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outside source build now possible, C API with inline functions, examples moved from 'test' directory to new 'example' directory

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This commit is contained in:
gsell
2013-05-16 12:46:37 +00:00
parent 22421d8d88
commit 72fa424a51
60 changed files with 2675 additions and 4780 deletions
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.gitattributes
+33 -43
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@@ -359,18 +359,41 @@ doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/buildlatex.ba
doc/tetrahedron_refinements/6-edges/edge_01-12-20-23-30-31_refined/output_file.jpg -text
doc/tetrahedron_refinements/README -text
doc/tetrahedron_refinements/text2vtk.py -text
examples/H5Block/BlockTestSpecs.txt -text
examples/H5Block/H5BlockDissolveGhosts.c -text
examples/H5Block/H5BlockParTestScalarField.c -text
examples/H5Block/H5BlockParTestScalarField.pbs -text
examples/H5Block/H5BlockParTestScalarFieldF.f90 -text
examples/H5Block/H5BlockTestAttributes.c -text
examples/H5Block/H5BlockTestAttributesF.f90 -text
examples/H5Block/Makefile.am -text
examples/H5Fed/Makefile.am -text
examples/H5Fed/map_tet2globalid.c -text
examples/H5Fed/map_triangle2globalid.c -text
examples/H5Fed/tetmesh_adjacencies.c -text
examples/H5Fed/tetmesh_read.c -text
examples/H5Fed/tetmesh_read_tags.c -text
examples/H5Fed/tetmesh_write.c -text
examples/H5Fed/tetmesh_write1.c -text
examples/H5Fed/tetmesh_write2.c -text
examples/H5Fed/tetmesh_write_tags.c -text
examples/H5Fed/trimesh_2gnuplot.c -text
examples/H5Fed/trimesh_adjacencies.c -text
examples/H5Fed/trimesh_read.c -text
examples/H5Fed/trimesh_write.c -text
examples/H5Fed/trimesh_write_dunetest.c -text
examples/H5Fed/write_boundary.c -text
examples/H5Part/Bench.c -text
examples/H5Part/H5ParallelTest.cc -text
examples/H5Part/H5PartAndreasTest.cc -text
examples/H5Part/H5PartTest.cc -text
examples/H5Part/H5PartTestParallel.cc -text
examples/H5Part/H5test.cc -text
examples/H5Part/H5testF.f -text
examples/H5Part/H5testFpar.f90 -text
examples/H5Part/Makefile.am -text
/license.txt -text
src/C++/H5Fed.cc -text
src/C++/H5Fed.hh -text
src/C++/Makefile.am -text
src/C/H5.c -text
src/C/H5Block.c -text
src/C/H5Block_readwrite.c -text
src/C/H5Part.c -text
src/C/H5_attachments.c -text
src/C/H5_attribs.c -text
src/C/Makefile.am -text
src/C/generate-h5b-readwrite.py -text
src/Fortran/H5.f90 -text
src/Fortran/H5Block.f90 -text
src/Fortran/H5Block_F.c -text
@@ -502,39 +525,6 @@ src/include/h5core/h5t_storemesh.h -text
src/include/h5core/h5t_tags.h -text
src/include/h5core/h5u_model.h -text
src/include/h5core/h5u_readwrite.h -text
test/H5Block/BlockTestSpecs.txt -text
test/H5Block/H5BlockDissolveGhosts.c -text
test/H5Block/H5BlockParTestScalarField.c -text
test/H5Block/H5BlockParTestScalarField.pbs -text
test/H5Block/H5BlockParTestScalarFieldF.f90 -text
test/H5Block/H5BlockTestAttributes.c -text
test/H5Block/H5BlockTestAttributesF.f90 -text
test/H5Block/Makefile.am -text
test/H5Fed/Makefile.am -text
test/H5Fed/map_tet2globalid.c -text
test/H5Fed/map_triangle2globalid.c -text
test/H5Fed/tetmesh_adjacencies.c -text
test/H5Fed/tetmesh_read.c -text
test/H5Fed/tetmesh_read_tags.c -text
test/H5Fed/tetmesh_write.c -text
test/H5Fed/tetmesh_write1.c -text
test/H5Fed/tetmesh_write2.c -text
test/H5Fed/tetmesh_write_tags.c -text
test/H5Fed/trimesh_2gnuplot.c -text
test/H5Fed/trimesh_adjacencies.c -text
test/H5Fed/trimesh_read.c -text
test/H5Fed/trimesh_write.c -text
test/H5Fed/trimesh_write_dunetest.c -text
test/H5Fed/write_boundary.c -text
test/H5Part/Bench.c -text
test/H5Part/H5ParallelTest.cc -text
test/H5Part/H5PartAndreasTest.cc -text
test/H5Part/H5PartTest.cc -text
test/H5Part/H5PartTestParallel.cc -text
test/H5Part/H5test.cc -text
test/H5Part/H5testF.f -text
test/H5Part/H5testFpar.f90 -text
test/H5Part/Makefile.am -text
test/Makefile.am -text
test/h5_attach_test.c -text
test/h5b_read.c -text
.gitignore
+27 -29
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@@ -15,14 +15,39 @@
/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++/Makefile
src/C++/Makefile.in
src/C/.deps
src/C/Makefile
src/C/Makefile.in
