Merge branch 'int8' into 'master'

Add support for hdf5 int8 types (int8, uint8)

See merge request H5hut/src!7

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+src/include/H5Block_io.h -text
+src/include/H5Block_model.h -text
+src/include/H5Fed.h -text
+src/include/H5Fed_adjacency.h -text
+src/include/H5Fed_model.h -text
+src/include/H5Fed_retrieve.h -text
+src/include/H5Fed_store.h -text
+src/include/H5Fed_tags.h -text
+src/include/H5Part.h -text
+src/include/H5Part_io.h -text
+src/include/H5Part_model.h -text
+src/include/H5_attribs.h -text
+src/include/H5_model.h -text
+src/include/H5hut.h -text
+src/include/Makefile.am -text
+src/include/h5core/Makefile.am -text
+src/include/h5core/h5.h -text
+src/include/h5core/h5_attribs.h -text
+src/include/h5core/h5_debug.h -text
+src/include/h5core/h5_errorhandling.h -text
+src/include/h5core/h5_model.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_io.h -text
+src/include/h5core/h5b_model.h -text
+src/include/h5core/h5t_adjacencies.h -text
+src/include/h5core/h5t_map.h -text
+src/include/h5core/h5t_model.h -text
+src/include/h5core/h5t_octree.h -text
+src/include/h5core/h5t_retrieve.h -text
+src/include/h5core/h5t_store.h -text
+src/include/h5core/h5t_tags.h -text
+src/include/h5core/h5u_io.h -text
+src/include/h5core/h5u_model.h -text
 test/Makefile.am -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
-test/write.c -text
+tools/H5PartMerge/AUTHORS -text
-tools/H5BlockBench.c -text
+tools/H5PartMerge/COPYING -text
-tools/H5PartBench.c -text
+tools/H5PartMerge/ChangeLog -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
+visit_plugins/operators/BinnerFilter/QvisBinnerWindow.h -text
+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
+visit_plugins/operators/RandomSample/H5PartRandomSampleCommonPluginInfo.C -text
+visit_plugins/operators/RandomSample/H5PartRandomSampleEnginePluginInfo.C -text
+visit_plugins/operators/RandomSample/H5PartRandomSampleGUIPluginInfo.C -text
+visit_plugins/operators/RandomSample/H5PartRandomSamplePluginInfo.C -text
+visit_plugins/operators/RandomSample/H5PartRandomSamplePluginInfo.h -text
+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
+visit_plugins/operators/RandomSample/QvisH5PartRandomSampleWindow.h -text
+visit_plugins/operators/RandomSample/RandomSample.xml -text
+visit_plugins/operators/RandomSample/avtH5PartRandomSampleFilter.C -text
+visit_plugins/operators/RandomSample/avtH5PartRandomSampleFilter.h -text
+visit_plugins/operators/RandomSample/icon.xpm -text

.gitignore

@@ -0,0 +1,95 @@
+*.tar.gz
+*.[oa]
+*.la
+*.lo
+*.so
+*.dSYM
+*~
+*.h5
+.deps
+.dirstamp
+.libs
+CMakeFiles
+INSTALL
+Makefile
+Makefile.in
+aclocal.m4
+attach_field_attributes
+dump_field_attributes
+autom4te.cache/
+compile
+config.guess
+config.h
+config.h.in
+config.log
+config.status
+config.sub
+configure
+depcomp
+py-compile
+examples/H5/attach_file
+examples/H5/examples.h
+examples/H5/h5hut.mod
+examples/H5/openclose
+examples/H5/openclosef
+examples/H5/query
+examples/H5/queryf
+examples/H5/read_file_attribs
+examples/H5/read_file_attribsf
+examples/H5/read_step_attribs
+examples/H5/read_step_attribsf
+examples/H5/write_file_attribs
+examples/H5/write_file_attribsf
+examples/H5/write_step_attribs
+examples/H5/write_step_attribsf
+examples/H5Block/H5BlockExampleF
+examples/H5Block/fields
+examples/H5Block/read_write
+examples/H5Part/Bench
+examples/H5Part/H5test
+examples/H5Part/H5testF
+examples/H5Part/core_vfd
+examples/H5Part/examples.h
+examples/H5Part/h5hut.mod
+examples/H5Part/particles
+examples/H5Part/read_canonicalview
+examples/H5Part/read_setnparticles
+examples/H5Part/read_setview
+examples/H5Part/read_strided
+examples/H5Part/write_core_vfd
+examples/H5Part/write_setnparticles
+examples/H5Part/write_setnumparticles
+examples/H5Part/write_setview
+examples/H5Part/write_setviewf
+examples/H5Part/write_strided
+has_field
+install-sh
+libtool
+ltmain.sh
+m4/
+missing
+src/Fortran/TestUnderscore
+src/Fortran/Underscore.h
+src/include/H5hut.f
+src/include/H5hutF.h
+stamp-h1
+test/h5b_test
+test/h5u_test
+test/h5_attach_test
+tools/h5hutcc
+tetmesh_adjacencies
+tetmesh_read
+tetmesh_read_tags
+tetmesh_write
+tetmesh_write1
+examples/H5Fed/tetmesh_write2
+examples/H5Fed/trimesh_2gnuplot
+examples/H5Fed/trimesh_adjacencies
+examples/H5Fed/trimesh_read
+examples/H5Fed/trimesh_write
+examples/H5Fed/trimesh_write_dunetest
+tetmesh_write_tags
+write_field
+*.gch
+ReferencePages
+vtk2h5grid

AUTHORS

@@ -6,6 +6,5 @@ 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.
+Please use h5part@lists.psi.ch for communication.

COPYING

@@ -1,6 +1,6 @@
 *** Copyright Notice ***
 
-H5Part  Copyright (c) 2006-2009, The Regents of the University of California,
+H5hut  Copyright (c) 2006-2016, 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.
@@ -25,7 +25,7 @@ and to permit others to do so.
 
 *** License agreement ***
 
-H5Part  Copyright (c) 2006-2009, The Regents of the University of California,
+H5hut  Copyright (c) 2006-2016, 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.

ChangeLog

@@ -0,0 +1,15 @@
+2018-09-14  Gsell Achim  <achi.gsell@psi.ch>
+
+	* C-API
+	- H5PartSetNumPoints() renamed to H5PartSetNumItems()
+	- H5PartGetNumPoints() renamed to H5PartGetNumItems()
+	- Dataset names longer then 64 bytes are handled as error.
+	- Same for step/iteration names.
+	* core API
+	- we use the term 'iteration' instead of 'step'
+	- we use the term 'item' instead of 'point'
+	- re-factor function and variable names
+	- in printing messages/debug output fixed
+	- do not flush (sync to disk) after writing a dataset by default,
+	  can be controlled by a property
+

GNUmakefile.orig

@@ -1,133 +0,0 @@
-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

@@ -1,437 +0,0 @@
-==============================================================================
-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

@@ -1,12 +1,17 @@
-# Trial by Antino Kim
+ACLOCAL_AMFLAGS = -I m4
-# Top level Makefile.am
+EXTRA_DIST =			\
-ACLOCAL_AMFLAGS=-I m4
+	autogen.sh 		\
+	ax_pkg_swig.m4
 
 SUBDIRS =			\
-	doc \
 	src			\
 	test			\
-	tools
+	tools			\
+	doc			\
+	examples/H5		\
+	examples/H5Part	 	\
+	examples/H5Block	\
+	examples/H5Fed
 
 MAINTAINERCLEANFILES = 		\
 	config.h 		\

Makefile.orig

@@ -1,59 +0,0 @@
-
-# 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

@@ -1,3 +1,58 @@
+#### H5PART trunk ############################################################
+
+* h5_file_t is now uintptr_t
+* experimental version of parallel H5Fed
+* new API function for file open using properties (similiar to hdf5 properties)
+
+#### H5PART 1.99.10 ############################################################
+
+* C99 compiler required
+* C API with inline functions
+
+
+#### H5PART 1.99.0 ############################################################
+
+rudimental implementation of a grid manager
+
+Important changes from version 1.6 to 1.99.0
+
+Renamed type:
+    H5PartFile -> h5_file_t
+    h5part_int64_t -> h5_int64_t
+    h5part_float64_t -> h5_float_t
+
+Renamed functions:
+    All function not related to a specific data model have been renamed from
+    H5PartFunction() to H5Function().
+
+    Example:
+       H5PartOpenFile() -> H5OpenFile()
+
+Removed functions:
+    To simplify the API, there is just one function to open a file. It's the
+    same function for serial and parallel code.
+
+#### 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.

README

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

@@ -1,54 +1,48 @@
 #!/bin/sh
 # Run this to generate all the initial makefiles, etc.
 
+ACLOCAL_FLAGS="-I m4 -I . $ACLOCAL_FLAGS"
+LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
+AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
+
+LIBTOOLIZE=`which libtoolize`
+if [ "$LIBTOOLIZE" = "" ]; then
+        LIBTOOLIZE=`which glibtoolize`
+fi
+if [ "$LIBTOOLIZE" = "" ]; then
+        echo "libtoolize not found" 1>&2
+        exit 1
+fi
+
 echo "+ making misc files ..."
 touch NEWS README AUTHORS ChangeLog
 echo
-echo
+$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
-echo
-echo "+ running aclocal ..."
-aclocal $ACLOCAL_FLAGS || {
-  echo
-  echo "aclocal failed - check that all needed development files are present on system"
-  exit 1
-}
-echo
-echo
-echo
-echo "+ running autoheader ... "
-autoheader || {
-  echo
-  echo "autoheader failed"
-  exit 1
-}
-echo
-echo
-echo
-echo "+ running libtoolize ... "
-libtoolize --force || {
-  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"
+	exit 1
+}
 echo
+echo "+ running autoheader ... "
+autoheader || {
+	echo "autoheader failed"
+	exit 1
+}
 echo
 echo "+ running autoconf ... "
 autoconf || {
-  echo
 	echo "autoconf failed"
 	exit 1
 }
 echo
-echo
-echo
 echo "+ running automake ... "
-automake -a -c --foreign || {
+automake $AUTOMAKE_FLAGS || {
-  echo
 	echo "automake failed"
 	exit 1
 }
-echo
-echo
-echo
 

