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compare: H5hut/src:H5Part-1.3.3
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H5hut/src:master H5hut/src:int8 H5hut/src:1.99.x H5hut/src:1.99 H5hut/src:1.6 H5hut/src:1.4 H5hut/src:1.2 H5hut/src:1.0
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1 Commits
1.99.12 .. H5Part-1.3.3

Author SHA1 Message Date
Kurt Stockinger 7d140c6cb6 Preparing tag 1.4 2007-08-29 01:43:58 +00:00
620 changed files with 15849 additions and 220389 deletions
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src/h5core/h5t_readwrite_trim.c -text
src/h5core/h5t_ref_elements.c -text
src/h5core/h5t_ref_elements_private.h -text
src/h5core/h5t_retrieve.c -text
src/h5core/h5t_retrieve_private.h -text
src/h5core/h5t_retrieve_tetm.c -text
src/h5core/h5t_retrieve_trim.c -text
src/h5core/h5t_store.c -text
src/h5core/h5t_store_private.h -text
src/h5core/h5t_store_tetm.c -text
src/h5core/h5t_store_trim.c -text
src/h5core/h5t_store_trim_private.h -text
src/h5core/h5t_tags.c -text
src/h5core/h5t_tags_private.h -text
src/h5core/h5t_types_private.h -text
src/h5core/h5u_errorhandling_private.h -text
src/h5core/h5u_model.c -text
src/h5core/h5u_readwrite.c -text
src/h5core/h5u_types_private.h -text
src/include/H5.h -text
src/include/H5Block.h -text
src/include/H5Block_readwrite.h -text
src/include/H5Fed.h -text
src/include/H5Fed_adjacency.h -text
src/include/H5Fed_inquiry.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/H5_attachments.h -text
src/include/H5_attribs.h -text
src/include/H5hut.h -text
src/include/Makefile.am -text
src/include/grephdr -text
src/include/h5core/Makefile.am -text
src/include/h5core/h5_attach.h -text
src/include/h5core/h5_attribs.h -text
src/include/h5core/h5_core.h -text
src/include/h5core/h5_errno.h -text
src/include/h5core/h5_errorhandling.h -text
src/include/h5core/h5_hdf5.h -text
src/include/h5core/h5_maps.h -text
src/include/h5core/h5_openclose.h -text
src/include/h5core/h5_readwrite.h -text
src/include/h5core/h5_syscall.h -text
src/include/h5core/h5_types.h -text
src/include/h5core/h5b_attribs.h -text
src/include/h5core/h5b_model.h -text
src/include/h5core/h5b_readwrite.h -text
src/include/h5core/h5t_adjacencies.h -text
src/include/h5core/h5t_core.h -text
src/include/h5core/h5t_inquiry.h -text
src/include/h5core/h5t_map.h -text
src/include/h5core/h5t_model.h -text
src/include/h5core/h5t_readwrite.h -text
src/include/h5core/h5t_ref_elements.h -text
src/include/h5core/h5t_retrieve.h -text
src/include/h5core/h5t_storemesh.h -text
src/include/h5core/h5t_tags.h -text
src/include/h5core/h5u_model.h -text
src/include/h5core/h5u_readwrite.h -text
src/TestUnderscore.f -text
src/TestUnderscoreC.c -text
test/Bench.c -text
test/BlockTestSpecs.txt -text
test/H5BlockDissolveGhosts.c -text
test/H5BlockParTestScalarField.c -text
test/H5BlockParTestScalarField.pbs -text
test/H5BlockParTestScalarFieldF.f90 -text
test/H5BlockTestAttributes.c -text
test/H5BlockTestAttributesF.f90 -text
test/H5ParallelTest.cc -text
test/H5PartAndreasTest.cc -text
test/H5PartTest.cc -text
test/H5PartTestParallel.cc -text
test/H5test.cc -text
test/H5testF.f -text
test/H5testFpar.f90 -text
test/Makefile.am -text
test/h5_attach_test.c -text
test/h5b_read.c -text
test/h5b_test.c -text
test/h5b_write.c -text
test/h5u_read.c -text
test/h5u_test.c -text
test/h5u_write.c -text
test/params.h -text
test/testframe.c -text
test/testframe.h -text
tools/H5PartMerge/AUTHORS -text
tools/H5PartMerge/COPYING -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
.gitignore
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/H5hut
/INSTALL
/Makefile
/Makefile.in
/aclocal.m4
/autom4te.cache
/build
/config.guess
/config.h
/config.h.in
/config.log
/config.status
/config.sub
/configure
/depcomp
doc/Makefile
doc/Makefile.in
examples/H5Block/H5BlockParTestScalarField
examples/H5Block/H5BlockTestAttributes
examples/H5Block/Makefile
examples/H5Block/Makefile.in
examples/H5Fed/.deps
examples/H5Fed/Makefile
examples/H5Fed/Makefile.in
examples/H5Fed/large_tet.h5
examples/H5Fed/simple_tet.h5
examples/H5Fed/simple_triangle.h5
examples/H5Fed/small_tet.h5
examples/H5Fed/tetmesh_adjacencies
examples/H5Fed/tetmesh_read
examples/H5Fed/tetmesh_read_tags
examples/H5Fed/tetmesh_write
examples/H5Fed/tetmesh_write2
examples/H5Fed/tetmesh_write_tags
examples/H5Fed/trimesh_adjacencies
examples/H5Fed/trimesh_read
examples/H5Fed/trimesh_write
examples/H5Fed/trimesh_write_dunetest
examples/H5Part/Bench
examples/H5Part/H5PartAndreasTest
examples/H5Part/H5PartTestP
examples/H5Part/H5test
examples/H5Part/Makefile
examples/H5Part/Makefile.in
/install-sh
/libtool
/ltmain.sh
/m4
/missing
src/.deps
src/C/.deps
src/C/Makefile
src/C/Makefile.in
src/C/libH5hutC.a
src/Fortran/.deps
src/Fortran/Makefile
src/Fortran/Makefile.in
src/Fortran/TestUnderscore
src/Fortran/Underscore.h
src/Makefile
src/Makefile.in
src/h5core/.deps
src/h5core/Makefile
src/h5core/Makefile.in
src/h5core/libH5hut.a
src/include/H5hutF.h
src/include/Makefile
src/include/Makefile.in
src/include/h5core/Makefile
src/include/h5core/Makefile.in
src/lib
/stamp-h1
/svn-prop.tmp
/test-driver
test/.deps
test/Makefile
test/Makefile.in
test/h5_attach.h5
test/h5_attach_test
test/h5b_test
test/h5u_test
tools/.deps
tools/Makefile
tools/Makefile.in
tools/h5PartDcToVtk
tools/h5PartSurfaceToVtk
tools/h5hutcc
tools/vtk2h5grid/.deps
tools/vtk2h5grid/Makefile
tools/vtk2h5grid/Makefile.in
tools/vtk2h5grid/cgun_full.h5
tools/vtk2h5grid/cgun_full.vtk
tools/vtk2h5grid/vtk2h5grid
COPYING
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*** Copyright Notice ***
H5hut Copyright (c) 2006-2010, The Regents of the University of California,
through Lawrence Berkeley National Laboratory (subject to receipt of any
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
Institut (Switzerland). All rights reserved.
If you have questions about your rights to use or distribute this
software, please contact Berkeley Lab's Technology Transfer Department
at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
NOTICE. This software was developed under partial funding from the U.S.
Department of Energy. As such, the U.S. Government has been granted for
itself and others acting on its behalf a paid-up, nonexclusive,
irrevocable, worldwide license in the Software to reproduce, prepare
derivative works, and perform publicly and display publicly. Beginning
five (5) years after the date permission to assert copyright is obtained
from the U.S. Department of Energy, and subject to any subsequent five
(5) year renewals, the U.S. Government is granted for itself and others
acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide
license in the Software to reproduce, prepare derivative works,
distribute copies to the public, perform publicly and display publicly,
and to permit others to do so.
*** License agreement ***
H5Part Copyright (c) 2006-2009, The Regents of the University of California,
through Lawrence Berkeley National Laboratory (subject to receipt of any
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
Institut (Switzerland). All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
(1) Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
(2) Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
(3) Neither the name of the University of California, Lawrence Berkeley
National Laboratory, U.S. Dept. of Energy, Paul Scherrer Institut
(Switzerland) nor the names of its contributors may be used to endorse
or promote products derived from this software without specific prior
written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
You are under no obligation whatsoever to provide any bug fixes,
patches, or upgrades to the features, functionality or performance of
the source code ("Enhancements") to anyone; however, if you choose to
make your Enhancements available either publicly, or directly to
Lawrence Berkeley National Laboratory, without imposing a separate
written license agreement for such Enhancements, then you hereby grant
the following license: a non-exclusive, royalty-free perpetual license
to install, use, modify, prepare derivative works, incorporate into
other computer software, distribute, and sublicense such enhancements or
derivative works thereof, in binary and source code form.
COPYRIGHT
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*** Copyright Notice ***
H5Part Copyright (c) 2006, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and the Paul Scherrer Institut (Switzerland). All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov referring to "H5Part (LBNL Ref CR-2255)"
NOTICE. This software was developed under partial funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
GNUmakefile.orig
Executable
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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 ($(PARALLEL), yes) #parallel
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
endif
else
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o
endif
endif
include rules.make
Makefile.am
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@@ -1,11 +1,11 @@
ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = autogen.sh
# Trial by Antino Kim
# Top level Makefile.am
SUBDIRS = \
doc \
src \
test \
tools \
doc
tools
MAINTAINERCLEANFILES = \
config.h \
Makefile.orig
Executable
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# This is a very rudimentary multiarchitecture makefile
# You need to uncomment the default block of make variables you need
# Some key things to watch for are the following defines
# -DREGRESSIONTEST : enables a main(){} inside of
# the H5Part.cc file that does simple regression testing.
# -DPARALLEL_IO : If you want to use parallel HDF5, you have to
# enable this. Otherwise, you get only the serial
# implementation of the library.
# MacOS-X Serial
#CXX = c++
#CC = cc
#F90 = xlf
#H5HOME = /usr/local
#CFLAGS = -O -g -I$(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
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#### H5PART 1.99.10 ###########################################################
Bugfixes in the malloc wrappers
Converter from vtk to H5hut added.
Bugfixes in the autotools files.
#### H5PART 1.99.9 ############################################################
Bugfix in option parsing in tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk
tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk removed from list of tools
to be compiled. These tools should be moved to another repository anyway.
#### H5PART 1.99.8 ############################################################
Bugfixes
#### H5PART 1.99.7 ############################################################
Linking problem on Linux fixed
#### H5PART 1.99.6 ############################################################
#### H5PART 1.99.5 ############################################################
#### H5PART 1.99.4 ############################################################
#### H5PART 1.99.3 ############################################################
#### H5PART 1.99.2 ############################################################
#### H5PART 1.99.1 ############################################################
#### H5PART 1.99 ############################################################
Renamed type:
H5PartFile -> h5_file_t
h5part_int64_t -> h5_int64_t
Renamed functions:
#### H5PART 1.6.6 ############################################################
Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
interface.
Added missing type normalization for int32 type.
Rewrite of h5pAttrib tool.
#### H5PART 1.6.5 ############################################################
Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
#### H5PART 1.6.4 ############################################################
Fixed bug where H5PartSetViewIndices was not setting an empty view when the
number of elements is 0.
Set a threshold on the HDF5 alignment parameter so that small metadata writes
are not aligned, which causes large gaps in the file.
#### H5PART 1.6.3 ############################################################
New build system uses libtool and can build shared libraries.
Fixed a bug that incorrectly identifies the number of selected points in a view
when using H5PartSetViewIndices.
Fixed bug in Fortran test reported by several people, as well as several
incorrect views set in the C test that were causing segfaults.
Fixed name mismatches in the Fortran interface, and an off-by-one indexing
problem.
#### H5PART 1.6.2 ############################################################
Removed H5PartSetViewEmpty
--------------------------
An empty view can now be selected with:
H5PartSetNumParticles(file, 0);
Bug Fixes to Attribute Calls in Fortran API
-------------------------------------------
Fixed a problem where attribute values were reverting to zero.
#### H5PART 1.6.1 ############################################################
Chunking in the H5Part API
--------------------------
There is now an H5Part equivalent H5PartSetChunkSize to the existing
H5BlockDefine3DChunkDims call. Both of these calls enable the chunking
mechanism in the underlying HDF5 layer. Chunking is used in combination
with the aligned open calls to pad datasets to alignment multiples
on disk.
All Steps Available on Write
----------------------------
Previously, existing steps in a file were only accessible in read-only mode.
Now, all steps are available in all modes, including write-truncate and
write-append. Thus, it is now possible to overwrite existing data in write
mode. To help alert the user to this possibility, a warning is issued every
time an existing dataset is written to. Warnings can be printed by setting
the verbosity to H5PART_VERB_WARN or higher.
New Throttling Routine
----------------------
Previously, a throttle factor of N meant that for P processors, the total
number of P writes were divided into N batches of P/N writes.
To better accommodate round-robin lustre striping, the new policy is to
execute P/N batches of N writes. Thus, matching N to the number of stripes
results in the desirable 1-1 matching of writers to stripes.
Other Fixes
-----------
* The configure script should correctly detect PGI compilers now.
* There was a small memory leak in the Fortran file open calls.
* There was a compile error with HDF5 1.6.x due to a missing assignment.
#### H5PART 1.6 ##############################################################
Updated Documentation
---------------------
The Fortran API has been added to the doxygen documentation. Most entries have
a reference to their respective C API call.
Regression Test Suite
---------------------
The test subdirectory has been reorganized to include a systematic series
of regression tests of common use cases for the API. The goal is to have both
complete coverage of the API (every call is exercised) and testing of some
unlikely or unsuspected values and cases.
Currently, the C test covers the entire H5Part API and the Fortran test is
still in development.
Benchmark Utilities
-------------------
Two benchmarking utilities, H5PartBench and H5BlockBench, have been added to
the tools collection. Both require the parallel library and have functionality
and syntax similar to the IOR benchmark:
http://sourceforge.net/projects/ior-sio/
File Mode Flags
---------------
Previously, the only flags used were H5PART_READ, H5PART_WRITE, and
H5PART_APPEND, and these were mutually exclusive. Additional flags have been
added to select the underlying virtual file driver (VFD) that HDF5 uses in
parallel mode and to accommodate the lustre filesystem:
H5PART_VFD_MPIPOSIX (use the MPI-POSIX driver, which bypasses MPI-IO)
H5PART_VFD_MPIIO_IND (use MPI-IO in independent mode)
H5PART_FS_LUSTRE (activate H5P tunings for the lustre stripe size)
These flags can be specified using the typical bitwise OR method, e.g.
char flag = H5PART_WRITE | H5PART_VFD_MPIPOSIX | H5PART_FS_LUSTRE;
will select write mode with these two additional options.
The parallel library now defaults to using the MPI-IO collective mode driver
(previously it used independent mode). The collective buffering algorithm in
the Cray XT4/5 environment has been substantially improved in the last year,
and defaulting to collective mode allows us to take advantage of these
improvements automatically.
There are also new open calls H5PartOpenAlign and H5PartOpenParallelAlign that
take an additional 'alignment' value. This value is passed to HDF5 and used to
pad out objects so that they align to filesystem boundaries. For instance, it
would make sense to use the stripe size as the alignment value when writing to
a lustre filesystem.
Unified 'View' Model
--------------------
Views are now supported in both read and write mode (previously only supported
in read mode). It is possible to specify non-sensical views: you could for
instance specify a read view that is larger than the dataset on disk. Or you
could create a write view that is larger than the data in memory. In those
cases, you will encounter an error when you try to perform a read or write
operation on a dataset.
There are two new methods for selecting views. H5PartSetNumParticlesStrided
selects a view with $n$ particles per processor, but such that the data in
memory is expected to have a 'stride' factor. For instance, if you have
particle data with fields $x$ and $y$ and a single array with entries
$x1,y1,x2,y2...$, then the stride factor is 2. Striding works for both reads
and writes and only affects the view of memory: individual fields are still
stored as individual arrays on disk.
The second new method is H5PartSetViewIndices, which allows for point
selections of datasets. You can pass a list of indices for the points you
want to select. This is useful, for instance, when interfacing with FastBit
to perform queries that select a small subset of non-contiguous particles.
Because views are now supported on write, it is possible to write a dataset
using multiple 'passes' or to leave some values unwritten.
Also, all views are now *inclusive*, so that a view of (0,9) corresponds
to the 10 items 0, 1, 2, ... 9.
Internal Handling of Dataspaces
-------------------------------
H5PartSetNumParticles and H5PartSetNumParticlesStrided now share the same
HDF5 dataspace state in the H5PartFile struct with the calls that modify
the view (H5PartSetView etc.). Previously, the memory and disk dataspaces
were regenerated from the view on every read access, which was unnecessary.
Autogeneration of API Calls
---------------------------
Python scripts have been added to automatically generate read/write call
variants for different data types.
Renamed Fortran Include
-----------------------
The automake system no longer greps the *F90.inc files to generate an include
called 'H5Part.inc'. Instead, the *F90.inc files have been renamed to *.f90,
and awk is used to generate an 'H5PartF.h' file (the same naming convention
as in MPI's 'mpif.h').
The change to *.f90 was necessary to facilitate integration of the Fortran
API into doxygen. Note that the *.f90 files will not compile, nor can they
be included directly. Simply use
include 'H5PartF.h'
in your Fortran code to include all the definitions for Fortran H5Part/H5Block
calls.
64 Char Limit on Dataset Names
------------------------------
Previously, a user could overrun internal buffers for dataset names. Now, a
fixed limit of 64 chars is imposed. Dataset names that are longer than this are
truncated and a warning is printed. We expect that most users are using
short canonical names like x, px, id, etc.
Changes to Existing API
-----------------------
The H5BlockGetFieldInfo and H5BlockGetFieldInfoByName calls now both include
a parameter for the 'type' of the field.
#### H5PART 1.4 ##############################################################
Error Handling
--------------
Now all functions, in which an error could occure, are returning a
README
+418
View File
@@ -0,0 +1,418 @@
==============================================================================
README file for H5Part configure
==============================================================================
+ 0. HDF5 library
-----------------
Make sure you have a working version of the HDF5 library in your computer. If you plan
to use parallel I/O you need to use a parallel HDF5 version. If you don't have the
library download the sources from http://hdf.ncsa.uiuc.edu/HDF5/
+ 1. Quick start (If you feel lucky...)
----------------------------------------
For many platforms, where compilers are installed in the "default" location
and all the environment variables are set correctly, it should be sufficient
to type:
./configure [OPTIONS] && make [install]
to have the libraries and test program compiled.
