H5Part 1.6.4 release

* H5MultiBlock: added halo exchange routine: still needs debugging

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-test/H5Block/Makefile.am -text
-test/H5Fed/Makefile.am -text
-test/H5Fed/map_tet2globalid.c -text
-test/H5Fed/map_triangle2globalid.c -text
-test/H5Fed/tetmesh_adjacencies.c -text
-test/H5Fed/tetmesh_read.c -text
-test/H5Fed/tetmesh_read_tags.c -text
-test/H5Fed/tetmesh_write.c -text
-test/H5Fed/tetmesh_write1.c -text
-test/H5Fed/tetmesh_write2.c -text
-test/H5Fed/tetmesh_write_tags.c -text
-test/H5Fed/trimesh_adjacencies.c -text
-test/H5Fed/trimesh_read.c -text
-test/H5Fed/trimesh_write.c -text
-test/H5Fed/trimesh_write_dunetest.c -text
-test/H5Fed/write_boundary.c -text
-test/H5Part/Bench.c -text
-test/H5Part/H5ParallelTest.cc -text
-test/H5Part/H5PartAndreasTest.cc -text
-test/H5Part/H5PartTest.cc -text
-test/H5Part/H5PartTestParallel.cc -text
-test/H5Part/H5test.cc -text
-test/H5Part/H5testF.f -text
-test/H5Part/H5testFpar.f90 -text
-test/H5Part/Makefile.am -text
 test/Makefile.am -text
-test/h5_attach_test.c -text
-test/h5b_read.c -text
-test/h5b_test.c -text
-test/h5b_write.c -text
-test/h5u_read.c -text
-test/h5u_test.c -text
-test/h5u_write.c -text
 test/params.h -text
+test/read.c -text
+test/test.c -text
+test/testf.F90 -text
 test/testframe.c -text
 test/testframe.h -text
-tools/H5PartMerge/AUTHORS -text
+test/write.c -text
-tools/H5PartMerge/COPYING -text
+tools/H5BlockBench.c -text
-tools/H5PartMerge/ChangeLog -text
+tools/H5PartBench.c -text
-tools/H5PartMerge/INSTALL -text
-tools/H5PartMerge/NEWS -text
-tools/H5PartMerge/README -text
-tools/H5PartMerge/autogen.sh -text
-tools/H5PartMerge/configure.ac -text
-tools/H5PartMerge/makefile.am -text
-tools/H5PartMerge/src/H5merge.cpp -text
-tools/H5PartMerge/src/optparse.cpp -text
-tools/H5PartMerge/src/optparse.hh -text
 tools/Makefile.am -text
 tools/README -text
-tools/h5PartDcToVtk.cc -text
-tools/h5PartSurfaceToVtk.cc -text
-tools/h5hutcc.in -text
 tools/h5pAttrib.cc -text
 tools/h5pToGNUplot.cc -text
 tools/homdynToH5p.cc -text
-visit_plugins/databases/H5Part/.depend -text
-visit_plugins/databases/H5Part/Makefile -text
-visit_plugins/databases/H5Part/README.txt -text
-visit_plugins/databases/H5Part/avth5partFileFormat.C -text
-visit_plugins/databases/H5Part/avth5partFileFormat.h -text
-visit_plugins/databases/H5Part/h5part.xml -text
-visit_plugins/databases/H5Part/h5partCommonPluginInfo.C -text
-visit_plugins/databases/H5Part/h5partEnginePluginInfo.C -text
-visit_plugins/databases/H5Part/h5partMDServerPluginInfo.C -text
-visit_plugins/databases/H5Part/h5partPluginInfo.C -text
-visit_plugins/databases/H5Part/h5partPluginInfo.h -text
-visit_plugins/operators/BinnerFilter/.depend -text
-visit_plugins/operators/BinnerFilter/Binner.xml -text
-visit_plugins/operators/BinnerFilter/BinnerCommonPluginInfo.C -text
-visit_plugins/operators/BinnerFilter/BinnerEnginePluginInfo.C -text
-visit_plugins/operators/BinnerFilter/BinnerFilter.C -text
-visit_plugins/operators/BinnerFilter/BinnerFilter.h -text
-visit_plugins/operators/BinnerFilter/BinnerFilter.java -text
-visit_plugins/operators/BinnerFilter/BinnerGUIPluginInfo.C -text
-visit_plugins/operators/BinnerFilter/BinnerMakefile -text
-visit_plugins/operators/BinnerFilter/BinnerPluginInfo.C -text
-visit_plugins/operators/BinnerFilter/BinnerPluginInfo.h -text
-visit_plugins/operators/BinnerFilter/BinnerScriptingPluginInfo.C -text
-visit_plugins/operators/BinnerFilter/BinnerViewerPluginInfo.C -text
-visit_plugins/operators/BinnerFilter/Binnerreplace.txt -text
-visit_plugins/operators/BinnerFilter/Makefile -text
-visit_plugins/operators/BinnerFilter/PyBinner.C -text
-visit_plugins/operators/BinnerFilter/PyBinner.h -text
-visit_plugins/operators/BinnerFilter/QvisBinnerWindow.C -text
-visit_plugins/operators/BinnerFilter/QvisBinnerWindow.h -text
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-visit_plugins/operators/BinnerFilter/avtBinnerFilter.h -text
-visit_plugins/operators/BinnerFilter/icon.xpm -text
-visit_plugins/operators/RandomSample/.depend -text
-visit_plugins/operators/RandomSample/H5PartRandomSampleAttributes.C -text
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.gitignore

@@ -1,80 +1,13 @@
-/H5hut
-/INSTALL
-/Makefile
 /Makefile.in
 /aclocal.m4
 /autom4te.cache
 /build
-/config.guess
-/config.h
 /config.h.in
-/config.log
-/config.status
-/config.sub
 /configure
-/depcomp
-doc/Makefile
 doc/Makefile.in
-/install-sh
-/libtool
 /ltmain.sh
 /m4
-/missing
+src/H5PartF.h
-src/.deps
-src/C++/Makefile
-src/C++/Makefile.in
-src/C/.deps
-src/C/Makefile
-src/C/Makefile.in
-src/C/libH5hutC.a
-src/Fortran/.deps
-src/Fortran/Makefile
-src/Fortran/Makefile.in
-src/Makefile
 src/Makefile.in
-src/h5core/.deps
-src/h5core/Makefile
-src/h5core/Makefile.in
-src/h5core/libH5hut.a
-src/include/H5hutF.h
-src/lib
-/stamp-h1
-/svn-prop.tmp
-test/.deps
-test/H5Block/H5BlockParTestScalarField
-test/H5Block/H5BlockTestAttributes
-test/H5Block/Makefile
-test/H5Block/Makefile.in
-test/H5Fed/.deps
-test/H5Fed/Makefile
-test/H5Fed/Makefile.in
-test/H5Fed/large_tet.h5
-test/H5Fed/simple_tet.h5
-test/H5Fed/simple_triangle.h5
-test/H5Fed/small_tet.h5
-test/H5Fed/tetmesh_adjacencies
-test/H5Fed/tetmesh_read
-test/H5Fed/tetmesh_read_tags
-test/H5Fed/tetmesh_write
-test/H5Fed/tetmesh_write2
-test/H5Fed/tetmesh_write_tags
-test/H5Fed/trimesh_adjacencies
-test/H5Fed/trimesh_read
-test/H5Fed/trimesh_write
-test/H5Fed/trimesh_write_dunetest
-test/H5Part/Bench
-test/H5Part/H5PartAndreasTest
-test/H5Part/H5PartTestP
-test/H5Part/H5test
-test/H5Part/Makefile
-test/H5Part/Makefile.in
-test/Makefile
 test/Makefile.in
-test/h5_attach.h5
-test/h5_attach_test
-test/h5b_test
-test/h5u_test
-tools/.deps
-tools/Makefile
 tools/Makefile.in
-tools/h5hutcc

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

@@ -1,6 +1,6 @@
 *** Copyright Notice ***
 
-H5hut  Copyright (c) 2006-2010, The Regents of the University of California,
+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.

