).
+
+  You must use the Fortran indexing scheme to access items in \c data.
+
+  \return \c H5PART_SUCCESS or error code
+*/
+h5part_int64_t
+H5MultiBlock3dReadFieldInt32 (
+	H5PartFile *f,		/*!< IN: file handle */
+	const char *name,	/*!< IN: name of dataset to read */
+	h5part_int32_t **data	/*!< OUT: ptr to read buffer */
+	) {
+
+	SET_FNAME( "H5MultiBlock3dReadFieldInt32" );
+
+	h5part_int64_t herr;
+
+	herr = _H5MultiBlock_read_data ( f, name, (char**) data, H5T_NATIVE_INT32 );
+	if ( herr < 0 ) return herr;
+
+	return H5PART_SUCCESS;
+}
+
+#endif // PARALLEL_IO

src/H5MultiBlockReadWrite.h

@@ -0,0 +1,71 @@
+
+#ifndef _H5MULTIBLOCK_READWRITE_H_
+#define _H5MULTIBLOCK_READWRITE_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+h5part_int64_t
+H5MultiBlock3dWriteFieldFloat64 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_float64_t *data
+	);
+
+h5part_int64_t
+H5MultiBlock3dReadFieldFloat64 (
+	H5PartFile *f,
+	const char *name,
+	h5part_float64_t **data
+	);
+
+h5part_int64_t
+H5MultiBlock3dWriteFieldFloat32 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_float32_t *data
+	);
+
+h5part_int64_t
+H5MultiBlock3dReadFieldFloat32 (
+	H5PartFile *f,
+	const char *name,
+	h5part_float32_t **data
+	);
+
+h5part_int64_t
+H5MultiBlock3dWriteFieldInt64 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_int64_t *data
+	);
+
+h5part_int64_t
+H5MultiBlock3dReadFieldInt64 (
+	H5PartFile *f,
+	const char *name,
+	h5part_int64_t **data
+	);
+
+h5part_int64_t
+H5MultiBlock3dWriteFieldInt32 (
+	H5PartFile *f,
+	const char *name,
+	const h5part_int32_t *data
+	);
+
+h5part_int64_t
+H5MultiBlock3dReadFieldInt32 (
+	H5PartFile *f,
+	const char *name,
+	h5part_int32_t **data
+	);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

src/H5MultiBlockTypes.h

@@ -0,0 +1,27 @@
+#ifndef _H5MULTIBLOCK_TYPES_H_
+#define _H5MULTIBLOCK_TYPES_H_
+
+struct H5MultiBlockStruct {
+	h5part_int64_t halo_radii[3];
+	h5part_int64_t block_dims[3];
+	h5part_int64_t halo_dims[3];
+	h5part_int64_t field_dims[3];
+	h5part_int64_t decomp[3];
+	h5part_int64_t offsets[3];
+	char field_edges;
+	int read;
+	int halo;
+	int have_decomp;
+        int proc_shift;
+};
+
+#define H5PART_ERR_DECOMP	-102
+
+#define H5MB_EDGE_X0 0x01
+#define H5MB_EDGE_X1 0x02
+#define H5MB_EDGE_Y0 0x04
+#define H5MB_EDGE_Y1 0x08
+#define H5MB_EDGE_Z0 0x10
+#define H5MB_EDGE_Z1 0x20
+
+#endif