==============================================================================
+ 2. configure line options
----------------------------
(1) Enable options
--enable-fortran
--enable-parallel
--enable-tools
--enable-python
--enable-64 (only for AIX and Irix)
(2) Setting compilers related variables manually
To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE. See below for descriptions of some of the useful variables.
Compiler environment variables:
CC C compiler command
CXX C++ compiler command
FC Fortran compiler command
(3) Setting prefix for installation manually
--prefix=PREFIX install files in PREFIX
For more information, type:
./configure --help
==============================================================================
+ 3. Platform specific settings for compiling libraries & test programs
------------------------------------------------------------------------
Building
make : builds the libraries and test programs
make install: builds and installs
make clean : removes extraneous object files
make distclean : returns configuration to unconfigured state
As tested on hosts:
(1) Davinci <davinci.nersc.gov> (Linux"SUSE"-ia64)
---------------------------------------------------
FIRST THING FIRST!! Type:
module load intel
to have the proper compilers set up for use.
module load hdf5_par
[NOTE: module load hdf5 does not work at this moment.
Possible installation error of HDF5 on Davinci.]
Brief profile:
CC = icc
CXX = icc
FC = ifort
MPICC = icc
MPICXX = icc
MPIFC = ifort
If default doesn't work, try:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
mpirun 2 H5testFpar
mpirun 2 H5PartTestP
NOTE: Number 2 above is a arbitrary number that indicates the number of processes.
(2) Jacquard <jacquard.nersc.gov> (Linux"SUSE"-x86_64)
-------------------------------------------------------
Brief profile:
CC = pathcc
CXX = pathCC
FC = pathf90
MPICC = mpicc
MPICXX = mpicxx
MPIFC = mpif90
If default doesn't work, try:
For C shell:
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
For Korn or Bourne shell:
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
In Jacquard, we need a script to run parallel programs, since Jacquard does not support interactive parallel processing. Instead, we need to submit the task to a queue. A sample script (run_H5testFpar.scr) may look like below:
+++++++++++++++++++++++++++++++++++++++
#!/bin/csh
#PBS -l nodes=1:ppn=2,walltime=00:05:00
#PBS -N H5testFpar
#PBS -o H5testFpar.out
#PBS -e H5testFpar.err
#PBS -q debug
#PBS -A mpccc
#PBS -V
setenv PBS_OWORKDIR /home/H5Part/test
cd $PBS_O_WORKDIR
mpirun -np 2 ./H5testFpar
+++++++++++++++++++++++++++++++++++++++
Then, we need to submit the task to a queue by running:
qsub run_H5testFpar.scr
After processed, the result will appear in H5testFpar.out, and error messages will appear in H5testFpar.err.
(3) Bassi <bassi.nersc.ogv> (AIX5.3.0.0-Power 3)
-------------------------------------------------
FIRST THING FIRST!! Type:
module load gcc
to have the proper compilers set up for use.
Brief profile:
CC = cc_r
CXX = cc_r
FC = xlf_r
MPICC = mpcc_r
MPICXX = mpcc_r
MPIFC = mpxlf_r
If default doesn't work, try:
For C shell:
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
For Korn or Bourne shell:
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
unsetenv MP_SINGLE_THREAD
poe ./H5PartTestP -procs 2 -nodes 1
poe ./H5testFpar -procs 2 -nodes 1
For more details on how to run parallel programs on Bassi, go to:
http://www.nersc.gov/nusers/resources/bassi/running_jobs/
(4) Starsky <starsky.lbl.gov> (Darwin8.5.0-PowerPC)
----------------------------------------------------
FIRST THING FIRST!! Set environment variables: (in tcsh)
setenv LD_LIBRARY_PATH /usr/local/g95/lib/gcc-lib/powerpc-apple-darwin8.5.0/4.0.3/
setenv PATH ${PATH}:/usr/local/g95/bin
NOTE: This environment variable setting is specifit to Starsky. It is to make configure find the fortran compiler.
Brief profile:
CC = gcc
CXX = g++
FC = g95
If default doesn't work, try:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(5) Linux AMD64 Visualization group workstations (Linux"SUSE"-x86_64)
---------------------------------------------------------
Brief profile:
CC = gcc
CXX = g++
FC = g95
If default doesn't work, try:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(6) Cray XT3 @ CSCS gele
1) modules/3.1.6 9) PrgEnv-pgi/1.4.26 17) xt-lustre-ss/1.4.26
2) MySQL/4.0.26 10) xt-pbs/5.3.4 18) Base-opts/1.4.26
3) acml/3.0 11) xt-service/1.4.26 19) subversion/1.3.2
4) pgi/6.1.4 12) xt-libc/1.4.26 20) zlib/1.2.3
5) totalview/7.2.0 13) xt-os/1.4.26 21) szip/2.0
6) xt-libsci/1.4.26 14) xt-catamount/1.4.26 22) hdf5/1.6.5
7) xt-mpt/1.4.26 15) xt-boot/1.4.26
8) xt-pe/1.4.26 16) xt-crms/1.4.26
CFLAGS="-I$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.
autogen.sh
+24 -26
View File
@@ -1,48 +1,46 @@
#!/bin/sh
# Run this to generate all the initial makefiles, etc.
ACLOCAL_FLAGS="-I m4 $ACLOCAL_FLAGS"
LIBTOOLIZE_FLAGS="--force $LIBTOOLIZE_FLAGS"
AUTOMAKE_FLAGS="--add-missing --copy --foreign $AUTOMAKE_FLAGS"
LIBTOOLIZE=`which libtoolize`
if [ "$LIBTOOLIZE" = "" ]; then
LIBTOOLIZE=`which glibtoolize`
fi
if [ "$LIBTOOLIZE" = "" ]; then
echo "libtoolize not found" 1>&2
exit 1
fi
echo "+ making misc files ..."
touch NEWS README AUTHORS ChangeLog
echo
$LIBTOOLIZE $LIBTOOLIZE_FLAGS || {
echo "libtoolize failed"
exit 1
}
echo
echo
echo "+ running aclocal ..."
aclocal $ACLOCAL_FLAGS || {
echo "aclocal failed - check that all needed development files are present on system"
exit 1
echo
echo "aclocal failed - check that all needed development files are present on system"
exit 1
}
echo
echo
echo
echo
echo "+ running autoheader ... "
autoheader || {
echo "autoheader failed"
exit 1
echo
echo "autoheader failed"
exit 1
}
echo
echo
echo
echo "+ running autoconf ... "
autoconf || {
echo "autoconf failed"
exit 1
echo
echo "autoconf failed"
exit 1
}
echo
echo
echo
echo "+ running automake ... "
automake $AUTOMAKE_FLAGS || {
echo "automake failed"
exit 1
automake -a -c --foreign || {
echo
echo "automake failed"
exit 1
}
echo
echo
echo
config.guess
Vendored Executable
+1469
View File
File diff suppressed because it is too large Load Diff
config.h.in
Executable
+44
View File
@@ -0,0 +1,44 @@
/* config.h.in. Generated from configure.ac by autoheader. */
/* "" */
#undef MY_BUILD_CPU
/* "" */
#undef MY_BUILD_OS
/* "" */
#undef MY_BUILD_VENDOR
/* "" */
#undef MY_GNUNAME
/* "" */
#undef MY_UNAME
/* Name of package */
#undef PACKAGE
/* Define to the address where bug reports for this package should be sent. */
#undef PACKAGE_BUGREPORT
/* Define to the full name of this package. */
#undef PACKAGE_NAME
/* Define to the full name and version of this package. */
#undef PACKAGE_STRING
/* Define to the one symbol short name of this package. */
#undef PACKAGE_TARNAME
/* Define to the version of this package. */
#undef PACKAGE_VERSION
/* Version number of package */
#undef VERSION
/* Define to 1 if on AIX 3.
System headers sometimes define this.
We just want to avoid a redefinition error message. */
#ifndef _ALL_SOURCE
# undef _ALL_SOURCE
#endif
config.sub
Vendored Executable
+1563
View File
File diff suppressed because it is too large Load Diff
configure.ac
+502 -284
View File
@@ -1,87 +1,77 @@
AC_INIT([H5hut], [1.99.12], [h5part@lists.psi.ch], H5hut)
AC_PREREQ(2.60)
AC_CONFIG_HEADERS(config.h)
AC_CONFIG_MACRO_DIR([m4])
AM_INIT_AUTOMAKE
# Every configure script must call AC_INIT before doing anything else.
# AC_INIT (package, version, [bug-report], [tarname])
AC_INIT([H5Part], [1.3.3], [h5part@lists.psi.ch], H5Part)
ENABLE_DEBUG='no'
ENABLE_C='yes'
ENABLE_FORTRAN='no'
ENABLE_PARALLEL='no'
# Ensure that a recent enough version of Autoconf is being used.
# If the version of Autoconf being used to create configure is earlier than version,
# print an error message to the standard error output and do not create configure.
#AC_PREREQ(2.59)
# should be called right after AC_INIT.
# configure scripts can create a C header file containing `#define' directives.
# The AC_CONFIG_HEADERS macro selects this kind of output.
AC_CONFIG_HEADER(config.h)
###############################################################################
# --enable-xxx and --with-xxx Arguments
AC_ARG_ENABLE(
[debug],
[AS_HELP_STRING([--enable-debug], [Compile with debug flags [default=no]])],
[ENABLE_DEBUG=$enableval])
AM_CONDITIONAL([ENABLE_DEBUG], [test "$ENABLE_DEBUG" = "yes"])
################# --enable-xxx and --with-xxx Argument ########################
###############################################################################
AC_ARG_ENABLE(
[c],
[AS_HELP_STRING([--enable-c],
[Compile the C interface [default=yes]])],
[ENABLE_C=$enableval])
AM_CONDITIONAL([ENABLE_C], [test "$ENABLE_C" = "yes"])
[64],
[AC_HELP_STRING([--enable-64],
[Compile using 64-bit flags [default=no]])],
[USE_64=$enableval])
AC_ARG_ENABLE(
[fortran],
[AS_HELP_STRING([--enable-fortran],
[AC_HELP_STRING([--enable-fortran],
[Compile the Fortran interface [default=no]])],
[ENABLE_FORTRAN=$enableval])
AM_CONDITIONAL([ENABLE_FORTRAN], [test "$ENABLE_FORTRAN" = "yes"])
[USE_FORTRAN=$enableval])
AC_ARG_ENABLE(
[parallel],
[AS_HELP_STRING([--enable-parallel],
[AC_HELP_STRING([--enable-parallel],
[Compile the MPI/IO interface [default=no]])],
[ENABLE_PARALLEL=$enableval])
AM_CONDITIONAL([ENABLE_PARALLEL], [test "$ENABLE_PARALLEL" = "yes"])
[USE_PARALLEL=$enableval])
AC_ARG_ENABLE(
[large-indices],
[AC_HELP_STRING([--enable-large-indices],
[Compile with 64bit local IDs and indices [default=no]])],
[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 "$ENABLE_VTKCONVERTER" = "yes"])
[tools],
[AC_HELP_STRING([--enable-tools],
[Compile h5part tools [default=no]])],
[USE_TOOLS=$enableval])
AC_ARG_WITH(
[hdf5],
[AS_HELP_STRING([--with-hdf5],
[path to HDF5 installation [default=""]])],
[HDF5_PREFIX=$withval], [])
AC_ARG_WITH(
[mpi],
[AS_HELP_STRING([--with-mpi],
[mpipath],
[AC_HELP_STRING([--with-mpipath],
[path to MPI installation [default=""]])],
[PATH=$MPI_PREFIX/bin:$PATH])
[MPIPATH=$withval], [MPIPATH=""])
AC_ARG_WITH(
[lustre],
[AS_HELP_STRING([--with-lustre],
[path to lustre user API [default=""]])],
[LUSTREPATH=$withval], [LUSTREPATH=""])
[hdf5path],
[AC_HELP_STRING([--with-hdf5path],
[path to HDF5 installation [default=""]])],
[HDF5PATH=$withval], [HDF5PATH=""])
AC_ARG_WITH(
[parmetis],
[AC_HELP_STRING([--with-parmetis],
[path to ParMETIS API [default=""]])],
[PARMETISPATH=$withval], [PARMETISPATH=""])
###############################################################################
################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
###############################################################################
SAVE_CC=$CC
SAVE_CXX=$CXX
SAVE_FC=$FC
SAVE_MPICC=$MPICC
SAVE_MPICXX=$MPICXX
SAVE_MPIFC=$MPIFC
SAVE_MPILIB=$MPILIB
SAVE_MPIINC=$MPIINC
SAVE_CFLAGS=$CFLAGS
CFLAGS=''
SAVE_FFLAGS=$FFLAGS
SAVE_MPIROOT=$MPIROOT
SAVE_HDF5ROOT=$HDF5ROOT
SAVE_LDFLAGS=$LDFLAGS
###############################################################################
############### PATH SERACH FUNCTION - to be used later... ####################
@@ -95,92 +85,117 @@ AC_ARG_WITH(
# @enddesc
#@@*/
PATH_Search() {
eval $1=""
if test $# -lt 4 ; then
h5part_basedir=""
else
h5part_basedir="$4/"
fi
for h5part_place in $2; do
AC_MSG_CHECKING([looking in $h5part_place ... ])
if test -r "$h5part_basedir$h5part_place/$3" ; then
AC_MSG_RESULT([found])
eval $1="$h5part_place"
break
fi
AC_MSG_RESULT([no])
done
return
PATH_Search()
{
eval $1=""
if test $# -lt 4 ; then
h5part_basedir=""
else
h5part_basedir="$4/"
fi
for h5part_place in $2
do
echo -n "looking in $h5part_place ... $ac_c" #1>&6
if test -r "$h5part_basedir$h5part_place/$3" ; then
echo "$ac_t"" found" #1>&6
eval $1="$h5part_place"
break
fi
if test -d "$h5part_basedir$h5part_place/$3" ; then
echo "$ac_t"" found" #1>&6
eval $1="$h5part_place"
break
fi
echo "$ac_t"" no" #1>&6
done
return
}
###############################################################################
# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING
############# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING ################
###############################################################################
# Compute the canonical host-system type variable, host, and its three
# individual parts host_cpu, host_vendor, and host_os.
AC_CANONICAL_HOST
AC_PROG_MAKE_SET
# debug enabled?
AC_MSG_CHECKING([if debug is enabled])
if test "X$ENABLE_DEBUG" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="$CFLAGS -g -Wall"
CXXFLAGS="$CFLAGS -g -Wall"
FFLAGS="$FFLAGS -g"
else
AC_MSG_RESULT([no])
uname=`uname -s`
if test $uname = "AIX"; then
AC_MSG_CHECKING([if system is AIX])
AC_MSG_RESULT([OK])
# If on AIX, define _ALL_SOURCE. Allows the use of some BSD functions.
# Should be called before any macros that run the C compiler.
AC_AIX
fi
# Determine a C/C++ compiler to use.
if test "x$ENABLE_PARALLEL" = "xyes"; then
CCOMPILERS="mpicc"
CXXCOMPILERS="mpic++"
else
CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
CXXCOMPILERS="pgcc pathcc icc g++ cc_r c++"
# DAVINCI SPECIFIC!!!
if test `uname -n` = "davinci"; then
echo "DAVINCI SPECIFIC TESTING FOR STDC++ LIBRARY!"
PATH_Search STDCXX_CHECK '/usr/lib64 /usr/lib' libstdc++.a
# if STDCXX_CHECK is set...
if test "$STDCXX_CHECK" = "/usr/lib64"; then
echo "STDCXX setting ..."
echo "STDCXX_CHECK = $STDCXX_CHECK ..."
STDCXX="-L/usr/lib64 -lstdc++"
echo "STDCXX = $STDCXX ..."
elif test "$STDCXX_CHECK" = "/usr/lib"; then
echo "STDCXX setting ..."
echo "STDCXX_CHECK = $STDCXX_CHECK ..."
STDCXX="-L/usr/lib -lstdc++"
echo "STDCXX = $STDCXX ..."
fi
fi
AC_PROG_CC($CCOMPILERS)
CC=`which $CC`
AC_PROG_CXX($CXXCOMPILERS)
CXX=`which $CXX`
AC_PROG_CC_C99
if test "x$ac_cv_prog_cc_c99" = "xno"; then
AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
exit 1
fi
# Determine a C compiler to use.
# If CC is not already set in the environment, check for gcc and cc, then
# for other C compilers.
# Set output variable CC to the name of the compiler found.
AC_PROG_CC(pathcc icc cc_r gcc cc)
# AC_PROG_CC doesn't pick up cc_r in Bassi. The following AC_PATH_PROGS
# is the fix.
AC_PATH_PROGS([BAS_CC], [cc_r], [], [$PATH])
# if BAS_CC not empty
if test -n "$BAS_CC"; then
echo "CC setting for Bassi ..."
