bug fixes in Fortran API for 1.6.2

* H5MultiBlock: added halo exchange routine: still needs debugging

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-src/include/H5_attachments.h -text
-src/include/H5_attribs.h -text
-src/include/H5hut.h -text
-src/include/Makefile.am -text
-src/include/grephdr -text
-src/include/h5core/Makefile.am -text
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-src/include/h5core/h5_core.h -text
-src/include/h5core/h5_errno.h -text
-src/include/h5core/h5_errorhandling.h -text
-src/include/h5core/h5_hdf5.h -text
-src/include/h5core/h5_maps.h -text
-src/include/h5core/h5_openclose.h -text
-src/include/h5core/h5_readwrite.h -text
-src/include/h5core/h5_syscall.h -text
-src/include/h5core/h5_types.h -text
-src/include/h5core/h5b_attribs.h -text
-src/include/h5core/h5b_model.h -text
-src/include/h5core/h5b_readwrite.h -text
-src/include/h5core/h5t_adjacencies.h -text
-src/include/h5core/h5t_core.h -text
-src/include/h5core/h5t_inquiry.h -text
-src/include/h5core/h5t_map.h -text
-src/include/h5core/h5t_model.h -text
-src/include/h5core/h5t_readwrite.h -text
-src/include/h5core/h5t_ref_elements.h -text
-src/include/h5core/h5t_retrieve.h -text
-src/include/h5core/h5t_storemesh.h -text
-src/include/h5core/h5t_tags.h -text
-src/include/h5core/h5u_model.h -text
-src/include/h5core/h5u_readwrite.h -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
-tools/vtk2h5grid/Makefile.am -text
-tools/vtk2h5grid/vtk2h5grid.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
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-visit_plugins/operators/BinnerFilter/avtBinnerFilter.C -text
-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
-visit_plugins/operators/RandomSample/H5PartRandomSampleAttributes.h -text
-visit_plugins/operators/RandomSample/H5PartRandomSampleAttributes.java -text
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-visit_plugins/operators/RandomSample/H5PartRandomSampleScriptingPluginInfo.C -text
-visit_plugins/operators/RandomSample/H5PartRandomSampleViewerPluginInfo.C -text
-visit_plugins/operators/RandomSample/Makefile -text
-visit_plugins/operators/RandomSample/PyH5PartRandomSampleAttributes.C -text
-visit_plugins/operators/RandomSample/PyH5PartRandomSampleAttributes.h -text
-visit_plugins/operators/RandomSample/QvisH5PartRandomSampleWindow.C -text
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-visit_plugins/operators/RandomSample/RandomSample.xml -text
-visit_plugins/operators/RandomSample/avtH5PartRandomSampleFilter.C -text
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.gitignore

@@ -1,102 +0,0 @@
-*.o
-*.lo
-*.la
-*~
-*.h5
-*.vtk
-.deps
-.libs
-/H5hut
-/INSTALL
-/Makefile
-/Makefile.in
-/aclocal.m4
-/autom4te.cache
-/build
-/compile
-/config.guess
-/config.h
-/config.h.in
-/config.log
-/config.status
-/config.sub
-/configure
-/depcomp
-doc/Makefile
-doc/Makefile.in
-examples/H5Block/H5BlockParTestScalarField
-examples/H5Block/H5BlockTestAttributes
-examples/H5Block/Makefile
-examples/H5Block/Makefile.in
-examples/H5Fed/.deps
-examples/H5Fed/Makefile
-examples/H5Fed/Makefile.in
-examples/H5Fed/large_tet.h5
-examples/H5Fed/simple_tet.h5
-examples/H5Fed/simple_triangle.h5
-examples/H5Fed/small_tet.h5
-examples/H5Fed/tetmesh_adjacencies
-examples/H5Fed/tetmesh_read
-examples/H5Fed/tetmesh_read_tags
-examples/H5Fed/tetmesh_write
-examples/H5Fed/tetmesh_write2
-examples/H5Fed/tetmesh_write_tags
-examples/H5Fed/trimesh_adjacencies
-examples/H5Fed/trimesh_read
-examples/H5Fed/trimesh_write
-examples/H5Fed/trimesh_write_dunetest
-examples/H5Part/Bench
-examples/H5Part/H5PartAndreasTest
-examples/H5Part/H5PartTestP
-examples/H5Part/H5test
-examples/H5Part/Makefile
-examples/H5Part/Makefile.in
-/install-sh
-/libtool
-/ltmain.sh
-/m4
-/missing
-src/.deps
-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/Fortran/TestUnderscore
-src/Fortran/Underscore.h
-src/Makefile
-src/Makefile.in
-src/h5core/.deps
-src/h5core/Makefile
-src/h5core/Makefile.in
-src/h5core/libH5hut.a
-src/include/H5hutF.h
-src/include/Makefile
-src/include/Makefile.in
-src/include/h5core/Makefile
-src/include/h5core/Makefile.in
-src/lib
-/stamp-h1
-/svn-prop.tmp
-/test-driver
-test/.deps
-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/h5PartDcToVtk
-tools/h5PartSurfaceToVtk
-tools/h5hutcc
-tools/vtk2h5grid/.deps
-tools/vtk2h5grid/Makefile
-tools/vtk2h5grid/Makefile.in
-tools/vtk2h5grid/cgun_full.h5
-tools/vtk2h5grid/cgun_full.vtk
-tools/vtk2h5grid/vtk2h5grid