ax_cxx_compile_stdcxx.m4

@@ -0,0 +1,982 @@
+# ===========================================================================
+#  https://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_CXX_COMPILE_STDCXX(VERSION, [ext|noext], [mandatory|optional])
+#
+# DESCRIPTION
+#
+#   Check for baseline language coverage in the compiler for the specified
+#   version of the C++ standard.  If necessary, add switches to CXX and
+#   CXXCPP to enable support.  VERSION may be '11' (for the C++11 standard)
+#   or '14' (for the C++14 standard).
+#
+#   The second argument, if specified, indicates whether you insist on an
+#   extended mode (e.g. -std=gnu++11) or a strict conformance mode (e.g.
+#   -std=c++11).  If neither is specified, you get whatever works, with
+#   preference for an extended mode.
+#
+#   The third argument, if specified 'mandatory' or if left unspecified,
+#   indicates that baseline support for the specified C++ standard is
+#   required and that the macro should error out if no mode with that
+#   support is found.  If specified 'optional', then configuration proceeds
+#   regardless, after defining HAVE_CXX${VERSION} if and only if a
+#   supporting mode is found.
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Benjamin Kosnik <bkoz@redhat.com>
+#   Copyright (c) 2012 Zack Weinberg <zackw@panix.com>
+#   Copyright (c) 2013 Roy Stogner <roystgnr@ices.utexas.edu>
+#   Copyright (c) 2014, 2015 Google Inc.; contributed by Alexey Sokolov <sokolov@google.com>
+#   Copyright (c) 2015 Paul Norman <penorman@mac.com>
+#   Copyright (c) 2015 Moritz Klammler <moritz@klammler.eu>
+#   Copyright (c) 2016 Krzesimir Nowak <qdlacz@gmail.com>
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved.  This file is offered as-is, without any
+#   warranty.
+
+#serial 7
+
+dnl  This macro is based on the code from the AX_CXX_COMPILE_STDCXX_11 macro
+dnl  (serial version number 13).
+
+AX_REQUIRE_DEFINED([AC_MSG_WARN])
+AC_DEFUN([AX_CXX_COMPILE_STDCXX], [dnl
+  m4_if([$1], [11], [ax_cxx_compile_alternatives="11 0x"],
+        [$1], [14], [ax_cxx_compile_alternatives="14 1y"],
+        [$1], [17], [ax_cxx_compile_alternatives="17 1z"],
+        [m4_fatal([invalid first argument `$1' to AX_CXX_COMPILE_STDCXX])])dnl
+  m4_if([$2], [], [],
+        [$2], [ext], [],
+        [$2], [noext], [],
+        [m4_fatal([invalid second argument `$2' to AX_CXX_COMPILE_STDCXX])])dnl
+  m4_if([$3], [], [ax_cxx_compile_cxx$1_required=true],
+        [$3], [mandatory], [ax_cxx_compile_cxx$1_required=true],
+        [$3], [optional], [ax_cxx_compile_cxx$1_required=false],
+        [m4_fatal([invalid third argument `$3' to AX_CXX_COMPILE_STDCXX])])
+  AC_LANG_PUSH([C++])dnl
+  ac_success=no
+  AC_CACHE_CHECK(whether $CXX supports C++$1 features by default,
+  ax_cv_cxx_compile_cxx$1,
+  [AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
+    [ax_cv_cxx_compile_cxx$1=yes],
+    [ax_cv_cxx_compile_cxx$1=no])])
+  if test x$ax_cv_cxx_compile_cxx$1 = xyes; then
+    ac_success=yes
+  fi
+
+  m4_if([$2], [noext], [], [dnl
+  if test x$ac_success = xno; then
+    for alternative in ${ax_cxx_compile_alternatives}; do
+      switch="-std=gnu++${alternative}"
+      cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch])
+      AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch,
+                     $cachevar,
+        [ac_save_CXX="$CXX"
+         CXX="$CXX $switch"
+         AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
+          [eval $cachevar=yes],
+          [eval $cachevar=no])
+         CXX="$ac_save_CXX"])
+      if eval test x\$$cachevar = xyes; then
+        CXX="$CXX $switch"
+        if test -n "$CXXCPP" ; then
+          CXXCPP="$CXXCPP $switch"
+        fi
+        ac_success=yes
+        break
+      fi
+    done
+  fi])
+
+  m4_if([$2], [ext], [], [dnl
+  if test x$ac_success = xno; then
+    dnl HP's aCC needs +std=c++11 according to:
+    dnl http://h21007.www2.hp.com/portal/download/files/unprot/aCxx/PDF_Release_Notes/769149-001.pdf
+    dnl Cray's crayCC needs "-h std=c++11"
+    for alternative in ${ax_cxx_compile_alternatives}; do
+      for switch in -std=c++${alternative} +std=c++${alternative} "-h std=c++${alternative}"; do
+        cachevar=AS_TR_SH([ax_cv_cxx_compile_cxx$1_$switch])
+        AC_CACHE_CHECK(whether $CXX supports C++$1 features with $switch,
+                       $cachevar,
+          [ac_save_CXX="$CXX"
+           CXX="$CXX $switch"
+           AC_COMPILE_IFELSE([AC_LANG_SOURCE([_AX_CXX_COMPILE_STDCXX_testbody_$1])],
+            [eval $cachevar=yes],
+            [eval $cachevar=no])
+           CXX="$ac_save_CXX"])
+        if eval test x\$$cachevar = xyes; then
+          CXX="$CXX $switch"
+          if test -n "$CXXCPP" ; then
+            CXXCPP="$CXXCPP $switch"
+          fi
+          ac_success=yes
+          break
+        fi
+      done
+      if test x$ac_success = xyes; then
+        break
+      fi
+    done
+  fi])
+  AC_LANG_POP([C++])
+  if test x$ax_cxx_compile_cxx$1_required = xtrue; then
+    if test x$ac_success = xno; then
+      AC_MSG_ERROR([*** A compiler with support for C++$1 language features is required.])
+    fi
+  fi
+  if test x$ac_success = xno; then
+    HAVE_CXX$1=0
+    AC_MSG_NOTICE([No compiler with C++$1 support was found])
+  else
+    HAVE_CXX$1=1
+    AC_DEFINE(HAVE_CXX$1,1,
+              [define if the compiler supports basic C++$1 syntax])
+  fi
+  AC_SUBST(HAVE_CXX$1)
+  m4_if([$1], [17], [AC_MSG_WARN([C++17 is not yet standardized, so the checks may change in incompatible ways anytime])])
+])
+
+
+dnl  Test body for checking C++11 support
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_11],
+  _AX_CXX_COMPILE_STDCXX_testbody_new_in_11
+)
+
+
+dnl  Test body for checking C++14 support
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_14],
+  _AX_CXX_COMPILE_STDCXX_testbody_new_in_11
+  _AX_CXX_COMPILE_STDCXX_testbody_new_in_14
+)
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_17],
+  _AX_CXX_COMPILE_STDCXX_testbody_new_in_11
+  _AX_CXX_COMPILE_STDCXX_testbody_new_in_14
+  _AX_CXX_COMPILE_STDCXX_testbody_new_in_17
+)
+
+dnl  Tests for new features in C++11
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_11], [[
+
+// If the compiler admits that it is not ready for C++11, why torture it?
+// Hopefully, this will speed up the test.
+
+#ifndef __cplusplus
+
+#error "This is not a C++ compiler"
+
+#elif __cplusplus < 201103L
+
+#error "This is not a C++11 compiler"
+
+#else
+
+namespace cxx11
+{
+
+  namespace test_static_assert
+  {
+
+    template <typename T>
+    struct check
+    {
+      static_assert(sizeof(int) <= sizeof(T), "not big enough");
+    };
+
+  }
+
+  namespace test_final_override
+  {
+
+    struct Base
+    {
+      virtual void f() {}
+    };
+
+    struct Derived : public Base
+    {
+      virtual void f() override {}
+    };
+
+  }
+
+  namespace test_double_right_angle_brackets
+  {
+
+    template < typename T >
+    struct check {};
+
+    typedef check<void> single_type;
+    typedef check<check<void>> double_type;
+    typedef check<check<check<void>>> triple_type;
+    typedef check<check<check<check<void>>>> quadruple_type;
+
+  }
+
+  namespace test_decltype
+  {
+
+    int
+    f()
+    {
+      int a = 1;
+      decltype(a) b = 2;
+      return a + b;
+    }
+
+  }
+
+  namespace test_type_deduction
+  {
+
+    template < typename T1, typename T2 >
+    struct is_same
+    {
+      static const bool value = false;
+    };
+
+    template < typename T >
+    struct is_same<T, T>
+    {
+      static const bool value = true;
+    };
+
+    template < typename T1, typename T2 >
+    auto
+    add(T1 a1, T2 a2) -> decltype(a1 + a2)
+    {
+      return a1 + a2;
+    }
+
+    int
+    test(const int c, volatile int v)
+    {
+      static_assert(is_same<int, decltype(0)>::value == true, "");
+      static_assert(is_same<int, decltype(c)>::value == false, "");
+      static_assert(is_same<int, decltype(v)>::value == false, "");
+      auto ac = c;
+      auto av = v;
+      auto sumi = ac + av + 'x';
+      auto sumf = ac + av + 1.0;
+      static_assert(is_same<int, decltype(ac)>::value == true, "");
+      static_assert(is_same<int, decltype(av)>::value == true, "");
+      static_assert(is_same<int, decltype(sumi)>::value == true, "");
+      static_assert(is_same<int, decltype(sumf)>::value == false, "");
+      static_assert(is_same<int, decltype(add(c, v))>::value == true, "");
+      return (sumf > 0.0) ? sumi : add(c, v);
+    }
+
+  }
+
+  namespace test_noexcept
+  {
+
+    int f() { return 0; }
+    int g() noexcept { return 0; }
+
+    static_assert(noexcept(f()) == false, "");
+    static_assert(noexcept(g()) == true, "");
+
+  }
+
+  namespace test_constexpr
+  {
+
+    template < typename CharT >
+    unsigned long constexpr
+    strlen_c_r(const CharT *const s, const unsigned long acc) noexcept
+    {
+      return *s ? strlen_c_r(s + 1, acc + 1) : acc;
+    }
+
+    template < typename CharT >
+    unsigned long constexpr
+    strlen_c(const CharT *const s) noexcept
+    {
+      return strlen_c_r(s, 0UL);
+    }
+
+    static_assert(strlen_c("") == 0UL, "");
+    static_assert(strlen_c("1") == 1UL, "");
+    static_assert(strlen_c("example") == 7UL, "");
+    static_assert(strlen_c("another\0example") == 7UL, "");
+
+  }
+
+  namespace test_rvalue_references
+  {
+
+    template < int N >
+    struct answer
+    {
+      static constexpr int value = N;
+    };
+
+    answer<1> f(int&)       { return answer<1>(); }
+    answer<2> f(const int&) { return answer<2>(); }
+    answer<3> f(int&&)      { return answer<3>(); }
+
+    void
+    test()
+    {
+      int i = 0;
+      const int c = 0;
+      static_assert(decltype(f(i))::value == 1, "");
+      static_assert(decltype(f(c))::value == 2, "");
+      static_assert(decltype(f(0))::value == 3, "");
+    }
+
+  }
+
+  namespace test_uniform_initialization
+  {
+
+    struct test
+    {
+      static const int zero {};
+      static const int one {1};
+    };
+
+    static_assert(test::zero == 0, "");
+    static_assert(test::one == 1, "");
+
+  }
+
+  namespace test_lambdas
+  {
+
+    void
+    test1()
+    {
+      auto lambda1 = [](){};
+      auto lambda2 = lambda1;
+      lambda1();
+      lambda2();
+    }
+
+    int
+    test2()
+    {
+      auto a = [](int i, int j){ return i + j; }(1, 2);
+      auto b = []() -> int { return '0'; }();
+      auto c = [=](){ return a + b; }();
