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compare: H5hut/src:H5Part-1.6.4
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68 Commits
1.99.13 .. H5Part-1.6.4

Author SHA1 Message Date
Marc Howison 1bda4e3c70 H5Part 1.6.4 release 2011-09-03 16:42:21 +00:00
gsell 819ddc4704 work around to use env.vars removed 2011-08-15 14:08:08 +00:00
gsell 3894452bc9 target 'clean' replaced with 'clean-local' 2011-08-15 13:27:48 +00:00
gsell 58be7a8318 ignore property edited 2011-08-15 10:15:29 +00:00
gsell 9a06157427 config.{guess,sub} removed from repo 2011-08-15 10:11:37 +00:00
gsell a44e2b6a05 missing H5P_DEFAULT added to H5Gopen() if 1.8 API is used 2011-08-15 10:08:58 +00:00
gsell ac8d16c0b6 libtoolize must be called first, use try 'glibtoolize' if 'libtoolize dosn't exists 2011-08-15 09:36:43 +00:00
gsell 6c944f2b16 meaningless comment removed 2011-08-15 09:34:15 +00:00
Marc Howison b1aa655b22 1.6.3 release 2011-07-25 14:09:43 +00:00
Marc Howison efb1e39233 more fixes to the new libtool build system 2011-07-19 01:31:21 +00:00
Marc Howison 5b611ab155 new build system for both H5hut and H5Part; preparing 1.6.3 release of H5Part 2011-07-16 18:30:25 +00:00
Marc Howison 66449ee44d fixed mismatched function names and uncorrected indices in Fortran API; incorporated bug report for Fortran test 2011-02-01 16:36:00 +00:00
Marc Howison d368a60202 bug fixes in Fortran API for 1.6.2 2010-07-28 21:44:48 +00:00
Marc Howison 6b4b556ff1 removed H5PartSetViewEmpty and enabled 0 as input to H5PartSetNumParticles 2010-06-29 16:39:29 +00:00
Marc Howison 0857443617 fixed spelling errors in NEWS 2010-06-11 17:48:42 +00:00
Marc Howison e3b93e4383 removed redundant VFD code in _H5Part_open and added an option for CORE VFD 2010-05-13 17:54:38 +00:00
Marc Howison 3e99a8ccfa fixed autoconf issue with PGI compilers and #define issue with OpenMPI 2010-05-03 20:04:34 +00:00
Marc Howison bb41cc3288 added documentation for file open flags; added flags to h5pt_openr_par_align(); added H5PartSetViewEmpty() and h5pt_setview_empty() calls for creating empty hyperslab selections (previously kludge was to use H5PartSetViewIndices with a null list); fixed memory leak with file open flags in the Fortran interface; fixed missing statement in 1.6.x logic for _H5Part_have_group() 2010-04-29 16:17:51 +00:00
Marc Howison cf1368291d fixed the H5PART_HAVE_HDF5_18 logic to work with the 1.9 snapshot; fixed broken test in _H5Part_have_group in the codepath for HDF5 1.6 2010-03-23 22:18:40 +00:00
Marc Howison 698b5e0c76 removed config.h.in 2010-03-11 23:04:27 +00:00
Marc Howison ea40b3272e fixes to lustre optimizations 2010-03-11 23:00:43 +00:00
Marc Howison 90f8506628 changed print functions to only print from proc 0 in parallel mode, except for 'debug detail' level which prints from all procs 2010-02-23 19:45:43 +00:00
Marc Howison a7727635a7 reverted the rename of xfer_prop because it is used in OPAL 2010-02-22 21:18:37 +00:00
Marc Howison 66476adf6a removed overloaded use of H5_USE_16_API so that it can be used with HDF 1.85 without invoking the HDF5 1.6 codepath in places 2010-02-22 18:35:37 +00:00
Marc Howison 1c4c62192d added chunking for H5Part; had to remove open object test because out-of-order file handle / property list closes were causing errors 2010-02-18 21:08:03 +00:00
Marc Howison fb660f8459 changed throttling routine; removed read-only restriction for setting step to existing steps; revised NEWS 2010-02-18 18:56:39 +00:00
Marc Howison 20bff7f87c fixes for HDF5 1.6.x 2010-02-17 03:19:20 +00:00
Marc Howison 64c2b96f27 incorporated fixes from Gunther for 1.6.0 release 2010-02-16 18:46:57 +00:00
Marc Howison 1d23bdab85 1.6 release: moved 1.5 to 1.6; copied 1.6 to tags/H5Part-1.6.0; copied 1.6 to 1.7 2010-02-16 17:06:40 +00:00
Marc Howison 0de2f00b08 fixed H5PartGetNumParticles to correctly count indexed views; added type parameter to H5BlockGetFieldInfo/ByName 2010-02-11 22:28:49 +00:00
Marc Howison 3300a665b5 updates to makefiles; added CrayXT configure crutch 2010-02-11 19:39:25 +00:00
Marc Howison f671d1ab9f fixed missing test/testf.F90 2010-02-11 17:42:56 +00:00
Marc Howison ec7184bf2d fixed missing test/read.c 2010-02-11 17:42:18 +00:00
Marc Howison 46574c2482 fixed bug in strided selection; added examples dir with a strided write Fortran program (more examples to come...) 2010-02-11 17:34:50 +00:00
Marc Howison 2bb96c6f69 updated NEWS with details about 1.6 changes; changed hsize_t type in H5PartSetViewIndices; fixes to the build system; fixed bugs that were preventing the use of H5PartSetView during writes; added open object checks to regression test 2010-02-10 23:33:32 +00:00
Marc Howison 181c03008f major changes in preparations for 1.6 release: will add details to CHANGES 2010-02-10 01:02:14 +00:00
Marc Howison 7c4126c2c8 integrated changes to iterators from Allen; refactored the HDF 1.6 vs. 1.8 API #ifs 2010-01-14 21:25:29 +00:00
Marc Howison 90c6032c34 fixed type id leaks found by Allen 2010-01-11 21:29:26 +00:00
Marc Howison f40afd9670 fixed H5Oget_info() bug from Allen 2010-01-11 20:37:05 +00:00
Marc Howison c8b49c520f fixed attribute read functions to use string type 2010-01-06 00:12:55 +00:00
Marc Howison a65e9586c5 fixed string attribute bug reported by Allen Sanderson 2010-01-05 23:26:23 +00:00
Marc Howison 3c6065e2f9 flags are now stored in H5PartFile struct; added the 'throttle' as a runtime parameter instead of a compiler flag; merged H5Bench into the tests suite; compiles but need to perform regression tests 2009-10-16 22:37:20 +00:00
Marc Howison c3cd4d7c99 set collective mode as default for H5Part 2009-10-12 22:13:19 +00:00
Marc Howison fdd69338ea updated doxygen groups for H5(Multi)Block 2009-10-07 18:12:03 +00:00
Marc Howison 5d4d62f5c2 typo in Fortran linkage; fixed doxygen to use parallel flag 2009-10-06 17:58:39 +00:00
Marc Howison 195d58693a added throttling for reading 2009-09-10 04:45:48 +00:00
Marc Howison d149d8a5dd added write throttling for large concurency jobs with MPI-POSIX VFD 2009-09-10 02:49:59 +00:00
Marc Howison 8dac86872b added a proc shift option to H5MultiBlock, used in I/O benchmarking to defeat caching 2009-08-30 18:02:04 +00:00
Marc Howison 15ad7b21c5 added MPI_Comm_f2c in Fortran-C bindings 2009-08-25 17:40:49 +00:00
Marc Howison 1b8073b82b added API calls for int32 and float32 step attribs 2009-08-18 15:47:50 +00:00
Marc Howison 06aef8a08f fixed bug in halo exchange when there is only one proc in the direction of the exchange 2009-07-10 21:34:44 +00:00
Marc Howison 57ce44db8b fixed format flag for H5MultiBlock timing output 2009-07-09 01:36:26 +00:00
Marc Howison 1104b9ff93 added timing output for H5MultiBlock reads 2009-07-08 20:14:56 +00:00
Marc Howison 01aa167339 changes to _H5Block_init so that only 1 dataset creation plist is created and reused 2009-07-06 21:31:42 +00:00
Marc Howison cd0391db7e added a test for existing datasets to write calls 2009-07-06 21:07:30 +00:00
Marc Howison 207e49716c Implemented two halo exchange routines: one uses an MPI vector datatype and the other manually packs and unpacks the send and recv buffers. The MPI datatype method is not currently working due to a "double free" error in libc. The manual buffering method has been debuged and works. 2009-07-06 16:42:03 +00:00
Marc Howison 97a14cc488 fixed Fortran compile error with gfortran (had to move f90 files to F90) 2009-07-02 18:46:06 +00:00
Marc Howison 13d7784c44 added file open flags for Fortran interface 2009-07-02 18:22:30 +00:00
Marc Howison 00b0e87f10 forgot to remove existing write attrib functions from H5BlockF.inc and H5BlockF.c after adding them to the code generator 2009-07-02 17:06:12 +00:00
Marc Howison 6d38bf442d * H5Block: added attribute writing functions to code generator: still need to add reading functions 
* H5MultiBlock: added halo exchange routine: still needs debugging
 2009-07-02 16:46:07 +00:00
Marc Howison 3d4da8653a fixed bug with layout debug info always printing the layout for proc 0 2009-06-24 18:45:23 +00:00
Marc Howison 0e853656cd * fixed bug in h5bl_defin3dchunkdims call that was using variables addresses ins 
* added new MultiBlock module that is used for efficiently loading regular
rectilinear grid blocks (using chunking) and handling ghost zones in a
distributed-memory environment
** still need to add the "halo exchange" routine for reshuffling ghost regions
** performed some basic testing of read/write functionality

~Mark
 2009-06-24 18:11:39 +00:00
Marc Howison 3d1ed0e92a found incorrect == comparison with read flag; replaced with & 2009-06-19 22:34:22 +00:00
Marc Howison b5e3756f57 fixed bug in H5Gopen2 where I was using the wrong group id 2009-06-19 18:34:57 +00:00
Marc Howison 122e913f08 Merged changes from LBL, including: 
* read/write call variants for different datatypes
* HDF5 properties tuned for lustre filesystems and the Cray XT (enabled using flags passed during file open)
* HDF5 chunking for field data
* HDF5 alignment (set during file open)
* support for both HDF5 1.6 and 1.8 using #if statements
* a new error reporting level: debug_detail (HDF5 errors are now printed at debug level 1 by default)

These changes have undergone limited testing.