CC=$BAS_CC
echo "CC = $CC ..."
fi
# Determine a C++ compiler to use.
# Check if the environment variable CXX or CCC (in that order) is set;
# if so, then set output variable CXX to its value.
# Otherwise, if the macro is invoked without an argument,
# then search for a C++ compiler under the likely names (first g++ and c++
# then other names).
# If none of those checks succeed, then as a last resort set CXX to g++.
AC_PROG_CXX(pathCC icc cc_r g++ gcc cc)
# Set output variable INSTALL to the path of a BSD-compatible install program,
# if one is found in the current PATH.
# Otherwise, set INSTALL to `dir/install-sh -c`
AC_PROG_INSTALL
AC_PROG_AWK
# Disable shared libraries by default: can be enabled with --enable-shared
LT_INIT([disable-shared])
AC_PROG_LIBTOOL
# AM_INIT_AUTOMAKE is required to use autoconf with automake
AM_INIT_AUTOMAKE()
AC_PROG_RANLIB
# Default prefix for bindir, etc... (eg >> ./build/bin)
AC_PREFIX_DEFAULT(`pwd`/build)
# Checks for header files.
AC_CHECK_HEADERS([fcntl.h limits.h stdint.h stdlib.h string.h sys/ioctl.h unistd.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_C_INLINE
AC_TYPE_INT16_T
AC_TYPE_INT32_T
AC_TYPE_INT64_T
AC_TYPE_SIZE_T
AC_TYPE_SSIZE_T
AC_TYPE_UINT16_T
AC_TYPE_UINT32_T
AC_TYPE_UINT64_T
AC_CHECK_TYPES([ptrdiff_t])
# Checks for library functions.
AC_FUNC_MALLOC
AC_FUNC_REALLOC
AC_CHECK_FUNCS([memmove memset pow strchr strdup strerror strstr])
# AC_DEFINE_UNQUOTED (variable, value, [description])
# Define the C preprocessor variable variable to value
@@ -192,198 +207,401 @@ AC_DEFINE_UNQUOTED(MY_GNUNAME, "${host_cpu}-${host_vendor}-${host_os}", "")
AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
###############################################################################
######################## CONFIGURE LINE OPTIONS ###############################
###############################################################################
# PROCESS ARGUMENTS
# C enabled?
AC_MSG_CHECKING([if C interface enabled])
if test "X$ENABLE_C" = "Xyes"; then
AC_MSG_RESULT([yes])
###################### 64-bit compilation enabled #############################
AC_MSG_CHECKING([if 64-bit compilation is enabled])
# If --enable-64 is set in the configure line
if test "X$USE_64" = "Xyes"; then
AC_MSG_RESULT([yes])
if test $uname = "AIX"; then
CFLAGS="$CFLAGS -q64"
FFLAGS="$FFLAGS -q64"
fi
if test $uname = "IRIX64"; then
CFLAGS="$CFLAGS -64"
FFLAGS="$FFLAGS -64 -fPIC -fno-second-underscore"
fi
else
AC_MSG_RESULT([no])
AC_MSG_RESULT([no])
fi
# fortran enabled?
############################ fortran enabled ##################################
AC_MSG_CHECKING([if fortran interface enabled])
if test "X$ENABLE_FORTRAN" = "Xyes"; then
AC_MSG_RESULT([yes])
if test "X$USE_FORTRAN" = "Xyes"; then
AC_MSG_RESULT([yes])
if test "X$ENABLE_PARALLEL" = "Xyes"; then
AC_PROG_FC(mpif90 mpif77)
else
AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
fi
FC=`which $FC`
if test -z "$FC" ; then
AC_MSG_ERROR([Cannot find a Fortran compiler!])
exit 1
fi
AC_PROG_FC(ifort xlf_r pathf90 g95 g90 ftn gfortran)
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 ! $uname = "AIX"; then
FFLAGS="${FFLAGS} -fPIC -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/Fortran && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
`cd src/Fortran && ${FC} ${FFLAGS} -c TestUnderscore.f`
`cd src/Fortran && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
`cd src/Fortran && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
if test -f src/Fortran/TestUnderscore ; then
`cd src/Fortran && ./TestUnderscore > Underscore.h`
AC_MSG_RESULT([ok])
else
AC_MSG_RESULT([nok])
AC_MSG_ERROR([Cannot determine the symbol convention for Fortran object files!])
exit 1
fi
AC_MSG_CHECKING([symbol convention in object files])
`cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
`cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
`cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
`cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o -lc`
if test -f src/TestUnderscore ; then
UNDERSCORE_H=Underscore.h
`cd src && ./TestUnderscore > Underscore.h`
AC_MSG_RESULT([ok])
else
AC_MSG_RESULT([nok])
AC_MSG_ERROR([Cannot build fortran executables!!!])
exit 1
fi
else
AC_MSG_RESULT([no])
AC_MSG_RESULT([no])
fi
######################## large indices enabled ###########################
AC_MSG_CHECKING([if large indices are enabled])
if test "X$USE_LARGE_INDICES" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="${CFLAGS} -DUSE_LARGE_INDICES"
else
AC_MSG_RESULT([no])
fi
######################## parallel interface enabled ###########################
AC_MSG_CHECKING([if parallel interface enabled])
if test "X$ENABLE_PARALLEL" = "Xyes"; then
AC_MSG_RESULT([yes])
CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
if test "X$USE_PARALLEL" = "Xyes"; then
AC_MSG_RESULT([yes])
if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
AC_MSG_CHECKING([for ParMETIS])
if test "X$PARMETISPATH" != "X"; then
CPPFLAGS="$CPPFLAGS -I$PARMETISPATH/include"
LDFLAGS="$LDFLAGS -L$PARMETISPATH/lib"
fi
CFLAGS="${CFLAGS} -DPARALLEL_IO -DH5_HAVE_PARALLEL -DMPICH_IGNORE_CXX_SEEK"
LIBS="$LIBS -lparmetis -lmetis"
AC_TRY_LINK([#include <parmetis.h>], [
ParMETIS_V3_PartGeom (NULL, NULL, NULL, NULL, NULL);],
[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
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 ); ],
[echo 'yes'; r='yes'], [echo "no"; r='no'] )
if test "X$r" = "Xno"; then
AC_MSG_ERROR([ParMETIS])
exit 1
fi
fi
else # --enable-parallel=no
AC_MSG_RESULT([no])
fi
if test "X$r" = "Xno"; then
AC_PATH_PROGS([MPICC], [mpicc mpcc_r], [], [$PATH])
AC_PATH_PROGS([MPICXX], [mpicxx mpcc_r], [], [$PATH])
if test -z "$MPICC" -o -z "$MPICXX"; then
AC_MSG_CHECKING([for MPI root ])
AC_MSG_RESULT([])
if test -n "$MPIROOT"; then
P=${MPIROOT}
elif test -n "$MPIHOME"; then
P=${MPIHOME}
elif test -n "$MPIPATH"; then
P=${MPIPATH}
else
P=''
P="$P /usr"
P="$P /usr/local"
P="$P /usr/local/mpi"
P="$P /usr/local/packages/mpi"
P="$P /usr/local/mpich2"
P="$P /usr/local/mpich"
P="$P /opt/xt-mpt/default/mpich2-64/P2"
fi
PATH_Search MPIROOT "$P" include/mpi.h
if test ! -n "$MPIROOT"; then
AC_MSG_ERROR([Cannot determine MPI root!!!])
exit 1
fi
###############################################################################
# LIBRARY PATHS
if test -z "${HDF5_PREFIX}"; then
# alternatives to HDF5_PREFIX
if test -n "${HDF5_DIR}"; then
HDF5_PREFIX=${HDF5_DIR}
if test -e "${MPIROOT}/bin/mpicc"; then
MPICC=${MPIROOT}/bin/mpicc
fi
if test -e "${MPIROOT}/bin/mpicxx"; then
MPICXX=${MPIROOT}/bin/mpicxx
fi
fi
fi
if test -n "${HDF5_PREFIX}"; then
CPPFLAGS="$CPPFLAGS -I$HDF5_PREFIX/include"
LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
fi
AC_CHECK_LIB([z], [compress2])
AC_CHECK_LIB([hdf5], [H5open])
AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes],
[AC_MSG_ERROR([Cannot compile and link a HDF5 program]);
exit 1])
if test -z "$MPICC" -o -z "$MPICXX"; then
MPIINC="${MPIINC} -I${MPIROOT}/include"
FFLAGS="${FFLAGS} -I${MPIROOT}/include"
AC_MSG_CHECKING([for name of MPI lib ])
if test -e ${MPIROOT}/lib/libmpi.a; then
MPILIB="-L${MPIROOT}/lib -lmpi"
elif test -e ${MPIROOT}/lib/libmpi.so; then
MPILIB="-L${MPIROOT}/lib -lmpi"
elif test -e ${MPIROOT}/lib/libmpich.a; then
MPILIB="-L${MPIROOT}/lib -lmpich"
elif test -e ${MPIROOT}/lib/libmpich.so; then
MPILIB="-L${MPIROOT}/lib -lmpich"
else
AC_MSG_RESULT([not found])
exit 1
fi
AC_MSG_RESULT([${MPILIB}])
fi
AC_MSG_CHECKING([for lustre API ])
if test -n "$MPICC"; then
CC=${MPICC}
fi
if test -n "$MPICXX"; then
CXX=${MPICXX}
fi
fi
MTARGET="libpH5Part.a"
TTARGET="H5PartTestP H5PartAndreasTest Bench"
TTARGET="${TTARGET} H5BlockTestAttributes"
TTARGET="${TTARGET} H5BlockParTestScalarField"
# parallel + fortran
if test "X$USE_FORTRAN" = "Xyes"; then
AC_PATH_PROGS([MPIFC], [mpxlf_r mpif90], [], [$PATH])
if test -z "${MPIFC}" ; then
if test -e "${MPIROOT}/bin/mpif90"; then
MPIFC=${MPIROOT}/bin/mpif90
fi
fi
# if MPIFC empty
if test ! -n "$MPIFC"; then
AC_MSG_CHECKING([ No MPIFC detected. Setting MPIFC to FC.])
MPIFC=$FC
echo "MPIFC = $MPIFC ..."
fi
if test -n "$MPIFC"; then
FC=${MPIFC}
fi
MTARGET="${MTARGET} libpH5PartF.a"
TTARGET="${TTARGET} H5testFpar"
TTARGET="${TTARGET} H5BlockParTestScalarFieldF"
fi
else # --enable-parallel=no
AC_MSG_RESULT([no])
MTARGET="libH5Part.a"
TTARGET="H5PartTest H5test"
TTARGET="${TTARGET} H5BlockTestAttributes"
if test "X$USE_FORTRAN" = "Xyes"; then
MTARGET="${MTARGET} libH5PartF.a"
TTARGET="${TTARGET} H5testF"
TTARGET="${TTARGET} H5BlockTestAttributesF"
fi
fi
AC_MSG_CHECKING([wheter tools are enabled])
if test "X$USE_TOOLS" = "Xyes"; then
AC_MSG_RESULT([yes])
BUILD_TOOLS="h5pAttrib h5pToGNUplot # homdynToH5p"
else
AC_MSG_RESULT([no])
fi
###############################################################################
######################### PATH CHECKING & SETTING #############################
###############################################################################
AC_MSG_CHECKING([for HDF5 root ])
AC_MSG_RESULT([])
if test -n "${LUSTREPATH}"; then
P=${LUSTREPATH}
elif test -n "${LUSTREROOT}" ; then
P=${LUSTREROOT}
elif test -n "${LUSTREHOME}" ; then
P=${LUSTREHOME}
elif test -n "${LUSTRE_DIR}" ; then
P=${LUSTRE_DIR}
if test -n "${HDF5ROOT}"; then
P=${HDF5ROOT}
elif test -n "${HDF5HOME}" ; then
P=${HDF5HOME}
elif test -n "${HDF5PATH}" ; then
P=${HDF5PATH}
else
P=''
P="$P /usr"
P="$P /usr/local"
P="$P /usr/local/lustre"
P="$P /opt/lustre"
P=''
P="$P /usr"
P="$P /usr/local"
P="$P /usr/local/hdf5"
P="$P /usr/local/packages/hdf5"
P="$P /apps/hdf5"
if test "X$USE_PARALLEL" = "Xyes"; then
P="$P /usr/local/phdf5"
P="$P /usr/local/hdf5/hdf5_par"
if test "X$USE_64" = "Xyes"; then
P="$P /usr/common/usg/hdf5/64/default/parallel"
else
P="$P /usr/common/usg/hdf5/32/default/parallel"
fi
else
P="$P /usr/local/hdf5/hdf5_serial"
if test "X$USE_64" = "Xyes"; then
P="$P /usr/common/usg/hdf5/64/default/serial"
else
P="$P /usr/common/usg/hdf5/32/default/serial"
fi
fi
fi
PATH_Search LUSTREROOT "$P" usr/include/lustre/liblustreapi.h
if test -z "$LUSTREROOT"; then
AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
else
CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
CPPFLAGS="$CPPFLAGS -I$LUSTREROOT/usr/include"
LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
LIBS="$LIBS -llustreapi"
PATH_Search HDF5ROOT "$P" include/hdf5.h
if test -z "$HDF5ROOT"; then
AC_MSG_ERROR([Cannot determine HDF5 root!!!])
exit 1
fi
LIBS="$LIBS -lm"
###############################################################################
# TOOLS
AC_MSG_CHECKING([if we have to compile the VTK to H5hut grid converter])
if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
AC_MSG_CHECKING([if we need to link to libsz ])
if test -n "$HDF5ROOT"; then
if test -f $HDF5ROOT/lib/libsz.a; then
AC_MSG_RESULT([yes])
# :TODO: add test whether we can compile/link a prog with vtk
else
SZLIB="-L$HDF5ROOT/lib/ -lsz"
else
AC_MSG_RESULT([no])
SZLIB=""
fi
fi
AC_MSG_CHECKING([for static zlib root ])
echo
PATH_Search ZLIBROOT '/apps/zlib' lib/libz.a
if test -n "$ZLIBROOT"; then
LDFLAGS="$LDFLAGS -L$ZLIBROOT/lib"
fi
###############################################################################
#################### MISC SETTINGS - path, flags, etc #########################
###############################################################################
H5P_LIB_LOC=`pwd`/src
###############################################################################
################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
###############################################################################
#if there was an external input for the variable...
if test -n "$SAVE_CC"; then
CC=$SAVE_CC
fi
if test -n "$SAVE_CXX"; then
CXX=$SAVE_CXX
fi
if test -n "$SAVE_FC"; then
FC=$SAVE_FC
fi
if test -n "$SAVE_MPICC"; then
MPICC=$SAVE_MPICC
fi
if test -n "$SAVE_MPICXX"; then
MPICXX=$SAVE_MPICXX
fi
if test -n "$SAVE_MPIFC"; then
MPIFC=$SAVE_MPIFC
fi
if test -n "$SAVE_MPILIB"; then
MPILIB=$SAVE_MPILIB
fi
if test -n "$SAVE_MPIINC"; then
MPIINC=$SAVE_MPIINC
fi
if test -n "$SAVE_CFLAGS"; then
CFLAGS="$SAVE_CFLAGS ${CFLAGS}"
fi
if test -n "$SAVE_FFLAGS"; then
FFLAGS=$SAVE_FFLAGS
fi
if test -n "$SAVE_MPIROOT"; then
MPIROOT=$SAVE_MPIROOT
fi
if test -n "$SAVE_HDF5ROOT"; then
HDF5ROOT=$SAVE_HDF5ROOT
fi
if test -n "$SAVE_LDFLAGS"; then
LDFLAGS=$SAVE_LDFLAGS
fi
if test -n "$MPICXX"; then
TOOLS_CXX=$MPICXX
TOOLS_H5PART_LIB="-lpH5Part"
TOOLS_HDFLIB="-L$HDF5ROOT/lib -lhdf5"
else
TOOLS_CXX=$CXX
TOOLS_H5PART_LIB="-lH5Part"
TOOLS_HDFLIB="-L$HDF5ROOT/lib -lhdf5"
fi
###############################################################################
# EXPORTING VARIABLES & CREATING OUTPUT FILES
AM_CPPFLAGS=$CPPFLAGS
AM_LDFLAGS=$LDFLAGS
AC_SUBST(HDF5_PREFIX)
############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
###############################################################################
# AC_SUBST (variable, [value])
# Create an output variable from a shell variable.
# Make AC_OUTPUT substitute the variable variable into output files (typically one or more `Makefile's).
# This means that AC_OUTPUT will replace instances of `@variable@' in input files with the value that
# the shell variable variable has when AC_OUTPUT is called.
# This value of variable should not contain literal newlines.
# If value is given, in addition assign it to variable.
AC_SUBST(MPIROOT)
AC_SUBST(HDF5ROOT)
AC_SUBST(MPIINC)
AC_SUBST(MPILIB)
AC_SUBST(MPICC)
AC_SUBST(MPICXX)
AC_SUBST(MPIFC)
AC_SUBST(MTARGET)
AC_SUBST(TTARGET)
AC_SUBST(SZLIB)
AC_SUBST(CFLAGS)
AC_SUBST(FFLAGS)
AC_SUBST(AM_CPPFLAGS)
AC_SUBST(AM_LDFLAGS)
AC_SUBST(STDCXX)
AC_SUBST(H5P_LIB_LOC)
AC_SUBST(UNDERSCORE_H)
AC_SUBST(BUILD_TOOLS)
AC_SUBST(LDFLAGS)
AC_SUBST(TOOLS_CXX)
AC_SUBST(TOOLS_H5PART_LIB)
AC_SUBST(TOOLS_HDFLIB)
# 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
src/h5core/Makefile
src/include/Makefile
src/include/h5core/Makefile
src/C/Makefile
src/Fortran/Makefile
test/Makefile
doc/Makefile
tools/Makefile
tools/h5hutcc
tools/vtk2h5grid/Makefile
Makefile
doc/Makefile
src/Makefile
test/Makefile
tools/Makefile
])
AC_OUTPUT
###############################################################################
# PRINTING SUMMARY
AC_MSG_RESULT([ ])
AC_MSG_RESULT([Summary:])
AC_MSG_RESULT([ ])
AC_MSG_RESULT([Host OS: $host_os])
AC_MSG_RESULT([Host CPU: $host_cpu])
AC_MSG_RESULT([Host vendor: $host_vendor])
AC_MSG_RESULT([CC = $CC])
AC_MSG_RESULT([CXX = $CXX])
AC_MSG_RESULT([FC = $FC])
AC_MSG_RESULT([CFLAGS = $CFLAGS])
AC_MSG_RESULT([FFLAGS = $FFLAGS])
AC_MSG_RESULT([AM_CPPFLAGS = $AM_CPPFLAGS])
AC_MSG_RESULT([AM_LDFLAGS = $AM_LDFLAGS])
AC_MSG_RESULT([LIBS = $LIBS])
AC_MSG_RESULT([HDF5_PREFIX = $HDF5_PREFIX])
AC_MSG_RESULT([LUSTREROOT = $LUSTREROOT])
AC_MSG_RESULT([ ])
########################## PRINTING SUMMARY ###################################
###############################################################################
echo
echo
echo "Summary for `(hostname || uname -n) 2>/dev/null | sed 1q`:"
echo
echo "Host OS: $host_os"
echo "Host CPU: $host_cpu"
echo "Host vendor: $host_vendor"
echo "Build libraries: $MTARGET"
echo "Build test programs: $TTARGET"
echo "Build tools: $BUILD_TOOLS"
echo "CC = $CC"
echo "CXX = $CXX"
echo "FC = $FC"
echo "MPICC = $MPICC"
echo "MPICXX = $MPICXX"
echo "MPIFC = $MPIFC"
echo "CFLAGS = $CFLAGS"
echo "FFLAGS = $FFLAGS"
echo "MPILIB = $MPILIB"
echo "MPIINC = $MPIINC"
echo "MPIROOT = $MPIROOT"
echo "HDF5ROOT = $HDF5ROOT"
echo "LDFLAGS = $LDFLAGS"
echo
depcomp
Executable
+529
View File
@@ -0,0 +1,529 @@
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
scriptversion=2005-02-09.22
# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
# 02111-1307, USA.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
case $1 in
'')
echo "$0: No command. Try \`$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
Run PROGRAMS ARGS to compile a file, generating dependencies
as side-effects.