+      auto d = [&](){ return c; }();
+      auto e = [a, &b](int x) mutable {
+        const auto identity = [](int y){ return y; };
+        for (auto i = 0; i < a; ++i)
+          a += b--;
+        return x + identity(a + b);
+      }(0);
+      return a + b + c + d + e;
+    }
+
+    int
+    test3()
+    {
+      const auto nullary = [](){ return 0; };
+      const auto unary = [](int x){ return x; };
+      using nullary_t = decltype(nullary);
+      using unary_t = decltype(unary);
+      const auto higher1st = [](nullary_t f){ return f(); };
+      const auto higher2nd = [unary](nullary_t f1){
+        return [unary, f1](unary_t f2){ return f2(unary(f1())); };
+      };
+      return higher1st(nullary) + higher2nd(nullary)(unary);
+    }
+
+  }
+
+  namespace test_variadic_templates
+  {
+
+    template <int...>
+    struct sum;
+
+    template <int N0, int... N1toN>
+    struct sum<N0, N1toN...>
+    {
+      static constexpr auto value = N0 + sum<N1toN...>::value;
+    };
+
+    template <>
+    struct sum<>
+    {
+      static constexpr auto value = 0;
+    };
+
+    static_assert(sum<>::value == 0, "");
+    static_assert(sum<1>::value == 1, "");
+    static_assert(sum<23>::value == 23, "");
+    static_assert(sum<1, 2>::value == 3, "");
+    static_assert(sum<5, 5, 11>::value == 21, "");
+    static_assert(sum<2, 3, 5, 7, 11, 13>::value == 41, "");
+
+  }
+
+  // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
+  // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function
+  // because of this.
+  namespace test_template_alias_sfinae
+  {
+
+    struct foo {};
+
+    template<typename T>
+    using member = typename T::member_type;
+
+    template<typename T>
+    void func(...) {}
+
+    template<typename T>
+    void func(member<T>*) {}
+
+    void test();
+
+    void test() { func<foo>(0); }
+
+  }
+
+}  // namespace cxx11
+
+#endif  // __cplusplus >= 201103L
+
+]])
+
+
+dnl  Tests for new features in C++14
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_14], [[
+
+// If the compiler admits that it is not ready for C++14, why torture it?
+// Hopefully, this will speed up the test.
+
+#ifndef __cplusplus
+
+#error "This is not a C++ compiler"
+
+#elif __cplusplus < 201402L
+
+#error "This is not a C++14 compiler"
+
+#else
+
+namespace cxx14
+{
+
+  namespace test_polymorphic_lambdas
+  {
+
+    int
+    test()
+    {
+      const auto lambda = [](auto&&... args){
+        const auto istiny = [](auto x){
+          return (sizeof(x) == 1UL) ? 1 : 0;
+        };
+        const int aretiny[] = { istiny(args)... };
+        return aretiny[0];
+      };
+      return lambda(1, 1L, 1.0f, '1');
+    }
+
+  }
+
+  namespace test_binary_literals
+  {
+
+    constexpr auto ivii = 0b0000000000101010;
+    static_assert(ivii == 42, "wrong value");
+
+  }
+
+  namespace test_generalized_constexpr
+  {
+
+    template < typename CharT >
+    constexpr unsigned long
+    strlen_c(const CharT *const s) noexcept
+    {
+      auto length = 0UL;
+      for (auto p = s; *p; ++p)
+        ++length;
+      return length;
+    }
+
+    static_assert(strlen_c("") == 0UL, "");
+    static_assert(strlen_c("x") == 1UL, "");
+    static_assert(strlen_c("test") == 4UL, "");
+    static_assert(strlen_c("another\0test") == 7UL, "");
+
+  }
+
+  namespace test_lambda_init_capture
+  {
+
+    int
+    test()
+    {
+      auto x = 0;
+      const auto lambda1 = [a = x](int b){ return a + b; };
+      const auto lambda2 = [a = lambda1(x)](){ return a; };
+      return lambda2();
+    }
+
+  }
+
+  namespace test_digit_separators
+  {
+
+    constexpr auto ten_million = 100'000'000;
+    static_assert(ten_million == 100000000, "");
+
+  }
+
+  namespace test_return_type_deduction
+  {
+
+    auto f(int& x) { return x; }
+    decltype(auto) g(int& x) { return x; }
+
+    template < typename T1, typename T2 >
+    struct is_same
+    {
+      static constexpr auto value = false;
+    };
+
+    template < typename T >
+    struct is_same<T, T>
+    {
+      static constexpr auto value = true;
+    };
+
+    int
+    test()
+    {
+      auto x = 0;
+      static_assert(is_same<int, decltype(f(x))>::value, "");
+      static_assert(is_same<int&, decltype(g(x))>::value, "");
+      return x;
+    }
+
+  }
+
+}  // namespace cxx14
+
+#endif  // __cplusplus >= 201402L
+
+]])
+
+
+dnl  Tests for new features in C++17
+
+m4_define([_AX_CXX_COMPILE_STDCXX_testbody_new_in_17], [[
+
+// If the compiler admits that it is not ready for C++17, why torture it?
+// Hopefully, this will speed up the test.
+
+#ifndef __cplusplus
+
+#error "This is not a C++ compiler"
+
+#elif __cplusplus <= 201402L
+
+#error "This is not a C++17 compiler"
+
+#else
+
+#if defined(__clang__)
+  #define REALLY_CLANG
+#else
+  #if defined(__GNUC__)
+    #define REALLY_GCC
+  #endif
+#endif
+
+#include <initializer_list>
+#include <utility>
+#include <type_traits>
+
+namespace cxx17
+{
+
+#if !defined(REALLY_CLANG)
+  namespace test_constexpr_lambdas
+  {
+
+    // TODO: test it with clang++ from git
+
+    constexpr int foo = [](){return 42;}();
+
+  }
+#endif // !defined(REALLY_CLANG)
+
+  namespace test::nested_namespace::definitions
+  {
+
+  }
+
+  namespace test_fold_expression
+  {
+
+    template<typename... Args>
+    int multiply(Args... args)
+    {
+      return (args * ... * 1);
+    }
+
+    template<typename... Args>
+    bool all(Args... args)
+    {
+      return (args && ...);
+    }
+
+  }
+
+  namespace test_extended_static_assert
+  {
+
+    static_assert (true);
+
+  }
+
+  namespace test_auto_brace_init_list
+  {
+
+    auto foo = {5};
+    auto bar {5};
+
+    static_assert(std::is_same<std::initializer_list<int>, decltype(foo)>::value);
+    static_assert(std::is_same<int, decltype(bar)>::value);
+  }
+
+  namespace test_typename_in_template_template_parameter
+  {
+
+    template<template<typename> typename X> struct D;
+
+  }
+
+  namespace test_fallthrough_nodiscard_maybe_unused_attributes
+  {
+
+    int f1()
+    {
+      return 42;
+    }
+
+    [[nodiscard]] int f2()
+    {
+      [[maybe_unused]] auto unused = f1();
+
+      switch (f1())
+      {
+      case 17:
+        f1();
+        [[fallthrough]];
+      case 42:
+        f1();
+      }
+      return f1();
+    }
+
+  }
+
+  namespace test_extended_aggregate_initialization
+  {
+
+    struct base1
+    {
+      int b1, b2 = 42;
+    };
+
+    struct base2
+    {
+      base2() {
+        b3 = 42;
+      }
+      int b3;
+    };
+
+    struct derived : base1, base2
+    {
+        int d;
+    };
+
+    derived d1 {{1, 2}, {}, 4};  // full initialization
+    derived d2 {{}, {}, 4};      // value-initialized bases
+
+  }
+
+  namespace test_general_range_based_for_loop
+  {
+
+    struct iter
+    {
+      int i;
+
+      int& operator* ()
+      {
+        return i;
+      }
+
+      const int& operator* () const
+      {
+        return i;
+      }
+
+      iter& operator++()
+      {
+        ++i;
+        return *this;
+      }
+    };
+
+    struct sentinel
+    {
+      int i;
+    };
+
+    bool operator== (const iter& i, const sentinel& s)
+    {
+      return i.i == s.i;
+    }
+
+    bool operator!= (const iter& i, const sentinel& s)
+    {
+      return !(i == s);
+    }
+
+    struct range
+    {
+      iter begin() const
+      {
+        return {0};
+      }
+
+      sentinel end() const
+      {
+        return {5};
+      }
+    };
+
+    void f()
+    {
+      range r {};
+
+      for (auto i : r)
+      {
+        [[maybe_unused]] auto v = i;
+      }
+    }
+
+  }
+
+  namespace test_lambda_capture_asterisk_this_by_value
+  {
+
+    struct t
+    {
+      int i;
+      int foo()
+      {
+        return [*this]()
+        {
+          return i;
+        }();
+      }
+    };
+
+  }
+
+  namespace test_enum_class_construction
+  {
+
+    enum class byte : unsigned char
+    {};
+
+    byte foo {42};
+
+  }
+
+  namespace test_constexpr_if
+  {
+
+    template <bool cond>
+    int f ()
+    {
+      if constexpr(cond)
+      {
+        return 13;
+      }
+      else
+      {
+        return 42;
+      }
+    }
+
+  }
+
+  namespace test_selection_statement_with_initializer
+  {
+
+    int f()
+    {
+      return 13;
+    }
+
+    int f2()
+    {
+      if (auto i = f(); i > 0)
+      {
+        return 3;
+      }
+
+      switch (auto i = f(); i + 4)
+      {
+      case 17:
+        return 2;
+
+      default:
+        return 1;
+      }
+    }
+
+  }
+
+#if !defined(REALLY_CLANG)
+  namespace test_template_argument_deduction_for_class_templates
+  {
+
+    // TODO: test it with clang++ from git
+
+    template <typename T1, typename T2>
+    struct pair
+    {
+      pair (T1 p1, T2 p2)
+        : m1 {p1},
+          m2 {p2}
+      {}
+
+      T1 m1;
+      T2 m2;
+    };
+
+    void f()
+    {
+      [[maybe_unused]] auto p = pair{13, 42u};
+    }
+
+  }
+#endif // !defined(REALLY_CLANG)
+
+  namespace test_non_type_auto_template_parameters
+  {
+
+    template <auto n>
+    struct B
+    {};
+
+    B<5> b1;
+    B<'a'> b2;
+
+  }
+
+#if !defined(REALLY_CLANG)
+  namespace test_structured_bindings
+  {
+
+    // TODO: test it with clang++ from git
+
+    int arr[2] = { 1, 2 };
+    std::pair<int, int> pr = { 1, 2 };
+
+    auto f1() -> int(&)[2]
+    {
+      return arr;
+    }
+
+    auto f2() -> std::pair<int, int>&
+    {
+      return pr;
+    }
+
+    struct S
+    {
+      int x1 : 2;
+      volatile double y1;
+    };
+
+    S f3()
+    {
+      return {};
+    }
+
+    auto [ x1, y1 ] = f1();
+    auto& [ xr1, yr1 ] = f1();
+    auto [ x2, y2 ] = f2();
+    auto& [ xr2, yr2 ] = f2();
+    const auto [ x3, y3 ] = f3();
+
+  }
+#endif // !defined(REALLY_CLANG)
+
+#if !defined(REALLY_CLANG)
+  namespace test_exception_spec_type_system
+  {
+
+    // TODO: test it with clang++ from git
+
+    struct Good {};
+    struct Bad {};
+
+    void g1() noexcept;
+    void g2();
+
+    template<typename T>
+    Bad
+    f(T*, T*);
+
+    template<typename T1, typename T2>
+    Good
+    f(T1*, T2*);
+
+    static_assert (std::is_same_v<Good, decltype(f(g1, g2))>);
+
+  }
+#endif // !defined(REALLY_CLANG)
+
+  namespace test_inline_variables
+  {
+
+    template<class T> void f(T)
+    {}
+
+    template<class T> inline T g(T)
+    {
+      return T{};
+    }
+
+    template<> inline void f<>(int)
+    {}
+
+    template<> int g<>(int)
+    {
+      return 5;
+    }
+
+  }
+
+}  // namespace cxx17
+
+#endif  // __cplusplus <= 201402L
+
+]])