@@ -41,33 +66,6 @@ src/lib
/stamp-h1
/svn-prop.tmp
test/.deps
test/H5Block/H5BlockParTestScalarField
test/H5Block/H5BlockTestAttributes
test/H5Block/Makefile
test/H5Block/Makefile.in
test/H5Fed/.deps
test/H5Fed/Makefile
test/H5Fed/Makefile.in
test/H5Fed/large_tet.h5
test/H5Fed/simple_tet.h5
test/H5Fed/simple_triangle.h5
test/H5Fed/small_tet.h5
test/H5Fed/tetmesh_adjacencies
test/H5Fed/tetmesh_read
test/H5Fed/tetmesh_read_tags
test/H5Fed/tetmesh_write
test/H5Fed/tetmesh_write2
test/H5Fed/tetmesh_write_tags
test/H5Fed/trimesh_adjacencies
test/H5Fed/trimesh_read
test/H5Fed/trimesh_write
test/H5Fed/trimesh_write_dunetest
test/H5Part/Bench
test/H5Part/H5PartAndreasTest
test/H5Part/H5PartTestP
test/H5Part/H5test
test/H5Part/Makefile
test/H5Part/Makefile.in
test/Makefile
test/Makefile.in
test/h5_attach.h5
configure.ac
+110 -181
View File
@@ -1,53 +1,55 @@
# Every configure script must call AC_INIT before doing anything else.
# AC_INIT (package, version, [bug-report], [tarname])
AC_INIT([H5hut], [1.99.6], [h5part@lists.psi.ch], H5hut)
# 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_INIT([H5hut], [1.99-trunk], [h5part@lists.psi.ch], H5hut)
AC_PREREQ(2.60)
# 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
BUILD_LIBS='libH5hut'
USE_C='yes'
ENABLE_DEBUG='no'
ENABLE_C='yes'
ENABLE_FORTRAN='no'
ENABLE_PARALLEL='no'
###############################################################################
################# --enable-xxx and --with-xxx Argument ########################
###############################################################################
# --enable-xxx and --with-xxx Arguments
AC_ARG_ENABLE(
[debug],
[AC_HELP_STRING([--enable-debug],
[Compile with debug flags [default=no]])],
[USE_DEBUG=$enableval])
[AS_HELP_STRING([--enable-debug], [Compile with debug flags [default=no]])],
[ENABLE_DEBUG=$enableval])
AM_CONDITIONAL([ENABLE_DEBUG], [test "$ENABLE_DEBUG" = "yes"])
AC_ARG_ENABLE(
[c],
[AC_HELP_STRING([--enable-c],
[AS_HELP_STRING([--enable-c],
[Compile the C interface [default=yes]])],
[USE_C=$enableval])
[ENABLE_C=$enableval])
AM_CONDITIONAL([ENABLE_C], [test "$ENABLE_C" = "yes"])
AC_ARG_ENABLE(
[fortran],
[AC_HELP_STRING([--enable-fortran],
[AS_HELP_STRING([--enable-fortran],
[Compile the Fortran interface [default=no]])],
[USE_FORTRAN=$enableval])
[ENABLE_FORTRAN=$enableval])
AM_CONDITIONAL([ENABLE_FORTRAN], [test "$ENABLE_FORTRAN" = "yes"])
AC_ARG_ENABLE(
[parallel],
[AC_HELP_STRING([--enable-parallel],
[AS_HELP_STRING([--enable-parallel],
[Compile the MPI/IO interface [default=no]])],
[USE_PARALLEL=$enableval])
[ENABLE_PARALLEL=$enableval])
AM_CONDITIONAL([ENABLE_PARALLEL], [test "$ENABLE_PARALLEL" = "yes"])
AC_ARG_ENABLE(
[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 "$ENABLE_EXPERIMENTAL" = "yes"])
AC_ARG_ENABLE(
[vtkconverter],
@@ -58,27 +60,28 @@ AM_CONDITIONAL([ENABLE_VTKCONVERTER], [test "$ENABLE_VTKCONVERTER" = "yes"])
AC_ARG_WITH(
[hdf5],
[AC_HELP_STRING([--with-hdf5],
[AS_HELP_STRING([--with-hdf5],
[path to HDF5 installation [default=""]])],
[HDF5PATH=$withval], [HDF5PATH=""])
[HDF5_PREFIX=$withval], [HDF5_PREFIX=""])
AC_ARG_WITH(
[mpi],
[AC_HELP_STRING([--with-mpi],
[AS_HELP_STRING([--with-mpi],
[path to MPI installation [default=""]])],
[MPIPATH=$withval;PATH=$MPIPATH/bin:$PATH], [MPIPATH=""])
[PATH=$MPI_PREFIX/bin:$PATH])
AC_ARG_WITH(
[lustre],
[AC_HELP_STRING([--with-lustre],
[AS_HELP_STRING([--with-lustre],
[path to lustre user API [default=""]])],
[LUSTREPATH=$withval], [LUSTREPATH=""])
AC_ARG_WITH(
[vtk],
[AS_HELP_STRING([--with-vtk],
[path to VTK installation [default=""]])],
[VTK_PREFIX=$withval], [VTK_PREFIX=""])
[parmetis],
[AC_HELP_STRING([--with-parmetis],
[path to ParMETIS API [default=""]])],
[PARMETISPATH=$withval], [PARMETISPATH=""])
###############################################################################
############### PATH SERACH FUNCTION - to be used later... ####################
@@ -111,33 +114,27 @@ 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$USE_DEBUG" = "Xyes"; then
if test "X$ENABLE_DEBUG" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="$CFLAGS -g"
CFLAGS="$CFLAGS -g -Wall"
CXXFLAGS="$CFLAGS -g -Wall"
FFLAGS="$FFLAGS -g"
else
AC_MSG_RESULT([no])