Environment variables:
depmode Dependency tracking mode.
source Source file read by `PROGRAMS ARGS'.
object Object file output by `PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
tmpdepfile Temporary file to use when outputing dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake@gnu.org>.
EOF
exit $?
;;
-v | --v*)
echo "depcomp $scriptversion"
exit $?
;;
esac
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
fi
# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
depfile=${depfile-`echo "$object" |
sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
# here, because this file can only contain one case statement.
if test "$depmode" = hp; then
# HP compiler uses -M and no extra arg.
gccflag=-M
depmode=gcc
fi
if test "$depmode" = dashXmstdout; then
# This is just like dashmstdout with a different argument.
dashmflag=-xM
depmode=dashmstdout
fi
case "$depmode" in
gcc3)
## gcc 3 implements dependency tracking that does exactly what
## we want. Yay! Note: for some reason libtool 1.4 doesn't like
## it if -MD -MP comes after the -MF stuff. Hmm.
"$@" -MT "$object" -MD -MP -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
mv "$tmpdepfile" "$depfile"
;;
gcc)
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
## -MM, not -M (despite what the docs say).
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
gccflag=-MD,
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
## The second -e expression handles DOS-style file names with drive letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
## This next piece of magic avoids the `deleted header file' problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
tr ' ' '
' < "$tmpdepfile" |
## Some versions of gcc put a space before the `:'. On the theory
## that the space means something, we add a space to the output as
## well.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
hp)
# This case exists only to let depend.m4 do its work. It works by
# looking at the text of this script. This case will never be run,
# since it is checked for above.
exit 1
;;
sgi)
if test "$libtool" = yes; then
"$@" "-Wp,-MDupdate,$tmpdepfile"
else
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
# the IRIX cc adds comments like `#:fec' to the end of the
# dependency line.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
tr '
' ' ' >> $depfile
echo >> $depfile
# The second pass generates a dummy entry for each header file.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
>> $depfile
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
aix)
# The C for AIX Compiler uses -M and outputs the dependencies
# in a .u file. In older versions, this file always lives in the
# current directory. Also, the AIX compiler puts `$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'`
tmpdepfile="$stripped.u"
if test "$libtool" = yes; then
"$@" -Wc,-M
else
"$@" -M
fi
stat=$?
if test -f "$tmpdepfile"; then :
else
stripped=`echo "$stripped" | sed 's,^.*/,,'`
tmpdepfile="$stripped.u"
fi
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
if test -f "$tmpdepfile"; then
outname="$stripped.o"
# Each line is of the form `foo.o: dependent.h'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile"
sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
icc)
# Intel's C compiler understands `-MD -MF file'. However on
# icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
# ICC 7.0 will fill foo.d with something like
# foo.o: sub/foo.c
# foo.o: sub/foo.h
# which is wrong. We want:
# sub/foo.o: sub/foo.c
# sub/foo.o: sub/foo.h
# sub/foo.c:
# sub/foo.h:
# ICC 7.1 will output
# foo.o: sub/foo.c sub/foo.h
# and will wrap long lines using \ :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
"$@" -MD -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
# Each line is of the form `foo.o: dependent.h',
# or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
# Some versions of the HPUX 10.20 sed can't process this invocation
# correctly. Breaking it into two sed invocations is a workaround.
sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
tru64)
# The Tru64 compiler uses -MD to generate dependencies as a side
# effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
# At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
# dependencies in `foo.d' instead, so we check for that too.
# Subdirectories are respected.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
# With Tru64 cc, shared objects can also be used to make a
# static library. This mecanism is used in libtool 1.4 series to
# handle both shared and static libraries in a single compilation.
# With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
#
# With libtool 1.5 this exception was removed, and libtool now
# generates 2 separate objects for the 2 libraries. These two
# compilations output dependencies in in $dir.libs/$base.o.d and
# in $dir$base.o.d. We have to check for both files, because
# one of the two compilations can be disabled. We should prefer
# $dir$base.o.d over $dir.libs/$base.o.d because the latter is
# automatically cleaned when .libs/ is deleted, while ignoring
# the former would cause a distcleancheck panic.
tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
tmpdepfile2=$dir$base.o.d # libtool 1.5
tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
"$@" -Wc,-MD
else
tmpdepfile1=$dir$base.o.d
tmpdepfile2=$dir$base.d
tmpdepfile3=$dir$base.d
tmpdepfile4=$dir$base.d
"$@" -MD
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
# That's a tab and a space in the [].
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
# dependency tracking mechanisms from slower ones.
dashmstdout)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
test -z "$dashmflag" && dashmflag=-M
# Require at least two characters before searching for `:'
# in the target name. This is to cope with DOS-style filenames:
# a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
"$@" $dashmflag |
sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
tr ' ' '
' < "$tmpdepfile" | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
dashXmstdout)
# This case only exists to satisfy depend.m4. It is never actually
# run, as this mode is specially recognized in the preamble.
exit 1
;;
makedepend)
"$@" || exit $?
# Remove any Libtool call
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# X makedepend
shift
cleared=no
for arg in "$@"; do
case $cleared in
no)
set ""; shift
cleared=yes ;;
esac
case "$arg" in
-D*|-I*)
set fnord "$@" "$arg"; shift ;;
# Strip any option that makedepend may not understand. Remove
# the object too, otherwise makedepend will parse it as a source file.
-*|$object)
;;
*)
set fnord "$@" "$arg"; shift ;;
esac
done
obj_suffix="`echo $object | sed 's/^.*\././'`"
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
sed '1,2d' "$tmpdepfile" | tr ' ' '
' | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
cpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test $1 != '--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
"$@" -E |
sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
msvisualcpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o,
# because we must use -o when running libtool.
"$@" || exit $?
IFS=" "
for arg
do
case "$arg" in
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
set fnord "$@"
shift
shift
;;
*)
set fnord "$@" "$arg"
shift
shift
;;
esac
done
"$@" -E |
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
echo " " >> "$depfile"
. "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
none)
exec "$@"
;;
*)
echo "Unknown depmode $depmode" 1>&2
exit 1
;;
esac
exit 0
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-end: "$"
# End:
doc/Building.html
+262
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>Building H5Part</title>
</head>
<body bgcolor="#F0F0F0">
<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
<UL>
<LI><a href="#Quickstart">Quickstart guide for the impatient.</a>
<LI><a href="#Details">Details of the Configuration Script</a>
<!-- <LI><a href="UsingC++.html">Using the C++ interface</a> -->
<LI><a href="#ConfigOptions">Important Configure Options</a>
<LI><a href="#EnvVariables">Important Environment Variables</a>
</UL>
<hr>
<a name="Quickstart">
<h2>Quickstart <i>for the impatient</i></h2>
</a>
<OL>
<LI><b>Configure</b>:<br>
For the serial implementation
<pre>
./configure
</pre>
For the parallel implementation configure with
<pre>
./configure --enable-parallel
</pre>
If you also want to build fortran bindings, add the
<code>--enable-fortran</code> flag to the configure line.
</LI><p>
<LI><b>Make the Library</b>:<br>
Type <code>make</code> to build the library. The libraries are
named accordingly.
<UL>
<LI>libH5Part.a: Serial C/C++ Library.</LI>
<LI>libpH5Part.a: Parallel C/C++ library.</LI>
<LI>libH5PartF.a: Serial F77/F90 library.</LI>
<LI>libpH5PartF.a: Parallel F77/F90 library.</LI>
</UL>
</LI><p>
<LI><b>Make Regression Tests and Examples</b>:<br>
Just type <code>make tests</code> to build regression tests
and/or example programs for H5Part. These tests are
<UL>
<LI>H5PartF: Fortran example (only build if --enable-fortran
is specified).</LI>
<LI>H5PartFpar: Parallel Fortran example (only built if both
--enable-fortran and --enable-parallel are specified).</LI>
<LI>H5PartTest: Serial C example. This test writes a sample
datafile and then reopens it for reading. It demonstrates
the most basic reading/writing capabilities.</LI>
<LI>H5PartTestP: Parallel C example (only built if
--enable-parallel is specified). This program only works
as an MPI/parallel program.</LI>
<LI>Bench: This program will only be built if
--enable-parallel is specified. It compares the
performance of raw binary
I/O (one file per processor), raw binary MPI-IO based
parallel I/O to a single file, and the parallel H5Part/HDF5 to
a single file. Generally, H5Part should be very close to the
MPI-IO implementation in terms of performance, but slower
than one-file-per-processor. If HDF5 is slower the
MPI-IO, it would indicate that some performance tuning
will be required for your platform (contact us, and we will
see what we can do!).</LI>
</UL>
</LI><p>
<LI><b>Building Your Own Programs</b>:<br>
There are many different subtleties to linking on various
computer platforms, but typically one does the following.
<UL>
<LI>C/C++ Serial:
<br><code>#include
&lt H5Part.h &gt </code> into your
source file.
<br><code>$CC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -o outfile
MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
</LI>
<LI>C/C++ Parallel:
<br><code>#include
&lt H5Part.h &gt </code> into your
source file.
<br><code>$MPICC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -DPARALLEL_IO
-DH5_HAVE_PARALLEL -o outfile
MyFile.cc -L<i>path_to_libH5Part.a</i> -lH5Part
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i></code>
</LI>
<LI>Fortran Serial:
<br><code>include
'H5Part.inc'</code> into your
source file.
<br><code>$FC -I<i>path_to_H5Part.h</i>
-I<i>path_to_hdf5.h</i> -o outfile
MyFile.cc -L<i>path_to_libH5PartF.a</i> -lH5PartF
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
</LI>
<LI>Fortran Parallel:
<br><code>include
'H5Part.inc'</code> into your
source file.
<br><code>$MPIF90 -I<i>path_to_H5Part.h</i>
-o outfile
MyFile.cc -L<i>path_to_libpH5PartF.a</i> -lpH5PartF
-L<i>path_to_libhdf5</i> -lhdf5 -lz <i>-lsz</i> -lc</code>
</LI><p>
</UL>
</OL>
<hr>
<a name="Details">
<h1>Details for H5Part Configure and Build</h1>
</a>
<a name="ConfigOptions">
<h2>Configure Options</h2>
</a>
H5Part uses GNU Autoconf to generate a Makefile from the makefile
template called <code>Makefile.in</code>.
The configure script pays attention to the following
configure options;<p>
<UL>
<LI><b>--prefix=PREFIX</b> Install files in PREFIX</LI>
<LI><b>--enable-fortran</b> By default H5part will make no attempt to
build Fortran bindings. If you add the
<code>--enable-fortran</code> flag to the ./configure line, it
will create a small test program to determine how to generate
the fortran bindings and then create a library that includes
those bindings. You may need to set the fortran compiler by
setting the <code>FC</code> environment variable in your shell.</LI>
<LI><b>--enable-parallel</b> The version of HDF5 that you build for
Parallel I/O differs from the library you would build for
serial I/O. Consequently, the H5Part libraries must be built
specifically for the kind of I/O you have in mind (parallel or
serial). The configure script will attempt to find an
<code>mpicc</code> if it is available. If no
<code>mpicc</code> is available it will use the regular
C-compiler and will try to locate the location of the MPI
include files and libraries. You can assist the configure
program in its search by setting the <code>MPIROOT</code>
environment variable.</LI>
<LI><b>--enable-tools</b> Builds the currently available tools
<br>
<b>h5pAttrib</b>, an inspection tool that prints the number of timesteps in a file
the file attributes, the step attributes, the dataset names and their values.
<br>
<b>h5pToGNUplot</b>, a converter to two column ASCII format to load in GNUplot.
</LI>
<LI><b>--enable-python</b><font color=red> Under construction</font> Option to build python bindings. It has not been tested.
</LI>
<LI><b>--help</b> Prints configure options.
</LI>
</UL>
<p>
<a name="MakeOptions">
<h2>Make Options</h2>
</a>
<UL>
<LI>make</LI>builds the libraries and test programs
<LI>make install</LI>builds and installs
<LI>make clean</LI>removes extraneous object files
<LI>make distclean</LI>returns configuration to unconfigured state
</UL>
<a name="EnvVariables">
<h2>Environment Variables for Configure</h2>
</a>
The
configuration script is of limited intelligence. Sometimes, you
have to define the following environment variables in order to
help it on its way. You will often only need to tell it where to
find the HDF5 libraries (<code>H5ROOT</code> for serial or
<code>PHDF5ROOT</code> for parallel builds). All of these
environment variables can also be overidden in the Makefile that
is generated by the autoconfigure script.
The configure script pays attention to the following
environment variables;
<p>
<UL>
<LI><b>CC</b>: Use the <code>CC</code> environment variable to tell the
configure script where to find the C compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>CXX</b>: Use the <code>CXX</code> environment variable to tell the
configure script where to find the C++ compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>FC</b>: Use the <code>FC</code> environment variable to tell the
configure script where to find the fortran compiler. You can
also directly modify this variable in the
<code>Makefile</code> that is generated by the autoconfigure</LI>
<LI><b>MPICC</b>: If you are building for parallel C I/O, then it is
useful to tell the configure script where to find the
<code>mpicc</code> script. Normally, <code>mpicc</code> is
merely a wrapper script for a build using a regular C-compiler.
If no <code>mpicc</code> is available, then the
<code>configure</code> script will attempt to locate the mpi
header files and libraries. In that case, it may be useful to
define the <code>MPI_HOME</code> environment variable.</LI>
<LI><b>MPICXX</b>If you are building for parallel C++</LI>
<LI><b>MPIFC</b>: If you are building for parallel Fortran I/O, then it is
useful to tell the configure script where to find the parallel fortran compiler.
<LI><b>MPIROOT</b>: Set this environment variable to help the
configure script to locate the MPI libraries that should be
used to build the parallel version of the libraries. This
variable will be ignored if configured only to build the
serial implementation of the library.</LI>
<LI><b>HDF5ROOT</b>: Find the path to your serial HDF5 installation. If you
are building the serial version of H5part, then you should set
the <code>PHDF5ROOT</code> environment variable.</LI>
</UL><p>
<h3>Common compiler environemt variables for NERSC platforms</h3>
<UL>
<LI><b>DaVinci</b>: Linux ia64 </LI>
CC=icc CXX=icc F90=ifort MPICC=icc MPIFC=ifort MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include
<LI><b>Bassi</b>: AIX</LI>
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r
<LI><b>Jacquard</b>: Linux x86_64</LI>
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90
<LI><b>Starsky.lbl.gov:</b> (Darwin) PowerPC</LI>
CC=gcc CXX=g++ FC=g95
</UL>
<br>
NOTE: You might need to set the MPI library path (MPILIB) and MPI includes (MPIIINC) if they are in non standard places. For example: <br>
MPILIB=-L/usr/lpp/ppe.poe/lib -lmpi_r MPIINC=-I/usr/lpp/ppe.poe/include/thread
<h3>How to set the variables for configure:</h3>
It is very simple just call env with the variables together with configure. Notice the quotes in MPILIB.
<pre>
% env CC=icc CXX=icc F90=ifort MPICC=icc MPILIB=-L/usr/lib/ -lmpi MPIINC=-I/usr/include ./configure (configure options follow here)
</pre>
In the worst case, you can edit the <code>src/Makefile.am</code> and <code>test/Makefile.am</code> as
needed to perform the proper build.
</div>
doc/BuildingHDF5.html
Executable
+64
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>Building HDF5</title>
</head>
<body>
<font face="arial,helvetica" size="+2" color="#555588"><h2>Building H5Part</h2></font>
<UL>
<LI><a href="#ConfigOptions">Configure Options</a>
<LI><a href="#EnvVariables">Important Environment Variables</a>
</UL>
<hr>
<a name="ConfigOptions">
<h2>Configure options</h2></a>
</a>
To set the installation path configure with
<pre>
./configure --prefix=your hdf5 installation full path, e.g.--prefix=/usr/local/hdf5
</pre>
For the serial implementation configure with
<pre>
./configure
</pre>
For the parallel implementation configure with
<pre>
./configure --enable-parallel
</pre>
To enable shared objects configure with
<pre>
./configure --enable-shared
</pre>
<a name="EnvVariables">
<h2>Environment Variables</h2></a>
</a>
To add HDF5 to your PATH and LD_LIBRARY_PATH edit your
.tcshr, or .cshrc depending on the shell you are using and add
<pre>
setenv HDF5 "your hdf5 installation full path"
setenv PATH ${PATH}:${HDF5}/bin
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5}/lib
</pre>
if you are using bash, add to your .bashrc
<pre>
export HDF5="your hdf5 installation full path"
export PATH=$PATH:${HDF5}/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF5}/lib
</pre>
Open a new terminal or do a
source .tcshr (.cshrc, .bashrc) in the one that you are using.
You can <a href="http://vis.lbl.gov/Research/AcceleratorSAPP/Downloading.html">continue <a/>downloading and installing H5Part.
</div>
doc/Downloading.html
+37
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@@ -0,0 +1,37 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Downloading HDF5 and H5Part</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>Downloading HDF5 and H5Part</title>
</head>
<body>
<font face="arial,helvetica" size="+2" color="#555588"><h2>Downloading H5Part</h2></font>
<UL>
<LI><a href="#hdf5">Downloading HDF5</a>
<LI><a href="#h5part">Downloading H5Part</a>
</UL>
<hr>
<a name="hdf5">
<h2>Downloading HDF5</h2></a>
You will need to download and install the HDF5 library and link H5Part with it.
<UL>
<LI><a href="ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.6.5.tar.gz">ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.6.5.tar.gz</a></LI>
<LI><a href="http://www.zlib.net/zlib-1.2.3.tar.gz">http://www.zlib.net/zlib-1.2.3.tar.gz</a></LI>
<LI><a href="ftp://ftp.hdfgroup.org/lib-external/szip/2.0/src/szip-2.0.tar.gz">ftp://ftp.hdfgroup.org/lib-external/szip/2.0/src/szib-2.0.tar.gz</a></LI>
</UL>
<P>
Note: you might already have libz in your system and you will not need libsz unless you build hdf5 with support for it.
</P>
<h2 id="h5part">Downloading H5Part</h2>
H5Part is available for download from Berkeley Labs Codeforge system <a href="https://codeforge.lbl.gov/projects/h5part/">https://codeforge.lbl.gov/projects/h5part</a>.