I will begin using this version for my H5Part projects so that I can test it more thoroughly.

~Mark
 2009-06-18 20:29:02 +00:00
gsell a2d2a02cd2 branch new development verson 2008-06-24 19:04:45 +00:00
gsell 249117c89e serial and parallel code merged 2008-06-24 18:59:06 +00:00
gsell 463ef08da9 branch stable 1.4 version 2007-09-21 09:53:26 +00:00
677 changed files with 20004 additions and 253514 deletions
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examples/H5Fed/tetmesh_read_tags.c -text
examples/H5Fed/tetmesh_write.c -text
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examples/H5Fed/tetmesh_write2.c -text
examples/H5Fed/tetmesh_write_tags.c -text
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src/h5core/h5t_retrieve_trim.c -text
src/h5core/h5t_store.c -text
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src/h5core/h5t_store_trim.c -text
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src/h5core/h5t_tags.c -text
src/h5core/h5t_tags_private.h -text
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src/h5core/h5u_errorhandling_private.h -text
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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
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src/include/H5Fed_retrieve.h -text
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src/include/H5Part.h -text
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test/H5BlockParTestScalarField.c -text
test/H5BlockParTestScalarField.pbs -text
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test/H5BlockTestAttributesF.F90 -text
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test/H5PartTestParallel.cc -text
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test/H5testF.f -text
test/H5testFpar.F90 -text
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test/h5b_read.c -text
test/h5b_test.c -text
test/h5b_write.c -text
test/h5u_read.c -text
test/h5u_test.c -text
test/h5u_write.c -text
test/params.h -text
test/read.c -text
test/test.c -text
test/testf.F90 -text
test/testframe.c -text
test/testframe.h -text
tools/H5PartMerge/AUTHORS -text
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
test/write.c -text
tools/H5BlockBench.c -text
tools/H5PartBench.c -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
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visit_plugins/databases/H5Part/avth5partFileFormat.C -text
visit_plugins/databases/H5Part/avth5partFileFormat.h -text
visit_plugins/databases/H5Part/h5part.xml -text
visit_plugins/databases/H5Part/h5partCommonPluginInfo.C -text
visit_plugins/databases/H5Part/h5partEnginePluginInfo.C -text
visit_plugins/databases/H5Part/h5partMDServerPluginInfo.C -text
visit_plugins/databases/H5Part/h5partPluginInfo.C -text
visit_plugins/databases/H5Part/h5partPluginInfo.h -text
visit_plugins/operators/BinnerFilter/.depend -text
visit_plugins/operators/BinnerFilter/Binner.xml -text
visit_plugins/operators/BinnerFilter/BinnerCommonPluginInfo.C -text
visit_plugins/operators/BinnerFilter/BinnerEnginePluginInfo.C -text
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visit_plugins/operators/BinnerFilter/BinnerFilter.h -text
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visit_plugins/operators/BinnerFilter/BinnerMakefile -text
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visit_plugins/operators/BinnerFilter/BinnerPluginInfo.h -text
visit_plugins/operators/BinnerFilter/BinnerScriptingPluginInfo.C -text
visit_plugins/operators/BinnerFilter/BinnerViewerPluginInfo.C -text
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visit_plugins/operators/BinnerFilter/Makefile -text
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visit_plugins/operators/BinnerFilter/PyBinner.h -text
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visit_plugins/operators/BinnerFilter/avtBinnerFilter.h -text
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visit_plugins/operators/RandomSample/.depend -text
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visit_plugins/operators/RandomSample/RandomSample.xml -text
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.gitignore
+1 -90
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@@ -1,102 +1,13 @@
*.o
*.lo
*.la
*~
*.h5
*.vtk
.deps
.libs
/H5hut
/INSTALL
/Makefile
/Makefile.in
/aclocal.m4
/autom4te.cache
/build
/compile
/config.guess
/config.h
/config.h.in
/config.log
/config.status
/config.sub
/configure
/depcomp
doc/Makefile
doc/Makefile.in
examples/H5Block/H5BlockParTestScalarField
examples/H5Block/H5BlockTestAttributes
examples/H5Block/Makefile
examples/H5Block/Makefile.in
examples/H5Fed/.deps
examples/H5Fed/Makefile
examples/H5Fed/Makefile.in
examples/H5Fed/large_tet.h5
examples/H5Fed/simple_tet.h5
examples/H5Fed/simple_triangle.h5
examples/H5Fed/small_tet.h5
examples/H5Fed/tetmesh_adjacencies
examples/H5Fed/tetmesh_read
examples/H5Fed/tetmesh_read_tags
examples/H5Fed/tetmesh_write
examples/H5Fed/tetmesh_write2
examples/H5Fed/tetmesh_write_tags
examples/H5Fed/trimesh_adjacencies
examples/H5Fed/trimesh_read
examples/H5Fed/trimesh_write
examples/H5Fed/trimesh_write_dunetest
examples/H5Part/Bench
examples/H5Part/H5PartAndreasTest
examples/H5Part/H5PartTestP
examples/H5Part/H5test
examples/H5Part/Makefile
examples/H5Part/Makefile.in
/install-sh
/libtool
/ltmain.sh
/m4
/missing
src/.deps
src/C/.deps
src/C/Makefile
src/C/Makefile.in
src/C/libH5hutC.a
src/Fortran/.deps
src/Fortran/Makefile
src/Fortran/Makefile.in
src/Fortran/TestUnderscore
src/Fortran/Underscore.h
src/Makefile
src/H5PartF.h
src/Makefile.in
src/h5core/.deps
src/h5core/Makefile
src/h5core/Makefile.in
src/h5core/libH5hut.a
src/include/H5hutF.h
src/include/Makefile
src/include/Makefile.in
src/include/h5core/Makefile
src/include/h5core/Makefile.in
src/lib
/stamp-h1
/svn-prop.tmp
/test-driver
test/.deps
test/Makefile
test/Makefile.in
test/h5_attach.h5
test/h5_attach_test
test/h5b_test
test/h5u_test
tools/.deps
tools/Makefile
tools/Makefile.in
tools/h5PartDcToVtk
tools/h5PartSurfaceToVtk
tools/h5hutcc
tools/vtk2h5grid/.deps
tools/vtk2h5grid/Makefile
tools/vtk2h5grid/Makefile.in
tools/vtk2h5grid/cgun_full.h5
tools/vtk2h5grid/cgun_full.vtk
tools/vtk2h5grid/vtk2h5grid
AUTHORS
+1
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@@ -6,5 +6,6 @@ Benedikt Oswald (PSI)
Wes Bethel (NERSC/LBNL)
John Shalf (NERSC/LBNL)
Cristina Siegerist (NERSC/LBNL)
Mark Howison (NERSC/LBNL)
Please use h5part@lists.psi.ch for communicaion.