GNUmakefile.orig

@@ -0,0 +1,133 @@
+UNAME := $(shell uname | perl -pe 's/(sn\d\d\d\d|jsimpson)/UNICOS\/mk/')
+# for host specific options
+HOST := $(shell hostname)
+
+# for processor-specific options
+ifeq ($(UNAME), Linux)
+PROC := $(shell uname -p)
+endif
+
+CXX = c++
+CC = cc
+H5HOME = /usr/local/hdf5
+CFLAGS = -g -I$(H5HOME)/include
+LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
+
+# MacOS-X Serial
+ifeq ($(UNAME), Darwin)
+ifeq ($(PARALLEL), yes)
+CXX = g++
+CC = mpicc
+H5HOME = /usr/local
+CFLAGS = -O -g -I$(H5HOME)/include -DPARALLEL_IO
+LDFLAGS = -L$(H5HOME)/lib -lmpich -lpmpich -lhdf5 -lz -lm
+else
+CXX = c++
+CC = cc
+F90 = xlf
+H5HOME = /usr/local
+CFLAGS = -O -g -I$(H5HOME)/include
+LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
+endif
+endif
+
+# SGI MIPS/Irix
+ifeq ($(UNAME), IRIX64)
+CXX = CC
+CC = cc
+F90 = f90
+ifeq ($(PARALLEL), yes)
+H5HOME = $(HDF5_DIR)
+CFLAGS = -64 -O3 -I$(H5HOME)/include -DPARALLEL_IO
+LDFLAGS = -64 -O3 -L$(H5HOME)/lib -lhdf5 -lz -lmpi -lm
+else
+H5HOME = /usr/local
+CFLAGS = -O3 -I$(H5HOME)/include
+LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
+endif
+endif
+
+# AIX/SP-2 Parallel/serial : Seaborg
+ifeq ($(UNAME), AIX)
+ifeq ($(PARALLEL), yes) # parallel
+CXX = mpCC_r
+CC = mpxlc_r
+# H5HOME = /usr/common/usg/hdf5_64/1.4.5-post2/parallel
+H5HOME = /usr/common/usg/hdf5_64/1.6.1/parallel
+# /usr/common/usg/hdf5/1.4.4/parallel
+H4HOME = /usr/common/usg/hdf/default
+OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
+CFLAGS = -q64 -I$(H5HOME)/include
+LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lsz -lm
+else # serial
+CXX = xlC
+CC = xlc
+H5HOME = /usr/common/usg/hdf5/1.4.4/serial
+H4HOME = /usr/common/usg/hdf/default
+OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
+CFLAGS = -g -bmaxdata:800000000  -bmaxstack:256000000 -I$(H5HOME)/include
+LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
+endif
+endif
+
+# Linux
+ifeq ($(UNAME), Linux)
+# if this machine is NERSC/Davinci Altix system
+ifeq ($(PROC), ia64)
+CC = icc 
+CXX = icc
+
+ifeq ($(PARALLEL), yes)
+# IA64 Linux Parallel
+ifeq ($(HOST), davinci)
+H5HOME = $(HDF5_PAR)
+MPILIB = -lmpi
+else
+H5HOME = /usr/local
+HDF5_PAR_LIB = -L$(H5HOME)/lib -lhdf5 -lz -lm
+HDF5_PAR_INCLUDE = -I$(H5HOME)/include
+MPIHOME = /usr/local
+MPILIB = -lmpich
+endif # HOST
+CFLAGS = -O3 -DPARALLEL_IO -DH5_HAVE_PARALLEL $(HDF5_PAR_INCLUDE) 
+LDFLAGS = $(HDF5_PAR_LIB) $(MPILIB)
+else # IA64 Linux Serial
+CFLAGS = -O3 $(HDF5_INCLUDE)
+LDFLAGS = $(HDF5_LIB) -lm
+endif # PARALLEL
+
+# else this is standard IA32 linux
+else
+ifeq ($(PARALLEL), yes)
+# Linux Parallel
+CC = gcc
+CXX = g++
+H5HOME = /usr/local
+MPIHOME = /usr/local
+CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include 
+LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
+else # Linux Serial
+CXX = g++
+CC = gcc
+CFLAGS = -O -g -I$(H5HOME)/include
+LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
+endif # !PARALLEL
+endif # PROC!ia64
+
+endif # !Linux
+
+ifeq ($(PARALLEL), yes) #parallel
+ifdef F90
+all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
+else
+all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
+endif
+else
+ifdef F90
+all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
+else
+all: H5PartTest H5PartTest.o H5Part.o
+endif
+endif
+
+include rules.make

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

@@ -1,6 +1,7 @@
-ACLOCAL_AMFLAGS = -I m4
+ACLOCAL_AMFLAGS=-I m4
 
 SUBDIRS = \
+	doc \
 	src \
 	test \
 	tools

Makefile.orig

@@ -0,0 +1,59 @@
+
+# This is a very rudimentary multiarchitecture makefile
+# You need to uncomment the default block of make variables you need
+# Some key things to watch for are the following defines
+#	-DREGRESSIONTEST : enables a main(){} inside of
+#		the H5Part.cc file that does simple regression testing.
+#	-DPARALLEL_IO : If you want to use parallel HDF5, you have to 
+#		enable this.  Otherwise, you get only the serial 
+#		implementation of the library.  
+
+# MacOS-X Serial
+#CXX = c++
+#CC = cc
+#F90 = xlf
+#H5HOME = /usr/local
+#CFLAGS = -O -g -I$(H5HOME)/include
+#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
+
+# AIX/SP-2 Parallel : Seaborg
+#CXX = mpCC_r
+#CC = mpcc_r
+#F90 = mpxlf
+#H5HOME = /usr/common/usg/hdf5/1.4.4/parallel
+#H4HOME = /usr/common/usg/hdf/default
+#OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
+#CFLAGS = -g -bmaxdata:800000000  -bmaxstack:256000000 -I$(H5HOME)/include
+#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
+
+# Linux Serial
+#CXX = g++
+#CC = gcc
+#F90 = g77  # or could be pgif90
+#CFLAGS = -O -g -I$(H5HOME)/include
+#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
+
+# Linux Jacquard
+CC = mpicc
+CXX = mpicxx
+F90 = mpif90
+H5HOME = /usr/common/usg/hdf5/1.6.3/parallel
+CFLAGS = -O2 -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
+LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
+
+# Linux Parallel
+#CC = gcc
+#CXX = g++
+#F90 = g77
+#H5HOME = /usr/local
+# /usr/common/usg/hdf5/1.6.3/parallel
+#MPIHOME = /usr/local
+#CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include 
+#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
+
+all: H5PartTest H5PartTest.o H5Part.o
+parallel: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest # parallel regression tests
+fortran: H5PartF.o # fortran bindings
+
+include rules.make
+

NEWS

@@ -0,0 +1,354 @@
+#### 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

@@ -0,0 +1,29 @@
+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. 
+

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

@@ -1,12 +1,11 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5hut], [1.99.6], [h5part@lists.psi.ch], H5hut)
+AC_INIT([H5Part], [1.6.4], [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(2.60)
+AC_PREREQ(2.59)
 
 # should be called right after AC_INIT.
 # configure scripts can create a C header file containing `#define' directives. 
@@ -18,8 +17,8 @@ AC_CONFIG_MACRO_DIR([m4])
 # AM_INIT_AUTOMAKE is required to use autoconf with automake
 AM_INIT_AUTOMAKE
 
-BUILD_LIBS='libH5hut'
+BUILD_LIBS='libH5Part'
-USE_C='yes'
+BUILD_TESTS='test'
 
 ###############################################################################
 ################# --enable-xxx and --with-xxx Argument ########################
@@ -31,12 +30,6 @@ AC_ARG_ENABLE(
 	[Compile with debug flags [default=no]])],
 	[USE_DEBUG=$enableval])
 
-AC_ARG_ENABLE(
-	[c],
-	[AC_HELP_STRING([--enable-c],
-	[Compile the C interface [default=yes]])],
-	[USE_C=$enableval])
-
 AC_ARG_ENABLE(
 	[fortran],
 	[AC_HELP_STRING([--enable-fortran],
@@ -49,24 +42,18 @@ AC_ARG_ENABLE(
 	[Compile the MPI/IO interface [default=no]])],
 	[USE_PARALLEL=$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=""])
 
-AC_ARG_WITH(
-	[mpi],
-	[AC_HELP_STRING([--with-mpi],
-	[path to MPI installation [default=""]])],
-	[MPIPATH=$withval;PATH=$MPIPATH/bin:$PATH], [MPIPATH=""])
-
-AC_ARG_WITH(
-	[lustre],
-	[AC_HELP_STRING([--with-lustre],
-	[path to lustre user API [default=""]])],
-	[LUSTREPATH=$withval], [LUSTREPATH=""])
-
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
 ###############################################################################
@@ -114,59 +101,29 @@ AC_PROG_MAKE_SET
 # Set output variable CC to the name of the compiler found.
 if test "x$USE_PARALLEL" = "xyes"; then
    	CCOMPILERS="mpicc cc"
-	CXXCOMPILERS="mpic++ c++"
+   	CXXCOMPILERS="mpic++ mpicxx CC"
 else
 	CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
-	CXXCOMPILERS="pgcc pathcc icc g++ cc_r c++"
+   	CXXCOMPILERS="pgCC pathCC icpc g++"
 fi
 
 AC_PROG_CC($CCOMPILERS)
-CC=`which $CC`
-AC_PROG_CXX($CXXCOMPILERS)
-CXX=`which $CXX`
 
-# Use macro to set C99 mode instead of checking for gcc, which breaks with
+# Only need C++ for some of the tools
-# parallel builds.
+#if test "x$USE_TOOLS" = "xyes"; then
-AC_PROG_CC_C99
+	AC_PROG_CXX($CXXCOMPILERS)
-if test "x$ac_cv_prog_cc_c99" = "xno"; then
+#fi
-	AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
-	exit 1
-fi
 
 # 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
-AC_PROG_AWK
 
-# Disable shared libraries by default: can be enabled with --enable-shared
+AC_PROG_AWK
-LT_INIT([disable-shared])
-AC_PROG_LIBTOOL
 