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

@@ -1,11 +1,13 @@
-ACLOCAL_AMFLAGS = -I m4
+# Trial by Antino Kim
-EXTRA_DIST = autogen.sh
+# Top level Makefile.am
 
 SUBDIRS = \
+	doc \
 	src \
 	test \
-	tools \
+	tools
-	doc 
+
+EXTRA_DIST = configure-crayxt
 
 MAINTAINERCLEANFILES = \
 	config.h \

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

@@ -1,77 +1,3 @@
-#### H5PART 1.99.10 ###########################################################
-
-Bugfixes in the malloc wrappers
-
-Converter from vtk to H5hut added.
-
-Bugfixes in the autotools files.
-
-#### H5PART 1.99.9 ############################################################
-
-Bugfix in option parsing in tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk
-
-tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk removed from list of tools
-to be compiled. These tools should be moved to another repository anyway.
-
-#### H5PART 1.99.8 ############################################################
-
-Bugfixes
-
-#### H5PART 1.99.7 ############################################################
-
-Linking problem on Linux fixed
-
-#### H5PART 1.99.6 ############################################################
-
-
-#### H5PART 1.99.5 ############################################################
-#### H5PART 1.99.4 ############################################################
-#### H5PART 1.99.3 ############################################################
-#### H5PART 1.99.2 ############################################################
-#### H5PART 1.99.1 ############################################################
-#### H5PART 1.99 ############################################################
-
-Renamed type: 
-    H5PartFile -> h5_file_t
-    h5part_int64_t -> h5_int64_t
-
-Renamed functions:
-    
-
-#### H5PART 1.6.6 ############################################################
-
-Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
-interface.
-
-Added missing type normalization for int32 type.
-
-Rewrite of h5pAttrib tool.
-
-#### 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

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. 
+

autogen.sh

@@ -1,48 +1,46 @@
 #!/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 [ "$LIBTOOLIZE" = "" ]; then
-        echo "libtoolize not found" 1>&2
-        exit 1
-fi
-
 echo "+ making misc files ..."
 touch NEWS README AUTHORS ChangeLog
 echo
-$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
+echo
-	echo "libtoolize failed"
-	exit 1
-}
 echo
 echo "+ running aclocal ..."
 aclocal $ACLOCAL_FLAGS || {
-	echo "aclocal failed - check that all needed development files are present on system"
+  echo
-	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 "autoheader failed"
+  echo
-	exit 1
+  echo "autoheader failed"
+  exit 1
 }
 echo
+echo
+echo
 echo "+ running autoconf ... "
 autoconf || {
-	echo "autoconf failed"
+  echo
-	exit 1
+  echo "autoconf failed"
+  exit 1
 }
 echo
+echo
+echo
 echo "+ running automake ... "
-automake $AUTOMAKE_FLAGS || {
+automake -a -c --foreign || {
-	echo "automake failed"
+  echo
-	exit 1
+  echo "automake failed"
+  exit 1
 }
+echo
+echo
+echo
 

configure-crayxt

@@ -0,0 +1,18 @@
+#!/bin/sh
+
+ ./configure \
+        $@ \
+        --enable-parallel \
+        --enable-fortran \
+        --enable-tools \
+        CC=cc CXX=CC FC=pgf90 \
+        MPICC=cc MPICXX=CC MPIFC=ftn
+sed -e 's/pgf90/ftn/g' <Makefile > newMakefile
+mv newMakefile Makefile
+sed -e 's/pgf90/ftn/g' <src/Makefile > newMakefile
+mv newMakefile src/Makefile
+sed -e 's/pgf90/ftn/g' <test/Makefile > newMakefile
+mv newMakefile test/Makefile
+sed -e 's/pgf90/ftn/g' <tools/Makefile > newMakefile
+mv newMakefile tools/Makefile
+

configure.ac

@@ -1,87 +1,88 @@
-AC_INIT([H5hut], [1.99.14], [h5part@lists.psi.ch], H5hut)
+# Every configure script must call AC_INIT before doing anything else.
-AC_PREREQ(2.60)
+# AC_INIT (package, version, [bug-report], [tarname])
-AC_CONFIG_HEADERS(config.h)
+AC_INIT([H5Part], [1.6.2], [h5part@lists.psi.ch], H5Part)
-AC_CONFIG_MACRO_DIR([m4])
-AM_INIT_AUTOMAKE
 