src/H5Part++.cc

@@ -1,234 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <hdf5.h>
-#include "H5Part++.hh"
-
-#include <fstream>
-#include <iomanip>
-#include <iostream>
-#include <string>
-using namespace std;
-
-#ifdef READTEST
-
-/*
-  A simple regression test that shows how you use this API
-  to write and read multi-timestep files of particle data.
-*/
-#ifdef PARALLEL_IO
-
-
-#else
-
-int main(int argc,char **argv){
-    const int sz=5;
-    double x[sz],y[sz],z[sz];
-    long long id[sz];
-    char name[64];
-    H5PartFile *file;
-    int i,t,nt,nds,myproc;
-    int nfattribs,nsattribs;
-
-    const string fn = string(argv[1]);
-
-    cout << "Open " << fn << endl;
-
-
-    file= H5PartOpenFile(fn.c_str(),H5PART_READ);
-    nt=H5PartGetNumSteps(file); /* get number of steps in file */
-    H5PartSetStep(file,0);
-    nds=H5PartGetNumDatasets(file); /* get number of datasets in timestep 0 */
-
-
-
-    puts("\n\n===============================");
-    for(i=0;i<nds;i++){ /* and print out those names */
-        H5PartGetDatasetName(file,i,name,64);
-        printf("\tDataset[%u] name=[%s]\n",
-            i,name);
-    }
-    puts("===============================\n\n");
-
-    nfattribs=H5PartGetNumFileAttribs(file);
-    printf("Number of datasteps in file is %u num file attribs=%d\n",
-        nt,nfattribs);
-
-    H5PartCloseFile(file);
-}
-#endif
-
-#endif
-
-
-#ifdef REGRESSIONTEST
-
-/*
-  A simple regression test that shows how you use this API
-  to write and read multi-timestep files of particle data.
-*/
-#ifdef PARALLEL_IO
-
-int main(int argc,char *argv[]){
-  int sz=5;
-  double *x,*y,*z;
-  long long *id;
-  char name[64];
-  H5PartFile *file;
-  int i,t,nt,nds;
-  int nprocs,myproc;
-  hid_t gid;
-  MPI_Comm comm=MPI_COMM_WORLD;
-
-  MPI_Init(&argc,&argv);
-  MPI_Comm_size(comm,&nprocs);
-  MPI_Comm_rank(comm,&myproc);
-
-  x=(double*)malloc(sz*nprocs*sizeof(double));
-  y=(double*)malloc(sz*nprocs*sizeof(double));
-  z=(double*)malloc(sz*nprocs*sizeof(double));
-  id=(long long*)malloc(sz*nprocs*sizeof(long long));
-  /* parallel file creation */
-  file=H5PartOpenFileParallel("parttest.h5",H5PART_WRITE,comm);
-  if(!file) {
-    perror("File open failed:  exiting!");
-    exit(0);
-  }
-
-  for(t=0;t<5;t++){
-    MPI_Barrier(comm);
-    for(i=0;i<sz;i++) {
-      x[i]=(double)(i+t)+10.0*(double)myproc;
-      y[i]=0.1 + (double)(i+t);
-      z[i]=0.2 + (double)(i+t*10);
-      id[i]=i+sz*myproc;
-    }
-    printf("Proc[%u] Writing timestep %u file=%u\n",myproc,t,file->file);
-    H5PartSetStep(file,t); /* must set the current timestep in file */
-    H5PartSetNumParticles(file,sz); /* then set number of particles to store */
-    /* now write different tuples of data into this timestep of the file */
-    H5PartWriteDataFloat64(file,"x",x); 
-    H5PartWriteDataFloat64(file,"y",y);
-    H5PartWriteDataFloat64(file,"z",z);
-    H5PartWriteDataInt64(file,"id",id);
-  }
-  printf("AllDone p[%u]\n",myproc);
-  H5PartCloseFile(file);
-    MPI_Barrier(comm);
-  printf("p[%u:%u] : OK, close file and reopen for reading \n",myproc,nprocs);
-  if(myproc==0){ /* now only proc 0 reads the file serially */
-    file= H5PartOpenFileSerial("parttest.h5",H5PART_READ);
-    nt=H5PartGetNumSteps(file); /* get number of steps in file */
-    H5PartSetStep(file,0);
-    nds=H5PartGetNumDatasets(file); /* get number of datasets in timestep 0 */
-
-    puts("\n\n===============================");
-    for(i=0;i<nds;i++){ /* and print out those names */