 # Default prefix for bindir, etc... (eg >> ./build/bin)
 AC_PREFIX_DEFAULT(`pwd`/build)
 
-# Checks for header files.
-AC_CHECK_HEADERS([fcntl.h limits.h stdint.h stdlib.h string.h sys/ioctl.h unistd.h])
-
-# Checks for typedefs, structures, and compiler characteristics.
-AC_HEADER_STDBOOL
-AC_C_INLINE
-AC_TYPE_INT16_T
-AC_TYPE_INT32_T
-AC_TYPE_INT64_T
-AC_TYPE_SIZE_T
-AC_TYPE_SSIZE_T
-AC_TYPE_UINT16_T
-AC_TYPE_UINT32_T
-AC_TYPE_UINT64_T
-AC_CHECK_TYPES([ptrdiff_t])
-
-# Checks for library functions.
-AC_FUNC_MALLOC
-AC_FUNC_REALLOC
-AC_CHECK_FUNCS([memmove memset pow strchr strdup strerror strstr])
-
 # 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. 
@@ -186,34 +143,24 @@ AC_MSG_CHECKING([if debug is enabled])
 if test "X$USE_DEBUG" = "Xyes"; then
     AC_MSG_RESULT([yes])
     CFLAGS="$CFLAGS -g"
+    CXXFLAGS="$CXXFLAGS -g"
     FFLAGS="$FFLAGS -g"
 else
     AC_MSG_RESULT([no])
 fi
 
-############################ fortran enabled ##################################
-AC_MSG_CHECKING([if C interface enabled])
-if test "X$USE_C" = "Xyes"; then
-	AC_MSG_RESULT([yes])
-	BINDINGS="$BINDINGS C"
-	LIB_C="libH5hutC.la"
-	BUILD_LIBS="$BUILD_LIBS libH5hutC"
-	BUILD_TESTS="$BUILD_TESTS h5u_test h5b_test"
-	BUILD_TOOLS="$BUILD_TOOLS h5hutcc h5PartDcToVtk h5PartSurfaceToVtk"
-fi
-
 ############################ fortran enabled ##################################
 AC_MSG_CHECKING([if fortran interface enabled])
 if test "X$USE_FORTRAN" = "Xyes"; then
 	AC_MSG_RESULT([yes])
-	BINDINGS="$BINDINGS Fortran"
+	LIB_FORTRAN="libH5PartF.la"
-	LIB_FORTRAN="libH5hutF.la"
+        BUILD_LIBS="$BUILD_LIBS libH5PartF"
-        BUILD_LIBS="$BUILD_LIBS libH5hutF"
+	BUILD_TESTS="$BUILD_TESTS testf"
 
 	if test "X$USE_PARALLEL" = "Xyes"; then
-		AC_PROG_FC(mpif90 mpif77)
+		AC_PROG_FC(mpif90 mpif77 ftn)
 	else
-		AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
+		AC_PROG_FC(pgf90 pathf90 ifort ftn xlf_r g95 g90 gfortran)
 	fi
 
 	if test -z "$FC" ; then
@@ -230,14 +177,14 @@ if test "X$USE_FORTRAN" = "Xyes"; then
 	fi
 
 	AC_MSG_CHECKING([symbol convention in object files])
-	`cd src/Fortran && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
+	`cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
-	`cd src/Fortran && ${FC} ${FFLAGS} -c TestUnderscore.f`
+	`cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
-	`cd src/Fortran && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
+	`cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
-	`cd src/Fortran && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
+	`cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
 
-	if test -f src/Fortran/TestUnderscore ; then
+	if test -f src/TestUnderscore ; then
 		UNDERSCORE_H=Underscore.h
-		`cd src/Fortran && ./TestUnderscore > Underscore.h`
+		`cd src && ./TestUnderscore > Underscore.h`
 		AC_MSG_RESULT([ok])
 	else
 		AC_MSG_RESULT([nok])
@@ -250,12 +197,19 @@ else
 fi
 
 
+# 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])
 if test "X$USE_PARALLEL" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 
 	CFLAGS="${CFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
+	CXXFLAGS="${CXXFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
+	FFLAGS="${FFLAGS} -DPARALLEL_IO"
 
 	AC_MSG_CHECKING([if we can compile MPI code without setting flags])
 	AC_TRY_LINK([#include "mpi.h"], [
@@ -269,28 +223,25 @@ if test "X$USE_PARALLEL" = "Xyes"; then
 		exit 1
 	fi
 
-	TPTARGET="${TPTARGET} H5PartTestP H5PartAndreasTest Bench"
-	TBTARGET="${TBTARGET} H5BlockTestAttributes"
-	TBTARGET="${TBTARGET} H5BlockParTestScalarField"
-
-	# parallel + fortran
-	if test "X$USE_FORTRAN" = "Xyes"; then
-		TPTARGET="${TPTARGET} H5testFpar"
-		TBTARGET="${TBTARGET} H5BlockParTestScalarFieldF"
-	fi
-
 else  # --enable-parallel=no
 	AC_MSG_RESULT([no])
-
-	TPTARGET="${TPTARGET} H5test"
-	TBTARGET="${TBTARGET} H5BlockTestAttributes"
-
-	if test "X$USE_FORTRAN" = "Xyes"; then
-		TPTARGET="${TPTARGET} H5testF"
-		TBTARGET="${TBTARGET} H5BlockTestAttributesF"
-	fi
 fi
 
+
+######################## tools enabled ###########################
+AC_MSG_CHECKING([whether tools are enabled])
+if test "X$USE_TOOLS" = "Xyes"; then
+    AC_MSG_RESULT([yes])
+    BUILD_TOOLS="h5pAttrib h5pToGNUplot homdynToH5p"
+    # tools + parallel
+    if test "X$USE_PARALLEL" = "Xyes"; then
+        BUILD_TOOLS="${BUILD_TOOLS} H5PartBench H5BlockBench"
+    fi
+else
+    AC_MSG_RESULT([no])
+fi
+
+
 ###############################################################################
 ######################### PATH CHECKING & SETTING #############################
 ###############################################################################
@@ -335,35 +286,22 @@ if test -n "$HDF5ROOT"; then
 	fi
 fi
 
-AC_MSG_CHECKING([for lustre API ])
-AC_MSG_RESULT([])
-if test -n "${LUSTREPATH}"; then
-	P=${LUSTREPATH}
-elif test -n "${LUSTREROOT}" ; then
-	P=${LUSTREROOT}
-elif test -n "${LUSTREHOME}" ; then
-	P=${LUSTREHOME}
-elif test -n "${LUSTRE_DIR}" ; then
-	P=${LUSTRE_DIR}
-else
-	P=''
-	P="$P /usr"
-	P="$P /usr/local"
-	P="$P /usr/local/lustre"
-	P="$P /opt/lustre"
-fi
-PATH_Search LUSTREROOT "$P" usr/include/lustre/liblustreapi.h
-if test -z "$LUSTREROOT"; then
-	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
-else
-        CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
-        INCLUDES="$INCLUDES -I$LUSTREROOT/usr/include"
-        LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
-        LIBS="$LIBS -llustreapi"
-fi
-
 LIBS="$LIBS -lz -lm"
 
+
+# Checks for header files.
+AC_CHECK_HEADERS([fcntl.h stdlib.h string.h unistd.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_HEADER_STDBOOL
+AC_TYPE_INT64_T
+AC_TYPE_SIZE_T
+AC_TYPE_SSIZE_T
+
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_CHECK_FUNCS([memset pow strchr strdup])
+
 ###############################################################################
 ############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
 ###############################################################################
@@ -374,17 +312,14 @@ LIBS="$LIBS -lz -lm"
 # 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(HDF5ROOT)
-AC_SUBST(LUSTREROOT)
 AC_SUBST(CFLAGS)
+AC_SUBST(CXXFLAGS)
 AC_SUBST(FFLAGS)
 AC_SUBST(INCLUDES)
 AC_SUBST(LDFLAGS)
 AC_SUBST(LIBS)
 AC_SUBST(UNDERSCORE_H)
-AC_SUBST(LIB_C)
 AC_SUBST(LIB_FORTRAN)
-AC_SUBST(BINDINGS)
 AC_SUBST(BUILD_TESTS)
 AC_SUBST(BUILD_TOOLS)
 
@@ -393,13 +328,9 @@ AC_SUBST(BUILD_TOOLS)
 AC_CONFIG_FILES([
 	Makefile
 	src/Makefile
-	src/C/Makefile
+	doc/Makefile
-	src/h5core/Makefile
-        src/Fortran/Makefile
 	test/Makefile
-        test/H5Fed/Makefile
 	tools/Makefile
-	tools/h5hutcc
 ])
 