-ENABLE_DEBUG='no'
+
-ENABLE_C='yes'
+# Ensure that a recent enough version of Autoconf is being used. 
-ENABLE_FORTRAN='no'
+# If the version of Autoconf being used to create configure is earlier than version, 
-ENABLE_PARALLEL='no'
+# 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)
 
 ###############################################################################
-# --enable-xxx and --with-xxx Arguments
+################# --enable-xxx and --with-xxx Argument ########################
-AC_ARG_ENABLE(
+###############################################################################
-	[debug],
-	[AS_HELP_STRING([--enable-debug], [Compile with debug flags [default=no]])],
-	[ENABLE_DEBUG=$enableval])
-AM_CONDITIONAL([ENABLE_DEBUG], [test "$ENABLE_DEBUG" = "yes"])
 
 AC_ARG_ENABLE(
-	[c],
+	[debug],
-	[AS_HELP_STRING([--enable-c],
+	[AC_HELP_STRING([--enable-debug],
-	[Compile the C interface [default=yes]])],
+	[Compile with debug support [default=no]])],
-	[ENABLE_C=$enableval])
+	[USE_DEBUG=$enableval])
-AM_CONDITIONAL([ENABLE_C], [test "$ENABLE_C" = "yes"])
+
+AC_ARG_ENABLE(
+	[shared],
+	[AC_HELP_STRING([--enable-shared],
+	[Compile with shared library support [default=no]])],
+	[USE_SHARED=$enableval])
+
+AC_ARG_ENABLE(
+	[64],
+	[AC_HELP_STRING([--enable-64],
+	[Compile using 64-bit flags [default=no]])],
+	[USE_64=$enableval])
 
 AC_ARG_ENABLE(
 	[fortran],
-	[AS_HELP_STRING([--enable-fortran],
+        [AC_HELP_STRING([--enable-fortran],
 	[Compile the Fortran interface [default=no]])],
-	[ENABLE_FORTRAN=$enableval])
+        [USE_FORTRAN=$enableval])
-AM_CONDITIONAL([ENABLE_FORTRAN], [test "$ENABLE_FORTRAN" = "yes"])
 
 AC_ARG_ENABLE(
 	[parallel],
-	[AS_HELP_STRING([--enable-parallel],
+        [AC_HELP_STRING([--enable-parallel],
 	[Compile the MPI/IO interface [default=no]])],
-	[ENABLE_PARALLEL=$enableval])
+        [USE_PARALLEL=$enableval])
-AM_CONDITIONAL([ENABLE_PARALLEL], [test "$ENABLE_PARALLEL" = "yes"])
 
 AC_ARG_ENABLE(
-	[large-indices],
+	[tools],
-	[AC_HELP_STRING([--enable-large-indices],
+        [AC_HELP_STRING([--enable-tools],
-	[Compile with 64bit local IDs and indices [default=no]])],
+	[Compile h5part tools [default=no]])],
-	[USE_LARGE_INDICES=$enableval])
+        [USE_TOOLS=$enableval])
-
-AC_ARG_ENABLE(
-        [experimental],
-        [AS_HELP_STRING([--enable-experimental],
-        [Compile experimental code [default=no]])],
-        [ENABLE_EXPERIMENTAL=$enableval])
-AM_CONDITIONAL([ENABLE_EXPERIMENTAL], [test "$ENABLE_EXPERIMENTAL" = "yes"])
-
-AC_ARG_ENABLE(
-	[vtkconverter],
-	[AS_HELP_STRING([--enable-vtkconverter],
-	[Compile the vtk to H5hut converter for grids [default=no]])],
-	[ENABLE_VTKCONVERTER=$enableval])
-AM_CONDITIONAL([ENABLE_VTKCONVERTER], [test "$ENABLE_VTKCONVERTER" = "yes"])
 
 AC_ARG_WITH(
-	[hdf5],
+	[mpipath],
-	[AS_HELP_STRING([--with-hdf5],
+	[AC_HELP_STRING([--with-mpipath],
-	[path to HDF5 installation [default=""]])],
-	[HDF5_PREFIX=$withval], [])
-
-AC_ARG_WITH(
-	[mpi],
-	[AS_HELP_STRING([--with-mpi],
 	[path to MPI installation [default=""]])],
-	[PATH=$MPI_PREFIX/bin:$PATH])
+        [MPIPATH=$withval], [MPIPATH=""])
 
 AC_ARG_WITH(
-	[lustre],
+	[hdf5path],
-	[AS_HELP_STRING([--with-lustre],
+	[AC_HELP_STRING([--with-hdf5path],
-	[path to lustre user API [default=""]])],
+	[path to HDF5 installation [default=""]])],
-	[LUSTREPATH=$withval], [LUSTREPATH=""])
+	[HDF5PATH=$withval], [HDF5PATH=""])
 
-AC_ARG_WITH(
+###############################################################################
-	[parmetis],
+################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-	[AC_HELP_STRING([--with-parmetis],
+###############################################################################
-	[path to ParMETIS API [default=""]])],
-	[PARMETISPATH=$withval], [PARMETISPATH=""])
 