-      H5PartGetDatasetName(file,i,name,64);
-      printf("\tDataset[%u] name=[%s]\n",
-	     i,name);
-    }
-    puts("===============================\n\n");
-    printf("Number of datasteps in file is %u\n",nt);
-    for(t=0;t<nt;t++){
-      int nparticles;
-      H5PartSetStep(file,t); /* select a timestep */
-      nparticles=(int)H5PartGetNumParticles(file);
-      printf("Step[%u] nparticles this step=%u\n",
-	     t,nparticles); /* get num particles this step *
-      H5PartReadParticleStep(file,t,/* do a mongo read of all data this step */
-			     x,y,z,id);
-      printf("\tid\t\tx\t\ty\t\tz\n");
-      puts("\t----------------------------------------------------");
-      for(i=0;i<nparticles;i++) {
-	printf("\t%llu\t%f\t%f\t%f\n\n",id[i],x[i],y[i],z[i]);
-      }
-    }
-    H5PartCloseFile(file);
-  }
-  if(x) free(x); 
-  if(y) free(y);
-  if(z) free(z);
-  if(id) free(id);
-  MPI_Barrier(comm);
-  fprintf(stderr,"proc[%u]:  done\n",myproc);
-  return MPI_Finalize();
-}
-
-#else
-
-  int main(int argc,char *argv){
-    const int sz=5;
-    double x[sz],y[sz],z[sz];
-  long long id[sz];
-  char name[64];
-  H5PartFile *file;
-  int i,t,nt,nds,myproc;
-  int nfattribs,nsattribs;
-
-  file=H5PartOpenFile("parttest.h5",H5PART_WRITE);
-  if(!file) {
-    perror("File open failed:  exiting!");
-    exit(0);
-  }
-  for(t=0;t<5;t++){
-    long long step=t;
-    printf("Writing timestep %u\n",t);
-    for(i=0;i<sz;i++) {
-      x[i]=(double)(i+t);
-      y[i]=0.1 + (double)(i+t);
-      z[i]=0.2 + (double)(i+t);
-      id[i]=i;
-    }
-    H5PartSetStep(file,t); /* must set the current timestep in file */
-    H5PartSetNumParticles(file,sz); /* then set number of particles to store */
-    /* now write different tuples of data into this timestep of the file */
-    H5PartWriteDataFloat64(file,"x",x); 
-    H5PartWriteDataFloat64(file,"y",y);
-    H5PartWriteDataFloat64(file,"z",z);
-    H5PartWriteDataInt64(file,"id",id);
-    H5PartWriteStepAttrib(file,"Step",H5T_NATIVE_INT64,&step,1);
-  }
-  H5PartCloseFile(file);
-  printf("OK, close file and reopen for reading\n");
-  file= H5PartOpenFile("parttest.h5",H5PART_READ);
-  nt=H5PartGetNumSteps(file); /* get number of steps in file */
-  H5PartSetStep(file,0);
-  nds=H5PartGetNumDatasets(file); /* get number of datasets in timestep 0 */
-
-  puts("\n\n===============================");
-  for(i=0;i<nds;i++){ /* and print out those names */
-    H5PartGetDatasetName(file,i,name,64);
-    printf("\tDataset[%u] name=[%s]\n",
-	   i,name);
-  }
-  puts("===============================\n\n");
-
-  nfattribs=H5PartGetNumFileAttribs(file);
-  printf("Number of datasteps in file is %u num file attribs=%d\n",
-	 nt,nfattribs);
-  for(t=0;t<nt;t++){
-    int nparticles;
-    H5PartSetStep(file,t); /* select a timestep */
-    nparticles=(int)H5PartGetNumParticles(file);
-    nsattribs=H5PartGetNumStepAttribs(file);
-    printf("Step[%u] nparticles this step=%u stepattribs=%u\n",
-	   t,nparticles,nsattribs); /* get num particles this step */
-    if(nsattribs>0){
-      char attrname[32];
-      H5PartGetStepAttribInfo(file,0,attrname,32,0,0);
-      printf("First Attrib name is [%s]\n",attrname);
-    }
-    H5PartReadParticleStep(file,t,/* do a mongo read of all data this step */
-			   x,y,z,id);
-    printf("\tid\t\tx\t\ty\t\tz\n");
-    puts("\t----------------------------------------------------");
-    for(i=0;i<sz;i++) {
-      printf("\t%llu\t%f\t%f\t%f\n\n",id[i],x[i],y[i],z[i]);
-    }
-  }
-  H5PartCloseFile(file);
-}
-#endif
-
-#endif