 AC_OUTPUT
@@ -420,10 +351,10 @@ 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([LUSTREROOT =         $LUSTREROOT])
 AC_MSG_RESULT([ ])

depcomp

@@ -0,0 +1,529 @@
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2005-02-09.22
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
+
+case $1 in
+  '')
+     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+  depmode     Dependency tracking mode.
+  source      Source file read by `PROGRAMS ARGS'.
+  object      Object file output by `PROGRAMS ARGS'.
+  DEPDIR      directory where to store dependencies.
+  depfile     Dependency file to output.
+  tmpdepfile  Temporary file to use when outputing dependencies.
+  libtool     Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "depcomp $scriptversion"
+    exit $?
+    ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+  echo "depcomp: Variables source, object and depmode must be set" 1>&2
+  exit 1
+fi
+
+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
+depfile=${depfile-`echo "$object" |
+  sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags.  We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write.  Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+  # HP compiler uses -M and no extra arg.
+  gccflag=-M
+  depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+   # This is just like dashmstdout with a different argument.
+   dashmflag=-xM
+   depmode=dashmstdout
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want.  Yay!  Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff.  Hmm.
+  "$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  mv "$tmpdepfile" "$depfile"
+  ;;
+
+gcc)
+## There are various ways to get dependency output from gcc.  Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+##   up in a subdir.  Having to rename by hand is ugly.
+##   (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+##   -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+##   than renaming).
+  if test -z "$gccflag"; then
+    gccflag=-MD,
+  fi
+  "$@" -Wp,"$gccflag$tmpdepfile"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+  sed -e 's/^[^:]*: / /' \
+      -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header).  We avoid this by adding
+## dummy dependencies for each header file.  Too bad gcc doesn't do
+## this for us directly.
+  tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'.  On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+hp)
+  # This case exists only to let depend.m4 do its work.  It works by
+  # looking at the text of this script.  This case will never be run,
+  # since it is checked for above.
+  exit 1
+  ;;
+
+sgi)
+  if test "$libtool" = yes; then
+    "$@" "-Wp,-MDupdate,$tmpdepfile"
+  else
+    "$@" -MDupdate "$tmpdepfile"
+  fi
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+
+  if test -f "$tmpdepfile"; then  # yes, the sourcefile depend on other files
+    echo "$object : \\" > "$depfile"
+
+    # Clip off the initial element (the dependent).  Don't try to be
+    # clever and replace this with sed code, as IRIX sed won't handle
+    # lines with more than a fixed number of characters (4096 in
+    # IRIX 6.2 sed, 8192 in IRIX 6.5).  We also remove comment lines;
+    # the IRIX cc adds comments like `#:fec' to the end of the
+    # dependency line.
+    tr ' ' '
+' < "$tmpdepfile" \
+    | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+    tr '
+' ' ' >> $depfile
+    echo >> $depfile
+
+    # The second pass generates a dummy entry for each header file.
+    tr ' ' '
+' < "$tmpdepfile" \
+   | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+   >> $depfile
+  else
+    # The sourcefile does not contain any dependencies, so just
+    # store a dummy comment line, to avoid errors with the Makefile
+    # "include basename.Plo" scheme.
+    echo "#dummy" > "$depfile"
+  fi
+  rm -f "$tmpdepfile"
+  ;;
+
+aix)
+  # The C for AIX Compiler uses -M and outputs the dependencies
+  # in a .u file.  In older versions, this file always lives in the
+  # current directory.  Also, the AIX compiler puts `$object:' at the
+  # start of each line; $object doesn't have directory information.
+  # Version 6 uses the directory in both cases.
+  stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
+  tmpdepfile="$stripped.u"
+  if test "$libtool" = yes; then
+    "$@" -Wc,-M
+  else
+    "$@" -M
+  fi
+  stat=$?
+
+  if test -f "$tmpdepfile"; then :
+  else
+    stripped=`echo "$stripped" | sed 's,^.*/,,'`
+    tmpdepfile="$stripped.u"
+  fi
+
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+
+  if test -f "$tmpdepfile"; then
+    outname="$stripped.o"
+    # Each line is of the form `foo.o: dependent.h'.
+    # Do two passes, one to just change these to
+    # `$object: dependent.h' and one to simply `dependent.h:'.
+    sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
+    sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
+  else
+    # The sourcefile does not contain any dependencies, so just
+    # store a dummy comment line, to avoid errors with the Makefile
+    # "include basename.Plo" scheme.
+    echo "#dummy" > "$depfile"
+  fi
+  rm -f "$tmpdepfile"
+  ;;
+
+icc)
+  # Intel's C compiler understands `-MD -MF file'.  However on
+  #    icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+  # ICC 7.0 will fill foo.d with something like
+  #    foo.o: sub/foo.c
+  #    foo.o: sub/foo.h
+  # which is wrong.  We want:
+  #    sub/foo.o: sub/foo.c
+  #    sub/foo.o: sub/foo.h
+  #    sub/foo.c:
+  #    sub/foo.h:
+  # ICC 7.1 will output
+  #    foo.o: sub/foo.c sub/foo.h
+  # and will wrap long lines using \ :
+  #    foo.o: sub/foo.c ... \
+  #     sub/foo.h ... \
+  #     ...
+
+  "$@" -MD -MF "$tmpdepfile"
+  stat=$?
+  if test $stat -eq 0; then :
+  else
+    rm -f "$tmpdepfile"
+    exit $stat
+  fi
+  rm -f "$depfile"
+  # Each line is of the form `foo.o: dependent.h',
+  # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+  # Do two passes, one to just change these to
+  # `$object: dependent.h' and one to simply `dependent.h:'.
+  sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+  # Some versions of the HPUX 10.20 sed can't process this invocation
+  # correctly.  Breaking it into two sed invocations is a workaround.
+  sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+    sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+tru64)
+   # The Tru64 compiler uses -MD to generate dependencies as a side
+   # effect.  `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+   # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+   # dependencies in `foo.d' instead, so we check for that too.
+   # Subdirectories are respected.
+   dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+   test "x$dir" = "x$object" && dir=
+   base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+   if test "$libtool" = yes; then
+      # With Tru64 cc, shared objects can also be used to make a
+      # static library.  This mecanism is used in libtool 1.4 series to
+      # handle both shared and static libraries in a single compilation.
+      # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+      #
+      # With libtool 1.5 this exception was removed, and libtool now
+      # generates 2 separate objects for the 2 libraries.  These two
+      # compilations output dependencies in in $dir.libs/$base.o.d and
+      # in $dir$base.o.d.  We have to check for both files, because
+      # one of the two compilations can be disabled.  We should prefer
+      # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+      # automatically cleaned when .libs/ is deleted, while ignoring
+      # the former would cause a distcleancheck panic.
+      tmpdepfile1=$dir.libs/$base.lo.d   # libtool 1.4
+      tmpdepfile2=$dir$base.o.d          # libtool 1.5
+      tmpdepfile3=$dir.libs/$base.o.d    # libtool 1.5
+      tmpdepfile4=$dir.libs/$base.d      # Compaq CCC V6.2-504
+      "$@" -Wc,-MD
+   else
+      tmpdepfile1=$dir$base.o.d
+      tmpdepfile2=$dir$base.d
+      tmpdepfile3=$dir$base.d
+      tmpdepfile4=$dir$base.d
+      "$@" -MD
+   fi
+
+   stat=$?
+   if test $stat -eq 0; then :
+   else
+      rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+      exit $stat
+   fi
+
+   for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+   do
+     test -f "$tmpdepfile" && break
+   done
+   if test -f "$tmpdepfile"; then
+      sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+      # That's a tab and a space in the [].
+      sed -e 's,^.*\.[a-z]*:[	 ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+   else
+      echo "#dummy" > "$depfile"
+   fi
+   rm -f "$tmpdepfile"
+   ;;
+
+#nosideeffect)
+  # This comment above is used by automake to tell side-effect
+  # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout, regardless of -o.
+  "$@" || exit $?
+
+  # Remove the call to Libtool.
+  if test "$libtool" = yes; then
+    while test $1 != '--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  # Remove `-o $object'.
+  IFS=" "
+  for arg
+  do
+    case $arg in
+    -o)
+      shift
+      ;;
+    $object)
+      shift
+      ;;
+    *)
+      set fnord "$@" "$arg"
+      shift # fnord
+      shift # $arg
+      ;;
+    esac
+  done
+
+  test -z "$dashmflag" && dashmflag=-M
+  # Require at least two characters before searching for `:'
+  # in the target name.  This is to cope with DOS-style filenames:
+  # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+  "$@" $dashmflag |
+    sed 's:^[  ]*[^: ][^:][^:]*\:[    ]*:'"$object"'\: :' > "$tmpdepfile"
+  rm -f "$depfile"
+  cat < "$tmpdepfile" > "$depfile"
+  tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+dashXmstdout)
+  # This case only exists to satisfy depend.m4.  It is never actually
+  # run, as this mode is specially recognized in the preamble.
+  exit 1
+  ;;
+
+makedepend)
+  "$@" || exit $?
+  # Remove any Libtool call
+  if test "$libtool" = yes; then
+    while test $1 != '--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+  # X makedepend
+  shift
+  cleared=no
+  for arg in "$@"; do
+    case $cleared in
+    no)
+      set ""; shift
+      cleared=yes ;;
+    esac
+    case "$arg" in
+    -D*|-I*)
+      set fnord "$@" "$arg"; shift ;;
+    # Strip any option that makedepend may not understand.  Remove
+    # the object too, otherwise makedepend will parse it as a source file.
+    -*|$object)
+      ;;
+    *)
+      set fnord "$@" "$arg"; shift ;;
+    esac
+  done
+  obj_suffix="`echo $object | sed 's/^.*\././'`"
+  touch "$tmpdepfile"
+  ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+  rm -f "$depfile"
+  cat < "$tmpdepfile" > "$depfile"
+  sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly.  Breaking it into two sed invocations is a workaround.
+    sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile" "$tmpdepfile".bak
+  ;;
+
+cpp)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout.
+  "$@" || exit $?
+
+  # Remove the call to Libtool.
+  if test "$libtool" = yes; then
+    while test $1 != '--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  # Remove `-o $object'.
+  IFS=" "
+  for arg
+  do
+    case $arg in
+    -o)
+      shift
+      ;;
+    $object)
+      shift
+      ;;
+    *)
+      set fnord "$@" "$arg"
+      shift # fnord
+      shift # $arg
+      ;;
+    esac
+  done
+
+  "$@" -E |
+    sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+    sed '$ s: \\$::' > "$tmpdepfile"
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  cat < "$tmpdepfile" >> "$depfile"
+  sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+msvisualcpp)
+  # Important note: in order to support this mode, a compiler *must*
+  # always write the preprocessed file to stdout, regardless of -o,
+  # because we must use -o when running libtool.
+  "$@" || exit $?
+  IFS=" "
+  for arg
+  do
+    case "$arg" in
+    "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+	set fnord "$@"
+	shift
+	shift
+	;;
+    *)
+	set fnord "$@" "$arg"
+	shift
+	shift
+	;;
+    esac
+  done
+  "$@" -E |
+  sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
+  rm -f "$depfile"
+  echo "$object : \\" > "$depfile"
+  . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"
+  echo "	" >> "$depfile"
+  . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+  rm -f "$tmpdepfile"
+  ;;
+
+none)
+  exec "$@"
+  ;;
+
+*)
+  echo "Unknown depmode $depmode" 1>&2
+  exit 1
+  ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-end: "$"
+# End:

doc/Doxyfile

@@ -3,8 +3,8 @@
 #---------------------------------------------------------------------------
 # Project related configuration options
 #---------------------------------------------------------------------------
-PROJECT_NAME           = H5hut
+PROJECT_NAME           = H5Part
-PROJECT_NUMBER         = 1.9.9
+PROJECT_NUMBER         = 1.6.1
 OUTPUT_DIRECTORY       = ./ReferencePages
 CREATE_SUBDIRS         = NO
 OUTPUT_LANGUAGE        = English
@@ -35,7 +35,7 @@ INHERIT_DOCS           = YES
 SEPARATE_MEMBER_PAGES  = NO
 TAB_SIZE               = 8
 ALIASES                = 
-OPTIMIZE_OUTPUT_FOR_C  = YES
+OPTIMIZE_OUTPUT_FOR_C  = NO
 OPTIMIZE_OUTPUT_JAVA   = NO
 BUILTIN_STL_SUPPORT    = NO
 DISTRIBUTE_GROUP_DOC   = NO
@@ -57,9 +57,9 @@ CASE_SENSE_NAMES       = YES
 HIDE_SCOPE_NAMES       = NO
 SHOW_INCLUDE_FILES     = NO
 INLINE_INFO            = YES
-SORT_MEMBER_DOCS       = NO
+SORT_MEMBER_DOCS       = YES
-SORT_BRIEF_DOCS        = NO
+SORT_BRIEF_DOCS        = YES
-SORT_BY_SCOPE_NAME     = NO
+SORT_BY_SCOPE_NAME     = YES
 GENERATE_TODOLIST      = YES
 GENERATE_TESTLIST      = YES
 GENERATE_BUGLIST       = YES
@@ -67,7 +67,7 @@ GENERATE_DEPRECATEDLIST= YES
 ENABLED_SECTIONS       = 
 MAX_INITIALIZER_LINES  = 30
 SHOW_USED_FILES        = NO
-SHOW_DIRECTORIES       = NO
+SHOW_DIRECTORIES       = YES
 FILE_VERSION_FILTER    = 
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
@@ -82,22 +82,28 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT			+= H5.dox
+INPUT                  += ../src/H5Part.c
-INPUT			+= ../src/h5core/
+INPUT                  += ../src/H5PartAttrib.c
-INPUT			+= ../src/C/
+INPUT		       += ../src/H5Block.c
-INPUT			+= ../src/Fortran/
+INPUT		       += ../src/H5BlockReadWrite.c
-FILE_PATTERNS          	= 
+INPUT		       += ../src/H5MultiBlock.c
-RECURSIVE              	= YES
+INPUT		       += ../src/H5MultiBlockReadWrite.c
-EXCLUDE                	=
+INPUT		       += ../src/H5Part.f90
-EXCLUDE_SYMLINKS       	= NO
+INPUT		       += ../src/H5PartAttrib.f90
-EXCLUDE_PATTERNS       	= 
+INPUT		       += ../src/H5Block.f90
-EXAMPLE_PATH           	= 
+INPUT		       += ../src/H5BlockReadWrite.f90
-EXAMPLE_PATTERNS       	= *
+FILE_PATTERNS          = 
-EXAMPLE_RECURSIVE      	= NO
+RECURSIVE              = YES
-IMAGE_PATH             	= 
+EXCLUDE                =
-INPUT_FILTER           	= 
+EXCLUDE_SYMLINKS       = NO
-FILTER_PATTERNS        	= 
+EXCLUDE_PATTERNS       = 
-FILTER_SOURCE_FILES    	= NO
+EXAMPLE_PATH           = 
+EXAMPLE_PATTERNS       = *
+EXAMPLE_RECURSIVE      = NO
+IMAGE_PATH             = 
+INPUT_FILTER           = 
+FILTER_PATTERNS        = 
+FILTER_SOURCE_FILES    = NO
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
@@ -120,8 +126,8 @@ IGNORE_PREFIX          =
 GENERATE_HTML          = YES
 HTML_OUTPUT            = .
 HTML_FILE_EXTENSION    = .html
-HTML_HEADER            =
+HTML_HEADER            = 
-HTML_FOOTER            =
+HTML_FOOTER            = doxyfooter 
 HTML_STYLESHEET        = 
 HTML_ALIGN_MEMBERS     = YES
 GENERATE_HTMLHELP      = NO
@@ -199,7 +205,7 @@ SKIP_FUNCTION_MACROS   = YES
 #---------------------------------------------------------------------------
 # Configuration::additions related to external references   
 #---------------------------------------------------------------------------
-TAGFILES               =
+TAGFILES               = 
 GENERATE_TAGFILE       = 
 ALLEXTERNALS           = NO
 EXTERNAL_GROUPS        = YES
@@ -208,7 +214,7 @@ PERL_PATH              = /usr/bin/perl
 # Configuration options related to the dot tool   
 #---------------------------------------------------------------------------
 CLASS_DIAGRAMS         = NO
-HIDE_UNDOC_RELATIONS   = YES
+HIDE_UNDOC_RELATIONS   = NO
 HAVE_DOT               = NO
 CLASS_GRAPH            = NO
 COLLABORATION_GRAPH    = NO
@@ -218,10 +224,10 @@ TEMPLATE_RELATIONS     = NO
 INCLUDE_GRAPH          = NO
 INCLUDED_BY_GRAPH      = NO
 CALL_GRAPH             = NO
-GRAPHICAL_HIERARCHY    = NO
+GRAPHICAL_HIERARCHY    = YES
-DIRECTORY_GRAPH        = NO
+DIRECTORY_GRAPH        = YES
 DOT_IMAGE_FORMAT       = png
-DOT_PATH               =
+DOT_PATH               = 
 DOTFILE_DIRS           = 
 MAX_DOT_GRAPH_WIDTH    = 1024
 MAX_DOT_GRAPH_HEIGHT   = 1024

doc/Examples/meshexample.txt

@@ -1,77 +0,0 @@
-NumLevels: 2
-
-NumVerticesOnLevel: 11 20 29
-
-Vertices:
-1	  0.0	  0.0
-2	 60.0	-70.0
-3	 90.0	-10.0
-4	140.0	-70.0
-5	180.0	-10.0
-6	240.0	-60.0
-7	220.0	 60.0
-8	140.0	 90.0
-9	200.0	120.0
-10	130.0	150.0
-11	 50.0	 80.0
-12	115.0	 40.0
-13	 95.0	 85.0
-14	 70.0	 35.0
-15	160.0	-40.0
-16	135.0	-10.0
-17	115.0	-40.0
-18	200.0	 25.0	
-19	180.0	 75.0
-20	160.0	 40.0
-
-21	125.0	 15.0
-22	112.5	-10.0
-23	102.5	 15.0
-24	147.5	 15.0
-25	137.5	 40.0
-26	150.0	 65.0
-27	127.5	 65.0
-28	117.5	 87.5
-29	105.0	 62.5
-
-NumElemsOnLevel: 12 24 36
-NumElems: 12 28 44
-
-Elements:
-ID	PID	CID	VertexIDs	Adj		Translation Tbl (dim num lvls - 1)
-1	-1	-1	1 2 3		2 11 -1		1
-2	-1	-1	2 3 4		3 -1 1		2
-3	-1	12	3 4 5		4 12 2		-1
-4	-1	-1	4 5 6		5 -1 3		3
-5	-1	-1	5 7 6		-1 4 6		4
-6	-1	17	8 5 7		5 7 12		-1
-7	-1	-1	8 9 7		-1 6 8		5
-8	-1	-1	10 8 9		7 -1 9		6
-9	-1	-1	11 10 8		8 10 -1		7
-10	-1	25	11 3 8		12 9 11		-1
-11	-1	-1	1 11 3		10 1 -1		8
-12	-1	21	3 8 5		6 3 10		-1
-13	3	-1	3 14 13		16 21 2		9
-14	3	-1	14 4 12		4 16 2		10
-15	3	-1	13 12 5		4 23 16		11
-16	3	-1	14 13 12	15 14 13	12
-17	6	-1	8 17 16		20 5 22		13
-18	6	-1	17 5 15		5 20 23		14
-19	6	-1	16 15 7		5 7 20		15
-20	6	-1	17 16 15	19 18 17	16
-21	12	-1	3 18 13		24 13 26	17
-22	12	-1	18 8 17		17 24 27	18
-23	12	-1	13 17 5		18 15 24	19
-24	12	-1	18 13 17	23 22 21	20
-25	10	-1	11 20 19	28 9 11		21
-26	10	-1	20 3 18		21 28 11	22
-27	10	-1	19 18 8		22 9 28		23
-28	10	-1	20 3 18		27 26 25	24
-
-3,0 3,1 4,2 2,3 16,4
-
-1 2 -1 3 4
-
-1    2       3
-1    3       6
-2 11 1 13 14 