</div>
doc/Doxyfile
+31 -33
View File
@@ -3,8 +3,8 @@
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
PROJECT_NAME = H5hut
PROJECT_NUMBER = 1.9.9
PROJECT_NAME = H5Part
PROJECT_NUMBER = 1.3.3
OUTPUT_DIRECTORY = ./ReferencePages
CREATE_SUBDIRS = NO
OUTPUT_LANGUAGE = English
@@ -35,7 +35,7 @@ INHERIT_DOCS = YES
SEPARATE_MEMBER_PAGES = NO
TAB_SIZE = 8
ALIASES =
OPTIMIZE_OUTPUT_FOR_C = YES
OPTIMIZE_OUTPUT_FOR_C = NO
OPTIMIZE_OUTPUT_JAVA = NO
BUILTIN_STL_SUPPORT = NO
DISTRIBUTE_GROUP_DOC = NO
@@ -57,7 +57,7 @@ CASE_SENSE_NAMES = YES
HIDE_SCOPE_NAMES = NO
SHOW_INCLUDE_FILES = NO
INLINE_INFO = YES
SORT_MEMBER_DOCS = NO
SORT_MEMBER_DOCS = YES
SORT_BRIEF_DOCS = NO
SORT_BY_SCOPE_NAME = NO
GENERATE_TODOLIST = YES
@@ -67,7 +67,7 @@ GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS =
MAX_INITIALIZER_LINES = 30
SHOW_USED_FILES = NO
SHOW_DIRECTORIES = NO
SHOW_DIRECTORIES = YES
FILE_VERSION_FILTER =
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
@@ -82,22 +82,20 @@ WARN_LOGFILE =
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
INPUT += H5.dox
INPUT += ../src/h5core/
INPUT += ../src/C/
INPUT += ../src/Fortran/
FILE_PATTERNS =
RECURSIVE = YES
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
EXAMPLE_PATH =
EXAMPLE_PATTERNS = *
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER =
FILTER_PATTERNS =
FILTER_SOURCE_FILES = NO
INPUT += ../src/H5Part.c
INPUT += ../src/H5Block.c
FILE_PATTERNS =
RECURSIVE = YES
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
EXAMPLE_PATH =
EXAMPLE_PATTERNS = *
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER =
FILTER_PATTERNS =
FILTER_SOURCE_FILES = NO
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
@@ -120,8 +118,8 @@ IGNORE_PREFIX =
GENERATE_HTML = YES
HTML_OUTPUT = .
HTML_FILE_EXTENSION = .html
HTML_HEADER =
HTML_FOOTER =
HTML_HEADER =
HTML_FOOTER = doxyfooter
HTML_STYLESHEET =
HTML_ALIGN_MEMBERS = YES
GENERATE_HTMLHELP = NO
@@ -193,13 +191,13 @@ EXPAND_ONLY_PREDEF = NO
SEARCH_INCLUDES = YES
INCLUDE_PATH =
INCLUDE_FILE_PATTERNS =
PREDEFINED = PARALLEL_IO
PREDEFINED =
EXPAND_AS_DEFINED =
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
TAGFILES =
TAGFILES = YES
GENERATE_TAGFILE =
ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
@@ -207,21 +205,21 @@ PERL_PATH = /usr/bin/perl
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
CLASS_DIAGRAMS = NO
CLASS_DIAGRAMS = YES
HIDE_UNDOC_RELATIONS = YES
HAVE_DOT = NO
CLASS_GRAPH = NO
COLLABORATION_GRAPH = NO
GROUP_GRAPHS = NO
HAVE_DOT = YES
CLASS_GRAPH = YES
COLLABORATION_GRAPH = YES
GROUP_GRAPHS = YES
UML_LOOK = NO
TEMPLATE_RELATIONS = NO
INCLUDE_GRAPH = NO
INCLUDED_BY_GRAPH = NO
CALL_GRAPH = NO
GRAPHICAL_HIERARCHY = NO
DIRECTORY_GRAPH = NO
GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
DOT_IMAGE_FORMAT = png
DOT_PATH =
DOT_PATH = /Applications/Graphviz.app/Contents/MacOS
DOTFILE_DIRS =
MAX_DOT_GRAPH_WIDTH = 1024
MAX_DOT_GRAPH_HEIGHT = 1024
doc/Examples/meshexample.dxf
-47962
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File diff suppressed because it is too large Load Diff
doc/Examples/meshexample.txt
-77
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@@ -1,77 +0,0 @@
NumLevels: 2
NumVerticesOnLevel: 11 20 29
Vertices:
1 0.0 0.0
2 60.0 -70.0
3 90.0 -10.0
4 140.0 -70.0
5 180.0 -10.0
6 240.0 -60.0
7 220.0 60.0
8 140.0 90.0
9 200.0 120.0
10 130.0 150.0
11 50.0 80.0
12 115.0 40.0
13 95.0 85.0
14 70.0 35.0
15 160.0 -40.0
16 135.0 -10.0
17 115.0 -40.0
18 200.0 25.0
19 180.0 75.0
20 160.0 40.0
21 125.0 15.0
22 112.5 -10.0
23 102.5 15.0
24 147.5 15.0
25 137.5 40.0
26 150.0 65.0
27 127.5 65.0
28 117.5 87.5
29 105.0 62.5
NumElemsOnLevel: 12 24 36
NumElems: 12 28 44
Elements:
ID PID CID VertexIDs Adj Translation Tbl (dim num lvls - 1)
1 -1 -1 1 2 3 2 11 -1 1
2 -1 -1 2 3 4 3 -1 1 2
3 -1 12 3 4 5 4 12 2 -1
4 -1 -1 4 5 6 5 -1 3 3
5 -1 -1 5 7 6 -1 4 6 4
6 -1 17 8 5 7 5 7 12 -1
7 -1 -1 8 9 7 -1 6 8 5
8 -1 -1 10 8 9 7 -1 9 6
9 -1 -1 11 10 8 8 10 -1 7
10 -1 25 11 3 8 12 9 11 -1
11 -1 -1 1 11 3 10 1 -1 8
12 -1 21 3 8 5 6 3 10 -1
13 3 -1 3 14 13 16 21 2 9
14 3 -1 14 4 12 4 16 2 10
15 3 -1 13 12 5 4 23 16 11
16 3 -1 14 13 12 15 14 13 12
17 6 -1 8 17 16 20 5 22 13
18 6 -1 17 5 15 5 20 23 14
19 6 -1 16 15 7 5 7 20 15
20 6 -1 17 16 15 19 18 17 16
21 12 -1 3 18 13 24 13 26 17
22 12 -1 18 8 17 17 24 27 18
23 12 -1 13 17 5 18 15 24 19
24 12 -1 18 13 17 23 22 21 20
25 10 -1 11 20 19 28 9 11 21
26 10 -1 20 3 18 21 28 11 22
27 10 -1 19 18 8 22 9 28 23
28 10 -1 20 3 18 27 26 25 24
3,0 3,1 4,2 2,3 16,4
1 2 -1 3 4
1 2 3
1 3 6
2 11 1 13 14
doc/Examples/simple_tet.vtk
-107
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@@ -1,107 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 18 90
4 0 3 2 1
4 0 4 3 1
4 0 5 6 7
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
4 0 11 12 13
4 11 5 14 15
4 12 14 6 16
4 13 15 16 7
4 11 12 13 15
4 11 12 14 15
4 12 13 15 16
4 12 14 15 16
CELL_TYPES 18
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 18
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
doc/Examples/simple_tet_level0.vtk
-59
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@@ -1,59 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 2 10
4 0 3 2 1
4 0 4 3 1
CELL_TYPES 2
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 2
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
doc/Examples/simple_tet_level1.vtk
-80
View File
@@ -1,80 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 9 45
4 0 4 3 1
4 0 5 6 7
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
CELL_TYPES 9
10
10
10
10
10
10
10
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 9
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
doc/Examples/simple_tet_level2.vtk
-101
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@@ -1,101 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 17 DOUBLE
-1 0 0
1 0 0
0 1 0
0 0 1
0 -1 0
-0.5 0 0.5
-0.5 0.5 0
0 0 0
0 0.5 0.5
0.5 0 0.5
0.5 0.5 0
-0.75 0 0.25
-0.75 0.25 0
-0.5 0 0
-0.5 0.25 0.25
-0.25 0 0.25
-0.25 0.25 0
CELLS 16 80
4 0 4 3 1
4 5 3 8 9
4 6 8 2 10
4 7 9 10 1
4 5 6 7 9
4 5 6 8 9
4 6 7 9 10
4 6 8 9 10
4 0 11 12 13
4 11 5 14 15
4 12 14 6 16
4 13 15 16 7
4 11 12 13 15
4 11 12 14 15
4 12 13 15 16
4 12 14 15 16
CELL_TYPES 16
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
10
POINT_DATA 17
SCALARS vertex_id int 1
LOOKUP_TABLE default
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
CELL_DATA 16
SCALARS cell_attribute_data int 1
LOOKUP_TABLE default
1
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
doc/Examples/trimesh_dgraph_level0.metis
-13
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@@ -1,13 +0,0 @@
12 14
2 11
1 3
2 4 12
3 5
4 6
5 7 12
6 8
7 9
8 10
9 11 12
1 10
3 6 10
doc/Examples/trimesh_dgraph_level0.metis.part.2
-12
View File
@@ -1,12 +0,0 @@
0
1
1
1
1
1
0
0
0
0
0
1
doc/Examples/trimesh_dgraph_level0.metis.part.3
-12
View File
@@ -1,12 +0,0 @@
1
1
2
2
2
0
0
0
0
1
1
2
doc/Examples/trimesh_dnode_level1.metis
-49
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@@ -1,49 +0,0 @@
24 35
%1
2 8
%2
1 9 10
%3
4 10 11
%4
3 14 15
%5
6 13 15
%6
5 7
%7
6 21 23
%8
1 21 22
%9
2 12 17
%10
2 3 12
%11
3 12 19
%12
9 10 11
%13
5 16 18
%14
4 16 19
%15
4 5 16
%16
13 14 15
%17
9 20 22
%18
13 20 23
%19
11 14 20
%20
17 18 19
%21
7 8 24
%22
8 17 24
%23
7 18 24
%24
21 22 23
doc/Examples/trimesh_dnode_level1.metis.part.2
-24
View File
@@ -1,24 +0,0 @@
1
1
0
0
0
0
1
1
1
1
0
1
0
0
0
0
1
0
0
0
1
1
1
1
doc/Examples/trimesh_level0.metis
-13
View File
@@ -1,13 +0,0 @@
12 1
1 2 3
2 3 4
3 4 6
4 5 6
5 6 7
6 7 8
7 8 11
8 10 11
8 9 10
3 8 9
1 3 9
3 6 8
doc/Examples/trimesh_level0.metis.epart.2
-12
View File
@@ -1,12 +0,0 @@
1
1
1
1
0
0
0
0
0
0
1
1
doc/Examples/trimesh_level0.metis.ngraph
-12
View File
@@ -1,12 +0,0 @@
11 22
2 3 9
1 3 4
1 2 4 6 8 9
2 3 6 5
4 6 7
3 4 5 7 8
5 6 8 11
6 7 11 10 9 3
8 10 3 1
8 11 9
7 8 10
doc/Examples/trimesh_level0.metis.npart.2
-11
View File
@@ -1,11 +0,0 @@
1
1
1
1
1
0
0
0
0
0
0
doc/Examples/trimesh_level1.metis
-41
View File
@@ -1,41 +0,0 @@
20 43
%1
2 3 11
%2
1 3 4
%3
1 2 14 13 18 20
%4
2 14 12 6
%5
12 6 15 17 13
%6
4 5 7
%7
6 15 16 9
%8
9 10 19 18 17 16
%9
7 8 10
%10
8 9 11
%11
1 20 19 10
%12
4 14 13 5
%13
3 14 12 5 17 18
%14
3 13 12 4
%15
5 17 17 7
%16
7 8 17 15
%17
5 15 16 8 18 13
%18
3 13 17 8 19 20
%19
8 11 20 18
%20
3 18 19 11
doc/Examples/trimesh_level1.metis.part.2
-20
View File
@@ -1,20 +0,0 @@
1
1
1
0
0
0
0
1
1
1
1
0
0
0
0
0
0
1
1
1
doc/H5.dox
-139
View File
@@ -1,139 +0,0 @@
/*!
\mainpage H5hut: A High-Performance I/O Library for Particle-based Simulations
Particle-based simulations running on large high-performance computing systems
over many time steps can generate an enormous amount of particle- and
field-based data for post-processing and analysis. Achieving high-performance
I/O for this data, effectively managing it on disk, and interfacing it with
analysis and visualization tools can be challenging, especially for domain
scientists who do not have I/O and data management expertise. We present the
H5hut library, an implementation of several data models for particle-based
simulations that encapsulates the complexity of HDF5 and is simple to use, yet
does not compromise performance.
Developers:
<UL>
<LI> Andreas Adelmann (PSI) </LI>
<LI> Achim Gsell (PSI) </LI>
<LI> Benedikt Oswald (PSI) </LI>
<LI> Mark Howison (NERSC/LBNL) </LI>
<LI> Prabhat (NERSC/LBNL) </LI>
<LI> Wes Bethel (NERSC/LBNL) </LI>
</UL>
Previous developers:
<UL>
<LI> John Shalf (NERSC/LBNL)</LI>
<LI> Cristina Siegerist (NERSC/LBNL)</LI>
</UL>
For more information, please contact the <a href="mailto:h5part@lists.psi.ch">h5part</a> mailing list.
*/
/*!
\defgroup h5hut_c_api H5hut C API
*/
/*!
\ingroup h5hut_c_api
\defgroup h5hut_file File Handling
*/
/*!
\ingroup h5hut_c_api
\defgroup h5hut_error Error Handling
*/
/*!
\ingroup h5hut_c_api
\defgroup h5hut_model Setting up the Data Model
*/
/*!
\ingroup h5hut_c_api
\defgroup h5hut_attrib Reading and Writing Attributes
*/
/*!
\defgroup h5part_c_api H5Part C API
*/
/*!
\ingroup h5part_c_api
\defgroup h5part_model Setting up the Data Model
*/
/*!
\ingroup h5part_c_api
\defgroup h5part_data Reading and Writing Datasets
*/
/*!
\defgroup h5block_c_api H5Block C API
*/
*/!
\ingroup h5block_c_api
\defgroup h5block_model Setting up the Data Model
*/
\ingroup h5block_c_api
\defgroup h5block_data Reading and Writing Datasets
*/
\ingroup h5block_c_api
\defgroup h5block_attrib Reading and Writing Attributes
*/
/*!
\defgroup h5fed_c_api H5Fed C API
*/
/*!
\defgroup h5hut_f90_api H5hut F90 API
*/
/*!
\ingroup h5hut_f90_api
\defgroup h5hut_file_f File Handling
*/
/*!
\ingroup h5hut_f90_api
\defgroup h5hut_model_f Setting up the Data Model
*/
/*!
\ingroup h5hut_f90_api
\defgroup h5hut_attrib_f Reading and Writing Attributes
!<
/*!
\defgroup h5part_f90_api H5Part F90 API
*/
/*!
\ingroup h5part_f90_api
\defgroup h5part_model_f Setting up the Data Model
*/
/*!
\ingroup h5part_f90_api
\defgroup h5part_data_f Reading and Writing Datasets
*/
/*!
\defgroup h5block_f90_api H5Block F90 API
*/
/*!
\ingroup h5block_f90_api
\defgroup h5block_model_f Setting up the Data Model
*/
/*!
\ingroup h5block_f90_api
\defgroup h5block_data_f Reading and Writing Datasets
*/
/*!
\ingroup h5block_f90_api
\defgroup h5block_attrib_f Reading and Writing Attributes
*/
doc/H5PartExpress.html
Executable
+14
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@@ -0,0 +1,14 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
Under construction, will be here soon.
</div>
doc/H5PartIDL.html
Executable
+15
View File
@@ -0,0 +1,15 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
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Under construction, will be here soon.
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<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Put your title here!!</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<head>
<title>H5Part Utility Tools</title>
</head>
<body>
<font face="arial,helvetica" size="+2" color="#555588"><h2>H5Part Utility Tools</h2></font>
<UL>
<LI><a href="h5pAttrib">h5pAttrib</a>
<LI><a href="h5pToGNUplot">h5pToGNUplot</a>
</UL>
<hr>
<a name="h5pAttrib">
<h2>h5pAttrib</h2>
</a>
<b>h5pAttrib</b> is an inspection tool that prints to stdout the number of timesteps in a file
the file attributes, the step attributes, the dataset names and their values. It's simpler to use than h5dump.
Usage options are given by typing:
<br><br>
<PRE>
% ./h5pAttrib -h
usage: h5pAttrib [OPTIONS] file
OPTIONS
-h, --help Print help page
-n, --nstep Print number of steps
-A, --fileA Print file attributes
-a, --stepA Print step attributes & values for time step n
-d, --dataset Print data sets names & values for time step n
-H, --header Print shorter version without the values
</PRE>
<h3>Examples</h3>
<OL>
<LI>
Show file attribute names & values of sample.h5part
</LI>
h5pAttrib -A sample.h5part
<LI>
Show step attribute names for time step 5 of sample.h5part
</LI>
h5pAttrib -a 5 -H sample.h5part
</OL>
<a name="h5pToGNUplot">
<h2>h5pToGNUplot</h2>
</a>
<b>h5pToGNUplot</b> is a converter from H5Part to two column ASCII text format for loading into GNUplot. Usage options are given by typing:
<br><br>
<PRE>
% ./h5pToGNUplot -h
usage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]
FLAGS
-h, --help Print help page
-1, --1var (REQUIRED) Takes first variable parameter
-2, --2var (REQUIRED) Takes second variable parameter
-i, --input (REQUIRED) Takes input file name
-t, --timestep (REQUIRED) Sets the timestep (Value -1 will result in dumping values of all timesteps.)
-o, --output (OPTIONAL) Takes output file name (without this flag, the program will print to stdout)
-n, --number (OPTIONAL) Sets number of output points
-s, --start (OPTIONAL) Sets the starting particle index
</PRE>
<h3>Examples</h3>
<OL>
<LI>
Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
</LI>
h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt
<LI>
Create a GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
using 1200 points from particle index 76
</LI>
h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt -s 76 -n 1200
</OL>
</div>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part: VisIt Plugins</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<font face="arial,helvetica"><h1>H5Part: VisIt Plugins</h1></font>
<font face="arial,helvetica" color="#555588"><h2>Introduction</h2></font>
<P>
<a href="http://www.llnl.gov/visit">VisIt</a> is an open source point-and-click 3D scientific visualization application that supports most of the common visualization techniques on structured and unstructured grids. One of its advantages is that it employs a distributed and parallel architecture in order to handle extremely large data sets interactively. VisIt's rendering and data processing capabilities are split into viewer and engine components that may be distributed across multiple machines. See this link for <a href="http://vis.lbl.gov/NERSC/Software/visit/">details</a> on how to run VisIt in NERSC.