+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_LDFLAGS=$LDFLAGS
 
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
@@ -95,92 +96,117 @@ AC_ARG_WITH(
 #   @enddesc
 #@@*/
 
-PATH_Search() {
+PATH_Search()
-	eval  $1=""
+{
-	if test $# -lt 4 ; then
+  eval  $1=""
-		h5part_basedir=""
+  if test $# -lt 4 ; then
-	else
+    h5part_basedir=""
-		h5part_basedir="$4/"
+  else
-	fi
+    h5part_basedir="$4/"
-	for h5part_place in $2; do
+  fi
-		AC_MSG_CHECKING([looking in $h5part_place ... ])
+  for h5part_place in $2
-		if test -r "$h5part_basedir$h5part_place/$3" ; then
+    do
-			AC_MSG_RESULT([found])
+      echo -n "looking in $h5part_place ... $ac_c" #1>&6
-			eval $1="$h5part_place"
+      if test -r "$h5part_basedir$h5part_place/$3" ; then
-			break
+        echo "$ac_t"" found" #1>&6
-		fi
+        eval $1="$h5part_place"
-		AC_MSG_RESULT([no])
+        break
-	done
+      fi
-	return
+      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
 }
 
+
+
 ###############################################################################
-# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING
+############# 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
 
-# debug enabled?
+
-AC_MSG_CHECKING([if debug is enabled])
+uname=`uname -s`
-if test "X$ENABLE_DEBUG" = "Xyes"; then
+if test $uname = "AIX"; then
-    AC_MSG_RESULT([yes])
+  AC_MSG_CHECKING([if system is AIX])
-    CFLAGS="$CFLAGS -g -Wall"
+  AC_MSG_RESULT([OK])
-    CXXFLAGS="$CFLAGS -g -Wall"
+
-    FFLAGS="$FFLAGS -g"
+  # If on AIX, define _ALL_SOURCE. Allows the use of some BSD functions. 
-else
+  # Should be called before any macros that run the C compiler.
-    AC_MSG_RESULT([no])
+  AC_AIX
 fi
 
-# Determine a C/C++ compiler to use. 
+
-if test "x$ENABLE_PARALLEL" = "xyes"; then
+# DAVINCI SPECIFIC!!!
-   	CCOMPILERS="mpicc"
+if test `uname -n` = "davinci"; then
-	CXXCOMPILERS="mpic++"
+   echo "DAVINCI SPECIFIC TESTING FOR STDC++ LIBRARY!"
-else
+   PATH_Search STDCXX_CHECK '/usr/lib64 /usr/lib' libstdc++.a
-	CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
+
-	CXXCOMPILERS="pgcc pathcc icc g++ cc_r c++"
+   # if STDCXX_CHECK is set...
+   if test "$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
 
-AC_PROG_CC($CCOMPILERS)
-CC=`which $CC`
-AC_PROG_CXX($CXXCOMPILERS)
-CXX=`which $CXX`
 
-AC_PROG_CC_C99
+# Determine a C compiler to use. 
-if test "x$ac_cv_prog_cc_c99" = "xno"; then
+# If CC is not already set in the environment, check for gcc and cc, then
-	AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
+# for other C compilers. 
-	exit 1
+# Set output variable CC to the name of the compiler found.
+AC_PROG_CC(pgcc pathcc icc cc_r gcc cc)
+
+# AC_PROG_CC doesn't pick up cc_r in Bassi. The following AC_PATH_PROGS
+# is the fix.
+AC_PATH_PROGS([BAS_CC], [cc_r], [], [$PATH])
+
+# if BAS_CC not empty
+if test -n "$BAS_CC"; then
+  echo "CC setting for Bassi ..."
+  CC=$BAS_CC
+  echo "CC =  $CC ..."
 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(pgCC 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. 
+# 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
+
-LT_INIT([disable-shared])
+# AM_INIT_AUTOMAKE is required to use autoconf with automake
-AC_PROG_LIBTOOL
+AM_INIT_AUTOMAKE()
+
+
+AC_PROG_RANLIB
 
 # 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
@@ -192,198 +218,431 @@ AC_DEFINE_UNQUOTED(MY_GNUNAME, "${host_cpu}-${host_vendor}-${host_os}", "")
 AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
 
 
+
+###############################################################################
+######################## CONFIGURE LINE OPTIONS ###############################
 ###############################################################################
-# PROCESS ARGUMENTS
 
-# C enabled?
+AC_MSG_CHECKING([if debug is enabled])
-AC_MSG_CHECKING([if C interface enabled])
+
-if test "X$ENABLE_C" = "Xyes"; then
+if test "X$USE_DEBUG" = "Xyes"; then
-	AC_MSG_RESULT([yes])
+    AC_MSG_RESULT([yes])
+    CFLAGS="$CFLAGS -g"
 else
-        AC_MSG_RESULT([no])
+    AC_MSG_RESULT([no])
 fi
 