doc/Examples/simple_tet.vtk

@@ -1,107 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 17 DOUBLE
--1 0 0
-1 0 0
-0 1 0
-0 0 1
-0 -1 0
--0.5 0 0.5
--0.5 0.5 0
-0 0 0
-0 0.5 0.5
-0.5 0 0.5
-0.5 0.5 0
--0.75 0 0.25
--0.75 0.25 0
--0.5 0 0
--0.5 0.25 0.25
--0.25 0 0.25
--0.25 0.25 0
-
-CELLS 18 90
-4	0 3 2 1
-4	0 4 3 1
-4	0 5 6 7
-4	5 3 8 9
-4	6 8 2 10
-4	7 9 10 1
-4	5 6 7 9
-4	5 6 8 9
-4	6 7 9 10
-4	6 8 9 10
-4	0 11 12 13
-4	11 5 14 15
-4	12 14 6 16
-4	13 15 16 7
-4	11 12 13 15
-4	11 12 14 15
-4	12 13 15 16
-4	12 14 15 16
-
-CELL_TYPES 18
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-
-POINT_DATA 17
-SCALARS vertex_id int 1
-LOOKUP_TABLE default
-0
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-
-CELL_DATA 18
-SCALARS cell_attribute_data int 1
-LOOKUP_TABLE default
-0
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-17
-

doc/Examples/simple_tet_level0.vtk

@@ -1,59 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 17 DOUBLE
--1 0 0
-1 0 0
-0 1 0
-0 0 1
-0 -1 0
--0.5 0 0.5
--0.5 0.5 0
-0 0 0
-0 0.5 0.5
-0.5 0 0.5
-0.5 0.5 0
--0.75 0 0.25
--0.75 0.25 0
--0.5 0 0
--0.5 0.25 0.25
--0.25 0 0.25
--0.25 0.25 0
-
-CELLS 2 10
-4	0 3 2 1
-4	0 4 3 1
-
-CELL_TYPES 2
-10
-10
-
-POINT_DATA 17
-SCALARS vertex_id int 1
-LOOKUP_TABLE default
-0
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-
-CELL_DATA 2
-SCALARS cell_attribute_data int 1
-LOOKUP_TABLE default
-0
-1
-

doc/Examples/simple_tet_level1.vtk

@@ -1,80 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 17 DOUBLE
--1 0 0
-1 0 0
-0 1 0
-0 0 1
-0 -1 0
--0.5 0 0.5
--0.5 0.5 0
-0 0 0
-0 0.5 0.5
-0.5 0 0.5
-0.5 0.5 0
--0.75 0 0.25
--0.75 0.25 0
--0.5 0 0
--0.5 0.25 0.25
--0.25 0 0.25
--0.25 0.25 0
-
-CELLS 9 45
-4	0 4 3 1
-4	0 5 6 7
-4	5 3 8 9
-4	6 8 2 10
-4	7 9 10 1
-4	5 6 7 9
-4	5 6 8 9
-4	6 7 9 10
-4	6 8 9 10
-
-CELL_TYPES 9
-10
-10
-10
-10
-10
-10
-10
-10
-10
-
-POINT_DATA 17
-SCALARS vertex_id int 1
-LOOKUP_TABLE default
-0
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-
-CELL_DATA 9
-SCALARS cell_attribute_data int 1
-LOOKUP_TABLE default
-0
-1
-2
-3
-4
-5
-6
-7
-8
-

doc/Examples/simple_tet_level2.vtk

@@ -1,101 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 17 DOUBLE
--1 0 0
-1 0 0
-0 1 0
-0 0 1
-0 -1 0
--0.5 0 0.5
--0.5 0.5 0
-0 0 0
-0 0.5 0.5
-0.5 0 0.5
-0.5 0.5 0
--0.75 0 0.25
--0.75 0.25 0
--0.5 0 0
--0.5 0.25 0.25
--0.25 0 0.25
--0.25 0.25 0
-
-CELLS 16 80
-4	0 4 3 1
-4	5 3 8 9
-4	6 8 2 10
-4	7 9 10 1
-4	5 6 7 9
-4	5 6 8 9
-4	6 7 9 10
-4	6 8 9 10
-4	0 11 12 13
-4	11 5 14 15
-4	12 14 6 16
-4	13 15 16 7
-4	11 12 13 15
-4	11 12 14 15
-4	12 13 15 16
-4	12 14 15 16
-
-CELL_TYPES 16
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-10
-
-POINT_DATA 17
-SCALARS vertex_id int 1
-LOOKUP_TABLE default
-0
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-
-CELL_DATA 16
-SCALARS cell_attribute_data int 1
-LOOKUP_TABLE default
-1
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-17
-

doc/Examples/trimesh_dgraph_level0.metis

@@ -1,13 +0,0 @@
-12 14
-2 11
-1 3
-2 4 12
-3 5
-4 6
-5 7 12
-6 8
-7 9
-8 10
-9 11 12
-1 10
-3 6 10

doc/Examples/trimesh_dgraph_level0.metis.part.2

@@ -1,12 +0,0 @@
-0
-1
-1
-1
-1
-1
-0
-0
-0
-0
-0
-1

doc/Examples/trimesh_dgraph_level0.metis.part.3

@@ -1,12 +0,0 @@
-1
-1
-2
-2
-2
-0
-0
-0
-0
-1
-1
-2

doc/Examples/trimesh_dnode_level1.metis

@@ -1,49 +0,0 @@
-24 35
-%1
-2 8
-%2
-1 9 10
-%3
-4 10 11
-%4
-3 14 15
-%5
-6 13 15
-%6
-5 7
-%7
-6 21 23
-%8
-1 21 22
-%9
-2 12 17
-%10
-2 3 12
-%11
-3 12 19
-%12
-9 10 11
-%13
-5 16 18
-%14
-4 16 19
-%15
-4 5 16
-%16
-13 14 15
-%17
-9 20 22
-%18
-13 20 23
-%19
-11 14 20
-%20
-17 18 19
-%21
-7 8 24
-%22
-8 17 24
-%23
-7 18 24
-%24
-21 22 23

doc/Examples/trimesh_dnode_level1.metis.part.2

@@ -1,24 +0,0 @@
-1
-1
-0
-0
-0
-0
-1
-1
-1
-1
-0
-1
-0
-0
-0
-0
-1
-0
-0
-0
-1
-1
-1
-1

doc/Examples/trimesh_level0.metis

@@ -1,13 +0,0 @@
-12 1
-1 2 3
-2 3 4
-3 4 6
-4 5 6
-5 6 7
-6 7 8
-7 8 11
-8 10 11
-8 9 10
-3 8 9
-1 3 9
-3 6 8

doc/Examples/trimesh_level0.metis.epart.2

@@ -1,12 +0,0 @@
-1
-1
-1
-1
-0
-0
-0
-0
-0
-0
-1
-1

doc/Examples/trimesh_level0.metis.ngraph

@@ -1,12 +0,0 @@
-11 22
- 2 3 9
- 1 3 4
- 1 2 4 6 8 9
- 2 3 6 5
- 4 6 7
- 3 4 5 7 8
- 5 6 8 11
- 6 7 11 10 9 3
- 8 10 3 1
- 8 11 9
- 7 8 10

doc/Examples/trimesh_level0.metis.npart.2

@@ -1,11 +0,0 @@
-1
-1
-1
-1
-1
-0
-0
-0
-0
-0
-0

doc/Examples/trimesh_level1.metis

@@ -1,41 +0,0 @@
-20 43
-%1
-2 3 11
-%2
-1 3 4
-%3
-1 2 14 13 18 20
-%4
-2 14 12 6
-%5
-12 6 15 17 13
-%6
-4 5 7
-%7
-6 15 16 9
-%8
-9 10 19 18 17 16
-%9
-7 8 10
-%10
-8 9 11
-%11
-1 20 19 10
-%12
-4 14 13 5
-%13
-3 14 12 5 17 18
-%14
-3 13 12 4
-%15
-5 17 17 7
-%16
-7 8 17 15
-%17
-5 15 16 8 18 13
-%18
-3 13 17 8 19 20
-%19
-8 11 20 18
-%20
-3 18 19 11