ax_cxx_compile_stdcxx_11.m4

@@ -0,0 +1,39 @@
+# =============================================================================
+#  https://www.gnu.org/software/autoconf-archive/ax_cxx_compile_stdcxx_11.html
+# =============================================================================
+#
+# SYNOPSIS
+#
+#   AX_CXX_COMPILE_STDCXX_11([ext|noext], [mandatory|optional])
+#
+# DESCRIPTION
+#
+#   Check for baseline language coverage in the compiler for the C++11
+#   standard; if necessary, add switches to CXX and CXXCPP to enable
+#   support.
+#
+#   This macro is a convenience alias for calling the AX_CXX_COMPILE_STDCXX
+#   macro with the version set to C++11.  The two optional arguments are
+#   forwarded literally as the second and third argument respectively.
+#   Please see the documentation for the AX_CXX_COMPILE_STDCXX macro for
+#   more information.  If you want to use this macro, you also need to
+#   download the ax_cxx_compile_stdcxx.m4 file.
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Benjamin Kosnik <bkoz@redhat.com>
+#   Copyright (c) 2012 Zack Weinberg <zackw@panix.com>
+#   Copyright (c) 2013 Roy Stogner <roystgnr@ices.utexas.edu>
+#   Copyright (c) 2014, 2015 Google Inc.; contributed by Alexey Sokolov <sokolov@google.com>
+#   Copyright (c) 2015 Paul Norman <penorman@mac.com>
+#   Copyright (c) 2015 Moritz Klammler <moritz@klammler.eu>
+#
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved. This file is offered as-is, without any
+#   warranty.
+
+#serial 18
+
+AX_REQUIRE_DEFINED([AX_CXX_COMPILE_STDCXX])
+AC_DEFUN([AX_CXX_COMPILE_STDCXX_11], [AX_CXX_COMPILE_STDCXX([11], [$1], [$2])])

ax_pkg_swig.m4

@@ -0,0 +1,135 @@
+# ===========================================================================
+#        http://www.gnu.org/software/autoconf-archive/ax_pkg_swig.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+#   AX_PKG_SWIG([major.minor.micro], [action-if-found], [action-if-not-found])
+#
+# DESCRIPTION
+#
+#   This macro searches for a SWIG installation on your system. If found,
+#   then SWIG is AC_SUBST'd; if not found, then $SWIG is empty.  If SWIG is
+#   found, then SWIG_LIB is set to the SWIG library path, and AC_SUBST'd.
+#
+#   You can use the optional first argument to check if the version of the
+#   available SWIG is greater than or equal to the value of the argument. It
+#   should have the format: N[.N[.N]] (N is a number between 0 and 999. Only
+#   the first N is mandatory.) If the version argument is given (e.g.
+#   1.3.17), AX_PKG_SWIG checks that the swig package is this version number
+#   or higher.
+#
+#   As usual, action-if-found is executed if SWIG is found, otherwise
+#   action-if-not-found is executed.
+#
+#   In configure.in, use as:
+#
+#     AX_PKG_SWIG(1.3.17, [], [ AC_MSG_ERROR([SWIG is required to build..]) ])
+#     AX_SWIG_ENABLE_CXX
+#     AX_SWIG_MULTI_MODULE_SUPPORT
+#     AX_SWIG_PYTHON
+#
+# LICENSE
+#
+#   Copyright (c) 2008 Sebastian Huber <sebastian-huber@web.de>
+#   Copyright (c) 2008 Alan W. Irwin
+#   Copyright (c) 2008 Rafael Laboissiere <rafael@laboissiere.net>
+#   Copyright (c) 2008 Andrew Collier
+#   Copyright (c) 2011 Murray Cumming <murrayc@openismus.com>
+#
+#   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 of the License, 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, see <http://www.gnu.org/licenses/>.
+#
+#   As a special exception, the respective Autoconf Macro's copyright owner
+#   gives unlimited permission to copy, distribute and modify the configure
+#   scripts that are the output of Autoconf when processing the Macro. You
+#   need not follow the terms of the GNU General Public License when using
+#   or distributing such scripts, even though portions of the text of the
+#   Macro appear in them. The GNU General Public License (GPL) does govern
+#   all other use of the material that constitutes the Autoconf Macro.
+#
+#   This special exception to the GPL applies to versions of the Autoconf
+#   Macro released by the Autoconf Archive. When you make and distribute a
+#   modified version of the Autoconf Macro, you may extend this special
+#   exception to the GPL to apply to your modified version as well.
+
+#serial 11
+
+AC_DEFUN([AX_PKG_SWIG],[
+        # Ubuntu has swig 2.0 as /usr/bin/swig2.0
+        AC_PATH_PROGS([SWIG],[swig swig2.0])
+        if test -z "$SWIG" ; then
+                m4_ifval([$3],[$3],[:])
+        elif test -n "$1" ; then
+                AC_MSG_CHECKING([SWIG version])
+                [swig_version=`$SWIG -version 2>&1 | grep 'SWIG Version' | sed 's/.*\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\).*/\1/g'`]
+                AC_MSG_RESULT([$swig_version])
+                if test -n "$swig_version" ; then
+                        # Calculate the required version number components
+                        [required=$1]
+                        [required_major=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_major" ; then
+                                [required_major=0]
+                        fi
+                        [required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
+                        [required_minor=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_minor" ; then
+                                [required_minor=0]
+                        fi
+                        [required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
+                        [required_patch=`echo $required | sed 's/[^0-9].*//'`]
+                        if test -z "$required_patch" ; then
+                                [required_patch=0]
+                        fi
+                        # Calculate the available version number components
+                        [available=$swig_version]
+                        [available_major=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_major" ; then
+                                [available_major=0]
+                        fi
+                        [available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
+                        [available_minor=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_minor" ; then
+                                [available_minor=0]
+                        fi
+                        [available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
+                        [available_patch=`echo $available | sed 's/[^0-9].*//'`]
+                        if test -z "$available_patch" ; then
+                                [available_patch=0]
+                        fi
+                        # Convert the version tuple into a single number for easier comparison.
+                        # Using base 100 should be safe since SWIG internally uses BCD values
+                        # to encode its version number.
+                        required_swig_vernum=`expr $required_major \* 10000 \
+                            \+ $required_minor \* 100 \+ $required_patch`
+                        available_swig_vernum=`expr $available_major \* 10000 \
+                            \+ $available_minor \* 100 \+ $available_patch`
+
+                        if test $available_swig_vernum -lt $required_swig_vernum; then
+                                AC_MSG_WARN([SWIG version >= $1 is required.  You have $swig_version.])
+                                SWIG=''
+                                m4_ifval([$3],[$3],[])
+                        else
+                                AC_MSG_CHECKING([for SWIG library])
+                                SWIG_LIB=`$SWIG -swiglib`
+                                AC_MSG_RESULT([$SWIG_LIB])
+                                m4_ifval([$2],[$2],[])
+                        fi
+                else
+                        AC_MSG_WARN([cannot determine SWIG version])
+                        SWIG=''
+                        m4_ifval([$3],[$3],[])
+                fi
+        fi
+        AC_SUBST([SWIG_LIB])
+])

configure-crayxt

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

configure.ac

@@ -1,72 +1,165 @@
-# Every configure script must call AC_INIT before doing anything else.
+#
-# AC_INIT (package, version, [bug-report], [tarname])
+#  Copyright (c) 2006-2018, The Regents of the University of California,
-AC_INIT([H5Part], [1.6.3], [h5part@lists.psi.ch], H5Part)
+#  through Lawrence Berkeley National Laboratory (subject to receipt of any
-
+#  required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
-# Ensure that a recent enough version of Autoconf is being used. 
+#  Institut (Switzerland).  All rights reserved.
-# If the version of Autoconf being used to create configure is earlier than version, 
+#
-# print an error message to the standard error output and do not create configure.
+#  License: see file COPYING in top level of source distribution.
-AC_PREREQ(2.59)
+#
-
+AC_INIT([H5hut], [2.0.0rc7], [h5part@lists.psi.ch], H5hut)
-# should be called right after AC_INIT.
+AC_PREREQ(2.60)
-# configure scripts can create a C header file containing `#define' directives. 
-# The AC_CONFIG_HEADERS macro selects this kind of output.
 AC_CONFIG_HEADERS(config.h)
-
 AC_CONFIG_MACRO_DIR([m4])
-
+LT_INIT
-# AM_INIT_AUTOMAKE is required to use autoconf with automake
 AM_INIT_AUTOMAKE
 