-# fortran enabled?
+# shared library
+AC_MSG_CHECKING([if shared libraries are enabled])
+
+if test "X$USE_SHARED" = "Xyes"; then
+    AC_MSG_RESULT([yes])
+    CFLAGS="$CFLAGS -fPIC"
+    FFLAGS="$FFLAGS -fPIC"
+else
+    AC_MSG_RESULT([no])
+fi
+
+###################### 64-bit compilation enabled #############################
+AC_MSG_CHECKING([if 64-bit compilation is enabled])
+
+
+# If --enable-64 is set in the configure line
+if test "X$USE_64:/f90
+" = "Xyes"; then
+    AC_MSG_RESULT([yes])
+    if test $uname = "AIX"; then
+        CFLAGS="$CFLAGS -q64"
+        FFLAGS="$FFLAGS -q64"
+    fi
+
+    if test $uname = "IRIX64"; then
+        CFLAGS="$CFLAGS -64"
+        FFLAGS="$FFLAGS -64 -fPIC -fno-second-underscore"
+    fi
+else
+    AC_MSG_RESULT([no])
+fi
+
+
+############################ fortran enabled ##################################
 AC_MSG_CHECKING([if fortran interface enabled])
-if test "X$ENABLE_FORTRAN" = "Xyes"; then
+if test "X$USE_FORTRAN" = "Xyes"; then
-	AC_MSG_RESULT([yes])
+    AC_MSG_RESULT([yes])
 
-	if test "X$ENABLE_PARALLEL" = "Xyes"; then
+    AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
-		AC_PROG_FC(mpif90 mpif77)
+    if test -z "$FC" ; then
-	else
+        AC_MSG_ERROR([Cannot find a fortran compiler!!!])
-		AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
+        exit 1
-	fi
+    fi
-        FC=`which $FC`
-	if test -z "$FC" ; then
-		AC_MSG_ERROR([Cannot find a Fortran compiler!])
-		exit 1
-	fi
 
-	if test $FC = "g90"; then
+    if test ! $uname = "AIX"; then
-		FFLAGS="${FFLAGS} -fno-second-underscore"
+        FFLAGS="${FFLAGS} -fPIC"
-	fi
+    fi
 
-	if test $FC = "g95"; then
+    if test $FC = "g90"; then
-		FFLAGS="${FFLAGS} -fno-second-underscore"
+	FFLAGS="${FFLAGS} -fno-second-underscore"
-	fi
+    fi
 
-	AC_MSG_CHECKING([symbol convention in object files])
+    if test $FC = "g95"; then
-	`cd src/Fortran && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
+	FFLAGS="${FFLAGS} -fno-second-underscore"
-	`cd src/Fortran && ${FC} ${FFLAGS} -c TestUnderscore.f`
+    fi
-	`cd src/Fortran && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
-	`cd src/Fortran && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
 
-	if test -f src/Fortran/TestUnderscore ; then
+    if test $FC = "gfortran"; then
-		`cd src/Fortran && ./TestUnderscore > Underscore.h`
+        FFLAGS="${FFLAGS} -DHAVE_GFORTRAN"
-		AC_MSG_RESULT([ok])
+    fi
-	else
-		AC_MSG_RESULT([nok])
-		AC_MSG_ERROR([Cannot determine the symbol convention for Fortran object files!])
-		exit 1
-	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 -lc`
+
+    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 build fortran executables!!!])
+        exit 1
+    fi
 else
-	AC_MSG_RESULT([no])
+    AC_MSG_RESULT([no])
 fi
 
-######################## large indices enabled ###########################
-AC_MSG_CHECKING([if large indices are enabled])
-if test "X$USE_LARGE_INDICES" = "Xyes"; then
-	AC_MSG_RESULT([yes])
-	CFLAGS="${CFLAGS} -DUSE_LARGE_INDICES"
-else
-	AC_MSG_RESULT([no])
-fi
 
 ######################## parallel interface enabled ###########################
 AC_MSG_CHECKING([if parallel interface enabled])
-if test "X$ENABLE_PARALLEL" = "Xyes"; then
+if test "X$USE_PARALLEL" = "Xyes"; then
-	AC_MSG_RESULT([yes])
+    AC_MSG_RESULT([yes])
-	CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
 
-        if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
+    CFLAGS="${CFLAGS} -DPARALLEL_IO -DH5_HAVE_PARALLEL -DMPICH_IGNORE_CXX_SEEK"
-        	AC_MSG_CHECKING([for ParMETIS])
-                if test "X$PARMETISPATH" != "X"; then
-                        CPPFLAGS="$CPPFLAGS -I$PARMETISPATH/include"
-	                LDFLAGS="$LDFLAGS -L$PARMETISPATH/lib"
-	        fi
 