doc/Examples/trimesh_level1.metis.part.2

@@ -1,20 +0,0 @@
-1
-1
-1
-0
-0
-0
-0
-1
-1
-1
-1
-0
-0
-0
-0
-0
-0
-1
-1
-1

doc/H5.dox

@@ -1,139 +0,0 @@
-/*!
-\mainpage H5hut: A High-Performance I/O Library for Particle-based Simulations
-
-Particle-based simulations running on large high-performance computing systems
-over many time steps can generate an enormous amount of particle- and
-field-based data for post-processing and analysis. Achieving high-performance
-I/O for this data, effectively managing it on disk, and interfacing it with
-analysis and visualization tools can be challenging, especially for domain
-scientists who do not have I/O and data management expertise. We present the
-H5hut library, an implementation of several data models for particle-based
-simulations that encapsulates the complexity of HDF5 and is simple to use, yet
-does not compromise performance.
-
-Developers:
-
-<UL>
-<LI> Andreas Adelmann (PSI) </LI>
-<LI> Achim Gsell (PSI) </LI>
-<LI> Benedikt Oswald (PSI) </LI>
-<LI> Mark Howison (NERSC/LBNL) </LI>
-<LI> Prabhat (NERSC/LBNL) </LI>
-<LI> Wes Bethel (NERSC/LBNL) </LI>
-</UL>
-
-Previous developers:
-
-<UL>
-<LI> John Shalf (NERSC/LBNL)</LI>
-<LI> Cristina Siegerist (NERSC/LBNL)</LI>
-</UL>
-
-For more information, please contact the <a href="mailto:h5part@lists.psi.ch">h5part</a> mailing list.
-
-*/
-
-/*!
-  \defgroup h5hut_c_api H5hut C API
-*/
-/*!
-  \ingroup h5hut_c_api
-  \defgroup h5hut_file File Handling
-*/
-/*!
-  \ingroup h5hut_c_api
-  \defgroup h5hut_error Error Handling
-*/
-/*!
-  \ingroup h5hut_c_api
-  \defgroup h5hut_model Setting up the Data Model
-*/
-/*!
-  \ingroup h5hut_c_api
-  \defgroup h5hut_attrib Reading and Writing Attributes
-*/  
-
-
-/*!
-  \defgroup h5part_c_api H5Part C API
-*/
-/*!
-  \ingroup h5part_c_api
-  \defgroup h5part_model	Setting up the Data Model
-*/
-/*!
-  \ingroup h5part_c_api
-  \defgroup h5part_data		Reading and Writing Datasets
-*/  
-
-
-/*!
-  \defgroup h5block_c_api H5Block C API
-*/
-*/!
-  \ingroup h5block_c_api
-  \defgroup h5block_model Setting up the Data Model
-*/
-  \ingroup h5block_c_api
-  \defgroup h5block_data Reading and Writing Datasets
-*/
-  \ingroup h5block_c_api
-  \defgroup h5block_attrib Reading and Writing Attributes
-*/
-
-
-
-/*!
-  \defgroup h5fed_c_api H5Fed C API
-*/
-
-
-/*!
-  \defgroup h5hut_f90_api H5hut F90 API
-*/
-
-/*!
-  \ingroup h5hut_f90_api
-  \defgroup h5hut_file_f File Handling
-*/
-
-/*!
-  \ingroup h5hut_f90_api
-  \defgroup h5hut_model_f Setting up the Data Model
-*/
-
-/*!
-  \ingroup h5hut_f90_api
-  \defgroup h5hut_attrib_f Reading and Writing Attributes
-!<
-
-
-/*!
-  \defgroup h5part_f90_api H5Part F90 API
-*/
-/*!
-  \ingroup h5part_f90_api
-  \defgroup h5part_model_f Setting up the Data Model
-*/
-/*!
-  \ingroup h5part_f90_api
-  \defgroup h5part_data_f Reading and Writing Datasets
-*/
-
-
-/*!
-  \defgroup h5block_f90_api H5Block F90 API
-*/
-/*!
-  \ingroup h5block_f90_api
-  \defgroup h5block_model_f Setting up the Data Model
-*/
-/*!
-  \ingroup h5block_f90_api
-  \defgroup h5block_data_f Reading and Writing Datasets
-*/
-/*!
-  \ingroup h5block_f90_api
-  \defgroup h5block_attrib_f Reading and Writing Attributes
-*/
-

doc/Makefile.am

@@ -1,13 +1,2 @@
 EXTRA_DIST = \
-	Doxyfile \
+	Doxyfile doxyfooter
-        H5.dox
-
-all:
-
-doc:
-
-doxydoc:
-	doxygen
-
-clean:
-	${RM} -rf ReferencePages TWiki

doc/doxyheader

@@ -1,6 +0,0 @@
-<HTML>
-    <HEAD>
-      <TITLE>H5/H5Part/H5Block/H5Fed API</TITLE>
-      <LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
-    </HEAD>
-    <BODY BGCOLOR="#FFFFFF">

doc/html2twiki

@@ -1,36 +0,0 @@
-#!/bin/bash
-
-shopt -s nullglob
-
-function html2twiki() {
-	declare	-rx	infile=$1
-	declare	-rx	outdir=$2
-	declare	-rx	fname=$( sed -n 's/.* member="\([a-zA-Z0-9_.]*\)::\([_a-zA-Z0-9]*\)" .*/\2/p' "${infile}" )
-	declare -rx	outfile="${outdir}/${fname}.txt"
-
-	grep -q " member=" "${infile}" || return 0
-
-	sed  '/Generated by/,/anchor/d' "${infile}" > "${outfile}"
-}
-
-mkdir -p TWiki/h5_core
-mkdir -p TWiki/H5
-mkdir -p TWiki/H5Part
-mkdir -p TWiki/H5Block
-mkdir -p TWiki/H5Fed
-
-for f in ReferencePages/group__h5__core_*.html; do
-	html2twiki $f  TWiki/h5_core
-done
-for f in ReferencePages/group__h5__c__api_*.html; do
-	html2twiki $f  TWiki/H5
-done
-for f in ReferencePages/group__h5part__c__api_*.html; do
-	html2twiki $f  TWiki/H5Part
-done
-for f in ReferencePages/group__h5block__c__api_*.html; do
-	html2twiki $f  TWiki/H5Block
-done
-for f in ReferencePages/group__h5fed__c__api_*.html; do
-	html2twiki $f  TWiki/H5Fed
-done

doc/tetrahedron_refinements/1-edge/edge_01_refined/01.txt

@@ -1,10 +0,0 @@
-TET no. 0:
-0.5, 0.5, 0.0
-0.0, 0.0, 1.0
-0.0, 0.0, 0.0
-0.0, 1.0, 0.0
-TET no. 1:
-0.5, 0.5, 0.0
-0.0, 0.0, 0.0
-0.0, 0.0, 1.0
-1.0, 0.0, 0.0

doc/tetrahedron_refinements/1-edge/edge_01_refined/01.vtk

@@ -1,25 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 5 DOUBLE
-0.5 0.5 0.0
-0.0 0.0 1.0
-0.0 0.0 0.0
-0.0 1.0 0.0
-1.0 0.0 0.0
-
-CELLS 2 10
-4	0  1  2  3 
-4	0  2  1  4 
-
-CELL_TYPES 2
-10
-10
-
-CELL_DATA 2
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1

doc/tetrahedron_refinements/1-edge/edge_12_refined/12.txt

@@ -1,10 +0,0 @@
-TET no. 0:
-0.0, 0.5, 0.5
-0.0, 0.0, 0.0
-1.0, 0.0, 0.0
-0.0, 1.0, 0.0
-TET no. 1:
-0.0, 0.5, 0.5
-1.0, 0.0, 0.0
-0.0, 0.0, 0.0
-0.0, 0.0, 1.0

doc/tetrahedron_refinements/1-edge/edge_12_refined/12.vtk

@@ -1,25 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 5 DOUBLE
-0.0 0.5 0.5
-0.0 0.0 0.0
-1.0 0.0 0.0
-0.0 1.0 0.0
-0.0 0.0 1.0
-
-CELLS 2 10
-4	0  1  2  3 
-4	0  2  1  4 
-
-CELL_TYPES 2
-10
-10
-
-CELL_DATA 2
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1

doc/tetrahedron_refinements/1-edge/edge_20_refined/20.txt

@@ -1,10 +0,0 @@
-TET no. 0:
-0.5, 0.0, 0.5
-0.0, 0.0, 0.0
-0.0, 1.0, 0.0
-0.0, 0.0, 1.0
-TET no. 1:
-0.5, 0.0, 0.5
-0.0, 1.0, 0.0
-0.0, 0.0, 0.0
-1.0, 0.0, 0.0

doc/tetrahedron_refinements/1-edge/edge_20_refined/20.vtk

@@ -1,25 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 5 DOUBLE
-0.5 0.0 0.5
-0.0 0.0 0.0
-0.0 1.0 0.0
-0.0 0.0 1.0
-1.0 0.0 0.0
-
-CELLS 2 10
-4	0  1  2  3 
-4	0  2  1  4 
-
-CELL_TYPES 2
-10
-10
-
-CELL_DATA 2
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1