COPYING
+1 -1
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@@ -1,6 +1,6 @@
*** Copyright Notice ***
H5hut Copyright (c) 2006-2010, The Regents of the University of California,
H5Part Copyright (c) 2006-2009, The Regents of the University of California,
through Lawrence Berkeley National Laboratory (subject to receipt of any
required approvals from the U.S. Dept. of Energy) and the Paul Scherrer
Institut (Switzerland). All rights reserved.
GNUmakefile.orig
Executable
+133
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@@ -0,0 +1,133 @@
UNAME := $(shell uname | perl -pe 's/(sn\d\d\d\d|jsimpson)/UNICOS\/mk/')
# for host specific options
HOST := $(shell hostname)
# for processor-specific options
ifeq ($(UNAME), Linux)
PROC := $(shell uname -p)
endif
CXX = c++
CC = cc
H5HOME = /usr/local/hdf5
CFLAGS = -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# MacOS-X Serial
ifeq ($(UNAME), Darwin)
ifeq ($(PARALLEL), yes)
CXX = g++
CC = mpicc
H5HOME = /usr/local
CFLAGS = -O -g -I$(H5HOME)/include -DPARALLEL_IO
LDFLAGS = -L$(H5HOME)/lib -lmpich -lpmpich -lhdf5 -lz -lm
else
CXX = c++
CC = cc
F90 = xlf
H5HOME = /usr/local
CFLAGS = -O -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif
endif
# SGI MIPS/Irix
ifeq ($(UNAME), IRIX64)
CXX = CC
CC = cc
F90 = f90
ifeq ($(PARALLEL), yes)
H5HOME = $(HDF5_DIR)
CFLAGS = -64 -O3 -I$(H5HOME)/include -DPARALLEL_IO
LDFLAGS = -64 -O3 -L$(H5HOME)/lib -lhdf5 -lz -lmpi -lm
else
H5HOME = /usr/local
CFLAGS = -O3 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif
endif
# AIX/SP-2 Parallel/serial : Seaborg
ifeq ($(UNAME), AIX)
ifeq ($(PARALLEL), yes) # parallel
CXX = mpCC_r
CC = mpxlc_r
# H5HOME = /usr/common/usg/hdf5_64/1.4.5-post2/parallel
H5HOME = /usr/common/usg/hdf5_64/1.6.1/parallel
# /usr/common/usg/hdf5/1.4.4/parallel
H4HOME = /usr/common/usg/hdf/default
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
CFLAGS = -q64 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lsz -lm
else # serial
CXX = xlC
CC = xlc
H5HOME = /usr/common/usg/hdf5/1.4.4/serial
H4HOME = /usr/common/usg/hdf/default
OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
endif
endif
# Linux
ifeq ($(UNAME), Linux)
# if this machine is NERSC/Davinci Altix system
ifeq ($(PROC), ia64)
CC = icc
CXX = icc
ifeq ($(PARALLEL), yes)
# IA64 Linux Parallel
ifeq ($(HOST), davinci)
H5HOME = $(HDF5_PAR)
MPILIB = -lmpi
else
H5HOME = /usr/local
HDF5_PAR_LIB = -L$(H5HOME)/lib -lhdf5 -lz -lm
HDF5_PAR_INCLUDE = -I$(H5HOME)/include
MPIHOME = /usr/local
MPILIB = -lmpich
endif # HOST
CFLAGS = -O3 -DPARALLEL_IO -DH5_HAVE_PARALLEL $(HDF5_PAR_INCLUDE)
LDFLAGS = $(HDF5_PAR_LIB) $(MPILIB)
else # IA64 Linux Serial
CFLAGS = -O3 $(HDF5_INCLUDE)
LDFLAGS = $(HDF5_LIB) -lm
endif # PARALLEL
# else this is standard IA32 linux
else
ifeq ($(PARALLEL), yes)
# Linux Parallel
CC = gcc
CXX = g++
H5HOME = /usr/local
MPIHOME = /usr/local
CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
else # Linux Serial
CXX = g++
CC = gcc
CFLAGS = -O -g -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
endif # !PARALLEL
endif # PROC!ia64
endif # !Linux
ifeq ($(PARALLEL), yes) #parallel
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
endif
else
ifdef F90
all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
else
all: H5PartTest H5PartTest.o H5Part.o
endif
endif
include rules.make
INSTALL
+437
View File
@@ -0,0 +1,437 @@
==============================================================================
README file for H5Part configure
==============================================================================
+ 0. HDF5 library
-----------------
Make sure you have a working version of the HDF5 library installed. If you plan
to use parallel I/O you need to use a parallel HDF5 version. Source files and
installation instructions are available from the HDF5 website:
http://www.hdfgroup.org/HDF5/
+ 1. Quick start (If you feel lucky...)
----------------------------------------
For many platforms, where compilers are installed in the "default" location
and all the environment variables are set correctly, it should be sufficient
to type:
./configure [OPTIONS] && make [install]
to have the libraries and test program compiled.
+ 2. Configure line options
----------------------------
To view a full list of configure option, use:
./configure --help
(1) Enable options
--enable-fortran
--enable-parallel
--enable-tools
--enable-python
--enable-64 (only for AIX and Irix)
(2) Setting compilers related variables manually
To assign environment variables (e.g., CC, CFLAGS...), specify them as
VAR=VALUE before running configure. For example, if you are using the bash
shell, you might type:
export CC=gcc
to set the default C compiler. See below for descriptions of some useful
variables.
Compiler environment variables:
CC C compiler command
CXX C++ compiler command
FC Fortran compiler command
MPICC MPI-enabled C compiler command
MPICXX MPI-enabled C++ compiler command
MPIFC MPI-enabled Fortran compiler command
CFLAGS flags to append when invoking the C compiler
Library environment variables:
LDFLAGS flags to append when invoking the linker
(3) Setting prefix for installation manually (by default, the package will
install itself in the 'build' subdirectory of your source directory)
--prefix=PREFIX install files in PREFIX
+ 3. Platform specific settings for compiling libraries & test programs
------------------------------------------------------------------------
Building
make : builds the libraries and test programs
make install: builds and installs
make clean : removes extraneous object files
make distclean : returns configuration to unconfigured state
As tested on hosts:
(0) Franklin <franklin.nersc.gov> (CNL - Cray XT4)
--------------------------------------------------
module add hdf5_par
module add zlib
module add szip
export CC=cc CXX=CC FC=ftn MPICC=cc MPICXX=CC MPIFC=ftn
export LDFLAGS=$HDF5
./configure --enable-fortran --enable-parallel --with-hdf5path=$HDF5_PAR_DIR --with-mpiposix
make install
(1) Davinci <davinci.nersc.gov> (Linux"SUSE"-ia64)
---------------------------------------------------
FIRST THING FIRST!! Type:
module load intel
to have the proper compilers set up for use.
module load hdf5_par
[NOTE: module load hdf5 does not work at this moment.
Possible installation error of HDF5 on Davinci.]
Brief profile:
CC = icc
CXX = icc
FC = ifort
MPICC = icc
MPICXX = icc
MPIFC = ifort
If default doesn't work, try:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=icc CXX=icc FC=ifort MPICC=icc MPICXX=icc MPIFC=ifort ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
mpirun 2 H5testFpar
mpirun 2 H5PartTestP
NOTE: Number 2 above is a arbitrary number that indicates the number of processes.