fi
# Determine a C/C++ compiler to use.
# If 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$USE_PARALLEL" = "xyes"; then
CCOMPILERS="mpicc cc"
CXXCOMPILERS="mpic++ c++"
if test "x$ENABLE_PARALLEL" = "xyes"; then
CCOMPILERS="mpicc"
CXXCOMPILERS="mpic++"
else
CCOMPILERS="pgcc pathcc icc gcc cc_r cc"
CXXCOMPILERS="pgcc pathcc icc g++ cc_r c++"
@@ -148,17 +145,12 @@ CC=`which $CC`
AC_PROG_CXX($CXXCOMPILERS)
CXX=`which $CXX`
# Use macro to set C99 mode instead of checking for gcc, which breaks with
# parallel builds.
AC_PROG_CC_C99
if test "x$ac_cv_prog_cc_c99" = "xno"; then
AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
exit 1
fi
# 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
@@ -201,34 +193,27 @@ AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
###############################################################################
######################## CONFIGURE LINE OPTIONS ###############################
###############################################################################
# PROCESS ARGUMENTS
############################ fortran enabled ##################################
# C enabled?
AC_MSG_CHECKING([if C interface enabled])
if test "X$USE_C" = "Xyes"; then
if test "X$ENABLE_C" = "Xyes"; then
AC_MSG_RESULT([yes])
BINDINGS="$BINDINGS C"
LIB_C="libH5hutC.la"
BUILD_LIBS="$BUILD_LIBS libH5hutC"
BUILD_TESTS="$BUILD_TESTS h5u_test h5b_test"
BUILD_TOOLS="$BUILD_TOOLS h5hutcc"
else
AC_MSG_RESULT([no])
fi
############################ fortran enabled ##################################
# fortran enabled?
AC_MSG_CHECKING([if fortran interface enabled])
if test "X$USE_FORTRAN" = "Xyes"; then
if test "X$ENABLE_FORTRAN" = "Xyes"; then
AC_MSG_RESULT([yes])
BINDINGS="$BINDINGS Fortran"
LIB_FORTRAN="libH5hutF.la"
BUILD_LIBS="$BUILD_LIBS libH5hutF"
if test "X$USE_PARALLEL" = "Xyes"; then
if test "X$ENABLE_PARALLEL" = "Xyes"; then
AC_PROG_FC(mpif90 mpif77)
else
AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
fi
FC=`which $FC`
if test -z "$FC" ; then
AC_MSG_ERROR([Cannot find a Fortran compiler!])
exit 1
@@ -249,12 +234,11 @@ if test "X$USE_FORTRAN" = "Xyes"; then
`cd src/Fortran && ${FC} ${FFLAGS} -o TestUnderscore TestUnderscore.o TestUnderscoreC.o`
if test -f src/Fortran/TestUnderscore ; then
UNDERSCORE_H=Underscore.h
`cd src/Fortran && ./TestUnderscore > Underscore.h`
AC_MSG_RESULT([ok])
else
AC_MSG_RESULT([nok])
AC_MSG_ERROR([Cannot determine the symbon convention for Fortran object files!])
AC_MSG_ERROR([Cannot determine the symbol convention for Fortran object files!])