</P>
<P>
VisIt achieves extensibility through the use of dynamically loaded plugins. All of VisIt's plots, operators, and database readers are implemented as plugins and are loaded at run-time from the plugin directory. New plugins can be added simply by installing them in this directory. VisIt comes with a graphical plugin creation tool, which greatly simplifies the process of creating new plugins. The user describes the properties of the plugin and then the tool generates most of the code necessary to implement the plugin. For example, in the case of an operator, the plugin creation tool creates the code necessary for the graphical user interface attribute window; the C++, Python, and Java interfaces; and the code necessary to interface to VisIt. The only code you need to write is the C++ code that actually performs the operation.
</P>
<font face="arial,helvetica" color="#555588"><h2>H5Part in VisIt</h2></font>
<font face="arial,helvetica" color="#555588"><h3>Database Reader Plugin</h3></font>
<P>
We wrote a Multiple Time Step Multiple Domain database reader to read H5Part data into VisIt. H5Part datasets should be named with the extension <font color=red>".h5part"</font> to be recognized by the reader since VisIt does not have a format selection mechanism at the time of reading. Figure 1 shows a Pseudocolor plot of a data set and Figure 2 shows a Scatter plot x-y (any combination of x, px, y, py, z, pz, id are possible).
</P>
<P>
<TABLE>
<TR>
<TD>
<a href="H5PartVisIt/cloud_visit.png"><img src="H5PartVisIt/cloud_visit.s.png" width=400 height=300></a>
</TD
></TR>
<TR>
<TD width=300>
Figure 1. VisIt User interface showing an H5Part particle file rendered as spheres using the Pseudocolor plot.
</TD>
</TR>
<TR>
<TD>
<a href="H5PartVisIt/cloud_visit_2D.png"><img src="H5PartVisIt/cloud_visit_2D.s.png" width=300 height=300></a>
</TD>
</TR>
<TR>
<TD>
Figure 2. A Scatter plot of the x-y projection of the particles.
</TD>
</TR>
</TABLE>
</P>
<P>
VisIt provides a Query interface, for single time steps and for time series. Figure 3 shows the query interace over time for the sum of the x position and the z position of the particoes.
</P>
<P>
<TABLE>
<TR>
<TD>
<a href="H5PartVisIt/visit_query1.png"><img src="H5PartVisIt/visit_query1.s.png" width=400 height=300></a>
</TD
></TR>
<TR>
<TD width=300>
Figure 3. VisIt's Time Query Output.
</TD>
</TR>
</TABLE>
</p>
<font face="arial,helvetica" color="#555588"><h2>Operator Plugins</h2></font>
<P>
<font face="arial,helvetica" color="#555588"><h3>Particle Random Sampler</h3></font>
</P>
<P>
<font face="arial,helvetica" color="#555588"><h3>Particle Binner</h3></font>
</P>
</div>
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doc/H5X_File_Format.txt
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2.1.1 File attributes
Attributes of the HDF5 root group are called "file attributes". There
are no restrictions on file attribute names. Names with "__" as prefix and
postfix are intended for internal use. Supported values for file attributes
are scalars and arrays of 64bit integer and 64bit floating point number as
well as string values. Arrays of strings are not supported.
are no restrictions on file attribute names. Supported values are
scalars and arrays of 64bit integer and 64bit floating point number as
well as string values, but not arrays of strings.
2.1.1.1 Predefined file attributes
@@ -64,28 +63,18 @@ Example: With __stepnumwidth__ := 5 the name of the step group with
number 42 is "Step#00042", with __stepnumwidth__ := 0 the name is
"Step#42".
Step groups may be unsorted in the HDF5 file und needn't be number
Step groups may be unsorted in the HDF5 file und may not be number
consecutively.
2.1.3 Other members of the root group
Other sub-groups of the root group are allowed, but the group names are restricted
to names not matching "Step#.*".
2.2 Format of a step group
2.2.1 Step attributes
Step attributes are HDF5 attributes asigned to a step group. There
are no restrictions on step attribute names. As with file attributes names
enclosed in "__" are intended for internal use. Supported values are the same
as for file attributes:
* 64bit integer value
* arrays of 64bit integer values
* 64bit floating point number
* array of 64bit floating point number
* strings
Note that array of strings are not supported!
are no restrictions on file attribute names. Supported values are
scalars and arrays of 64bit integer and 64bit floating point number as
well as string values, but not arrays of strings.
2.2.2 Predefined step attributes
@@ -158,13 +147,5 @@ n-dimensional vector values with n := 1.
2.3 Step properties [NEW]
Why? Much faster than step attributes if you need to access consecutive values
Group of root group with name "StepProperties"
Members are datasets
Supported values are the same as for step attributes
Mapping of value to step via object index of step group
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<html><head><title>H5Part Tools How-to</title>
<meta http-equiv="Content-Type" content="text/html; charset=euc-kr"></head>
<body bgcolor="#ffffff" text="#000000">
<table border="0" cellpadding="0" cellspacing="0" width="987">
<tbody><tr>
<td height="6050" width="27"></td>
<td colspan="3" valign="top">
<div id="body">
<div id="mainleft"><font face="Arial, Helvetica, sans-serif"><a name="TOP"></a>
</font></div>
<div id="maincenter"> <font face="arial,helvetica">
<h1 align="center"><font face="Arial, Helvetica, sans-serif"><b><font color="#666699">H5Part
Tools How-to</font></b></font></h1>
</font><font color="#555588" face="arial,helvetica">
<h2><font color="#666699" face="Arial, Helvetica, sans-serif">Table
of Contents</font></h2>
</font>
<p><font face="Arial, Helvetica, sans-serif"><b><a href="#Quick%20Guide">
[1] Quick Guide</a></b> </font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pAttrib</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
<b><br>
<a href="#timesteps">[2] To see number of timesteps in a h5part file</a><br>
<br>
<a href="#file%20attributes">[3] To see file attributes in a h5part
file</a><br>
<br>
<a href="#step%20attributes"> [4] To see step attributes in a h5part
file</a><br>
<br>
<a href="#dataset">[5] To see dataset in a h5part file</a><br>
<br>
<a href="#flags">[6] Providing more than one flag at once for h5pAttrib</a></b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pToGNUplot</font></b></font><font face="Arial, Helvetica, sans-serif"><br>
<br>
<b><a href="#parameters">[7] What parameters to provide</a><br>
<br>
<a href="#input%20file">[8] How to create an input file to GNUplot</a></b></font></p>
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="Quick Guide">[1]
Quick Guide</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">Executing the program with
-h option will display a concise help page.</font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">./h5pAttrib
-h</font></font></p>
<p><font face="Courier New, Courier, mono">usage: h5pAttrib [OPTIONS]
file</font></p>
<p><font face="Courier New, Courier, mono"> OPTIONS<br>
-h, --help Print help page<br>
-n, --nstep Print number of steps<br>
-A, --fileA Print file attributes<br>
-a n, --stepA n Print step attributes &amp; values for time step n<br>
-d n, --dataset n Print data sets names &amp; values for time step
n<br>
-H, --header Print shorter version without the values</font></p>
<p><font face="Courier New, Courier, mono"> Examples:</font></p>
<p><font face="Courier New, Courier, mono"> 1) Show file attribute names
&amp; values of sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> h5pAttrib -A sample.h5part<br>
OR<br>
h5pAttrib --fileA sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> 2) Show step attribute names
for time step 5 of sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"> h5pAttrib -a 5 -H sample.h5part<br>
OR<br>
h5pAttrib --stepA 5 -H sample.h5part</font></p>
<p><font face="Courier New, Courier, mono"><br>
<b><font size="+1">$&gt;</font></b> ./h5pToGNUplot -h</font></p>
<p><font face="Courier New, Courier, mono">usage: h5pToGNUplot -t TIMESTEP
-1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]</font></p>
<p><font face="Courier New, Courier, mono"> FLAGS<br>
-h, --help Print help page</font><br>
<font face="Courier New, Courier, mono">-1 par, --1var par (REQUIRED)
Takes first variable parameter to "par"<br>
-2 par, --2var par (REQUIRED) Takes second variable parameter to "par"<br>
-i file, --input file (REQUIRED) Takes input file name to "file"<br>
</font><font face="Courier New, Courier, mono">-t step, --timestep
step (REQUIRED) Sets the timestep to "step" (Value -1 will
result in dumping values of all timesteps.)<br>
-o file, --output file (OPTIONAL) Takes output file name to "file"
(without this flag, the program will print to stdout)<br>
-n num, --number num (OPTIONAL) Sets number of output points to "num"<br>
-s idx, --start idx (OPTIONAL) Sets the starting particle index to
"idx"</font></p>
<p><font face="Courier New, Courier, mono"><br>
Examples:</font></p>
<p><font face="Courier New, Courier, mono"> 1) Create GNU plot file
output.txt from sample.h5part by ploting x vs px for timestep 54</font></p>
<p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x
-2 px -i sample.h5part -o output.txt</font></p>
<p><font face="Courier New, Courier, mono"> 2) Create GNU plot file
output.txt from sample.h5part by ploting x vs px for timestep 54<br>
using 1200 points from particle index 76</font></p>
<p><font face="Courier New, Courier, mono"> h5pToGNUplot -t 54 -1 x
-2 px -i sample.h5part -o output.txt -s 76 -n 1200</font></p>
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pAttrib</font></b></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="timesteps">[2]
To see number of timesteps in a h5part file</a></font></h2>
<p>Executing the program h5pAttrib with -n flag will display the number
of timesteps in the file.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -n sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing number of timesteps
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">There are total 252 number
of timesteps.<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font><font face="Arial, Helvetica, sans-serif"><br>
</font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#666699" face="Arial, Helvetica, sans-serif"><br>
<font color="#555588"><a name="file attributes">[3] To see file attributes
in a h5part file</a></font></font></h2>
<p>File attribute contains information about the file. (file description
etc...) Executing the program h5pAttrib with -A flag will display
the file attributes in the file.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -A sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing file attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of file attributes
for file sample.h5part is 0 ...<br>
There are no file attributes.<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of file attributes.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p align="center">&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="step attributes">[4]
To see step attributes in a h5part file</a></font></h2>
<p>Step attribute contains information that belongs to a specific step.
(step name, timestep number, etc...) Executing the program h5pAttrib
with -a flag will display the step attributes in the file.<br>
Note that the timestep index should follow -a flag.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">
./h5pAttrib -a 2 sample.h5part</font></font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing step attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of step attributes
for timestep #2 is 10 ...</font></p>
<p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_INT64<br>
Printing 1 element value(s):<br>
COUNT[0]: 2</font></p>
<p><font face="Courier New, Courier, mono">Attribute #1 = Spos<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_DOUBLE<br>
Printing 1 element value(s):<br>
COUNT[0]: 0.143580</font></p>
<p><font face="Courier New, Courier, mono">Attribute #2 = structLen<br>
There are 1 elements in the attribute<br>
Attribute Type is H5T_NATIVE_DOUBLE<br>
Printing 1 element value(s):<br>
COUNT[0]: 2.393000</font></p>
<p><font face="Courier New, Courier, mono">.<br>
.<br>
.</font></p>
<p><font face="Courier New, Courier, mono"><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of step attributes.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
<a name="dataset">[5] To see dataset in a h5part file</a></font></h2>
<p>Executing the program h5pAttrib with -d flag will display the datasets
information in the file. (dataset name, type, number of elements,
etc...) Executing the program h5pAttrib with -d flag will display
the datasets information in the file.<br>
Note that the timestep index should follow -d flag.</p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -d 2 -H sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing names of datasets
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of datasets for
timestep #2 is 7 ...</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
Dataset Type is H5T_NATIVE_INT64<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 67587</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p><font face="Arial, Helvetica, sans-serif"><br>
<i>NOTE: -H option will omit the list of values of datasets.</i></font></p>
<p>&nbsp; </p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<p>&nbsp;</p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="flags">[6]
Providing more than one flag at once</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">When more than one flags
are provided, one result after another will be displayed.</font></p>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b></font></p>
<p><font face="Arial, Helvetica, sans-serif" size="+1"><b><font face="Courier New, Courier, mono">$&gt;</font></b></font><font face="Courier New, Courier, mono">
./h5pAttrib -H -a 1 -d 1 sample.h5part</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing step attributes
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of step attributes
for timestep #1 is 10 ...</font></p>
<p><font face="Courier New, Courier, mono">Attribute #0 = Step<br>
Attribute #1 = Spos<br>
Attribute #2 = structLen<br>
Attribute #3 = org<br>
Attribute #4 = maxX<br>
Attribute #5 = minX<br>
Attribute #6 = maxP<br>
Attribute #7 = minP<br>
Attribute #8 = centroid<br>
Attribute #9 = nloc<br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono"><br>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">Printing names of datasets
for: sample.h5part ...</font></p>
<p><font face="Courier New, Courier, mono">The number of datasets for
timestep #1 is 7 ...</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #0 = id<br>
Dataset Type is H5T_NATIVE_INT64<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #1 = px<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #2 = py<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #3 = pz<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #4 = x<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #5 = y<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">Dataset Name #6 = z<br>
Dataset Type is H5T_NATIVE_DOUBLE<br>
Number of elements: 60214</font></p>
<p><font face="Courier New, Courier, mono">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</font></p>
<p><font face="Courier New, Courier, mono">done</font></p>
<p>&nbsp;</p>
<div align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></div>
</div>
</div>
</td>
</tr>
<tr>
<td height="80"></td>
<td colspan="3" valign="top">
<h2><font face="Arial, Helvetica, sans-serif" size="+1"><b><font color="#999999">---
For h5pToGNUplot</font></b></font></h2>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><a name="parameters">[7]
What parameters to provide</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif">When you execute the program
with -h option, it displays what flags are necessary and what flags are
optional.</font></p>
</td>
</tr>
<tr>
<td height="200"></td>
<td valign="top" width="137">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Short Version</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">-h<br>
-1<br>
-2<br>
-i<br>
-t<br>
-o<br>
-n<br>
-s </font></p>
</td>
<td valign="top" width="144">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Long Version</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">--help<br>
--1var<br>
--2var<br>
--input<br>
--timestep<br>
--output<br>
--number<br>
--start </font></p>
</td>
<td valign="top" width="679">
<p align="left"><b><font face="Arial, Helvetica, sans-serif">Meanings</font></b></p>
<p><font face="Arial, Helvetica, sans-serif">Print help page<br>
(REQUIRED) Takes first variable parameter<br>
(REQUIRED) Takes second variable parameter<br>
(REQUIRED) Takes input file name<br>
(REQUIRED) Sets the timestep (Value -1 will result in dumping values of
all timesteps.)<br>
(OPTIONAL) Takes output file name (without this flag, the program will
print to stdout)<br>
(OPTIONAL) Sets number of output points<br>
(OPTIONAL) Sets the starting particle index</font> </p>
</td>
</tr>
<tr>
<td height="1786"></td>
<td colspan="3" valign="top">
<p>&nbsp;</p>
<p align="center"><font face="Arial, Helvetica, sans-serif"><a href="#TOP">&lt;back
to top&gt;</a></font></p>
<h2><font color="#555588" face="Arial, Helvetica, sans-serif"><br>
<a name="input file">[8] How to create an input file to GNUplot</a></font></h2>
<p><font face="Arial, Helvetica, sans-serif"><b>EXAMPLE&gt;&gt;</b><br>
<i>Create input file to GNUplot that plots x vs. y.</i></font></p>
<p><font face="Arial, Helvetica, sans-serif"><b><font face="Courier New, Courier, mono" size="+1">$&gt;</font></b><font face="Courier New, Courier, mono">
./h5pToGNUplot -1 x -2 y -t 1 -i sample.h5part -o output.txt<br>
<b><font size="+1">$&gt;</font></b> cat output.txt<br>
-0.390779 -0.254793<br>
-0.396527 -0.252781<br>
-0.375362 -0.285137<br>
-0.396527 -0.252781<br>
-0.379917 -0.283147<br>
-0.390779 -0.254793<br>
-0.387536 -0.287346<br>
-0.371787 -0.319797<br>
-0.379917 -0.283147<br>
-0.378967 -0.326058<br>
-0.378976 -0.326078<br>
-0.387536 -0.287346<br>
-0.378957 -0.326069<br>
-0.379917 -0.283147<br>
-0.388762 -0.265390<br>
-0.371787 -0.319797<br>
-0.390779 -0.254793<br>
-0.376825 -0.266804<br>
-0.379917 -0.283147<br>
-0.375362 -0.285137<br>
...</font></font></p>
<p><font face="Courier New, Courier, mono"><i>Then run GNUplot...</i></font></p>
<p><font face="Courier New, Courier, mono"><b><font size="+1">$&gt;</font></b>
gnuplot</font></p>
<p><font face="Courier New, Courier, mono"> G N U P L O T<br>
Version 4.0 patchlevel 0<br>
last modified Thu Apr 15 14:44:22 CEST 2004<br>
System: Linux 2.6.11.4-21.11-smp</font></p>
<p><font face="Courier New, Courier, mono"> Copyright (C) 1986 - 1993, 1998,
2004<br>
Thomas Williams, Colin Kelley and many others</font></p>
<p><font face="Courier New, Courier, mono"> This is gnuplot version 4.0.
Please refer to the documentation<br>
for command syntax changes. The old syntax will be accepted<br>
throughout the 4.0 series, but all save files use the new syntax.</font></p>
<p><font face="Courier New, Courier, mono"> Type `help` to access the on-line
reference manual.<br>
The gnuplot FAQ is available from<br>
http://www.gnuplot.info/faq/</font></p>
<p><font face="Courier New, Courier, mono"> Send comments and requests for
help to<br>
&lt;gnuplot-info@lists.sourceforge.net&gt;<br>
Send bugs, suggestions and mods to<br>
&lt;gnuplot-bugs@lists.sourceforge.net&gt;</font></p>
<p><font face="Courier New, Courier, mono"><br>
Terminal type set to 'x11'<br>
<font size="+1"><b>gnuplot&gt;</b></font> plot "output.txt"</font></p>
<p><font face="Arial, Helvetica, sans-serif"><i>This will open a GNUplot
window that plots output.txt.</i></font></p>
<p align="center"><img src="H5tools_files/snapshot1.jpg" height="541" width="672"><br>
<font face="Arial, Helvetica, sans-serif">&lt;Sample screen shot of GNUplot
with input datafile generated by h5pToGNUplot&gt;</font></p>
</td>
</tr>
<tr>
<td height="44"></td>
<td></td>
<td></td>
<td></td>
</tr>
</tbody></table>
</body></html>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part, Logical Internal HDF5 File Layout</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<font face="arial,helvetica"><h1>H5Part: Logical Internal HDF5 File Layout</h1></font>
<P>
HDF5 is extremely flexible in the sense that it allows the user to define a higher level data model to describe domain-specific data relationships. This flexibility however makes it necessary to develop an agreement on the logical layout of the data. The H5Part data model consists of Particle groups corresponding to the simulation time steps, each with seven datasets corresponding to x, px, y, py, z, pz, id for each particle. Attributes can be added to the file and to the datasets.