(2) Jacquard <jacquard.nersc.gov> (Linux"SUSE"-x86_64)
-------------------------------------------------------
Brief profile:
CC = pathcc
CXX = pathCC
FC = pathf90
MPICC = mpicc
MPICXX = mpicxx
MPIFC = mpif90
If default doesn't work, try:
For C shell:
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
For Korn or Bourne shell:
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=pathcc CXX=pathCC FC=pathf90 MPICC=mpicc MPICXX=mpicxx MPIFC=mpif90 ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
In Jacquard, we need a script to run parallel programs, since Jacquard does not support interactive parallel processing. Instead, we need to submit the task to a queue. A sample script (run_H5testFpar.scr) may look like below:
+++++++++++++++++++++++++++++++++++++++
#!/bin/csh
#PBS -l nodes=1:ppn=2,walltime=00:05:00
#PBS -N H5testFpar
#PBS -o H5testFpar.out
#PBS -e H5testFpar.err
#PBS -q debug
#PBS -A mpccc
#PBS -V
setenv PBS_OWORKDIR /home/H5Part/test
cd $PBS_O_WORKDIR
mpirun -np 2 ./H5testFpar
+++++++++++++++++++++++++++++++++++++++
Then, we need to submit the task to a queue by running:
qsub run_H5testFpar.scr
After processed, the result will appear in H5testFpar.out, and error messages will appear in H5testFpar.err.
(3) Bassi <bassi.nersc.ogv> (AIX5.3.0.0-Power 3)
-------------------------------------------------
FIRST THING FIRST!! Type:
module load gcc
to have the proper compilers set up for use.
Brief profile:
CC = cc_r
CXX = cc_r
FC = xlf_r
MPICC = mpcc_r
MPICXX = mpcc_r
MPIFC = mpxlf_r
If default doesn't work, try:
For C shell:
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
For Korn or Bourne shell:
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
For Korn or Bourne shell:
CC=cc_r CXX=cc_r FC=xlf_r MPICC=mpcc_r MPICXX=mpcc_r MPIFC=mpxlf_r ./configure --enable-fortran --enable-parallel && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(ii) Parallel test
run:
unsetenv MP_SINGLE_THREAD
poe ./H5PartTestP -procs 2 -nodes 1
poe ./H5testFpar -procs 2 -nodes 1
For more details on how to run parallel programs on Bassi, go to:
http://www.nersc.gov/nusers/resources/bassi/running_jobs/
(4) Starsky <starsky.lbl.gov> (Darwin8.5.0-PowerPC)
----------------------------------------------------
FIRST THING FIRST!! Set environment variables: (in tcsh)
setenv LD_LIBRARY_PATH /usr/local/g95/lib/gcc-lib/powerpc-apple-darwin8.5.0/4.0.3/
setenv PATH ${PATH}:/usr/local/g95/bin
NOTE: This environment variable setting is specifit to Starsky. It is to make configure find the fortran compiler.
Brief profile:
CC = gcc
CXX = g++
FC = g95
If default doesn't work, try:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(5) Linux AMD64 Visualization group workstations (Linux"SUSE"-x86_64)
---------------------------------------------------------
Brief profile:
CC = gcc
CXX = g++
FC = g95
If default doesn't work, try:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure && make install
And, of course, you should add configure options, such as --enable-fortran --enable-parallel.
On this host, executing:
For C shell:
env CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
For Korn or Bourne shell:
CC=gcc CXX=g++ FC=g95 ./configure --enable-fortran && make install
has functioned correctly.
To run test program, go to test directory:
(i) Serial test
run:
./H5testF
./H5PartTest
(6) Cray XT3 @ CSCS gele
1) modules/3.1.6 9) PrgEnv-pgi/1.4.26 17) xt-lustre-ss/1.4.26
2) MySQL/4.0.26 10) xt-pbs/5.3.4 18) Base-opts/1.4.26
3) acml/3.0 11) xt-service/1.4.26 19) subversion/1.3.2
4) pgi/6.1.4 12) xt-libc/1.4.26 20) zlib/1.2.3
5) totalview/7.2.0 13) xt-os/1.4.26 21) szip/2.0
6) xt-libsci/1.4.26 14) xt-catamount/1.4.26 22) hdf5/1.6.5
7) xt-mpt/1.4.26 15) xt-boot/1.4.26
8) xt-pe/1.4.26 16) xt-crms/1.4.26
CFLAGS="-I$H5HOME/include -DF77_SINGLE_UNDERSCORE" LDFLAGS="-L$H5HOME/lib -L$ZHOME/lib" ./configure --enable-parallel --enable-fortran
(7) merlin00 / merlin3
Currently Loaded Modulefiles:
1) hdf5/hdf5-1.6.5 2) root/root-5.10.00 3) mpi/mpich2-1.0.3-pgi-6.1 4) pgi/pgi_64-6.1
FC=mpif90 ./configure --enable-parallel --enable-fortran
==============================================================================
+ 4. Trouble shooting (Things to check for...)
--------------------------------------------
(0) Have you set the LD_LIBRARY_PATH?
---Some systems require the user to manually set the environment variable, LD_LIBRARY_PATH. To do so:
set the environment variable HDF5ROOT or PHDF5ROOT to point to your installation of HDF5 (serial and/or parallel respectively).
For Korn or Bourne shell:
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HDF5ROOT}/lib;export LD_LIBRARY_PATH
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:{PHDF5ROOT}/lib;export LD_LIBRARY_PATH
For C shell:
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HDF5ROOT}/lib
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${PHDF5ROOT}/lib
Note that the values of HDF5ROOT & PHDF5ROOT will be in the "summary" section when you run configure.
Not properly set LD_LIBRARY_PATH value may result in a runtime error:
./H5PartTest: error while loading shared libraries: libhdf5.so.0: cannot open shared object file: No such file or directory
(1) Are the compilers set correctly?
---Check with: which COMPILER
(2) Have you installed HDF5?
---You can get it at: http://vis.lbl.gov/Research/AcceleratorSAPP/index.html
(3) Have you loaded the proper modules?
---It is necessary in Davinci & Bassi, and configure && make install may not work without it.
Makefile.am
+3 -4
View File
@@ -1,11 +1,10 @@
ACLOCAL_AMFLAGS = -I m4
EXTRA_DIST = autogen.sh
ACLOCAL_AMFLAGS=-I m4
SUBDIRS = \
doc \
src \
test \
tools \
doc
tools
MAINTAINERCLEANFILES = \
config.h \
Makefile.orig
Executable
+59
View File
@@ -0,0 +1,59 @@
# This is a very rudimentary multiarchitecture makefile
# You need to uncomment the default block of make variables you need
# Some key things to watch for are the following defines
# -DREGRESSIONTEST : enables a main(){} inside of
# the H5Part.cc file that does simple regression testing.
# -DPARALLEL_IO : If you want to use parallel HDF5, you have to
# enable this. Otherwise, you get only the serial
# implementation of the library.
# MacOS-X Serial
#CXX = c++
#CC = cc
#F90 = xlf
#H5HOME = /usr/local
#CFLAGS = -O -g -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# AIX/SP-2 Parallel : Seaborg
#CXX = mpCC_r
#CC = mpcc_r
#F90 = mpxlf
#H5HOME = /usr/common/usg/hdf5/1.4.4/parallel
#H4HOME = /usr/common/usg/hdf/default
#OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
#CFLAGS = -g -bmaxdata:800000000 -bmaxstack:256000000 -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
# Linux Serial
#CXX = g++
#CC = gcc
#F90 = g77 # or could be pgif90
#CFLAGS = -O -g -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# Linux Jacquard
CC = mpicc
CXX = mpicxx
F90 = mpif90
H5HOME = /usr/common/usg/hdf5/1.6.3/parallel
CFLAGS = -O2 -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
# Linux Parallel
#CC = gcc
#CXX = g++
#F90 = g77
#H5HOME = /usr/local
# /usr/common/usg/hdf5/1.6.3/parallel
#MPIHOME = /usr/local
#CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include
#LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
all: H5PartTest H5PartTest.o H5Part.o
parallel: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest # parallel regression tests
fortran: H5PartF.o # fortran bindings
include rules.make
NEWS
-53
View File
@@ -1,56 +1,3 @@
#### H5PART 1.99.10 ###########################################################
Bugfixes in the malloc wrappers
Converter from vtk to H5hut added.