exit 1
fi
@@ -262,91 +246,54 @@ else
AC_MSG_RESULT([no])
fi
######################## large indices enabled ###########################
AC_MSG_CHECKING([if large indices are enabled])
if test "X$USE_LARGE_INDICES" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="${CFLAGS} -DUSE_LARGE_INDICES"
else
AC_MSG_RESULT([no])
fi
######################## parallel interface enabled ###########################
AC_MSG_CHECKING([if parallel interface enabled])
if test "X$USE_PARALLEL" = "Xyes"; then
if test "X$ENABLE_PARALLEL" = "Xyes"; then
AC_MSG_RESULT([yes])
AM_CPPFLAGS="${AM_CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
CFLAGS="${CFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
AC_MSG_CHECKING([for ParMETIS])
if test "X$PARMETISPATH" != "X"; then
AM_CPPFLAGS="$AM_CPPFLAGS -I$PARMETISPATH/include"
AM_LDFLAGS="$AM_LDFLAGS -L$PARMETISPATH/lib"
fi
AC_MSG_CHECKING([if we can compile MPI code without setting flags])
AC_TRY_LINK([#include "mpi.h"], [
MPI_Comm comm;
int n;
MPI_Comm_size( comm, &n ); ],
[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
if test "X$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
TPTARGET="${TPTARGET} H5PartTestP H5PartAndreasTest Bench"
TBTARGET="${TBTARGET} H5BlockTestAttributes"
TBTARGET="${TBTARGET} H5BlockParTestScalarField"
# parallel + fortran
if test "X$USE_FORTRAN" = "Xyes"; then
TPTARGET="${TPTARGET} H5testFpar"
TBTARGET="${TBTARGET} H5BlockParTestScalarFieldF"
fi
LIBS="$LIBS -lparmetis -lmetis"
AC_TRY_LINK([#include <parmetis.h>], [
ParMETIS_V3_PartGeom (NULL, NULL, NULL, NULL, NULL);],
[AC_MSG_RESULT([yes]); r='yes'], [AC_MSG_RESULT([no]); r='no'] )
if test "X$r" = "Xno"; then
AC_MSG_ERROR([ParMETIS])
exit 1
fi
fi
else # --enable-parallel=no
AC_MSG_RESULT([no])
TPTARGET="${TPTARGET} H5test"
TBTARGET="${TBTARGET} H5BlockTestAttributes"
if test "X$USE_FORTRAN" = "Xyes"; then
TPTARGET="${TPTARGET} H5testF"
TBTARGET="${TBTARGET} H5BlockTestAttributesF"
fi
fi
###############################################################################
######################### PATH CHECKING & SETTING #############################
###############################################################################
AC_MSG_CHECKING([for HDF5 root ])
AC_MSG_RESULT([])
if test -n "${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/hdf5"
P="$P /usr/local/packages/hdf5"
P="$P /apps/hdf5"
P="$P /opt/hdf5"
fi
PATH_Search HDF5ROOT "$P" include/hdf5.h
if test -z "$HDF5ROOT"; then
AC_MSG_ERROR([Cannot find an HDF5 library!])
exit 1
# LIBRARY PATHS
if test -n "${HDF5_PREFIX}" ; then
AM_CPPFLAGS="$AM_CPPFLAGS -I$HDF5_PREFIX/include"
AM_LDFLAGS="$AM_LDFLAGS -L$HDF5_PREFIX/lib"
fi
AC_CHECK_LIB([z], [compress2])
AC_CHECK_LIB([hdf5], [H5open])
AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes],
[AC_MSG_ERROR([Cannot compile and link a HDF5 program]);
exit 1])
AM_CPPFLAGS="$AM_CPPFLAGS -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
AC_MSG_CHECKING([for lustre API ])
AC_MSG_RESULT([])
@@ -370,12 +317,12 @@ 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"
AM_CPPFLAGS=="$AM_CPPFLAGS -I$LUSTREROOT/usr/include"
LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
AM_CPPFLAGS="$AM_CPPFLAGS -I$LUSTREROOT/usr/include"
AM_LDFLAGS="$AM_LDFLAGS -L$LUSTREROOT/usr/lib"
LIBS="$LIBS -llustreapi"
fi
LIBS="$LIBS -lz -lm"
LIBS="$LIBS -lm"
###############################################################################
# TOOLS
@@ -388,39 +335,25 @@ else
fi
###############################################################################
############## EXPORTING VARIABLES & CREATING OUTPUT FILES ####################
###############################################################################
# AC_SUBST (variable, [value])
# Create an output variable from a shell variable. Make AC_OUTPUT substitute
# the variable variable into output files (typically one or more `Makefile's).
# This means that AC_OUTPUT will replace instances of `@variable@' in input
# files with the value that the shell variable variable has when AC_OUTPUT is
# called. This value of variable should not contain literal newlines. If
# value is given, in addition assign it to variable.
AC_SUBST(HDF5ROOT)
AC_SUBST(LUSTREROOT)
# EXPORTING VARIABLES & CREATING OUTPUT FILES
AC_SUBST(HDF5_PREFIX)
AC_SUBST(CFLAGS)
AC_SUBST(FFLAGS)
AC_SUBST(AM_CPPFLAGS)
AC_SUBST(LDFLAGS)
AC_SUBST(LIBS)
AC_SUBST(UNDERSCORE_H)
AC_SUBST(LIB_C)
AC_SUBST(LIB_FORTRAN)
AC_SUBST(BINDINGS)
AC_SUBST(BUILD_TESTS)
AC_SUBST(BUILD_TOOLS)
AC_SUBST(AM_LDFLAGS)
# Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'),
# substituting the output variable values.
AC_CONFIG_FILES([
Makefile
src/Makefile
src/C/Makefile
src/h5core/Makefile
src/include/Makefile
src/C/Makefile
src/Fortran/Makefile
test/Makefile
test/H5Fed/Makefile
doc/Makefile
examples/H5Part/Makefile
examples/H5Block/Makefile
examples/H5Fed/Makefile
tools/Makefile
tools/h5hutcc
tools/vtk2h5grid/Makefile
@@ -429,25 +362,21 @@ AC_CONFIG_FILES([
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([FFLAGS = $FFLAGS])
AC_MSG_RESULT([INCLUDES = $INCLUDES])
AC_MSG_RESULT([LDFLAGS = $LDFLAGS])
AC_MSG_RESULT([AM_CPPFLAGS = $AM_CPPFLAGS])
AC_MSG_RESULT([AM_LDFLAGS = $AM_LDFLAGS])
AC_MSG_RESULT([LIBS = $LIBS])
AC_MSG_RESULT([HDF5ROOT = $HDF5ROOT])
AC_MSG_RESULT([HDF5_PREFIX = $HDF5_PREFIX])
AC_MSG_RESULT([LUSTREROOT = $LUSTREROOT])
AC_MSG_RESULT([ ])
test/H5Block/BlockTestSpecs.txt → examples/H5Block/BlockTestSpecs.txt
View File
test/H5Block/H5BlockDissolveGhosts.c → examples/H5Block/H5BlockDissolveGhosts.c
View File
test/H5Block/H5BlockParTestScalarField.c → examples/H5Block/H5BlockParTestScalarField.c
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test/H5Block/H5BlockParTestScalarField.pbs → examples/H5Block/H5BlockParTestScalarField.pbs
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test/H5Block/H5BlockParTestScalarFieldF.f90 → examples/H5Block/H5BlockParTestScalarFieldF.f90
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test/H5Block/H5BlockTestAttributes.c → examples/H5Block/H5BlockTestAttributes.c
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test/H5Block/H5BlockTestAttributesF.f90 → examples/H5Block/H5BlockTestAttributesF.f90
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test/H5Block/Makefile.am → examples/H5Block/Makefile.am
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test/H5Fed/Makefile.am → examples/H5Fed/Makefile.am
+1 -4
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@@ -1,10 +1,7 @@
# test level Makefile.am
OBJEXT = o
AM_LDFLAGS = -L../../src/lib @LDFLAGS@
LIBS = -lH5hutC -lH5hut @LIBS@
AM_CPPFLAGS = -I../../src/include @AM_CPPFLAGS@
AM_CPPFLAGS += -I$(top_srcdir)/src/include
noinst_PROGRAMS = \
tetmesh_write \
test/H5Fed/map_tet2globalid.c → examples/H5Fed/map_tet2globalid.c
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test/H5Fed/map_triangle2globalid.c → examples/H5Fed/map_triangle2globalid.c
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test/H5Fed/tetmesh_adjacencies.c → examples/H5Fed/tetmesh_adjacencies.c
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test/H5Fed/tetmesh_read.c → examples/H5Fed/tetmesh_read.c
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test/H5Fed/tetmesh_read_tags.c → examples/H5Fed/tetmesh_read_tags.c
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test/H5Fed/tetmesh_write.c → examples/H5Fed/tetmesh_write.c
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test/H5Fed/tetmesh_write1.c → examples/H5Fed/tetmesh_write1.c
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test/H5Fed/tetmesh_write2.c → examples/H5Fed/tetmesh_write2.c
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test/H5Fed/tetmesh_write_tags.c → examples/H5Fed/tetmesh_write_tags.c
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test/H5Fed/trimesh_2gnuplot.c → examples/H5Fed/trimesh_2gnuplot.c
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test/H5Fed/trimesh_adjacencies.c → examples/H5Fed/trimesh_adjacencies.c
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test/H5Fed/trimesh_read.c → examples/H5Fed/trimesh_read.c
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test/H5Fed/trimesh_write.c → examples/H5Fed/trimesh_write.c
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test/H5Fed/trimesh_write_dunetest.c → examples/H5Fed/trimesh_write_dunetest.c
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test/H5Fed/write_boundary.c → examples/H5Fed/write_boundary.c
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test/H5Part/Bench.c → examples/H5Part/Bench.c
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test/H5Part/H5ParallelTest.cc → examples/H5Part/H5ParallelTest.cc
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test/H5Part/H5PartAndreasTest.cc → examples/H5Part/H5PartAndreasTest.cc
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test/H5Part/H5PartTest.cc → examples/H5Part/H5PartTest.cc
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test/H5Part/H5PartTestParallel.cc → examples/H5Part/H5PartTestParallel.cc
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test/H5Part/H5test.cc → examples/H5Part/H5test.cc
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test/H5Part/H5testF.f → examples/H5Part/H5testF.f
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test/H5Part/H5testFpar.f90 → examples/H5Part/H5testFpar.f90
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test/H5Part/Makefile.am → examples/H5Part/Makefile.am
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src/C++/H5Fed.cc
-193
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@@ -1,193 +0,0 @@
/*
Implementation file for implementing the H5Fed application programming
interface (API) in the C++ language.
Copyright 2006-2007
Paul Scherrer Institut, Villigen, Switzerland;
Benedikt Oswald;
Achim Gsell
All rights reserved.
Authors
Benedikt Oswald, Achim Gsell
Warning
This code is under development.
*/
/*!
Some conventions:
Functions:
Name:
ThisIsAFunction()
Return values:
-1 or NULL signals an error
\note
In function names we use the words \b get and \b store insteed of
\b read and \b write, because no I/O is actually done in these
functions.