</P>
<center><img src="layout.png"></center>
<PRE>
HDF5 "parttest.h5" {
GROUP "/" {
GROUP "Particles#0" {
DATASET "id" {
DATATYPE H5T_STD_I64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "px" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "py" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "pz" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "x" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "y" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
DATASET "z" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 10 ) / ( 10 ) }
}
}
</PRE>
<P>
See <a href="http://www-vis.lbl.gov/Publications/2002/hdf5.pdf">hdf5.pdf</a> for an introduction on the use of HDF5.
</P>
</div>
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EXTRA_DIST = \
Doxyfile \
H5.dox \
Makefile.in
all:
doc:
doxydoc:
doxygen
clean:
${RM} -rf ReferencePages TWiki
EXTRA_DIST = \
Doxyfile doxyfooter \
$(wildcard *.html) \
$(wildcard *.png) \
$(wildcard H5PartVisIt/*.png) \
$(wildcard H5tools/*.html) \
$(wildcard H5tools/H5tools_files/*.jpg)
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part, the C/C++ API</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<h1>The C/C++ Application Programming Interface (API)</h1>
<UL>
<LI><a href="#Opening">Opening, Closing, and Validating Datafiles</a>
<LI><a href="#SetStep">Setting the Simulation Timestep</a>
<LI><a href="#SetNumParticles">Setting the Number of Particles</a>
<LI><a href="#Writing">Writing Datasets</a>
<LI><a href="#ReadingNumTimeSteps">Reading the Number of Time Steps</a>
<LI><a href="#ReadingNumParticles">Reading the Number of Particles</a>
<LI><a href="#Reading">Reading Datasets</a>
<LI><a href="#DatasetsInfo">Reading the Number and the Names of Datasets</a>
<LI><a href="#AttributesInfo">Attributes Interface</a>
<LI><a href="#WriteAttribs">Writing Additional Attributes</a>
<LI><a href="#ReadAttribs">Reading Attributes</a>
</UL>
<br>
<a href="ReferencePages/index.html">Reference Manual (Doxygen)</a>
<br>
<hr>
<a name="Opening"><h2>Opening Datafiles</h2></a>
<P>
Just like the familiar <code>FILE*</code> type for C stdio operations, all
H5Part file operations require a file handle. The type of this handle is
<code>(H5PartFile*)</code>.
<br>
<code>H5PartOpenFile()</code> is
used to open a serial file and
<code>HDFPartOpenFileParallel()</code> is used to open a file for
Parallel I/O (in an MPI program).
After you open the file handle you can use the same set of
subroutines for operations on the file regardless of whether the
file is a parallel or serial I/O file.
The libraries manage all of this internally.<p>
</P>
<b>C Prototypes</b><br>
<P>
<b>Serial File</b><br>
<code>H5PartFile *H5PartOpenFile(const char *filename, unsigned
accessmode);</code><br>
<b>Parallel File</b><br>
<code>H5PartFile *H5PartOpenFileParallel(char *filename,int
accessmode,MPI_Comm communicator);</code><br>
<DT><i>filename</i>: </DT><DD>The name of the IEEEIO data file to
open. The typical extension for these files is <i>.h5</i></DD>
<DT><i>accessmode</i>: </DT><DD>The accessmode for the file. This is
one of 2 different access modes<br>
<code>H5PART_READ</code> : Opens a file in read-only mode.</DT><br>
<code>H5PART_WRITE</code> : Opens a file in write-only mode.
If the
file does not exist, it will be created. If it does
exist, it will be
truncated.
<DT><i>communicator</i>: </DT>
<DD>This argument is only available if the program has been
compiled with the <code>PARALLEL_IO</code> C-preprocessor flag
defined. It is used to pass in the communicator that will be
used for all collective I/O operations that target the same
file on disk.</DD>
<DT><i>Returns</i>:</DT><DD>A new filehandle with an open file or NULL if error.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
. . . code . . .
/* Open an HDF5 file for writing */
H5PartFile *writer = H5PartOpenFile("datafileout.h5",H5PART_WRITE);
/* Open an HDF5 file for Parallel I/O */
H5PartFile *writer = H5PartOpenFileParallel("datafileout.h5",H5PART_WRITE,MPI_COMM_WORLD);
/* open HDF5 file for reading */
H5PartFile *reader = H5PartOpenFile("datafilein.h5",H5PART_READ);
/* open HDF5 file for parallel reads */
H5PartFile *reader = H5PartOpenFileParallel("datafilein.h5",H5PART_READ,MPI_COMM_WORLD);
. . . more code . . .
</pre> <br>
<hr>
<h2>Closing Datafiles</h2>
<P>
To close the file, you simply use H5PartCloseFile() for both
parallel and serial files. You must call H5PartCloseFile() on any
file descriptor created by H5PartFileOpen() regardless of
whether the file turns out to be valid or not.
</P>
<b>C Prototypes</b><br>
<P>
<code>void H5PartCloseFile(H5PartFile *fileID);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
H5PartOpenFile() or H5PartOpenFileParallel().</DD>
<DT><i>Returns</i>:</DT><DD>void.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *file;
... code ...
file=H5PartOpenFileParallel("parttest.h5",H5PART_WRITE,comm);
... more code ...
H5PartCloseFile(file);
</pre>
<br>
<hr>
<h2>Validating Datafiles</h2>
<P>
You can test if the file was opened successfully using the
H5PartFileIsValid() function. It returns 1 if valid, 0 if invalid.<p>
</P>
<b>C Prototype</b><br>
<P>
<code>int H5PartFileIsValid(H5PartFile *fileID);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
H5PartOpenFile() or H5PartOpenFileParallel().</DD>
<DT><i>Returns</i>:</DT><DD>1 if valid, 0 if invalid.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<P>
Here is an example of validating a newly opened file. Even if
the file is invalid, you must use H5PartCloseFile() to reclaim
the file handle.
</P>
<pre>
#include &lt H5Part.h &gt
. . . code . . .
H5PartFile *fileID = H5PartOpenFile("datafileout.h5",H5PART_WRITE);
if(!H5PartFileIsValid(fileID)){
puts("The file you specified does not exist or is not in a
readable format");
H5PartClose(fileID); /* must reclaim fileID even if file is invalid */
. . . do other cleanup . . .
}
. . . more code . . .
</pre><br>
<hr>
<a name="SetStep">
<h2>Setting the Timestep</h2>
</a>
<P>
When writing data to a file the current time step must be set (even if there is only one). In a file with N time steps, the steps are numbered from 0 to N-1.
</P>
<b>C Prototype</b><br>
<P>
<code>void H5PartSetStep((H5PartFile *fileID,int step);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
H5PartOpenFile() or H5PartOpenFileParallel().</DD>
<DT><i>step</i>: </DT><DD>An integer time step.
</DD>
<DT><i>Returns</i>: </DT><DD>void.</DD>
</DL>
<br><b>Example Use</b><br>
</P>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
int timeStep;
....
H5PartSetStep(fileID,timeStep);
....
</pre>
<hr>
<a name="SetNumParticles">
</a>
<h2>Setting the Number of Particles</h2>
<P>
H5PartSetNumParticles: This function's sole purpose is to
prevent needless creation of new HDF5 DataSpace handles if
the number of particles is invariant throughout the sim.
That's its only reason for existence. After you call this
subroutine, all subsequent operations will assume this
number of particles will be written.
</P>
<b>C Prototype</b><br>
<P>
<code>void H5PartSetNumParticles(H5PartFile *fileID,long long nparticles);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
H5PartOpenFile() or H5PartOpenFileParallel().</DD>
<DT><i>nparticles</i>: </DT><DD>A long long integer specifying the number of particles.
</DD>
<DT><i>Returns</i>: </DT><DD>void.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
long long nparticles;
....
H5PartSetStep(fileID,nparticles);
....
</pre>
<hr>
<a name="Writing">
<h2>Writing Datasets</h2>
</a>
<P>
After setting the number of particles with
<a href="#SetNumParticles">H5PartSetNumParticles()</a>
and the current timestep using
<a href="#SetStep">H5PartSetStep()</a>, you can start
writing datasets into the file. Each dataset has a name
associated with it (chosen by the user) in order to facilitate
later retrieval. The writing routines also implicitly store
the datatype of the array so that the array can be
reconstructed properly on other systems with incompatible type
representations. The data is committed to disk before the
routine returns. All data that is written after setting the
timestep is associated with that timestep. While the number of
particles can change for each timestep, you cannot change the
number of particles in the middle of a given timestep.
</P>
<b>C Prototypes</b><br>
<P>
<code>int H5PartWriteDataFloat64(H5PartFile *fileID,char
*name,double *array);</code></br>
<code>int H5PartWriteDataInt64(H5PartFile *fileID,char
*name,double *array);</code>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>array</i>: </DT><DD>A buffer containing an array of
particle data to commit to disk. The datatype for
elements in the buffer is implicit in the name of the
subroutine call.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
double *x,*y,*z;
int timeStep;
long long nparticles;
...
H5PartSetStep(fileID,timeStep); /* must set the current timestep in file */
H5PartSetNumParticles(fileID,nparticles); /* then set number of particles to store */
/* now write different tuples of data into this timestep of the file */
H5PartWriteDataFloat64(fileID,"x",x);
H5PartWriteDataFloat64(fileID,"y",y);
H5PartWriteDataFloat64(file,"z",z);
..
</pre>
<hr>
<a name="ReadingNumTimeSteps">
<h2>Reading the Number of Time Steps</h2>
</a>
<P>
This reads the number of datasteps that are
currently stored in the datafile.
It works for both reading and writing of files, but is probably
only typically used when you are reading.
</P>
<b>C Prototype</b><br>
<P>
<code>int H5PartGetNumSteps (H5PartFile *fileID);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by <a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i>: </DT><DD>The number of timesteps currently stored in the file.
</DL>
</P>
<hr>
<a name="ReadingNumParticles">
<h2>Reading the Number of Particles</h2>
</a>
<P>
This reads the number of particles that are
currently stored in the current time step.
It will arbitrarily select a timestep if you haven't
already set the timestep with H5PartSetStep().
</P>
<b>C Prototype</b><br>
<P>
<code>long long H5PartGetNumParticles (H5PartFile *fileID);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by <a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i>: </DT><DD>The number of particles in current timestep.
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
int timeStep;
long long nparticles;
H5PartSetStep(fileID,0);
nparticles=H5PartGetNumParticles(fileID);
...
</pre>
<hr>
<a name="Reading">
<h2>Reading Datasets</h2>
</a>
<P>
After setting the time step and getting the number of particles to allocate the data arrays, you can start to read the data.
</P>
<b>C Prototypes</b><br>
<P>
<code>int H5PartReadDataFloat64(H5PartFile *fileID,char *name,double *array);</code><br>
<code>int H5PartReadDataInt64(H5PartFile *fileID,char *name,long long *array);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>array</i>: </DT><DD>A buffer to which the particle data will be read.i
The datatype for
elements in the buffer is implicit in the name of the
subroutine call.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
double *x,*y,*z;
int timeStep;
long long nparticles;
H5PartSetStep(fileID,0);
nparticles=H5PartGetNumParticles(fileID);
...
H5PartReadDataFloat64(file,"x",x);
H5PartReadDataFloat64(file,"y",y);
H5PartReadDataFloat64(file,"z",z);
...
</pre>
<hr>
<a name="DatasetsInfo"><h2>Reading the Number and Names of Datasets</h2></a>
<P>
H5Part provides funtions to find out how many datasets are stored at a particular timestep
and what their names are if you don't know what they are a-priori.
</P>
<b>C Prototypes</b><br>
<P>
<code>int H5PartGetNumDatasets(H5PartFile *fileID);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i>: </DT><DD>The number of datasets.</DD>
</DL>
</P>
<P>
<code>int H5PartGetDatasetName(H5PartFile *fileID,int index,char *name,int maxlen);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>index</i>:</DT><DD> integer specifying the index of the dataset. If the number of datasets is
nds, the range of index is 0 to nds-1.</DD>
<DT><i>name</i>:</DT><DD> A null-terminated string for the name of the dataset.</DD>
<DT><i>maxlen</i>:</DT><DD> An integer specifying the maximum length of the name array.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
char name[64];
int index, nds;
...
nds=H5PartGetNumDatasets(fileID);
for(index=0;index&lt nds;index++){
H5PartGetDatasetName(fileID,index,name,64);
printf("\tDataset[%u] name=[%s]\n", index,name);
}
...
</pre>
<hr>
<a name="AttributesInfo">
<h2>Attributes Interface</h2></a>
<P>
In the current H5Part implemtation there are two types of attributes: file attributes which are bound to the file
and step attributes which are bound to the current timestep. You
must set the timestep explicitly before writing the attributes (just
as you must do when you write a new dataset. Currently there are no
attributes that are bound to a particular data array, but this could
easily be done if required.
</P>
<P>H5PartGetNumStepAttribs and H5PartGetNumFileAttribs return the number of attributes bound to a step and to a file respectively. H5PartGetStepAttribInfo and H5PartGetFileAttribInfo return the name, type and number of elements of type "type" bound to a step and a file respectively.
</P>
<b>C Prototypes:</b><br>
<code>int H5PartGetNumStepAttribs(H5PartFile *fileID);
</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i> </DT><DD> The number of step attributes for the current step.</DD>
</DL>
<code>int H5PartGetNumFileAttribs(H5PartFile *fileID);
</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>Returns</i> </DT><DD> The number of file attributes.</DD>
</DL>
<code>void H5PartGetStepAttribInfo(H5PartFile *fileID,int idx, char *name,size_t maxnamelen,hid_t *type,int *nelem);
</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>idx</i>: </DT><DD>Index of the attribute.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string with the name of the attribute.</DD>
<DT><i>maxnamelen</i></DT><DD>the length of the name of the attribute.</DD>
<DT><i>type</i>: </DT><DD>One of the following: H5T_NATIVE_DOUBLE H5T_NATIVE_INT64 H5T_NATIVE_CHAR.</DD>
<DT><i>nelem</i>: </DT><DD>Number of elements of type "type".</DD>
<DT><i>Returns</i> </DT><DD> void.</DD>
</DL>
<code>void H5PartGetFileAttribInfo(H5PartFile *fileID,int idx, char *name,size_t maxnamelen, hid_t *type,int *nelem);
</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>idx</i>: </DT><DD>Index of the attribute.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string with the name of the attribute.</DD>
<DT><i>maxnamelen</i></DT><DD>the length of the name of the attribute.</DD>
<DT><i>type</i>: </DT><DD>One of the following: H5T_NATIVE_DOUBLE H5T_NATIVE_INT64 H5T_NATIVE_CHAR.</DD>
<DT><i>nelem</i>: </DT><DD>Number of elements of type "type".</DD>
<DT><i>Returns</i> </DT><DD> void.</DD>
</DL>
<a name="WriteAttribs">
<h2>Writing Attributes</h2>
</a>
<P>
An attribute can be bound to the file or after setting the time step to this time step.
</P>
<b>C Prototypes: Generic Attributes</b><br>
<P>
<code>int H5PartWriteFileAttrib(H5PartFile *fileID,char *name, hid_t type,void *value,int nelem);</code><br>
<code>int H5PartWriteStepAttrib(H5PartFile *fileID,char *name, hid_t type,void *value,int nelem);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>type</i>: One of H5T_NATIVE_DOUBLE, H5T_NATIVE_INT64, H5T_NATIVE_CHAR.</DD>
<DT><i>value</i>: value of the attribute.</DD>
<DT><i>nelem</i>: number of elements of type "type".</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
double actPos;
...
H5PartWriteStepAttrib(file_m,"Spos",H5T_NATIVE_DOUBLE,&actPos,1);
...
</pre>
<b>C Prototypes: String Attributes</b><br>
<P>
<code>int H5PartWriteStepAttribString(H5PartFile *fileID,char *name, char *attrib);</code><br>
<code>int H5PartWriteFileAttribString(H5PartFile *fileID,char *name, char *attrib);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>attrib</i>: the attribute character string.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
char *newattrib;
char *newname;
...
H5PartWriteFileAttribString(fileID, newname,newattrib);
...
</pre>
<hr>
<a name="ReadAttribs">
<h2>Reading Attributes</h2>
</a>
<P>
<P>
As with the writing of attributes, there are two basic reading interfaces one that reads file bound attributes and one that reads
step bound attributes. If the step is not set the current one will be used.
</P>
</P>
<b>C Prototypes</b><br>
<P>
<code>void H5PartReadStepAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
<code>void H5PartReadAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
<code>int H5PartReadFileAttrib(H5PartFile *fileID,char *name,void *value);</code><br>
<DL>
<DT><i>fileID</i>: </DT><DD>A FileHandle opened by
<a href="#Opening">H5PartOpenFile()</a> or
<a href="#Opening">H5PartOpenFileParallel()</a>.</DD>
<DT><i>name</i>: </DT><DD>A null-terminated string for the
name of the array. When retrieving datasets from disk,
you ask for them by name. There are no restrictions on
naming of arrays, but it is useful to arrive at some common
naming convention when sharing data with other groups.</DD>
<DT><i>value</i>: value of the attribute.</DD>
<DT><i>Returns</i>: </DT><DD>1 on success, 0 on failure.</DD>
</DL>
</P>
<br>
NOTE: H5PartReadAttrib has been superseeded by H5PartSetStep.
<br>
<br><b>Example Use</b><br>
<pre>
#include &lt H5Part.h &gt
H5PartFile *fileID;
int step;
char name[MAXNAME];
...
H5PartSetStep(fileID, step);
if (H5PartReadStepAttrib(file, "filename", &name[0]) == 1){
printf("Read step from file: %s\n", name);
}
...