Bugfixes in the autotools files.
#### H5PART 1.99.9 ############################################################
Bugfix in option parsing in tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk
tools/h5PartDcToVtk and tools/h5PartSurfaceToVtk removed from list of tools
to be compiled. These tools should be moved to another repository anyway.
#### H5PART 1.99.8 ############################################################
Bugfixes
#### H5PART 1.99.7 ############################################################
Linking problem on Linux fixed
#### H5PART 1.99.6 ############################################################
#### H5PART 1.99.5 ############################################################
#### H5PART 1.99.4 ############################################################
#### H5PART 1.99.3 ############################################################
#### H5PART 1.99.2 ############################################################
#### H5PART 1.99.1 ############################################################
#### H5PART 1.99 ############################################################
Renamed type:
H5PartFile -> h5_file_t
h5part_int64_t -> h5_int64_t
Renamed functions:
#### H5PART 1.6.6 ############################################################
Fixed typo (Write instead of Read) in the h5bl_3d_read_scalar_field* Fortran
interface.
Added missing type normalization for int32 type.
Rewrite of h5pAttrib tool.
#### H5PART 1.6.5 ############################################################
Fixed several build errors reported by Iuri Prilepov on Ubuntu 11.04.
#### H5PART 1.6.4 ############################################################
Fixed bug where H5PartSetViewIndices was not setting an empty view when the
README
+29
View File
@@ -0,0 +1,29 @@
Website:
http://vis.lbl.gov/Research/AcceleratorSAPP/
Particle based simulations of accelerator beam-lines, especially in six
dimensional phase space, generate vast amounts of data. Even though a subset of
statistical information regarding phase space or analysis needs to be preserved,
reading and writing such enormous restart files on massively parallel
supercomputing systems remains challenging.
H5Part is a very simple data storage schema and provides an API that simplifies
the reading/writing of the data to the HDF5 file format. An important
foundation for a stable visualization and data analysis environment is a stable
and portable file storage format and its associated APIs. The presence of a
"common file storage format," including associated APIs, will help foster a
fundamental level of interoperability across the project's software
infrastructure. It will also help ensure that key data analysis capabilities
are present during the earliest phases of the software development effort.
H5Part is built on top of the HDF5 (Hierarchical Data Format). HDF5 offers a
self-describing machine-independent binary file format that supports scalable
parallel I/O performance for MPI codes on a variety of supercomputing systems,
and works equally well on laptop computers. The API is available for C, C++, and
Fortran codes. The H5Part file format and APIs enable disparate research groups
with different simulation implementations to transparently share datasets and
data analysis tools. For instance, the common file format will enable groups
that depend on completely different simulation implementations to share data
analysis tools.
configure-crayxt
Executable
+20
View File
@@ -0,0 +1,20 @@
#!/bin/sh
F90=gfortran
./configure \
$@ \
--enable-parallel \
--enable-fortran \
--enable-tools \
CC=cc CXX=CC FC=$F90 \
MPICC=cc MPICXX=CC MPIFC=ftn
sed -e 's/$F90/ftn/g' <Makefile > newMakefile
mv newMakefile Makefile
sed -e 's/$F90/ftn/g' <src/Makefile > newMakefile
mv newMakefile src/Makefile
sed -e 's/$F90/ftn/g' <test/Makefile > newMakefile
mv newMakefile test/Makefile
sed -e 's/$F90/ftn/g' <tools/Makefile > newMakefile
mv newMakefile tools/Makefile
configure.ac
+193 -222
View File
@@ -1,87 +1,58 @@
AC_INIT([H5hut], [1.99.13], [h5part@lists.psi.ch], H5hut)
AC_PREREQ(2.60)
# Every configure script must call AC_INIT before doing anything else.
# AC_INIT (package, version, [bug-report], [tarname])
AC_INIT([H5Part], [1.6.4], [h5part@lists.psi.ch], H5Part)
# Ensure that a recent enough version of Autoconf is being used.
# If the version of Autoconf being used to create configure is earlier than version,
# print an error message to the standard error output and do not create configure.
AC_PREREQ(2.59)
# 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_HEADERS(config.h)
AC_CONFIG_MACRO_DIR([m4])
# AM_INIT_AUTOMAKE is required to use autoconf with automake
AM_INIT_AUTOMAKE
ENABLE_DEBUG='no'
ENABLE_C='yes'
ENABLE_FORTRAN='no'
ENABLE_PARALLEL='no'
BUILD_LIBS='libH5Part'
BUILD_TESTS='test'
###############################################################################
# --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"])
[debug],
[AC_HELP_STRING([--enable-debug],
[Compile with debug flags [default=no]])],
[USE_DEBUG=$enableval])
AC_ARG_ENABLE(
[fortran],
[AS_HELP_STRING([--enable-fortran],
[AC_HELP_STRING([--enable-fortran],
[Compile the Fortran interface [default=no]])],
[ENABLE_FORTRAN=$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=$enableval])
AC_ARG_WITH(
[hdf5],
[AS_HELP_STRING([--with-hdf5],
[AC_HELP_STRING([--with-hdf5],
[path to HDF5 installation [default=""]])],
[HDF5_PREFIX=$withval], [])
AC_ARG_WITH(
[mpi],
[AS_HELP_STRING([--with-mpi],
[path to MPI installation [default=""]])],
[PATH=$MPI_PREFIX/bin:$PATH])
AC_ARG_WITH(
[lustre],
[AS_HELP_STRING([--with-lustre],
[path to lustre user API [default=""]])],
[LUSTREPATH=$withval], [LUSTREPATH=""])
AC_ARG_WITH(
[parmetis],
[AC_HELP_STRING([--with-parmetis],
[path to ParMETIS API [default=""]])],
[PARMETISPATH=$withval], [PARMETISPATH=""])
[HDF5PATH=$withval], [HDF5PATH=""])
###############################################################################
############### PATH SERACH FUNCTION - to be used later... ####################
@@ -114,74 +85,45 @@ PATH_Search() {
return
}
###############################################################################
# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING
###############################################################################
############# MISC SETTINGS INCLUDING C & C++ COMPILER SETTING ################
###############################################################################
# Compute the canonical host-system type variable, host, and its three
# individual parts host_cpu, host_vendor, and host_os.
AC_CANONICAL_HOST
AC_PROG_MAKE_SET
# debug enabled?
AC_MSG_CHECKING([if debug is enabled])
if test "X$ENABLE_DEBUG" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="$CFLAGS -g -Wall"
CXXFLAGS="$CFLAGS -g -Wall"
FFLAGS="$FFLAGS -g"
else
AC_MSG_RESULT([no])
fi
# Determine a C/C++ compiler to use.
if test "x$ENABLE_PARALLEL" = "xyes"; then
CCOMPILERS="mpicc"
CXXCOMPILERS="mpic++"
# 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.
if test "x$USE_PARALLEL" = "xyes"; then
CCOMPILERS="mpicc cc"
CXXCOMPILERS="mpic++ mpicxx CC"
else
CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
CXXCOMPILERS="pgcc pathcc icc g++ cc_r c++"
CXXCOMPILERS="pgCC pathCC icpc g++"
fi
AC_PROG_CC($CCOMPILERS)
CC=`which $CC`
AC_PROG_CXX($CXXCOMPILERS)
CXX=`which $CXX`
AC_PROG_CC_C99
if test "x$ac_cv_prog_cc_c99" = "xno"; then
AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
exit 1
fi
# Only need C++ for some of the tools
#if test "x$USE_TOOLS" = "xyes"; then
AC_PROG_CXX($CXXCOMPILERS)
#fi
# Set output variable INSTALL to the path of a BSD-compatible install program,
# if one is found in the current PATH.
# Otherwise, set INSTALL to `dir/install-sh -c`
AC_PROG_INSTALL
AC_PROG_AWK
# Disable shared libraries by default: can be enabled with --enable-shared
LT_INIT([disable-shared])
AC_PROG_LIBTOOL
AC_PROG_AWK
# Default prefix for bindir, etc... (eg >> ./build/bin)
AC_PREFIX_DEFAULT(`pwd`/build)