-BUILD_LIBS='libH5Part'
+ENABLE_DEBUG='no'
-BUILD_TESTS='test'
+ENABLE_C='yes'
+ENABLE_FORTRAN='no'
+ENABLE_PARALLEL='no'
+ENABLE_PYTHON='no'
 
 ###############################################################################
-################# --enable-xxx and --with-xxx Argument ########################
+# --enable-xxx and --with-xxx Arguments
-###############################################################################
-
 AC_ARG_ENABLE(
 	[debug],
-	[AC_HELP_STRING([--enable-debug],
+	[AS_HELP_STRING([--enable-debug], [Compile with debug flags [default=no]])],
-	[Compile with debug flags [default=no]])],
+	[ENABLE_DEBUG=$enableval])
-	[USE_DEBUG=$enableval])
+AM_CONDITIONAL([ENABLE_DEBUG], [test "$ENABLE_DEBUG" = "yes"])
+
+AC_ARG_ENABLE(
+	[c],
+	[AS_HELP_STRING([--enable-c],
+	[Compile the C interface [default=yes]])],
+	[ENABLE_C=$enableval])
+AM_CONDITIONAL([ENABLE_C], [test "$ENABLE_C" = "yes"])
 
 AC_ARG_ENABLE(
 	[fortran],
-	[AC_HELP_STRING([--enable-fortran],
+	[AS_HELP_STRING([--enable-fortran],
 	[Compile the Fortran interface [default=no]])],
-	[USE_FORTRAN=$enableval])
+	[ENABLE_FORTRAN=$enableval])
+AM_CONDITIONAL([ENABLE_FORTRAN], [test "$ENABLE_FORTRAN" = "yes"])
+
+AC_ARG_ENABLE(
+	[python],
+	[AS_HELP_STRING([--enable-python],
+	[Compile the Python interface [default=no]])],
+	[ENABLE_PYTHON=$enableval])
+AM_CONDITIONAL([ENABLE_PYTHON], [test "$ENABLE_PYTHON" = "yes"])
 
 AC_ARG_ENABLE(
 	[parallel],
-	[AC_HELP_STRING([--enable-parallel],
+	[AS_HELP_STRING([--enable-parallel],
 	[Compile the MPI/IO interface [default=no]])],
-	[USE_PARALLEL=$enableval])
+	[ENABLE_PARALLEL=$enableval])
+AM_CONDITIONAL([ENABLE_PARALLEL], [test "$ENABLE_PARALLEL" = "yes"])
 
 AC_ARG_ENABLE(
-	[tools],
+	[large-indices],
-        [AC_HELP_STRING([--enable-tools],
+	[AC_HELP_STRING([--enable-large-indices],
-	[Compile h5part tools [default=no]])],
+	[Compile with 64bit local IDs and indices [default=no]])],
-        [USE_TOOLS=$enableval])
+	[USE_LARGE_INDICES=$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_ENABLE(
+	[examples],
+	[AS_HELP_STRING([--enable-examples],
+	[Compile the H5hut examples [default=no]])],
+	[ENABLE_EXAMPLES=$enableval])
+AM_CONDITIONAL([ENABLE_EXAMPLES], [test "$ENABLE_EXAMPLES" = "yes"])
 
 AC_ARG_WITH(
 	[hdf5],
-	[AC_HELP_STRING([--with-hdf5],
+	[AS_HELP_STRING([--with-hdf5],
 	[path to HDF5 installation [default=""]])],
-	[HDF5PATH=$withval], [HDF5PATH=""])
+	[HDF5_PREFIX=$withval], [])
 
-###############################################################################
+AC_ARG_WITH(
-################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
+	[mpi],
-###############################################################################
+	[AS_HELP_STRING([--with-mpi],
+	[path to MPI installation [default=""]])],
+	[PATH=$MPI_PREFIX/bin:$PATH])
+
+AC_ARG_WITH(
+	[lustre],
+	[AS_HELP_STRING([--with-lustre],
+	[path to lustre user API [default=""]])],
+	[LUSTREPATH=$withval], [LUSTREPATH=""])
+
+AC_ARG_WITH(
+	[parmetis],
+	[AC_HELP_STRING([--with-parmetis],
+	[path to ParMETIS API [default=""]])],
+	[PARMETIS_PREFIX=$withval], [])
+
+AC_ARG_WITH(
+	[vtk],
+	[AC_HELP_STRING([--with-vtk],
+	[VTK installation path [default=""]])],
+	[VTK_PREFIX=$withval], [])
+
+# Determine a C/C++ compiler to use. 
+if test "x$ENABLE_PARALLEL" = "xyes"; then
+   	if test "x$MPICC" != "x"; then
+	   	CC=$MPICC
+	fi
+   	if test "x$MPICXX" != "x"; then
+	   	CXX=$MPICXX
+	fi
+   	if test "x$MPIFC" != "x"; then
+	   	FC=$MPIFC
+	else
+		FC=''
+		F77=''
+		F90=''
+	fi
+   	c_compilers="mpicc cc"
+	cxx_compilers="mpic++ CC"
+	fc_compiler="mpif90 mpif77 mpifort"
+else
+	c_compilers="pgcc pathcc icc gcc cc_r cc"
+	cxx_compilers="pgcc pathcc icc g++ cc_r c++"
+	fc_compiler="pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran"
+fi
+
+AC_PROG_CC($c_compilers)
+if test "x$ac_cv_prog_cc_c89" = "xno"; then
+	AC_MSG_ERROR([C compiler not found!])
+fi
+
+AC_PROG_CXX($cxx_compilers)
+
+if test "X$ENABLE_FORTRAN" = "Xyes"; then
+   	AC_PROG_FC($fc_compiler)
+	if test "x$FC" = "x"; then
+	   	AC_MSG_ERROR([Fortran compiler not found!])
+	fi
+fi
+
+CC=`which $CC`
+CXX=`which $CXX`
+FC=`which $FC`
+
+AX_CXX_COMPILE_STDCXX_11
+AC_PROG_CC_C99
+if test "x$ac_cv_prog_cc_c99" = "xno"; then
+	AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
+fi
 
-SAVE_CC=$CC
-SAVE_CXX=$CXX
-SAVE_FC=$FC
-SAVE_CFLAGS=$CFLAGS
-SAVE_CXXFLAGS=$CXXFLAGS
-SAVE_FFLAGS=$FFLAGS
-SAVE_INCLUDES=$INCLUDES
-SAVE_LDFLAGS=$LDFLAGS
-SAVE_LIBS=$LIBS
 
 ###############################################################################
 ############### PATH SERACH FUNCTION - to be used later... ####################
@@ -99,45 +192,62 @@ PATH_Search() {
 	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
         
-# Determine a C/C++ compiler to use. 
+CFLAGS="$CFLAGS -Wall"
-# If CC is not already set in the environment, check for gcc and cc, then
+CXXFLAGS="$CFLAGS -Wall"
-# for other C compilers. 
+FFLAGS="$FFLAGS -Wall"
-# Set output variable CC to the name of the compiler found.
+
-if test "x$USE_PARALLEL" = "xyes"; then
+# debug enabled?
-   	CCOMPILERS="mpicc cc"
+AC_MSG_CHECKING([if debug is enabled])
-   	CXXCOMPILERS="mpic++ mpicxx CC"
+if test "X$ENABLE_DEBUG" = "Xyes"; then
+	AC_MSG_RESULT([yes])
+	CFLAGS="$CFLAGS -g3 -O0"
+	CXXFLAGS="$CFLAGS -g3 -O0"
+	FFLAGS="$FFLAGS -g3 -O0"
 else
-	CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
+	AC_MSG_RESULT([no])
-   	CXXCOMPILERS="pgCC pathCC icpc g++"
+	CFLAGS="$CFLAGS -O3"
+	CXXFLAGS="$CFLAGS -O3"
+	FFLAGS="$FFLAGS -O3"
 fi
 
-AC_PROG_CC($CCOMPILERS)
 
-# Only need C++ for some of the tools
-#if test "x$USE_TOOLS" = "xyes"; then
-	AC_PROG_CXX($CXXCOMPILERS)
-#fi
-
-# Set output variable INSTALL to the path of a BSD-compatible install program,
-# if one is found in the current PATH. 
-# Otherwise, set INSTALL to `dir/install-sh -c`
 AC_PROG_INSTALL
-
 AC_PROG_AWK
 
+# Disable shared libraries by default: can be enabled with --enable-shared
+LT_INIT([disable-shared])
+AC_PROG_LIBTOOL
+
 # Default prefix for bindir, etc... (eg >> ./build/bin)
 AC_PREFIX_DEFAULT(`pwd`/build)
 