-                LIBS="$LIBS -lparmetis -lmetis"
+    AC_MSG_CHECKING([if we can compile MPI code without setting flags])
-	        AC_TRY_LINK([#include <parmetis.h>], [
+    AC_TRY_LINK([#include "mpi.h"], [
-	                ParMETIS_V3_PartGeom (NULL, NULL, NULL, NULL, NULL);],
+        MPI_Comm comm;
-		        [AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
+	int n;
+	MPI_Comm_size( comm, &n ); ], 
+	[echo 'yes'; r='yes'], [echo "no"; r='no'] )
 
-	        if test "X$r" = "Xno"; then
+    if test "X$r" = "Xno"; then
-		        AC_MSG_ERROR([ParMETIS])
+        AC_PATH_PROGS([MPICC], [mpicc mpcc_r], [], [$PATH])
-		        exit 1
+        AC_PATH_PROGS([MPICXX], [mpicxx mpcc_r], [], [$PATH])
-	        fi
+        if test -z "$MPICC" -o -z "$MPICXX"; then 
-        fi
+            AC_MSG_CHECKING([for MPI root ])
-else  # --enable-parallel=no
+            AC_MSG_RESULT([])
-	AC_MSG_RESULT([no])
+            if test -n "$MPIROOT"; then
-fi
+                P=${MPIROOT}
+            elif test -n "$MPIHOME"; then
+                P=${MPIHOME}
+            elif test -n "$MPIPATH"; then
+                P=${MPIPATH}
+            else
+                P=''
+                P="$P /usr"
+                P="$P /usr/local"
+                P="$P /usr/local/mpi"
+                P="$P /usr/local/packages/mpi"
+                P="$P /usr/local/mpich2"
+                P="$P /usr/local/mpich"
+                P="$P /opt/xt-mpt/default/mpich2-64/P2"
+            fi
+            PATH_Search MPIROOT "$P" include/mpi.h
+            if test ! -n "$MPIROOT"; then
+		AC_MSG_ERROR([Cannot determine MPI root!!!])
+                exit 1
+            fi
 
-###############################################################################
+	    if test -e "${MPIROOT}/bin/mpicc"; then
-# LIBRARY PATHS
+	       MPICC=${MPIROOT}/bin/mpicc
-if test -z "${HDF5_PREFIX}"; then
+	    fi
-	# alternatives to HDF5_PREFIX
+
-	if test -n "${HDF5_DIR}"; then
+	    if test -e "${MPIROOT}/bin/mpicxx"; then
-		HDF5_PREFIX=${HDF5_DIR}
+	       MPICXX=${MPIROOT}/bin/mpicxx
+	    fi
 	fi
-fi
+
-if test -n "${HDF5_PREFIX}"; then
+        if test -z "$MPICC" -o -z "$MPICXX"; then 
-        CPPFLAGS="$CPPFLAGS -I$HDF5_PREFIX/include"
+            MPIINC="${MPIINC} -I${MPIROOT}/include"
-        LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
+            FFLAGS="${FFLAGS} -I${MPIROOT}/include"
-fi
+            AC_MSG_CHECKING([for name of MPI lib ])
-AC_CHECK_LIB([z], [compress2])
+            if test -e ${MPIROOT}/lib/libmpi.a; then
-AC_CHECK_LIB([hdf5], [H5open])
+                MPILIB="-L${MPIROOT}/lib -lmpi"
-AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes], 
+            elif test -e ${MPIROOT}/lib/libmpi.so; then
-        [AC_MSG_ERROR([Cannot compile and link a HDF5 program]); 
+                MPILIB="-L${MPIROOT}/lib -lmpi"
-        exit 1])
+            elif test -e ${MPIROOT}/lib/libmpich.a; then
+                MPILIB="-L${MPIROOT}/lib -lmpich"
+            elif test -e ${MPIROOT}/lib/libmpich.so; then
+                MPILIB="-L${MPIROOT}/lib -lmpich"
+            else
+                AC_MSG_RESULT([not found])
+                exit 1
+            fi
+            AC_MSG_RESULT([${MPILIB}])
+	fi
+
+        if test -n "$MPICC"; then
+	    CC=${MPICC}
+        fi 
+  
+        if test -n "$MPICXX"; then
+	    CXX=${MPICXX}
+        fi
+    fi
+
+    H5P_LIB_NAME="-lpH5Part"
+    MTARGET="libpH5Part.a"
+    TTARGET="test"
 