# Checks for header files.
AC_CHECK_HEADERS([fcntl.h limits.h stdint.h stdlib.h string.h sys/ioctl.h unistd.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_C_INLINE
AC_TYPE_INT16_T
AC_TYPE_INT32_T
AC_TYPE_INT64_T
AC_TYPE_SIZE_T
AC_TYPE_SSIZE_T
AC_TYPE_UINT16_T
AC_TYPE_UINT32_T
AC_TYPE_UINT64_T
AC_CHECK_TYPES([ptrdiff_t])
# Checks for library functions.
AC_FUNC_MALLOC
AC_FUNC_REALLOC
AC_CHECK_FUNCS([memmove memset pow strchr strdup strerror strstr])
# AC_DEFINE_UNQUOTED (variable, value, [description])
# Define the C preprocessor variable variable to value
# Use this macro instead of AC_DEFINE when variable or value is a shell variable.
@@ -193,27 +135,34 @@ AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
###############################################################################
# PROCESS ARGUMENTS
######################## CONFIGURE LINE OPTIONS ###############################
###############################################################################
# C enabled?
AC_MSG_CHECKING([if C interface enabled])
if test "X$ENABLE_C" = "Xyes"; then
AC_MSG_RESULT([yes])
AC_MSG_CHECKING([if debug is enabled])
if test "X$USE_DEBUG" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="$CFLAGS -g"
CXXFLAGS="$CXXFLAGS -g"
FFLAGS="$FFLAGS -g"
else
AC_MSG_RESULT([no])
AC_MSG_RESULT([no])
fi
# fortran enabled?
############################ fortran enabled ##################################
AC_MSG_CHECKING([if fortran interface enabled])
if test "X$ENABLE_FORTRAN" = "Xyes"; then
if test "X$USE_FORTRAN" = "Xyes"; then
AC_MSG_RESULT([yes])
LIB_FORTRAN="libH5PartF.la"
BUILD_LIBS="$BUILD_LIBS libH5PartF"
BUILD_TESTS="$BUILD_TESTS testf"
if test "X$ENABLE_PARALLEL" = "Xyes"; then
AC_PROG_FC(mpif90 mpif77)
if test "X$USE_PARALLEL" = "Xyes"; then
AC_PROG_FC(mpif90 mpif77 ftn)
else
AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
AC_PROG_FC(pgf90 pathf90 ifort ftn xlf_r g95 g90 gfortran)
fi
FC=`which $FC`
if test -z "$FC" ; then
AC_MSG_ERROR([Cannot find a Fortran compiler!])
exit 1
@@ -228,17 +177,18 @@ if test "X$ENABLE_FORTRAN" = "Xyes"; then
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`
`cd src && rm -f TestUnderscore.o TestUnderscoreC.o TestUnderscore`
`cd src && ${FC} ${FFLAGS} -c TestUnderscore.f`
`cd src && ${CC} ${CFLAGS} -c TestUnderscoreC.c`
`cd src && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
if test -f src/Fortran/TestUnderscore ; then
`cd src/Fortran && ./TestUnderscore > Underscore.h`
if test -f src/TestUnderscore ; then
UNDERSCORE_H=Underscore.h
`cd src && ./TestUnderscore > Underscore.h`
AC_MSG_RESULT([ok])
else
AC_MSG_RESULT([nok])
AC_MSG_ERROR([Cannot determine the symbol convention for Fortran object files!])
AC_MSG_ERROR([Cannot determine the symbon convention for Fortran object files!])
exit 1
fi
@@ -246,144 +196,165 @@ else
AC_MSG_RESULT([no])
fi
######################## large indices enabled ###########################
AC_MSG_CHECKING([if large indices are enabled])
if test "X$USE_LARGE_INDICES" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="${CFLAGS} -DUSE_LARGE_INDICES"
else
AC_MSG_RESULT([no])
fi
# Disable shared libraries by default: can be enabled with --enable-shared
LT_INIT([disable-shared])
AC_PROG_LIBTOOL
######################## parallel interface enabled ###########################
AC_MSG_CHECKING([if parallel interface enabled])
if test "X$ENABLE_PARALLEL" = "Xyes"; then
if test "X$USE_PARALLEL" = "Xyes"; then
AC_MSG_RESULT([yes])
CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
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="${CFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
CXXFLAGS="${CXXFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
FFLAGS="${FFLAGS} -DPARALLEL_IO"
LIBS="$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 ); ],
[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
if test "X$r" = "Xno"; then
AC_MSG_ERROR([MPI wrapper can't compile or link MPI program! Please set the INCLUDE and LIBS variables manually.])
exit 1
fi
if test "X$r" = "Xno"; then
AC_MSG_ERROR([ParMETIS])
exit 1
fi
fi
else # --enable-parallel=no
AC_MSG_RESULT([no])
fi
######################## tools enabled ###########################
AC_MSG_CHECKING([whether tools are enabled])
if test "X$USE_TOOLS" = "Xyes"; then
AC_MSG_RESULT([yes])
BUILD_TOOLS="h5pAttrib h5pToGNUplot homdynToH5p"
# tools + parallel
if test "X$USE_PARALLEL" = "Xyes"; then
BUILD_TOOLS="${BUILD_TOOLS} H5PartBench H5BlockBench"
fi
else
AC_MSG_RESULT([no])
fi
###############################################################################
######################### PATH CHECKING & SETTING #############################
###############################################################################
# LIBRARY PATHS
if test -z "${HDF5_PREFIX}"; then
# alternatives to HDF5_PREFIX
if test -n "${HDF5_DIR}"; then
HDF5_PREFIX=${HDF5_DIR}
fi
fi
if test -n "${HDF5_PREFIX}"; then
CPPFLAGS="$CPPFLAGS -I$HDF5_PREFIX/include"
LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
fi
AC_CHECK_LIB([z], [compress2])
AC_CHECK_LIB([hdf5], [H5open])
AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes],
[AC_MSG_ERROR([Cannot compile and link a HDF5 program]);
exit 1])
AC_MSG_CHECKING([for lustre API ])
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 "${HDF5PATH}" ; then
P=${HDF5PATH}
elif test -n "${HDF5ROOT}"; then
P=${HDF5ROOT}
elif test -n "${HDF5HOME}" ; then
P=${HDF5HOME}
elif test -n "${HDF5_DIR}" ; then
P=${HDF5_DIR}
else
P=''
P="$P /usr"
P="$P /usr/local"
P="$P /usr/local/lustre"
P="$P /opt/lustre"
P="$P /usr/local/hdf5"
P="$P /usr/local/packages/hdf5"
P="$P /apps/hdf5"
P="$P /opt/hdf5"
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 find an HDF5 library!])
exit 1
fi
LIBS="$LIBS -lm"
INCLUDES="$INCLUDES -I$HDF5ROOT/include"
LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
LIBS="$LIBS -lhdf5"
AC_MSG_CHECKING([if we need to link to libsz ])
if test -n "$HDF5ROOT"; then
if test -f $HDF5ROOT/lib/libsz.a; then
AC_MSG_RESULT([yes])
LDFLAGS="$LDFLAGS -L$HDF5ROOT/lib"
LIBS="$LIBS -lsz"
else
AC_MSG_RESULT([no])
fi
fi
LIBS="$LIBS -lz -lm"
# Checks for header files.
AC_CHECK_HEADERS([fcntl.h stdlib.h string.h unistd.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_TYPE_INT64_T
AC_TYPE_SIZE_T
AC_TYPE_SSIZE_T
# Checks for library functions.
AC_FUNC_MALLOC
AC_CHECK_FUNCS([memset pow strchr strdup])
###############################################################################
# TOOLS
AC_MSG_CHECKING([if we have to compile the VTK to H5hut grid converter])
if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
AC_MSG_RESULT([yes])
# :TODO: add test whether we can compile/link a prog with vtk
else
AC_MSG_RESULT([no])
fi
############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
###############################################################################
# EXPORTING VARIABLES & CREATING OUTPUT FILES
AM_CPPFLAGS=$CPPFLAGS
AM_LDFLAGS=$LDFLAGS
AC_SUBST(HDF5_PREFIX)
# 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(CFLAGS)
AC_SUBST(CXXFLAGS)
AC_SUBST(FFLAGS)
AC_SUBST(AM_CPPFLAGS)
AC_SUBST(AM_LDFLAGS)
AC_SUBST(INCLUDES)
AC_SUBST(LDFLAGS)
AC_SUBST(LIBS)
AC_SUBST(UNDERSCORE_H)
AC_SUBST(LIB_FORTRAN)
AC_SUBST(BUILD_TESTS)
AC_SUBST(BUILD_TOOLS)
# Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'),
# substituting the output variable values.
AC_CONFIG_FILES([
Makefile
src/Makefile
src/h5core/Makefile
src/include/Makefile
src/include/h5core/Makefile
src/C/Makefile
src/Fortran/Makefile
doc/Makefile
test/Makefile
doc/Makefile
tools/Makefile
tools/h5hutcc
tools/vtk2h5grid/Makefile
])
AC_OUTPUT
###############################################################################
# PRINTING SUMMARY
########################## PRINTING SUMMARY ###################################
###############################################################################
AC_MSG_RESULT([ ])
AC_MSG_RESULT([Summary:])
AC_MSG_RESULT([ ])
AC_MSG_RESULT([Host OS: $host_os])
AC_MSG_RESULT([Host CPU: $host_cpu])
AC_MSG_RESULT([Host vendor: $host_vendor])
AC_MSG_RESULT([Build libraries: $BUILD_LIBS])
AC_MSG_RESULT([Build test programs: $BUILD_TESTS])
AC_MSG_RESULT([Build tools: $BUILD_TOOLS])
AC_MSG_RESULT([CC = $CC])
AC_MSG_RESULT([CXX = $CXX])
AC_MSG_RESULT([FC = $FC])
AC_MSG_RESULT([CFLAGS = $CFLAGS])
AC_MSG_RESULT([CXXFLAGS = $CXXFLAGS])
AC_MSG_RESULT([FFLAGS = $FFLAGS])
AC_MSG_RESULT([AM_CPPFLAGS = $AM_CPPFLAGS])
AC_MSG_RESULT([AM_LDFLAGS = $AM_LDFLAGS])
AC_MSG_RESULT([INCLUDES = $INCLUDES])
AC_MSG_RESULT([LDFLAGS = $LDFLAGS])
AC_MSG_RESULT([LIBS = $LIBS])
AC_MSG_RESULT([HDF5_PREFIX = $HDF5_PREFIX])
AC_MSG_RESULT([LUSTREROOT = $LUSTREROOT])
AC_MSG_RESULT([HDF5ROOT = $HDF5ROOT])
AC_MSG_RESULT([ ])
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/Doxyfile
+36 -30
View File
@@ -3,8 +3,8 @@
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
PROJECT_NAME = H5hut
PROJECT_NUMBER = 1.9.9
PROJECT_NAME = H5Part
PROJECT_NUMBER = 1.6.1
OUTPUT_DIRECTORY = ./ReferencePages
CREATE_SUBDIRS = NO
OUTPUT_LANGUAGE = English
@@ -35,7 +35,7 @@ INHERIT_DOCS = YES
SEPARATE_MEMBER_PAGES = NO
TAB_SIZE = 8
ALIASES =
OPTIMIZE_OUTPUT_FOR_C = YES
OPTIMIZE_OUTPUT_FOR_C = NO
OPTIMIZE_OUTPUT_JAVA = NO
BUILTIN_STL_SUPPORT = NO
DISTRIBUTE_GROUP_DOC = NO
@@ -57,9 +57,9 @@ CASE_SENSE_NAMES = YES
HIDE_SCOPE_NAMES = NO
SHOW_INCLUDE_FILES = NO
INLINE_INFO = YES
SORT_MEMBER_DOCS = NO
SORT_BRIEF_DOCS = NO
SORT_BY_SCOPE_NAME = NO
SORT_MEMBER_DOCS = YES
SORT_BRIEF_DOCS = YES
SORT_BY_SCOPE_NAME = YES
GENERATE_TODOLIST = YES
GENERATE_TESTLIST = YES
GENERATE_BUGLIST = YES
@@ -67,7 +67,7 @@ GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS =
MAX_INITIALIZER_LINES = 30
SHOW_USED_FILES = NO
SHOW_DIRECTORIES = NO
SHOW_DIRECTORIES = YES
FILE_VERSION_FILTER =
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
@@ -82,22 +82,28 @@ WARN_LOGFILE =
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
INPUT += H5.dox
INPUT += ../src/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/H5PartAttrib.c
INPUT += ../src/H5Block.c
INPUT += ../src/H5BlockReadWrite.c
INPUT += ../src/H5MultiBlock.c
INPUT += ../src/H5MultiBlockReadWrite.c
INPUT += ../src/H5Part.f90
INPUT += ../src/H5PartAttrib.f90
INPUT += ../src/H5Block.f90
INPUT += ../src/H5BlockReadWrite.f90
FILE_PATTERNS =
RECURSIVE = YES
EXCLUDE =
EXCLUDE_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 +126,8 @@ 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
@@ -199,7 +205,7 @@ SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
TAGFILES =
TAGFILES =
GENERATE_TAGFILE =
ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
@@ -208,7 +214,7 @@ PERL_PATH = /usr/bin/perl
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
CLASS_DIAGRAMS = NO
HIDE_UNDOC_RELATIONS = YES
HIDE_UNDOC_RELATIONS = NO
HAVE_DOT = NO
CLASS_GRAPH = NO
COLLABORATION_GRAPH = NO
@@ -218,10 +224,10 @@ TEMPLATE_RELATIONS = NO
INCLUDE_GRAPH = NO
INCLUDED_BY_GRAPH = NO
CALL_GRAPH = NO
GRAPHICAL_HIERARCHY = NO
DIRECTORY_GRAPH = NO
GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
DOT_IMAGE_FORMAT = png
DOT_PATH =
DOT_PATH =
DOTFILE_DIRS =
MAX_DOT_GRAPH_WIDTH = 1024
MAX_DOT_GRAPH_HEIGHT = 1024
doc/Examples/meshexample.dxf
-47962
View File
File diff suppressed because it is too large Load Diff
doc/Examples/meshexample.txt
-77
View File
@@ -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
View File
@@ -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
View File
@@ -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
View File
@@ -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
View File
@@ -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
View File
@@ -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/Makefile.am
+2 -14
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@@ -1,14 +1,2 @@
EXTRA_DIST = \
Doxyfile \
H5.dox \
Makefile.in
all:
doc:
doxydoc:
doxygen
clean:
${RM} -rf ReferencePages TWiki
EXTRA_DIST = \
Doxyfile doxyfooter
doc/doxyheader
-6
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@@ -1,6 +0,0 @@
<HTML>
<HEAD>
<TITLE>H5/H5Part/H5Block/H5Fed API</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
doc/html2twiki
-36
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@@ -1,36 +0,0 @@
#!/bin/bash
shopt -s nullglob
function html2twiki() {
declare -rx infile=$1
declare -rx outdir=$2
declare -rx fname=$( sed -n 's/.* member="\([a-zA-Z0-9_.]*\)::\([_a-zA-Z0-9]*\)" .*/\2/p' "${infile}" )
declare -rx outfile="${outdir}/${fname}.txt"
grep -q " member=" "${infile}" || return 0
sed '/Generated by/,/anchor/d' "${infile}" > "${outfile}"
}
mkdir -p TWiki/h5_core
mkdir -p TWiki/H5
mkdir -p TWiki/H5Part
mkdir -p TWiki/H5Block
mkdir -p TWiki/H5Fed
for f in ReferencePages/group__h5__core_*.html; do
html2twiki $f TWiki/h5_core
done
for f in ReferencePages/group__h5__c__api_*.html; do
html2twiki $f TWiki/H5
done
for f in ReferencePages/group__h5part__c__api_*.html; do
html2twiki $f TWiki/H5Part
done
for f in ReferencePages/group__h5block__c__api_*.html; do
html2twiki $f TWiki/H5Block
done
for f in ReferencePages/group__h5fed__c__api_*.html; do
html2twiki $f TWiki/H5Fed
done
doc/meshexample.dxf
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doc/tetrahedron_refinements/1-edge/edge_01_refined/01.txt
-10
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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
-25
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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
doc/tetrahedron_refinements/1-edge/edge_01_refined/01_smal.png
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doc/tetrahedron_refinements/1-edge/edge_12_refined/12.txt
-10
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@@ -1,10 +0,0 @@
TET no. 0:
0.0, 0.5, 0.5
0.0, 0.0, 0.0
1.0, 0.0, 0.0
0.0, 1.0, 0.0
TET no. 1:
0.0, 0.5, 0.5
1.0, 0.0, 0.0
0.0, 0.0, 0.0
0.0, 0.0, 1.0
doc/tetrahedron_refinements/1-edge/edge_12_refined/12.vtk
-25
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@@ -1,25 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.0 0.5 0.5
0.0 0.0 0.0
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_12_refined/12_small.png
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doc/tetrahedron_refinements/1-edge/edge_20_refined/20.txt
-10
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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
doc/tetrahedron_refinements/1-edge/edge_20_refined/20.vtk
-25