+# Checks for header files.
+AC_CHECK_HEADERS([fcntl.h limits.h stdint.h stdlib.h string.h sys/ioctl.h unistd.h])
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_HEADER_STDBOOL
+AC_C_INLINE
+AC_TYPE_INT16_T
+AC_TYPE_INT32_T
+AC_TYPE_INT64_T
+AC_TYPE_SIZE_T
+AC_TYPE_SSIZE_T
+AC_TYPE_UINT16_T
+AC_TYPE_UINT32_T
+AC_TYPE_UINT64_T
+AC_CHECK_TYPES([ptrdiff_t])
+
+# Checks for library functions.
+AC_FUNC_MALLOC
+AC_FUNC_REALLOC
+AC_CHECK_FUNCS([memmove memset pow strchr strdup strerror strstr])
+
 # AC_DEFINE_UNQUOTED (variable, value, [description])
 # Define the C preprocessor variable variable to value
 # Use this macro instead of AC_DEFINE when variable or value is a shell variable. 
@@ -149,268 +259,305 @@ AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
 
 
 ###############################################################################
-######################## CONFIGURE LINE OPTIONS ###############################
+# PROCESS ARGUMENTS
-###############################################################################
-
-AC_MSG_CHECKING([if debug is enabled])
-
-if test "X$USE_DEBUG" = "Xyes"; then
-    AC_MSG_RESULT([yes])
-    CFLAGS="$CFLAGS -g"
-    CXXFLAGS="$CXXFLAGS -g"
-    FFLAGS="$FFLAGS -g"
-else
-    AC_MSG_RESULT([no])
-fi
-
-############################ fortran enabled ##################################
-AC_MSG_CHECKING([if fortran interface enabled])
-if test "X$USE_FORTRAN" = "Xyes"; then
-	AC_MSG_RESULT([yes])
-	LIB_FORTRAN="libH5PartF.la"
-        BUILD_LIBS="$BUILD_LIBS libH5PartF"
-	BUILD_TESTS="$BUILD_TESTS testf"
-
-	if test "X$USE_PARALLEL" = "Xyes"; then
-		AC_PROG_FC(mpif90 mpif77 ftn)
-	else
-		AC_PROG_FC(pgf90 pathf90 ifort ftn xlf_r g95 g90 gfortran)
-	fi
-
-	if test -z "$FC" ; then
-		AC_MSG_ERROR([Cannot find a Fortran compiler!])
-		exit 1
-	fi
-
-	if test $FC = "g90"; then
-		FFLAGS="${FFLAGS} -fno-second-underscore"
-	fi
-
-	if test $FC = "g95"; then
-		FFLAGS="${FFLAGS} -fno-second-underscore"
-	fi
-
-	AC_MSG_CHECKING([symbol convention in object files])
-	`cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
-	`cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
-	`cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
-	`cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
-
-	if test -f src/TestUnderscore ; then
-		UNDERSCORE_H=Underscore.h
-		`cd src && ./TestUnderscore > Underscore.h`
-		AC_MSG_RESULT([ok])
-	else
-		AC_MSG_RESULT([nok])
-		AC_MSG_ERROR([Cannot determine the symbon convention for Fortran object files!])
-		exit 1
-	fi
-
-else
-	AC_MSG_RESULT([no])
-fi
-
-
-# Disable shared libraries by default: can be enabled with --enable-shared
-LT_INIT([disable-shared])
-AC_PROG_LIBTOOL
-
-
-######################## parallel interface enabled ###########################
-AC_MSG_CHECKING([if parallel interface enabled])
-if test "X$USE_PARALLEL" = "Xyes"; then
-	AC_MSG_RESULT([yes])
-
-	CFLAGS="${CFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
-	CXXFLAGS="${CXXFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
-	FFLAGS="${FFLAGS} -DPARALLEL_IO"
-
-	AC_MSG_CHECKING([if we can compile MPI code without setting flags])
-	AC_TRY_LINK([#include "mpi.h"], [
-		MPI_Comm comm;
-		int n;
-		MPI_Comm_size( comm, &n ); ], 
-		[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
-
-	if test "X$r" = "Xno"; then
-		AC_MSG_ERROR([MPI wrapper can't compile or link MPI program! Please set the INCLUDE and LIBS variables manually.])
-		exit 1
-	fi
-
-else  # --enable-parallel=no
-	AC_MSG_RESULT([no])
-fi
-
-
-######################## tools enabled ###########################
-AC_MSG_CHECKING([whether tools are enabled])
-if test "X$USE_TOOLS" = "Xyes"; then
-    AC_MSG_RESULT([yes])
-    BUILD_TOOLS="h5pAttrib h5pToGNUplot homdynToH5p"
-    # tools + parallel
-    if test "X$USE_PARALLEL" = "Xyes"; then
-        BUILD_TOOLS="${BUILD_TOOLS} H5PartBench H5BlockBench"
-    fi
-else
-    AC_MSG_RESULT([no])
-fi
-
 
 ###############################################################################
-######################### PATH CHECKING & SETTING #############################
+# check libraries
-###############################################################################
 
-AC_MSG_CHECKING([for HDF5 root ])
+AC_CHECK_LIB([z], [compress2])
+
+# hdf5
+if test -z "${HDF5_PREFIX}"; then
+	# alternatives to HDF5_PREFIX
+	if test -n "${HDF5_DIR}"; then
+		HDF5_PREFIX=${HDF5_DIR}
+	fi
+fi
+if test -n "${HDF5_PREFIX}"; then
+        CPPFLAGS="$CPPFLAGS -I$HDF5_PREFIX/include"
+        LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
+fi
+AC_CHECK_LIB([hdf5], [H5open])
+AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes], 
+        [AC_MSG_ERROR([Cannot compile and link a HDF5 program])])
+AC_MSG_CHECKING([checking whether hdf5 lib supports parallel IO])
+AC_COMPILE_IFELSE([AC_LANG_SOURCE([[
+#include "hdf5.h"
+#ifndef H5_HAVE_PARALLEL
+# error macro not defined
+#endif
+]])], [H5_HAVE_PARALLEL="yes"], [H5_HAVE_PARALLEL="no"])
+AC_MSG_RESULT([$H5_HAVE_PARALLEL])
+
+# lustre
+AC_MSG_CHECKING([for lustre API ])
 AC_MSG_RESULT([])
-if test -n "${HDF5PATH}" ; then
+if test -n "${LUSTREPATH}"; then
-	P=${HDF5PATH}
+	P=${LUSTREPATH}
-elif test -n "${HDF5ROOT}"; then
+elif test -n "${LUSTREROOT}" ; then
-	P=${HDF5ROOT}
+	P=${LUSTREROOT}
-elif test -n "${HDF5HOME}" ; then
+elif test -n "${LUSTREHOME}" ; then
-	P=${HDF5HOME}
+	P=${LUSTREHOME}
-elif test -n "${HDF5_DIR}" ; then
+elif test -n "${LUSTRE_DIR}" ; then
-	P=${HDF5_DIR}
+	P=${LUSTRE_DIR}
 else
 	P=''
 	P="$P /usr"
 	P="$P /usr/local"
-	P="$P /usr/local/hdf5"
+	P="$P /usr/local/lustre"
-	P="$P /usr/local/packages/hdf5"
+	P="$P /opt/lustre"
-	P="$P /apps/hdf5"
-	P="$P /opt/hdf5"
 fi
-PATH_Search HDF5ROOT "$P" include/hdf5.h
+PATH_Search LUSTREROOT "$P" usr/include/lustre/liblustreapi.h
-if test -z "$HDF5ROOT"; then
+if test -z "$LUSTREROOT"; then
-	AC_MSG_ERROR([Cannot find an HDF5 library!])
+	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
-	exit 1
+else
+        CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
+        CPPFLAGS="$CPPFLAGS -I$LUSTREROOT/usr/include"
+        LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
+        LIBS="$LIBS -llustreapi"
 fi
 
-INCLUDES="$INCLUDES -I$HDF5ROOT/include"
+LIBS="$LIBS -lm"
-LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
-LIBS="$LIBS -lhdf5"
 
-AC_MSG_CHECKING([if we need to link to libsz ])
+
-if test -n "$HDF5ROOT"; then
+
-	if test -f $HDF5ROOT/lib/libsz.a; then
+############################ enabled bindings ###############################
+
+# C enabled?
+AC_MSG_CHECKING([if C interface enabled])
+if test "X$ENABLE_C" = "Xyes"; then
 	AC_MSG_RESULT([yes])
-		LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
+else
-                LIBS="$LIBS -lsz"
+        AC_MSG_RESULT([no])
+fi
+
+# fortran enabled?
+AC_MSG_CHECKING([if fortran interface enabled])
+if test "X$ENABLE_FORTRAN" = "Xyes"; then
+	AC_MSG_RESULT([yes])
+	AC_LANG_PUSH(Fortran)
+	
+	# Query Fortran symbol mangling. __AC_FC_NAME_MANGLING sets
+	# ac_cv_{f77,fc}_mangling. The value contains three fields, separated
+	# by commas:
+	#
+	# lower case / upper case:
+	#    case translation of the Fortran symbols
+	# underscore / no underscore:
+	#    whether the compiler appends "_" to symbol names
+	# extra underscore / no extra underscore:
+	#    whether the compiler appends an extra "_" to symbol names already
+	#    containing at least one underscore
+	__AC_FC_NAME_MANGLING
+	if test "X${ac_cv_fc_mangling}" == "Xlower case, no underscore, no extra underscore"; then
+	    	CPPFLAGS+=" -DFC_MANGLING_LOWERCASE_NO_UNDERSCORE"
+	elif test "X${ac_cv_fc_mangling}" == "Xlower case, underscore, no extra underscore"; then
+	    	CPPFLAGS+=" -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE"
+	elif test "X${ac_cv_fc_mangling}" == "Xlower case, underscore, extra underscore"; then
+	    	CPPFLAGS+=" -DFC_MANGLING_LOWERCASE_DOUBLE_UNDERSCORE"
+	elif test "X${ac_cv_fc_mangling}" == "Xupper case, no underscore, no extra underscore"; then
+	    	CPPFLAGS+=" -DFC_MANGLING_UPPERCASE_NO_UNDERSCORE"
+	elif test "X${ac_cv_fc_mangling}" == "Xupper case, underscore, no extra underscore"; then
+	    	CPPFLAGS+=" -DFC_MANGLING_UPPERCASE_SINGLE_UNDERSCORE"
+	elif test "X${ac_cv_fc_mangling}" == "Xupper case, underscore, extra underscore"; then
+	    	CPPFLAGS+=" -DFC_MANGLING_UPPERCASE_DOUBLE_UNDERSCORE"
+	fi
+	AC_LANG_POP(Fortran)
+else
+	AC_MSG_RESULT([no])
+fi
+
+# python enabled?
+if test "X$ENABLE_PYTHON" = "Xyes"; then
+
+    	AM_PATH_PYTHON([2.5])
+    	AX_PKG_SWIG([1.3], [], [ AC_MSG_ERROR([SWIG is required to build..]) ])
+    	#SWIG_ENABLE_CXX
+    	#SWIG_PYTHON
+
+    	PYTHON_PREFIX=`python-config --prefix`
+    	PYTHON_EXEC_PREFIX=`python-config --exec-prefix`
+
+    	# make sure numpy is available..
+    	AC_MSG_CHECKING([for numpy support])
+    	NUMPY_INCLUDE=`${PYTHON} -c 'import numpy; print numpy.get_include()'`
+
+	if test "X$?" = "X0" ; then
+		AC_MSG_RESULT([$NUMPY_INCLUDE])
     	else
 		AC_MSG_RESULT([no])
+ 		exit 1
     	fi
+   	AC_SUBST([NUMPY_INCLUDE])
+
+    	#check for parallel support
+    	if test "X$ENABLE_PARALLEL" = "Xyes"; then
+        	AC_MSG_CHECKING([for mpi4py support])
+        	MPI4PY_INCLUDE=`${PYTHON} -c 'import mpi4py; print mpi4py.get_include()'`
+
+        	if test "X$?" = "X0" ; then
+			AC_MSG_RESULT([$MPI4PY_INCLUDE])
+        	else
+            		AC_MSG_RESULT([no])
+            		exit 1
+        	fi
+		AC_SUBST([MPI4PY_INCLUDE])
+    	fi
+
+	AC_MSG_RESULT([ok])
+
+else
+    	AC_MSG_CHECKING([if python interface is enabled])
+    	AC_MSG_RESULT([no])
 fi
 