doc/tetrahedron_refinements/1-edge/edge_23_refined/23.txt

@@ -1,10 +0,0 @@
-TET no. 0:
-0.0, 0.0, 0.5
-1.0, 0.0, 0.0
-0.0, 1.0, 0.0
-0.0, 0.0, 0.0
-TET no. 1:
-0.0, 0.0, 0.5
-0.0, 1.0, 0.0
-1.0, 0.0, 0.0
-0.0, 0.0, 1.0

doc/tetrahedron_refinements/1-edge/edge_23_refined/23.vtk

@@ -1,25 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 5 DOUBLE
-0.0 0.0 0.5
-1.0 0.0 0.0
-0.0 1.0 0.0
-0.0 0.0 0.0
-0.0 0.0 1.0
-
-CELLS 2 10
-4	0  1  2  3 
-4	0  2  1  4 
-
-CELL_TYPES 2
-10
-10
-
-CELL_DATA 2
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1

doc/tetrahedron_refinements/1-edge/edge_30_refined/30.txt

@@ -1,10 +0,0 @@
-TET no. 0:
-0.5, 0.0, 0.0
-0.0, 1.0, 0.0
-0.0, 0.0, 1.0
-0.0, 0.0, 0.0
-TET no. 1:
-0.5, 0.0, 0.0
-0.0, 0.0, 1.0
-0.0, 1.0, 0.0
-1.0, 0.0, 0.0

doc/tetrahedron_refinements/1-edge/edge_30_refined/30.vtk

@@ -1,25 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 5 DOUBLE
-0.5 0.0 0.0
-0.0 1.0 0.0
-0.0 0.0 1.0
-0.0 0.0 0.0
-1.0 0.0 0.0
-
-CELLS 2 10
-4	0  1  2  3 
-4	0  2  1  4 
-
-CELL_TYPES 2
-10
-10
-
-CELL_DATA 2
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1

doc/tetrahedron_refinements/1-edge/edge_31_refined/31.txt

@@ -1,10 +0,0 @@
-TET no. 0:
-0.0, 0.5, 0.0
-0.0, 0.0, 1.0
-1.0, 0.0, 0.0
-0.0, 0.0, 0.0
-TET no. 1:
-0.0, 0.5, 0.0
-1.0, 0.0, 0.0
-0.0, 0.0, 1.0
-0.0, 1.0, 0.0

doc/tetrahedron_refinements/1-edge/edge_31_refined/31.vtk

@@ -1,25 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 5 DOUBLE
-0.0 0.5 0.0
-0.0 0.0 1.0
-1.0 0.0 0.0
-0.0 0.0 0.0
-0.0 1.0 0.0
-
-CELLS 2 10
-4	0  1  2  3 
-4	0  2  1  4 
-
-CELL_TYPES 2
-10
-10
-
-CELL_DATA 2
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1

doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12.txt

@@ -1,15 +0,0 @@
-TET no. 0:
-0.5, 0.5, 0.0
-0.0, 1.0, 0.0
-0.0, 0.5, 0.5
-0.0, 0.0, 0.0
-TET no. 1:
-0.0, 0.5, 0.5
-1.0, 0.0, 0.0
-0.5, 0.5, 0.0
-0.0, 0.0, 0.0
-TET no. 2:
-1.0, 0.0, 0.0
-0.0, 0.5, 0.5
-0.0, 0.0, 1.0
-0.0, 0.0, 0.0

doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12.vtk

@@ -1,29 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 6 DOUBLE
-0.5 0.5 0.0
-0.0 1.0 0.0
-0.0 0.5 0.5
-0.0 0.0 0.0
-1.0 0.0 0.0
-0.0 0.0 1.0
-
-CELLS 3 15
-4	0  1  2  3 
-4	2  4  0  3 
-4	4  2  5  3 
-
-CELL_TYPES 3
-10
-10
-10
-
-CELL_DATA 3
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1
-2

doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.txt

@@ -1,15 +0,0 @@
-TET no. 0:
-0.5, 0.0, 0.5
-1.0, 0.0, 0.0
-0.5, 0.5, 0.0
-0.0, 0.0, 0.0
-TET no. 1:
-0.5, 0.5, 0.0
-0.0, 0.0, 1.0
-0.5, 0.0, 0.5
-0.0, 0.0, 0.0
-TET no. 2:
-0.0, 0.0, 1.0
-0.5, 0.5, 0.0
-0.0, 1.0, 0.0
-0.0, 0.0, 0.0

doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.vtk

@@ -1,29 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 6 DOUBLE
-0.5 0.0 0.5
-1.0 0.0 0.0
-0.5 0.5 0.0
-0.0 0.0 0.0
-0.0 0.0 1.0
-0.0 1.0 0.0
-
-CELLS 3 15
-4	0  1  2  3 
-4	2  4  0  3 
-4	4  2  5  3 
-
-CELL_TYPES 3
-10
-10
-10
-
-CELL_DATA 3
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1
-2

doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23.txt

@@ -1,20 +0,0 @@
-TET no. 0:
-1.0, 0.0, 0.0
-0.5, 0.5, 0.0
-0.0, 0.0, 0.5
-0.0, 0.0, 0.0
-TET no. 1:
-0.5, 0.5, 0.0
-0.0, 1.0, 0.0
-0.0, 0.0, 0.5
-0.0, 0.0, 0.0
-TET no. 2:
-0.5, 0.5, 0.0
-0.0, 0.0, 0.5
-0.0, 1.0, 0.0
-0.0, 0.0, 1.0
-TET no. 3:
-1.0, 0.0, 0.0
-0.0, 0.0, 0.5
-0.5, 0.5, 0.0
-0.0, 0.0, 1.0

doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23.vtk

@@ -1,32 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 6 DOUBLE
-1.0 0.0 0.0
-0.5 0.5 0.0
-0.0 0.0 0.5
-0.0 0.0 0.0
-0.0 1.0 0.0
-0.0 0.0 1.0
-
-CELLS 4 20
-4	0  1  2  3 
-4	1  4  2  3 
-4	1  2  4  5 
-4	0  2  1  5 
-
-CELL_TYPES 4
-10
-10
-10
-10
-
-CELL_DATA 4
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1
-2
-3

doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30.txt

@@ -1,15 +0,0 @@
-TET no. 0:
-0.5, 0.5, 0.0
-1.0, 0.0, 0.0
-0.5, 0.0, 0.0
-0.0, 0.0, 1.0
-TET no. 1:
-0.5, 0.0, 0.0
-0.0, 1.0, 0.0
-0.5, 0.5, 0.0
-0.0, 0.0, 1.0
-TET no. 2:
-0.0, 1.0, 0.0
-0.5, 0.0, 0.0
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-0.0, 0.0, 1.0

doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30.vtk

@@ -1,29 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 6 DOUBLE
-0.5 0.5 0.0
-1.0 0.0 0.0
-0.5 0.0 0.0
-0.0 0.0 1.0
-0.0 1.0 0.0
-0.0 0.0 0.0
-
-CELLS 3 15
-4	0  1  2  3 
-4	2  4  0  3 
-4	4  2  5  3 
-
-CELL_TYPES 3
-10
-10
-10
-
-CELL_DATA 3
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1
-2

doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31.txt

@@ -1,15 +0,0 @@
-TET no. 0:
-0.0, 0.5, 0.0
-0.0, 1.0, 0.0
-0.5, 0.5, 0.0
-0.0, 0.0, 1.0
-TET no. 1:
-0.5, 0.5, 0.0
-0.0, 0.0, 0.0
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-0.0, 0.0, 1.0
-TET no. 2:
-0.0, 0.0, 0.0
-0.5, 0.5, 0.0
-1.0, 0.0, 0.0
-0.0, 0.0, 1.0

doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31.vtk

@@ -1,29 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 6 DOUBLE
-0.0 0.5 0.0
-0.0 1.0 0.0
-0.5 0.5 0.0
-0.0 0.0 1.0
-0.0 0.0 0.0
-1.0 0.0 0.0
-
-CELLS 3 15
-4	0  1  2  3 
-4	2  4  0  3 
-4	4  2  5  3 
-
-CELL_TYPES 3
-10
-10
-10
-
-CELL_DATA 3
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1
-2

doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.txt

@@ -1,15 +0,0 @@
-TET no. 0:
-0.0, 0.5, 0.5
-0.0, 0.0, 1.0
-0.5, 0.0, 0.5
-0.0, 0.0, 0.0
-TET no. 1:
-0.5, 0.0, 0.5
-0.0, 1.0, 0.0
-0.0, 0.5, 0.5
-0.0, 0.0, 0.0
-TET no. 2:
-0.0, 1.0, 0.0
-0.5, 0.0, 0.5
-1.0, 0.0, 0.0
-0.0, 0.0, 0.0

doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.vtk

@@ -1,29 +0,0 @@
-# vtk DataFile Version 2.0
-VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
-ASCII
-DATASET UNSTRUCTURED_GRID
-
-POINTS 6 DOUBLE
-0.0 0.5 0.5
-0.0 0.0 1.0
-0.5 0.0 0.5
-0.0 0.0 0.0
-0.0 1.0 0.0
-1.0 0.0 0.0
-
-CELLS 3 15
-4	0  1  2  3 
-4	2  4  0  3 
-4	4  2  5  3 
-
-CELL_TYPES 3
-10
-10
-10
-
-CELL_DATA 3
-SCALARS cell_attribute_data float 1
-LOOKUP_TABLE default
-0
-1
-2