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@@ -1,25 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.5 0.0 0.5
0.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
1.0 0.0 0.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_20_refined/20_small.png
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doc/tetrahedron_refinements/1-edge/edge_23_refined/23.txt
-10
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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
-25
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@@ -1,25 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.0 0.0 0.5
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 0.0
0.0 0.0 1.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_23_refined/23_small.png
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doc/tetrahedron_refinements/1-edge/edge_30_refined/30.txt
-10
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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
-25
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@@ -1,25 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.5 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
0.0 0.0 0.0
1.0 0.0 0.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_30_refined/30_small.png
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doc/tetrahedron_refinements/1-edge/edge_31_refined/31.txt
-10
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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
-25
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@@ -1,25 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 5 DOUBLE
0.0 0.5 0.0
0.0 0.0 1.0
1.0 0.0 0.0
0.0 0.0 0.0
0.0 1.0 0.0
CELLS 2 10
4 0 1 2 3
4 0 2 1 4
CELL_TYPES 2
10
10
CELL_DATA 2
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
doc/tetrahedron_refinements/1-edge/edge_31_refined/31_small.png
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doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12.txt
-15
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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
-29
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@@ -1,29 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 6 DOUBLE
0.5 0.5 0.0
0.0 1.0 0.0
0.0 0.5 0.5
0.0 0.0 0.0
1.0 0.0 0.0
0.0 0.0 1.0
CELLS 3 15
4 0 1 2 3
4 2 4 0 3
4 4 2 5 3
CELL_TYPES 3
10
10
10
CELL_DATA 3
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
2
doc/tetrahedron_refinements/2-edges/edge_01-12_refined/01-12_smal.png
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doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.txt
-15
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@@ -1,15 +0,0 @@
TET no. 0:
0.5, 0.0, 0.5
1.0, 0.0, 0.0
0.5, 0.5, 0.0
0.0, 0.0, 0.0
TET no. 1:
0.5, 0.5, 0.0
0.0, 0.0, 1.0
0.5, 0.0, 0.5
0.0, 0.0, 0.0
TET no. 2:
0.0, 0.0, 1.0
0.5, 0.5, 0.0
0.0, 1.0, 0.0
0.0, 0.0, 0.0
doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20.vtk
-29
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@@ -1,29 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 6 DOUBLE
0.5 0.0 0.5
1.0 0.0 0.0
0.5 0.5 0.0
0.0 0.0 0.0
0.0 0.0 1.0
0.0 1.0 0.0
CELLS 3 15
4 0 1 2 3
4 2 4 0 3
4 4 2 5 3
CELL_TYPES 3
10
10
10
CELL_DATA 3
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
2
doc/tetrahedron_refinements/2-edges/edge_01-20_refined/01-20_small.png
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doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23.txt
-20
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@@ -1,20 +0,0 @@
TET no. 0:
1.0, 0.0, 0.0
0.5, 0.5, 0.0
0.0, 0.0, 0.5
0.0, 0.0, 0.0
TET no. 1:
0.5, 0.5, 0.0
0.0, 1.0, 0.0
0.0, 0.0, 0.5
0.0, 0.0, 0.0
TET no. 2:
0.5, 0.5, 0.0
0.0, 0.0, 0.5
0.0, 1.0, 0.0
0.0, 0.0, 1.0
TET no. 3:
1.0, 0.0, 0.0
0.0, 0.0, 0.5
0.5, 0.5, 0.0
0.0, 0.0, 1.0
doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23.vtk
-32
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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
1.0 0.0 0.0
0.5 0.5 0.0
0.0 0.0 0.5
0.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
CELLS 4 20
4 0 1 2 3
4 1 4 2 3
4 1 2 4 5
4 0 2 1 5
CELL_TYPES 4
10
10
10
10
CELL_DATA 4
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
2
3
doc/tetrahedron_refinements/2-edges/edge_01-23_refined/01-23_smal.png
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TET no. 0:
0.5, 0.5, 0.0
1.0, 0.0, 0.0
0.5, 0.0, 0.0
0.0, 0.0, 1.0
TET no. 1:
0.5, 0.0, 0.0
0.0, 1.0, 0.0
0.5, 0.5, 0.0
0.0, 0.0, 1.0
TET no. 2:
0.0, 1.0, 0.0
0.5, 0.0, 0.0
0.0, 0.0, 0.0
0.0, 0.0, 1.0
doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30.vtk
-29
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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
1.0 0.0 0.0
0.5 0.0 0.0
0.0 0.0 1.0
0.0 1.0 0.0
0.0 0.0 0.0
CELLS 3 15
4 0 1 2 3
4 2 4 0 3
4 4 2 5 3
CELL_TYPES 3
10
10
10
CELL_DATA 3
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
2
doc/tetrahedron_refinements/2-edges/edge_01-30_refined/01-30_small.png
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doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31.txt
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TET no. 0:
0.0, 0.5, 0.0
0.0, 1.0, 0.0
0.5, 0.5, 0.0
0.0, 0.0, 1.0
TET no. 1:
0.5, 0.5, 0.0
0.0, 0.0, 0.0
0.0, 0.5, 0.0
0.0, 0.0, 1.0
TET no. 2:
0.0, 0.0, 0.0
0.5, 0.5, 0.0
1.0, 0.0, 0.0
0.0, 0.0, 1.0
doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31.vtk
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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
0.0 0.5 0.0
0.0 1.0 0.0
0.5 0.5 0.0
0.0 0.0 1.0
0.0 0.0 0.0
1.0 0.0 0.0
CELLS 3 15
4 0 1 2 3
4 2 4 0 3
4 4 2 5 3
CELL_TYPES 3
10
10
10
CELL_DATA 3
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
2
doc/tetrahedron_refinements/2-edges/edge_01-31_refined/01-31_small.png
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doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.png
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doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.pvsm
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doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.txt
-15
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@@ -1,15 +0,0 @@
TET no. 0:
0.0, 0.5, 0.5
0.0, 0.0, 1.0
0.5, 0.0, 0.5
0.0, 0.0, 0.0
TET no. 1:
0.5, 0.0, 0.5
0.0, 1.0, 0.0
0.0, 0.5, 0.5
0.0, 0.0, 0.0
TET no. 2:
0.0, 1.0, 0.0
0.5, 0.0, 0.5
1.0, 0.0, 0.0
0.0, 0.0, 0.0
doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20.vtk
-29
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@@ -1,29 +0,0 @@
# vtk DataFile Version 2.0
VTK LEGACY FILE FORMAT ASCII - tetrahedral sample file for H5FED test
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 6 DOUBLE
0.0 0.5 0.5
0.0 0.0 1.0
0.5 0.0 0.5
0.0 0.0 0.0
0.0 1.0 0.0
1.0 0.0 0.0
CELLS 3 15
4 0 1 2 3
4 2 4 0 3
4 4 2 5 3
CELL_TYPES 3
10
10
10
CELL_DATA 3
SCALARS cell_attribute_data float 1
LOOKUP_TABLE default
0
1
2
doc/tetrahedron_refinements/2-edges/edge_12-20_refined/12-20_small.png
BIN
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doc/tetrahedron_refinements/2-edges/edge_12-23_refined/12-23.png
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