-LIBS="$LIBS -lz -lm"
+######################## large indices enabled ###########################
-
+AC_MSG_CHECKING([if large indices are enabled])
-
+if test "X$USE_LARGE_INDICES" = "Xyes"; then
-# Checks for header files.
+	AC_MSG_RESULT([yes])
-AC_CHECK_HEADERS([fcntl.h stdlib.h string.h unistd.h])
+	CFLAGS="${CFLAGS} -DUSE_LARGE_INDICES"
-
+else
-# Checks for typedefs, structures, and compiler characteristics.
+	AC_MSG_RESULT([no])
-AC_HEADER_STDBOOL
-AC_TYPE_INT64_T
-AC_TYPE_SIZE_T
-AC_TYPE_SSIZE_T
-
-# Checks for library functions.
-AC_FUNC_MALLOC
-AC_CHECK_FUNCS([memset pow strchr strdup])
-
-
-###############################################################################
-################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
-###############################################################################
-
-#if there was an external input for the variable...
-if test -n "$SAVE_CC"; then
-	CC="$SAVE_CC"
 fi
 
-if test -n "$SAVE_CXX"; then
+######################## parallel interface enabled ###########################
-	CXX="$SAVE_CXX"
+AC_MSG_CHECKING([if parallel interface enabled])
-fi
+if test "X$ENABLE_PARALLEL" = "Xyes"; then
+	AC_MSG_RESULT([yes])
 
-if test -n "$SAVE_FC"; then
+	AS_IF([test "x$H5_HAVE_PARALLEL" = "xno"],
-	FC="$SAVE_FC"
+	        [AC_MSG_ERROR([hdf5 does not support parallel IO!])])
-fi
 
-if test -n "$SAVE_CFLAGS"; then
+	if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
-	CFLAGS="$SAVE_CFLAGS"
+	   	AC_MSG_ERROR([VTK to H5hut grid converter cannot be compiled parallel!])
-fi
+	fi
+	CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
 
-if test -n "$SAVE_CXXFLAGS"; then
+        if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
-	CFLAGS="$SAVE_CXXFLAGS"
+		CPPFLAGS="$CPPFLAGS -DWITH_PARALLEL_H5GRID"
-fi
+        	AC_MSG_CHECKING([for ParMETIS])
+                if test "X$PARMETIS_PREFIX" != "X"; then
+                        CPPFLAGS="$CPPFLAGS -I$PARMETIS_PREFIX/include"
+	                LDFLAGS="$LDFLAGS -L$PARMETIS_PREFIX/lib"
+	        fi
 
-if test -n "$SAVE_FFLAGS"; then
+                LIBS="$LIBS -lparmetis -lmetis"
-	FFLAGS="$SAVE_FFLAGS"
+	        AC_TRY_LINK([#include <parmetis.h>], [
-fi
+	                ParMETIS_V3_PartGeom (NULL, NULL, NULL, NULL, NULL);],
+		        [AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
 
-if test -n "$SAVE_INCLUDES"; then
+	        if test "X$r" = "Xno"; then
-	INCLUDES="$SAVE_INCLUDES"
+		        AC_MSG_ERROR([ParMETIS])
-fi
+	        fi
-
+        fi
-if test -n "$SAVE_LDFLAGS"; then
+else  # --enable-parallel=no
-	LDFLAGS="$SAVE_LDFLAGS"
+	AC_MSG_RESULT([no])
-fi
+	AS_IF([test "x$H5_HAVE_PARALLEL" = "xyes"],
-
+	        [AC_MSG_ERROR([hdf5 with support for parallel IO cannot be used for non-parallel H5hut!])])
-if test -n "$SAVE_LIBS"; then
-	LIBS="$SAVE_LIBS"
 fi
 
 ###############################################################################
-############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
+# TOOLS
+AC_MSG_CHECKING([if we have to compile the VTK to H5hut grid converter])
+if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
+	AC_MSG_RESULT([yes])
+	if test -n "$VTK_PREFIX"; then
+		SAVE_C_INCLUDE_PATH="$C_INCLUDE_PATH"
+		SAVE_CPLUS_INCLUDE_PATH="$CPLUS_INCLUDE_PATH"
+		SAVE_LIBRARY_PATH="$LIBRARY_PATH"
+		C_INCLUDE_PATH="$C_INCLUDE_PATH $VTK_PREFIX/include"
+		CPLUS_INCLUDE_PATH="$CPLUS_INCLUDE_PATH $VTK_PREFIX/include"
+		LIBRARY_PATH="$LIBRARY_PATH $VTK_PREFIX/lib"
+	fi
+	AC_MSG_CHECKING([VTK inlcude files])
+	VTK_INCLUDES=`cmake --find-package -DNAME=VTK -DCOMPILER_ID=GNU -DLANGUAGE=C -DMODE=COMPILE 2>/dev/null`
+	if test "X$?" != "X0"; then
+		AC_MSG_RESULT([no])
+	        AC_MSG_ERROR([Cannot compile VTK to H5hut converter])
+	else
+		AC_MSG_RESULT([yes])
+	fi
+	AC_MSG_CHECKING([VTK libraries])
+	VTK_LIBS=`cmake --find-package -DNAME=VTK -DCOMPILER_ID=GNU -DLANGUAGE=C -DMODE=LINK 2>/dev/null`
+	if test "X$?" != "X0"; then
+		AC_MSG_RESULT([no])
+	        AC_MSG_ERROR([Cannot compile VTK to H5hut converter]); 
+	else
+		AC_MSG_RESULT([yes])
+	fi
+
+else
+	AC_MSG_RESULT([no])
+fi
+
 ###############################################################################
-# AC_SUBST (variable, [value])
+# EXAMPLES
-# Create an output variable from a shell variable.  Make AC_OUTPUT substitute
+AC_MSG_CHECKING([if we have to compile the H5hut examples])
-# the variable variable into output files (typically one or more `Makefile's).
+if test "X$ENABLE_EXAMPLES" = "Xyes"; then
-# This means that AC_OUTPUT will replace instances of `@variable@' in input
+	AC_MSG_RESULT([yes])
-# files with the value that the shell variable variable has when AC_OUTPUT is
+else
-# called.  This value of variable should not contain literal newlines.  If
+	AC_MSG_RESULT([no])
-# value is given, in addition assign it to variable. 
+fi
+
+###############################################################################
+# EXPORTING VARIABLES & CREATING OUTPUT FILES
+AM_CPPFLAGS=$CPPFLAGS
+AM_LDFLAGS=$LDFLAGS
+
+AC_SUBST(HDF5_PREFIX)
 AC_SUBST(CFLAGS)
-AC_SUBST(CXXFLAGS)
 AC_SUBST(FFLAGS)
-AC_SUBST(INCLUDES)
+AC_SUBST(AM_CPPFLAGS)
-AC_SUBST(LDFLAGS)
+AC_SUBST(AM_LDFLAGS)
-AC_SUBST(LIBS)
+AC_SUBST(VTK_INCLUDES)
-AC_SUBST(UNDERSCORE_H)
+AC_SUBST(VTK_LIBS)
-AC_SUBST(LIB_FORTRAN)
-AC_SUBST(BUILD_TESTS)
-AC_SUBST(BUILD_TOOLS)
-
-# Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'),
-# substituting the output variable values.
 AC_CONFIG_FILES([
 	Makefile
 	src/Makefile
-	doc/Makefile
+	src/h5core/Makefile
+	src/include/Makefile
+	src/include/h5core/Makefile
+        src/C/Makefile
+        src/Fortran/Makefile
+        src/Python/Makefile
 	test/Makefile
+        doc/Makefile
 	tools/Makefile
+	tools/h5hutcc
+        tools/vtk2h5grid/Makefile
+        examples/H5/Makefile
+        examples/H5Part/Makefile
+        examples/H5Block/Makefile
+        examples/H5Fed/Makefile
 ])
 