*/
/** include proprietary header files */
#include "H5Fed.hh"
/** \brief make the C API functions available so that
* we can used them in the implementation of the H5Fed class
* member functions implementations.
*/
//extern "C"
//{
// #include "../../H5Fed.h"
//}
/** activate namespaces */
using namespace std;
namespace H5Fed
{
/*!
\defgroup h5fed_cpp_api H5Fed CPP API
*/
/** \brief implement constructor without arguments */
H5Fed::H5Fed()
{
/** initialize internal variables */
filename_.erase();
}
/** \brief implement constructor without arguments */
H5Fed::H5Fed(std::string filename)
{
/** initialize internal variables */
filename_.erase();
filename_.append(filename);
}
/** \brief implement constructor */
H5Fed::~H5Fed()
{
/** initialize internal variables */
filename_.erase();
}
/** \brief Set name of H5Fed file to be accessed */
H5FED_RETURN_CODE H5Fed::filename(std::string filename)
{
/** initialize internal variables */
filename_.erase();
filename_.append(filename);
return(OKCODE);
}
/** \brief retrieve name of H5Fed file to be accessed */
std::string H5Fed::filename()
{
return(filename_);
}
/*!
\ingroup h5fed_cpp_api
Open file. This function is available in the paralell
and serial version. In the serial case \c comm may have any value.
\return
\return
\note
File is always opened in read/writer mode!
\note
Implement as wrapper of \c H5_open_file()!
*/
H5FED_RETURN_CODE H5Fed::open_file()
{
return(OKCODE);
}
/*!
\ingroup h5fed_cpp_api
Close file. This function is available in the paralell
and serial version. In the serial case \c comm may have
any value.
\return
\return
\note
File is always opened in read/writer mode!
\note
Implement as wrapper of \c H5_open_file()!
*/
H5FED_RETURN_CODE H5Fed::closeFile()
{
return(OKCODE);
}
/****** STORE routines*****************************************************/
/*!
\ingroup h5fed_c_api
Stores the the coordinates of a specific vertex at level \c level
with id \c vertex_id of the tetrahedral mesh.
\return value \c >=0 on success
\return \c -1 on error
*/
H5FED_RETURN_CODE H5Fed::storeVertexCoordinate(
unsigned int level, /*!< mesh level */
unsigned int vertex_id, /*!< global vertex id */
std::vector<double> /*!< 3-tuple of coordinates */
)
{
return(OKCODE);
}
/*!
\ingroup h5fed_c_api
Stores the 4-tuple, that contains the specific indices describing
a tetrahedron with id \c tet_id at level \c level of the tetrahedral
mesh.
\return value \c >=0 on success
\return \c -1 on error
*/
H5FED_RETURN_CODE H5Fed::H5FedStoreTetrahedron (
const unsigned int level, /*!< mesh level */
const unsigned int tet_id, /*!< global tetrahedron id */
const unsigned int parent_id, /*!< parent id if level \c >0 else \x -1 */
const std::vector<unsigned int> tet /*!< 4-tuple with vertex id's */
)
{
return(OKCODE);
}
}
src/C++/H5Fed.hh
-165
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@@ -1,165 +0,0 @@
/*
Header file for declaring the H5Fed application programming
interface (API) in the C++ language. The header files follows
the declaration of the C application programming interface.
Copyright 2006-2007
Paul Scherrer Institut, Villigen, Switzerland;
Benedikt Oswald;
Achim Gsell
All rights reserved.
Authors
Benedikt Oswald, Achim Gsell
Warning
This code is under development.
*/
/*!
Some conventions:
Functions:
Name:
ThisIsAFunction()
Return values:
-1 or NULL signals an error
\note
In function names we use the words \b get and \b store insteed of
\b read and \b write, because no I/O is actually done in these
functions.
*/
/** include standard header files */
#include <iostream>
#include <ostream>
#include <iterator>
#include <fstream>
#include <vector>
#include <iomanip>
#include <string>
#include <complex>
/** include fundamental HDF5 header files */
#include <hdf5.h>
#ifndef H5FED_HH
#define H5FED_HH
namespace H5Fed
{
/** \brief Define return codes */
enum H5FED_RETURN_CODE{OKCODE=0,ERROR=-1};
class H5Fed
{
public:
/** \brief infrastructure routines */
H5Fed(); /** \brief Constructor without argument */
H5Fed(std::string filename); /** \brief Constructor without argument */
~H5Fed(); /** \brief Class destructor */
H5FED_RETURN_CODE filename(std::string filename); /** \brief Set name of H5Fed file to be accessed */
std::string filename(); /** \brief retrieve name of H5Fed file to be accessed */
/****** General routines *****************************************************/
H5FED_RETURN_CODE open_file(); /** \brief open the file */
H5FED_RETURN_CODE closeFile(); /** \brief close the file */
/****** INQUIRY routines *****************************************************/
/****** STORE routines*****************************************************/
/*!
\ingroup h5fed_c_api
Stores the the coordinates of a specific vertex at level \c level
with id \c vertex_id of the tetrahedral mesh.