 
-AC_MSG_CHECKING([for lustre API ])
+    # parallel + fortran
+    if test "X$USE_FORTRAN" = "Xyes"; then
+        AC_PATH_PROGS([MPIFC], [mpxlf_r mpif90], [], [$PATH])
+
+        FFLAGS="${FFLAGS} -DPARALLEL_IO"
+
+	if test -z "${MPIFC}" ; then
+	    if test -e "${MPIROOT}/bin/mpif90"; then
+	       MPIFC=${MPIROOT}/bin/mpif90
+	    fi
+	fi
+ 
+        # if MPIFC empty
+        if test ! -n "$MPIFC"; then
+            AC_MSG_CHECKING([ No MPIFC detected. Setting MPIFC to FC.])
+            MPIFC=$FC
+            echo "MPIFC =  $MPIFC ..."
+        fi 
+
+	if test -n "$MPIFC"; then
+	    FC=${MPIFC}
+	fi
+ 
+        H5P_LIB_NAME="-lpH5PartF"
+        MTARGET="${MTARGET} libpH5PartF.a"
+        TTARGET="${TTARGET} testf"
+    fi
+
+else  # --enable-parallel=no
+    AC_MSG_RESULT([no])
+
+    H5P_LIB_NAME="-lH5Part"
+    MTARGET="libH5Part.a"
+    TTARGET="test"
+
+    if test "X$USE_FORTRAN" = "Xyes"; then
+        H5P_LIB_NAME="-lH5PartF"
+        MTARGET="${MTARGET} libH5PartF.a"
+        TTARGET="${TTARGET} testf"
+    fi
+fi
+
+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="${BUILD_TOOLS} H5PartBench H5BlockBench"
+    fi
+else
+    AC_MSG_RESULT([no])
+fi
+
+###############################################################################
+######################### PATH CHECKING & SETTING #############################
+###############################################################################
+
+AC_MSG_CHECKING([for HDF5 root ])
 AC_MSG_RESULT([])
-if test -n "${LUSTREPATH}"; then
+if test -n "${HDF5ROOT}"; then
-	P=${LUSTREPATH}
+    P=${HDF5ROOT}
-elif test -n "${LUSTREROOT}" ; then
+elif test -n "${HDF5HOME}" ; then
-	P=${LUSTREROOT}
+    P=${HDF5HOME}
-elif test -n "${LUSTREHOME}" ; then
+elif test -n "${HDF5PATH}" ; then
-	P=${LUSTREHOME}
+    P=${HDF5PATH}
-elif test -n "${LUSTRE_DIR}" ; then
-	P=${LUSTRE_DIR}
 else
-	P=''
+    P=''
-	P="$P /usr"
+    P="$P /usr"
-	P="$P /usr/local"
+    P="$P /usr/local"
-	P="$P /usr/local/lustre"
+    P="$P /usr/local/hdf5"
-	P="$P /opt/lustre"
+    P="$P /usr/local/packages/hdf5"
+    P="$P /apps/hdf5"
+
+    if test "X$USE_PARALLEL" = "Xyes"; then
+        P="$P /usr/local/phdf5"
+        P="$P /usr/local/hdf5/hdf5_par"
+        if test "X$USE_64" = "Xyes"; then
+            P="$P /usr/common/usg/hdf5/64/default/parallel"
+        else
+            P="$P /usr/common/usg/hdf5/32/default/parallel"
+        fi
+    else
+        P="$P /usr/local/hdf5/hdf5_serial"
+        if test "X$USE_64" = "Xyes"; then
+            P="$P /usr/common/usg/hdf5/64/default/serial"
+        else
+            P="$P /usr/common/usg/hdf5/32/default/serial"
+        fi
+    fi
 fi
-PATH_Search LUSTREROOT "$P" usr/include/lustre/liblustreapi.h
+PATH_Search HDF5ROOT "$P" include/hdf5.h
-if test -z "$LUSTREROOT"; then
+if test -z "$HDF5ROOT"; then
-	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
+    AC_MSG_ERROR([Cannot determine HDF5 root!!!])
-else
+    exit 1
-        CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
-        CPPFLAGS="$CPPFLAGS -I$LUSTREROOT/usr/include"
-        LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
-        LIBS="$LIBS -llustreapi"
 fi
 
-LIBS="$LIBS -lm"
+AC_MSG_CHECKING([if we need to link to libsz ])
-
+if test -n "$HDF5ROOT"; then
-###############################################################################
+    if test -f $HDF5ROOT/lib/libsz.a; then
-# TOOLS
-AC_MSG_CHECKING([if we have to compile the VTK to H5hut grid converter])
-if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
 	AC_MSG_RESULT([yes])
-        # :TODO: add test whether we can compile/link a prog with vtk
+        SZLIB="-L$HDF5ROOT/lib/ -lsz"
-else
+    else
 	AC_MSG_RESULT([no])
+        SZLIB=""
+    fi
+fi
+
+AC_MSG_CHECKING([for static zlib root ])
+echo
+PATH_Search ZLIBROOT '/apps/zlib' lib/libz.a
+if test -n "$ZLIBROOT"; then
+    LDFLAGS="$LDFLAGS -L$ZLIBROOT/lib"
+fi
+
+FCFLAGS=${FFLAGS}
+CXXFLAGS=${CFLAGS}
+
+
+###############################################################################
+#################### MISC SETTINGS - path, flags, etc #########################
+###############################################################################
+
+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 ${CFLAGS}"
+fi
+
+if test -n "$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_LDFLAGS"; then
+LDFLAGS=$SAVE_LDFLAGS
 fi
 