 AC_OUTPUT
 
 ###############################################################################
-########################## PRINTING SUMMARY ###################################
+# PRINTING SUMMARY
-###############################################################################
 AC_MSG_RESULT([ ])
 AC_MSG_RESULT([Summary:])
 AC_MSG_RESULT([ ])
 AC_MSG_RESULT([Host OS:             $host_os])
 AC_MSG_RESULT([Host CPU:            $host_cpu])
 AC_MSG_RESULT([Host vendor:         $host_vendor])
-AC_MSG_RESULT([Build libraries:     $BUILD_LIBS])
-AC_MSG_RESULT([Build test programs: $BUILD_TESTS])
-AC_MSG_RESULT([Build tools:         $BUILD_TOOLS])
 AC_MSG_RESULT([CC =                 $CC])
 AC_MSG_RESULT([CXX =                $CXX])
 AC_MSG_RESULT([FC =                 $FC])
 AC_MSG_RESULT([CFLAGS =             $CFLAGS])
-AC_MSG_RESULT([CXXFLAGS =           $CXXFLAGS])
 AC_MSG_RESULT([FFLAGS =             $FFLAGS])
-AC_MSG_RESULT([INCLUDES =           $INCLUDES])
+AC_MSG_RESULT([AM_CPPFLAGS =        $AM_CPPFLAGS])
-AC_MSG_RESULT([LDFLAGS =            $LDFLAGS])
+AC_MSG_RESULT([AM_LDFLAGS =         $AM_LDFLAGS])
 AC_MSG_RESULT([LIBS =               $LIBS])
-AC_MSG_RESULT([HDF5ROOT =           $HDF5ROOT])
+AC_MSG_RESULT([HDF5_PREFIX =        $HDF5_PREFIX])
+AC_MSG_RESULT([LUSTREROOT =         $LUSTREROOT])
+
+if test "x$ENABLE_PYTHON" = "xyes"; then
+	AC_MSG_RESULT([PYTHON =             $PYTHON])
+	AC_MSG_RESULT([SWIG =               $SWIG])
+	AC_MSG_RESULT([NUMPY_INCLUDE =      $NUMPY_INCLUDE])
+	if test "x$ENABLE_PARALLEL" = "xyes"; then
+		AC_MSG_RESULT([MPI4PY_INCLUDE =     $MPI4PY_INCLUDE])
+	fi
+fi
 AC_MSG_RESULT([ ])

depcomp

@@ -1,529 +0,0 @@
-#! /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/Examples/meshexample.txt

@@ -0,0 +1,77 @@
+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

@@ -0,0 +1,107 @@
+# 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

@@ -0,0 +1,59 @@
+# 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

@@ -0,0 +1,80 @@
+# 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

@@ -0,0 +1,101 @@
+# 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

@@ -0,0 +1,13 @@
+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

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

doc/Examples/trimesh_dgraph_level0.metis.part.3

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

doc/Examples/trimesh_dnode_level1.metis

@@ -0,0 +1,49 @@
+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

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

@@ -0,0 +1,13 @@
+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

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

doc/Examples/trimesh_level0.metis.ngraph

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

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

doc/Examples/trimesh_level1.metis

@@ -0,0 +1,41 @@
+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

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

doc/H5.dox

@@ -0,0 +1,171 @@
+/*!
+\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> Mark Howison (NERSC/LBNL) </LI>
+<LI> Prabhat (NERSC/LBNL) </LI>
+<LI> Wes Bethel (NERSC/LBNL) </LI>
+</UL>
+
+Previous developers:
+
+<UL>
+<LI> Benedikt Oswald (PSI) </LI>
+<LI> Cristina Siegerist (NERSC/LBNL)</LI>
+<LI> John Shalf (NERSC/LBNL)</LI>
+</UL>
+
+For more information, please contact the
+ <a href="mailto:h5part@lists.psi.ch">h5part</a> mailing list.
+
+\defgroup c_api                                 C API
+@{
+    \note The C API is implemented with '\c static \c inline' functions to minimize overhead.
+    \defgroup h5_c_api                  H5
+    @{
+        \defgroup h5_file		File interface
+
+	In this section we document the interface for accessing H5hut files.
+	
+        \defgroup h5_model          	Setting up the data model
+
+	The fundamental data model of H5hut is pretty simple. There
+	are (time-)steps to group data, that's it. In this section we
+	document the interface to these (time-)steps.
+	
+        \defgroup h5_file_attribs   	File attributes interface
+
+        File attributes are small datasets that can be used to
+        describe specific properties of a file. The H5hut API provides
+        functions to attach (write), read and inquire file attributes.
+
+        \defgroup h5_step_attribs   	Step attributes interface
+
+        Step attributes are similar to file attributes but are
+        attached to (time-)steps. They can be used to describe
+        specific properties of a specific step. The H5hut API provides
+        functions to attach (write), read and inquire step attributes.
+
+	\defgroup h5_attach		Attaching files
+
+	Sometimes it is required (or at least useful) to attach
+	additional information to H5hut files. H5hut provides
+	functions to attach other files to H5hut files. The attached
+	files can be of any type.
+	
+        \defgroup h5_log            	Controlling verbosity level
+
+	Controlling the verbosity level of H5hut. By default only
+	error messages are printed. For debugging it might be helpful
+	to increase the verbosity level.
+	
+        \defgroup h5_debug          	Controlling debug output
+
+	Debug output mainly intended for developers.
+
+        \defgroup h5_error          	Error handling interface
+
+	H5hut comes with two error handler. The default error handler
+	prints an error message (which can be suppressed by setting
+	the verbosity level to \c 0), sets an internal error number
+	and returns to the calling program with the value \c
+	H5_FAILURE. It is up to the programmer to handle the error
+	properly. In certain use-cases it make sense just to abort the
+	program, so no additional error handling is needed.  H5hut
+	provides an abort error-handler for this use-cases-
+	
+    @}
+    \defgroup h5part_c_api              H5Part
+    @{
+        \defgroup h5part_model          Setting up the data model
+
+	The H5Part data model interface provides functions to set and
+	inquire (per core) views on datasets.
+	
+        \defgroup h5part_io         	Dataset interface
+
+	The dataset interface provides functions to read and write
+	datasets. The following data types are supported:
+
+	- 64-bit floating point numbers (\c h5_float64_t)
+	- 32-bit floating point numbers (\c h5_float32_t)
+	- 64-bit integers (\c h5_int64_t)
+	- 32-bit integers (\c h5_int32_t)
+
+	\note Before you can write or read a dataset, you have to
+	define a "view" on the dataset for each core.
+
+    @}
+    \defgroup h5block_c_api             H5Block
+    @{
+        \defgroup h5block_model         Setting up the data model
+
+	The H5Block data model interface provides functions to set and
+	inquire (per core) views on fields. 
+
+	\defgroup h5block_io            Interface to block structured data
+
+	H5Block provides functions to store and retrieve
+
+	- 3-dimensional fields with scalar values
+	- 3-dimensional fields with 3-dimensional vectors as values
+
+	The following datatypes are supported:
+	
+	- 64-bit floating point numbers (\c h5_float64_t)
+	- 32-bit floating point numbers (\c h5_float32_t)
+	- 64-bit integers (\c h5_int64_t)
+	- 32-bit integers (\c h5_int32_t)
+
+	\defgroup h5block_attrib	Attaching attributes to field data
+
+        Field attributes are small datasets that can be used to
+        describe specific properties of a field like origin, spacing
+        or coordinates. The H5hut API provides functions to attach
+        (write), read and inquire file attributes.
+                    
+   @}
+@}
+*/
+
+/*!
+        \defgroup f90_api                               Fortran90 API
+        @{
+                \defgroup h5_f90_api                    H5
+                @{
+                        \defgroup h5_file_f             file interface
+                        \defgroup h5_model_f            setting up the data model
+                        \defgroup h5_file_attribs_f     reading and writing file attributes
+                        \defgroup h5_step_attribs_f     reading and writing step attributes	
+			\defgroup h5_log_f		control verbosity level
+			\defgroup h5_debug_f		control debug output
+		        \defgroup h5_error_f            error handling interface
+		@}
+                \defgroup h5part_f90_api                H5Part
+                @{
+                        \defgroup h5part_model_f        setting up the data model
+                        \defgroup h5part_io_f           reading and writing datasets
+                @}
+                \defgroup h5block_f90_api               H5Block
+                @{
+                        \defgroup h5block_model_f       setting up the data model
+                        \defgroup h5block_io_f          reading and writing datasets
+                        \defgroup h5block_attrib_f      reading and writing attributes
+                @}
+        @}
+*/
+

doc/Makefile.am

@@ -1,2 +1,14 @@
 EXTRA_DIST = \
-	Doxyfile doxyfooter
+	Doxyfile \
+        H5.dox
+
+all:
+
+doc:
+
+doxydoc:
+	doxygen
+
+clean-local:
+	$(RM) -r ReferencePages TWiki
+	$(RM) *~

doc/TracFooter.html

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

doc/TracHeader.html

@@ -0,0 +1,4 @@
+<style type="text/css">
+        h1 { text-align: center; }
+</style>
+

doc/doxyheader

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

doc/html2twiki

@@ -0,0 +1,36 @@
+#!/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/postprocess.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python
+
+from lxml import etree
+from lxml.html import builder as E
+import os
+import re
+
+tree   = etree.parse('tagfile')
+tags = tree.xpath ('//member[@kind="function"]')
+tags_per_files = {}
+for tag in tags:
+     name = tag.find("name").text
+     anchor = tag.find("anchor").text
+     anchorfile = tag.find("anchorfile").text
+     if anchorfile in tags_per_files:
+         tags_per_files[anchorfile].append([name, anchor])
+     else:
+         tags_per_files[anchorfile] = [[name, anchor]]
+
+
+prefix = None
+for line in open("Doxyfile", "r"):
+     if re.search ("^OUTPUT_DIRECTORY", line):
+          prefix = line.split("=")[-1].strip()
+
+if not prefix:
+     prefix = "."
+
+parser = etree.HTMLParser()
+for filename,anchors in tags_per_files.items():
+     print "Processing file: %s/%s" % (prefix, filename)
+     tree = etree.parse ("%s/%s" % (prefix, filename), parser)
+     for name,id in anchors:
+          anchor = tree.xpath ('//a[@id="%s"]' % id)
+          el = E.A(id="%s" % name)
+          anchor[0].addnext (el)
+
+     f = open ("%s/%s" % (prefix, filename), "w")
+     f.write (etree.tostring (tree))

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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,25 @@
+# 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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,25 @@
+# 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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,25 @@
+# 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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,25 @@
+# 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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,25 @@
+# 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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,25 @@
+# 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

@@ -0,0 +1,15 @@
+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

@@ -0,0 +1,29 @@
+# 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

@@ -0,0 +1,15 @@
+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

@@ -0,0 +1,29 @@
+# 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

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

@@ -0,0 +1,32 @@
+# 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

@@ -0,0 +1,15 @@
+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

@@ -0,0 +1,29 @@
+# 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