\return value \c >=0 on success
\return \c -1 on error
*/
H5FED_RETURN_CODE storeVertexCoordinate(
unsigned int level, /*!< mesh level */
unsigned int vertex_id, /*!< global vertex id */
std::vector<double> /*!< 3-tuple of coordinates */
);
/*!
\ingroup h5fed_c_api
Stores the 4-tuple, that contains the specific indices describing
a tetrahedron with id \c tet_id at level \c level of the tetrahedral
mesh.
\return value \c >=0 on success
\return \c -1 on error
*/
H5FED_RETURN_CODE H5FedStoreTetrahedron (
const unsigned int level, /*!< mesh level */
const unsigned int tet_id, /*!< global tetrahedron id */
const unsigned int parent_id, /*!< parent id if level \c >0 else \x -1 */
const std::vector<unsigned int> tet /*!< 4-tuple with vertex id's */
);
/****** UPWARD ADJACENCY routines *********************************************/
/****** DOWNWARD ADJACENCY routines *********************************************/
/****** routines for accessing degrees of freedom DoF *************************/
protected:
private:
/** book keeping */
std::string filename_; /** \brief Name of H5Fed file to be accessed */
};
}
#endif /** H5FED_HH */
src/C++/Makefile.am
-18
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@@ -1,18 +0,0 @@
# COMPILERS
CC = @CC@
CXX = @CXX@
LIBS = @LIBS@
AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
OBJEXT = o
lib_LIBRARIES = libH5XX.a
include_HEADERS = H5Fed.hh
libH5XX_a_SOURCES = H5Fed.cc
libH5XX.a: $(libH5XX_a_OBJECTS)
${AR} rucs $@ $^
%.o : %.cc
$(CXX) $(CFLAGS) $(INC) -c $<
src/C/H5.c
-379
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@@ -1,379 +0,0 @@
/*
Copyright 2007-2008
Paul Scherrer Institut, Villigen, Switzerland;
Benedikt Oswald;
Achim Gsell
All rights reserved.
Authors
Achim Gsell
Warning
This code is under development.
*/
/*!
Some conventions:
Functions:
Name:
thisIsAFunction()
Return values:
negative value or NULL signals an error
Macros:
UPPERCASE_WITH_UNDERSCORE
\note
In function names we use the words \b get and \b store insteed of
\b read and \b write, because no I/O is actually done in these
functions.
*/
#include "h5core/h5_core.h"
#include "H5.h"
/****** General routines *****************************************************/
/*!
\ingroup h5hut_file
Open file with name \c filbename. This function is available in the parallel
and serial version. In the serial case \c comm may have any value.
File mode flags are:
- H5_O_RDONLY: only reading allowed
- H5_O_WRONLY: create new file, dataset must not exist
- H5_O_APPEND: allows to append a new datasets to an existing file
- H5_O_RDWR: dataset may exist
You can also select a "virtual file driver" in the HDF5 layer using:
- H5_VFD_INDEPENDENT: MPI-IO in independent (asynchronous) mode
- H5_VFD_MPIPOSIX: parallel I/O implemented directly by HDF5, bypassing MPI-IO
\return File handle.
\return NULL on error.
*/
h5_file_p
H5OpenFile (
const char* filename, /*!< file name */
h5_int32_t flags, /*!< file open flags */
MPI_Comm comm /*!< MPI communicator */
) {
H5_API_ENTER (h5_file_p, "filename='%s', flags=%d, ...",filename,flags);
H5_API_RETURN (h5_open_file (filename, flags, comm, 0));
}
/*!
\ingroup h5hut_file
Close file and free all memory associated with the file handle.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5CloseFile (
h5_file_t* const f /*!< file handle */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_close_file (f));
}
/*!
\ingroup h5hut_file
Verify that the file handle points to a valid H5hut file structure.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5CheckFile (
h5_file_t* const f /*!< file handle */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_check_filehandle (f));
}
h5_err_t
H5FlushStep (
h5_file_t* const f /*!< file handle */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_flush_step (f));
}
h5_err_t
H5FlushFile (
h5_file_t* const f /*!< file handle */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_flush_file (f));
}
/*!
\ingroup h5hut_model
Define format of the step names.
Example: ==H5SetStepNameFormat( f, "Step", 6 )== defines step names
like ==Step#000042==.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5SetStepNameFormat (
h5_file_t* const f, /*!< Handle to file */
const char* name, /*!< Prefix */
const h5_int64_t width /*!< Width of the number */
) {
H5_API_ENTER (h5_err_t,
"f=%p, name='%s', width=%lld",
f, name, (long long) width);
H5_API_RETURN (h5_set_stepname_fmt (f, name, width));
}
/*!
\ingroup h5hut_model
Get format of the step names.
\return value \c >=0 on success
\return -1 on error
*/
h5_err_t
H5GetStepNameFormat (
h5_file_t* const f, /*!< Handle to file */
char* name, /*!< OUT: Prefix */
const h5_size_t l_name, /*!< length of buffer name */
int* width /*!< OUT: Width of the number */
) {
H5_API_ENTER (h5_err_t,
"f=%p, name=%p, l_name=%llu, width=%p",
f, name, (unsigned long long)l_name, width);
H5_API_RETURN (h5_get_stepname_fmt (f, name, l_name, width));
}
/*!