 ###############################################################################
-# EXPORTING VARIABLES & CREATING OUTPUT FILES
+############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
-AM_CPPFLAGS=$CPPFLAGS
+###############################################################################
-AM_LDFLAGS=$LDFLAGS
+# AC_SUBST (variable, [value])
-
+# Create an output variable from a shell variable. 
-AC_SUBST(HDF5_PREFIX)
+# 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(MPIINC)
+AC_SUBST(MPILIB)
+AC_SUBST(MPICC)
+AC_SUBST(MPICXX)
+AC_SUBST(MPIFC)
+AC_SUBST(MTARGET)
+AC_SUBST(TTARGET)
+AC_SUBST(SZLIB)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)
-AC_SUBST(AM_CPPFLAGS)
+AC_SUBST(STDCXX)
-AC_SUBST(AM_LDFLAGS)
+AC_SUBST(H5P_LIB_LOC)
+AC_SUBST(H5P_LIB_NAME)
+AC_SUBST(UNDERSCORE_H)
+AC_SUBST(BUILD_TOOLS)
+AC_SUBST(LDFLAGS)
 
+# Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'),
+# substituting the output variable values.
 AC_CONFIG_FILES([
-	Makefile
+Makefile
-	src/Makefile
+doc/Makefile
-	src/h5core/Makefile
+src/Makefile
-	src/include/Makefile
+test/Makefile
-	src/include/h5core/Makefile
+tools/Makefile
-        src/C/Makefile
-        src/Fortran/Makefile
-	test/Makefile
-        doc/Makefile
-	tools/Makefile
-	tools/h5hutcc
-        tools/vtk2h5grid/Makefile
 ])
 
 AC_OUTPUT
 
 ###############################################################################
-# PRINTING SUMMARY
+########################## PRINTING SUMMARY ###################################
-AC_MSG_RESULT([ ])
+###############################################################################
-AC_MSG_RESULT([Summary:])
+echo
-AC_MSG_RESULT([ ])
+echo
-AC_MSG_RESULT([Host OS:             $host_os])
+echo "Summary for `(hostname || uname -n) 2>/dev/null | sed 1q`:"
-AC_MSG_RESULT([Host CPU:            $host_cpu])
+echo
-AC_MSG_RESULT([Host vendor:         $host_vendor])
+echo "Host OS:             $host_os"
-AC_MSG_RESULT([CC =                 $CC])
+echo "Host CPU:            $host_cpu"
-AC_MSG_RESULT([CXX =                $CXX])
+echo "Host vendor:         $host_vendor"
-AC_MSG_RESULT([FC =                 $FC])
+echo "Build libraries:     $MTARGET"
-AC_MSG_RESULT([CFLAGS =             $CFLAGS])
+echo "Build test programs: $TTARGET"
-AC_MSG_RESULT([FFLAGS =             $FFLAGS])
+echo "Build tools:         $BUILD_TOOLS"
-AC_MSG_RESULT([AM_CPPFLAGS =        $AM_CPPFLAGS])
+echo "CC =                 $CC"
-AC_MSG_RESULT([AM_LDFLAGS =         $AM_LDFLAGS])
+echo "CXX =                $CXX"
-AC_MSG_RESULT([LIBS =               $LIBS])
+echo "FC =                 $FC"
-AC_MSG_RESULT([HDF5_PREFIX =        $HDF5_PREFIX])
+echo "MPICC =              $MPICC"
-AC_MSG_RESULT([LUSTREROOT =         $LUSTREROOT])
+echo "MPICXX =             $MPICXX"
-AC_MSG_RESULT([ ])
+echo "MPIFC =              $MPIFC"
+echo "CFLAGS =             $CFLAGS"
+echo "FFLAGS =             $FFLAGS"
+echo "MPILIB =             $MPILIB"
+echo "MPIINC =             $MPIINC"
+echo "MPIROOT =            $MPIROOT"
+echo "HDF5ROOT =           $HDF5ROOT"
+echo "LDFLAGS =            $LDFLAGS"
+echo

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
 #---------------------------------------------------------------------------
@@ -121,7 +127,7 @@ GENERATE_HTML          = YES
 HTML_OUTPUT            = .
 HTML_FILE_EXTENSION    = .html
 HTML_HEADER            = 
-HTML_FOOTER            =
+HTML_FOOTER            = doxyfooter 
 HTML_STYLESHEET        = 
 HTML_ALIGN_MEMBERS     = YES
 GENERATE_HTMLHELP      = NO
@@ -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
@@ -218,8 +224,8 @@ 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               = 
 DOTFILE_DIRS           = 

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

@@ -1,14 +1,2 @@
-EXTRA_DIST = 		\
+EXTRA_DIST = \
-	Doxyfile	\
+	Doxyfile doxyfooter
-        H5.dox		\
-	Makefile.in
-
-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
-0.0, 0.0, 0.0
-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
-0.0, 0.5, 0.0
-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