</pre>
</div>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5part, the Fortran API</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<h1>The FORTRAN Application Programming Interface (API)</h1>
<P>
These references contain the information on how to access the H5Part API using FORTRAN bindings. All pointers are cast to haddr_t (a unint64_t) within the C/C++ code. In fortran, these pointers (handles) are carried as INTEGER*8
</P>
<UL>
<LI><a href="#Opening">Opening, Closing, and Validating Datafiles</a>
<LI><a href="#SetStep">Setting the Simulation Timestep</a>
<LI><a href="#SetNumParticles">Setting the Number of Particles</a>
<LI><a href="#Writing">Writing Datasets</a>
<LI><a href="#ReadingNumTimeSteps">Reading the Number of Time Steps</a>
<LI><a href="#ReadingNumTimeSteps">Reading the Number of Particles</a>
<LI><a href="#Reading">Reading Datasets</a>
<LI><a href="#DatasetsInfo">Reading the Number and the Names of Datasets</a>
<LI><a href="#AttributesInfo">Attributes Interface</a>
<LI><a href="#WriteAttribs">Writing Additional Attributes</a>
<LI><a href="#ReadAttribs">Reading Attributes</a>
</UL>
<hr>
<a name="Opening"><h2>Opening Datafiles</h2></a>
<P>
Like the familiar OPEN in FORTRAN files can be opened to read and write. Different functions are used for the serial and parallel case.
</P>
<b>FORTRAN Prototypes</b><br>
<P>
<b>Serial File</b><br>
<code>INTEGER*8 h5pt_openr</code><br>
<code>FUNCTION h5pt_openw(file)<br>
in CHARACTER file(*) : the filename to open for writing </code><br>
returns INTEGER*8 : and open filehandle for serial reads</code><br>
<br>
<code>INTEGER*8 h5pt_openw</code><br>
<code>FUNCTION h5pt_openw(file)<br>
in CHARACTER file(*) : the filename to open for writing<br>
returns INTEGER*8 : and open filehandle for serial writes</code><br>
<br>
<b>Parallel File</b><br>
<code>INTEGER*8 h5pt_openr_par</code><br>
<code>FUNCTION h5pt_openr_par(file,mpi_communicator)<br>
in CHARACTER file(*) : the filename to open for writing<br>
in INTEGER mpi_communicator : the MPI_Communicator used by the program<br>
returns INTEGER*8 : and open filehandle for parallel reads</code><br>
<br>
<code>INTEGER*8 h5pt_openw_par</code><br>
<code>FUNCTION h5pt_openw_par(file,mpi_communicator)<br>
in CHARACTER file(*) : the filename to open for writing<br>
in INTEGER mpi_communicator : the MPI_Communicator used by the program<br>
returns INTEGER*8 : and open filehandle for parallel reads</code><br>
</P>
<P>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
...
file = h5pt_openw("testfilef.h5")
...
</pre>
</P>
<hr>
<h2>Closing Datafiles</h2>
<P>
To close the file, you simply use h5pt_close() for both parallel and serial files. You must call h5pt_close() on any file descriptor created by h5pt_open*() regardless of whether the file turns out to be valid or not.</P>
<b>FORTRAN Prototype</b><br>
<code>EXTERNAL h5pt_close</code><br>
<code>SUBROUTINE h5pt_close(filehandle)<br>
in INTEGER*8 filehandle : close this open filehandle</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
...
call h5pt_close(file)
...
</pre>
</P>
<hr>
<h2> Validating Datafiles</h2>
<P>
You can test if the file was opened successfully using the
h5p_isvalid() function. It returns 1 if valid, 0 if invalid.
</P>
<b>FORTRAN Prototype</b><br>
<code>INTEGER h5pt_isvalid</code><br>
<code>FUNCTION h5pt_isvalid(filehandle)<br>
in INTEGER*8 filehandle: an open filehandle <br>
returns INTEGER : 1 if the file is valid, 0 if it is not</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER status
...
status = h5pt_isvalid(file)
...
</pre>
</P>
<hr>
<a name="SetStep">
<h2>Setting the Timestep</h2>
</a>
<P>
When writing data to a file the current time step must be set (even if there is only one). In a file with N time steps, the steps are numbered from 0 to N-1.
</P>
<b>FORTRAN Prototype</b><br>
<code>EXTERNAL h5pt_setstep</code><br>
<code>SUBROUTINE h5pt_setstep(filehandle,step)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER step : Set the current timestep in the file to this
</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER I
INTEGER nstep
...
do I=1,nstep
call h5pt_setstep(file,I)
... more code ...
enddo
</pre>
</P>
<hr>
<a name="SetNumParticles">
</a>
<h2>Setting the Number of Particles</h2>
<P>
This function's sole purpose is to
prevent needless creation of new HDF5 DataSpace handles if
the number of particles is invariant throughout the sim.
That's its only reason for existence. After you call this
subroutine, all subsequent operations will assume this
number of particles will be written.
</P>
<b>FORTRAN Prototype</b><br>
<code>EXTERNAL h5pt_setnpoints</code><br>
<code>SUBROUTINE h5pt_setnpoints(filehandle,npoints)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER*8 npoints : The number of particles on *this* processor</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER*8 npoints
...
call h5pt_setnpoints(file,npoints)
...
</pre>
<hr>
<a name="Writing">
<h2>Writing Datasets</h2>
</a>
<P>
After setting the number of particles with
<a href="#SetNumParticles">h5pt_setnpoints()</a>
and the current timestep using
<a href="#SetStep">h5pt_setstep()</a>, you can start
writing datasets into the file. Each dataset has a name
associated with it (chosen by the user) in order to facilitate
later retrieval. The writing routines also implicitly store
the datatype of the array so that the array can be
reconstructed properly on other systems with incompatible type
representations. The data is committed to disk before the
routine returns. All data that is written after setting the
timestep is associated with that timestep. While the number of
particles can change for each timestep, you cannot change the
number of particles in the middle of a given timestep.
</P>
<b>FORTRAN Prototypes</b><br>
<P>
The two data types supported for the moment are REAL*8 and INTEGER*8 (float64 and int64).
</P>
<code>EXTERNAL h5pt_writedata_r8</code><br>
<code>SUBROUTINE h5pt_writedata_r8(filehandle,name,data)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the data we are writing eg. "X" or "Y" or "PX" etc...<br>
in REAL*8 data(*) : The dataarray to write</code><br>
<br>
<code>EXTERNAL h5pt_writedata_i8</code><br>
<code>SUBROUTINE h5pt_writedata_i8(filehandle,name,data)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the data we are writing eg. "X" or "Y" or "PX" etc...<br>
in INTEGER*8 data(*) : The dataarray to write</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER nstep
INTEGER I
REAL*8,ALLOCATABLE:: X(:)
...
do I=1,nstep
call h5pt_setstep(file,I)
call h5pt_writedata_r8(file,"x",X)
enddo
...
</pre>
<hr>
<a name="ReadingNumTimeSteps">
<h2>Reading the Number of Time Steps</h2>
</a>
<P>
This reads the number of datasteps that are
currently stored in the datafile.
It works for both reading and writing of files, but is probably
only typically used when you are reading.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getnsteps</code><br>
<code>FUNCTION h5pt_getnsteps(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER : number of timesteps stored in the file</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER nstep
file = h5pt_openr("testfilef.h5")
nstep = h5pt_getnsteps(file)
</pre>
<hr>
<a name="ReadingNumParticles">
<h2>Reading the Number of Particles</h2>
</a>
<P>
This reads the number of particles that are currently stored in the current time step. It will arbitrarily select a timestep if you haven't already set the timestep with H5PartSetStep().
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getnpointss</code><br>
<code>FUNCTION h5pt_getnpoints(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER : number of particles in the current time step</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER*8 npoints
INTEGET step;
file = h5pt_openr("testfilef.h5")
call h5pt_setstep(file,0)
npoints = h5pt_getnpoints(file)
...
</pre>
<hr>
<a name="Reading">
<h2>Reading Datasets</h2>
</a>
<P>
After setting the time step and getting the number of particles to allocate the data arrays, you can start to read the data.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_readdata_r8</code><br>
<code>FUNCTION h5pt_readdata_r8(filehandle,name,data)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the data we are writing, eg. "X" or "Y" or "PX" etc...<br>
out REAL*8 data(*) : The data array to read. The number of points to read is either the number within
the view setby h5pt_setview() or the default (the total number of particles in the file).<br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER err
INTEGER*8,ALLOCATABLE:: ID(:)
...
call h5pt_setstep(file,step)
err=h5pt_readdata_i8(file,"id",ID)
...
</pre>
<hr>
<a name="DatasetsInfo"><h2>Reading the Number and Names of Datasets</h2></a>
<P>
H5Part provides funtions to find out how many datasets are stored at a particular timestep
and what their names are if you don't know what they are a-priori.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getndatasets</code><br>
<code>FUNCTION h5pt_getndatasets(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER*8 : number of datasets stored per timestep</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER ndata
...
call h5pt_setstep(file,1)
ndata = h5pt_getndatasets(file)
...
</pre>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getdatasetname</code><br>
<code>FUNCTION h5pt_getdatasetname(filehandle,index,name)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER index : Index for a given dataset name<br>
out CHARACTER name(*) returns the name of the dataset at that index<br>
returns INTEGER, 1 on success 0 on failure.</code><br>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
INTEGER err
CHARACTER,ALLOCATABLE:: name(:)
...
err=h5pt_getdatasetname(file, 1, name)
...
</pre>
<hr>
<a name="AttributesInfo">
<h2>Attributes Interface</h2></a>
<P>
In the current H5Part implemtation there are two types of attributes: file attributes which are bound to the file
and step attributes which are bound to the current timestep. You
must set the timestep explicitly before writing the attributes (just
as you must do when you write a new dataset. Currently there are no
attributes that are bound to a particular data array, but this could
easily be done if required.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_getnstepattribs</code><br>
<code>FUNCTION h5pt_getnstepattribs(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER : number of attributes bound to this particular step<br>
</code>
<br>
<code>INTEGER h5pt_getnfileattribs</code><br>
<code>FUNCTION h5pt_getnfileattribs(filehandle)<br>
in INTEGER*8 filehandle : an open filehandle<br>
returns INTEGER : number of attributes bound to the file<br>
</code>
<br>
<code>INTEGER h5pt_getstepattribinfo</code><br>
<code>FUNCTION h5pt_getstepattribinfo(filehandle,idx,attribname,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER idx : index of the attribute being queried<br>
out CHARACTER name(*) : The name of the attribute<br>
out INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure.<br>
</code>
<br>
<code>INTEGER h5pt_getfileattribinfo</code><br>
<code>FUNCTION h5pt_getfileattribinfo(filehandle,idx,attribname,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in INTEGER idx : index of the attribute being queried<br>
out CHARACTER name(*) : The name of the attribute<br>
out INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure.
</code>
<br>
<hr>
<a name="WriteAttribs">
<h2>Writing Attributes</h2>
</a>
<P>
An attribute can be bound to the file or after setting the time step to this time step.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_writefileattrib_r8</code><br>
<code>
FUNCTION h5pt_writefileattrib_r8(filehandle,name,attrib,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in REAL*8 attrib(*) : The array of data to write into the attribute<br>
in INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writefileattrib_i8</code><br>
<code>FUNCTION h5pt_writefileattrib_i8(filehandle,name,attrib,nelem)<br>
in INTEGER*8 filehandle : The filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in INTEGER*8 attrib(*) : The array of data to write into the attribute<br>
in INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writefileattrib_string</code><br>
<code>FUNCTION h5pt_writefileattrib_string(filehandle,name,string)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in CHARACTER*8 attrib(*) : The array of data to write into the attribute<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writestepattrib_r8</code><br>
<code>FUNCTION h5pt_writestepattrib_r8(filehandle,name,attrib,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in REAL*8 attrib(*) : The array of data to write into the attribute<br>
in INTEGER nelem : Number of elements in the attrib array
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writestepattrib_i8</code><br>
<code>FUNCTION h5pt_writestepattrib_i8(filehandle,name,attrib,nelem)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in INTEGER*8 attrib(*) : The array of data to write into the attribute<br>
in INTEGER nelem : Number of elements in the attrib array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_writestepattrib_string</code><br>
<code>FUNCTION h5pt_writestepattrib_string(filehandle,name,string)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER name(*) : The name of the attribute<br>
in CHARACTER*8 attrib(*) : The array of data to write into the attribute<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
REAL*8 REALTIME
INTEGER err
...
err=h5pt_writefileattrib_string(file,"Annotation","Testing 1 2 3")
err=h5pt_writestepattrib_r8(file,"RealTime",REALTIME,1)
...
</pre>
<hr>
<a name="ReadAttribs">
<h2>Reading Attributes</h2>
</a>
<P>
As with the writing of attributes, there are two basic reading interfaces one that reads file bound attributes and one that reads
step bound attributes. If the step is not set the current one will be used.
</P>
<b>FORTRAN Prototypes</b><br>
<code>INTEGER h5pt_readstepattrib</code><br>
<code>FUNCTION h5pt_readstepattrib(filehandle,name,data)<br>
in INTEGER*8 filehandle : an open filehandle<br>
in CHARACTER attributename(*) : name of the attribute to read<br>
out <anytype> data(*) : the attribute data will be read into this array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<br>
<code>INTEGER h5pt_readfileattrib</code><br>
<code>FUNCTION h5pt_readfileattrib(filehandle,name,data)<br>
in INTEGER*8 filehandle an open filehandle<br>
in CHARACTER attributename(*) : name of the attribute to read<br>
out <anytype> data(*) : the attribute data will be read into this array<br>
returns INTEGER, 1 on success 0 on failure<br>
</code>
<b>Example Use</b><br>
<pre>
include 'H5Part.inc'
INTEGER*8 file
REAL*8 REALTIME
...
call h5pt_setstep(file,0)
err=h5pt_readstepattrib(file,"RealTime",data)
...
</pre>
</div>
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<HTML>
<HEAD>
<TITLE>H5/H5Part/H5Block/H5Fed API</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>H5Part: a Portable High Performance Parallel Data Interface to HDF5</title>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="keywords" content="scientific visualization">
<meta name="sitemap" content="put a brief descriptive phrase here that will show up in the site map:foo">
<div id="maincenter">
<font face="arial,helvetica"><h1>H5Part: a Portable High Performance Parallel Data Interface to HDF5</h1></font>
<!--<h2><font color="red"> THESE PAGES ARE UNDER CONSTRUCTION, September 2006</h2></font>-->
<font face="arial,helvetica" color="#555588"><h2>Motivation</h2></font>
<P>
<TABLE>
<TR>
<TD>
<a href="collision_6.png"><img src="collision_6.s.png" width=300 height=300></a>
</TD
></TR>
<TR>
<TD>
Beam-beam collision simulation.
</TD>
</TR>
</TABLE>
</P>
<P>
Particle based simulations of accelerator beam-lines, especially in
six dimensional phase space, generate vast amounts of data. Even
though a subset of statistical information regarding phase space
or analysis needs to be preserved, reading and writing such
enormous restart files on massively parallel supercomputing
systems remains challenging.<p>
</P>
<P>
H5Part is a very simple data storage schema and provides an
API that simplifies the reading/writing of the data to the HDF5
file format. An important foundation for a stable visualization and data
analysis environment is a stable and portable file storage format and
its associated APIs. The presence of a "common file storage format,"
including associated APIs, will help foster a fundamental level of
interoperability across the project's software infrastructure. It will
also help ensure that key data analysis capabilities are present
during the earliest phases of the software development effort.
</P>
<P>
H5Part is built on top of the <a href="http://hdf.ncsa.uiuc.edu/HDF5">HDF5 (Hierarchical Data Format).</a>
HDF5 offers a self-describing machine-independent
binary file format that supports scalable parallel I/O
performance for MPI codes on a variety of supercomputing
systems, and works equally well on laptop computers. The API is
available for C, C++, and Fortran codes. The H5Part file format and APIs
enable disparate research groups with different simulation
implementations to transparently share datasets and data
analysis tools. For instance, the common file format will enable
groups that depend on completely different simulation
implementations to share data analysis tools.
</P>
<font face="arial,helvetica" color="#555588"><h2>H5Part file organization and API</h2></font>
<P>
The proposed file storage format uses HDF5 for the lowlevel
file storage and a simple API to provide a high-level
interface to that file format. A programmer can either use
the H5Part API to access the data files or write directly to
the file format using some simple conventions for organizing
and naming the objects stored in the file.
</P>
<P>
In order to store Particle Data in the HDF5 file format,
we have formalized the hierarchical arrangement of the
datasets and naming conventions for the groups and associated
datasets. The sample H5Part API formally encodes
these conventions in order to provide a simple and uniform
way to access these files from C, C++, and Fortran codes.
The API makes it easier to write very portable data adaptors
for visualization tools in order to expand the number of
tools available to access the data. Even so, anyone can use
the HDF5 h5ls utility to examine the organization of the
H5Part files and even write their own HDF5-based interface
for reading and writing the file format. The standards
offered by the sample API are completely independent of
the standard for organizing data within the file.The file
format supports the storage of multiple timesteps
of datasets that contain multiple fields.
</P>
<!--
<font face="arial,helvetica" color="#555588"><h2>Requirements Specification</h2></font>
<UL>
<LI><a href="H5PartSpecs.html">H5Part API specifications
</UL>
</a>
-->
<font face="arial,helvetica" color="#555588"><h2>Downloading and Installing H5Part</h2></font>
<UL>
<LI><a href="Downloading.html">Downloading HDF5 and H5Part
<LI><a href="BuildingHDF5.html">Building the HDF5 Library</a>
<LI><a href="Building.html">Building the H5Part Library</a>
</UL>
<font face="arial,helvetica" color="#555588"><h2>Bindings</h2></font>
<UL>
<LI><a href="UsingC.html">Using the C/C++ interface</a>
<LI><a href="UsingF.html">Using the F77/F90 interface</a>
<LI><a href="InternalLayout.html">Logical Internal HDF5 File</a>
<LI><a href="H5PartTools.html">H5Part Utility Tools</a>
<LI><a href="ReferencePages/index.html">Reference Manual</a> (Note: Requires doxygen
to be run in the directory /doc)
</UL>
<font face="arial,helvetica" color="#555588"><h2>H5Part Visualization Tools</h2></font>
<UL>
<!--<LI><a href="H5PartExpress.html">H5Part Express Reader</a>-->
<LI><a href="H5PartVisIt.html">H5Part VisIt Reader</a>
<!--<LI><a href="H5PartIDL.html">H5Part IDL Reader</a>-->
<LI><a href="http://www.cscs.ch/a-display.php?id=170">H5Part sparticles Reader: developed at CSCS, Switzerland</a>
<LI><a href="http://vis.lbl.gov/Vignettes/PartView/index.html">PartView Visualization Application</a>
</UL>
</div>
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#!/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
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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
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# 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
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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
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# 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
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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
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# 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
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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
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# 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_23_refined/23_small.png
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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
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# 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_30_refined/30_small.png
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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
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# 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/1-edge/edge_31_refined/31_small.png
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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
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# 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_01-12_refined/01-12_smal.png
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doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12_small.png
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doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.png
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