\ingroup h5hut_model
Set the current step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5SetStep (
h5_file_t* const f, /*!< [in] Handle to open file */
const h5_id_t step /*!< [in] Step to set. */
) {
H5_API_ENTER (h5_err_t, "f=%p, step=%lld", f, (long long)step);
H5_API_RETURN (h5_set_step (f, step));
}
/*!
\ingroup h5hut_model
Get current step.
\return \c H5_SUCCESS or error code
*/
h5_id_t
H5GetStep (
h5_file_t* const f /*!< Handle to open file */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_get_step (f));
}
/*!
\ingroup h5hut_file
Get the number of processors.
\param[in] f File handle.
\return Number of processors.
\return \c -1 on error.
*/
int
H5GetNumProcs (
h5_file_t* const f
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_get_num_procs(f));
}
/*!
\ingroup h5hut_model
Get the number of time-steps that are currently stored in the file
\c f.
It works for both reading and writing of files, but is probably
only typically used when you are reading.
\param[in] f File handle.
\return number of time-steps or error code
*/
h5_ssize_t
H5GetNumSteps (
h5_file_t* const f
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_get_num_steps(f));
}
/*!
\ingroup h5_inquiry
Query whether a particular step already exists in the file.
\param[in] f File handle.
\param[in] stepno Step number to query for existence
\return true or false
*/
h5_err_t
H5HasStep (
h5_file_t* const f,
h5_id_t stepno
) {
H5_API_ENTER (h5_err_t,
"f=%p, stepno=%lld",
f, (long long)stepno);
H5_API_RETURN (h5_has_step (f, stepno));
}
/*!
\ingroup h5hut_model
Start traversing steps.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5StartTraverseSteps (
h5_file_t* const f /*!< Handle to open file */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_start_traverse_steps (f));
}
/*!
\ingroup h5hut_model
Traverse steps.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5TraverseSteps (
h5_file_t* const f /*!< Handle to open file */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_traverse_steps (f));
}
/*!
\ingroup h5hut_file
Set the `throttle` factor, which causes HDF5 write and read
calls to be issued in that number of batches.
This can prevent large concurrency parallel applications that
use independent writes from overwhelming the underlying
parallel file system.
Throttling only works with the H5_VFD_MPIPOSIX or
H5_VFD_INDEPENDENT drivers and is only available in
the parallel library.
\return \c H5_SUCCESS
*/
#ifdef PARALLEL_IO
h5_err_t
H5SetThrottle (
h5_file_t* f,
int factor
) {
H5_API_ENTER (h5_err_t, "f=%p, factor=%d", f, factor);
H5_API_RETURN (h5_set_throttle(f, factor));
}
#endif // PARALLEL_IO
/*!
\ingroup h5hut_error
Set verbosity level to \c level.
\return \c H5_SUCCESS
*/
h5_err_t
H5SetVerbosityLevel (
const h5_id_t level
) {
return h5_set_debuglevel (level);
}
/*!
\ingroup h5hut_error
Set error handler to \c handler.
\return \c H5_SUCCESS
*/
h5_err_t
H5SetErrorHandler (
h5_errorhandler_t handler
) {
H5_API_ENTER (h5_err_t, "handler=%p", handler);
H5_API_RETURN (h5_set_errorhandler (handler));
}
/*!
\ingroup h5hut_error
Get current error handler.
\return Pointer to error handler.
*/
h5_errorhandler_t
H5GetErrorHandler (
void
) {
H5_API_ENTER (h5_errorhandler_t, "%s", "void");
H5_API_RETURN (h5_get_errorhandler());
}
h5_err_t
H5ReportErrorhandler (
const char* fmt,
va_list ap
) {
return h5_report_errorhandler (fmt, ap);
}
h5_err_t
H5AbortErrorhandler (
const char* fmt,
va_list ap
) {
return h5_abort_errorhandler (fmt, ap);
}
/*!
\ingroup h5hut_error
Get last error code.
\return error code
*/
h5_err_t
H5GetErrno (
void
) {
return h5_get_errno ();
}
src/C/H5Block.c
-676
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@@ -1,676 +0,0 @@
/*!
\defgroup h5block_c_api H5Block C API
*/
/*!
\internal
\defgroup h5block_kernel H5Block Kernel
*/
/*!
\internal
\defgroup h5block_private H5Block Private
*/
/*!
\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
*/
/*!
\note
Different field sizes are allowed in the same time-step.
\note
The same layout can be used, if the size of the field matches the
size of the layout. If the size of the layout doesn't match the
size of the field, an error will be indicated.
\note
In write mode partitions are shrinked to make them non-overlaping. This
process may shrink the partitions more than required.
\note
In read-mode partitions may not cross boundaries. This means, if the grid
size is (X, Y, Z), all partitions must fit into this grid.
\todo
check whether layout is reasonable
API function names
*/
#include <stdlib.h>
#include <string.h>
#include "H5hut.h"
#include "h5core/h5_core.h"
/********************** defining the layout **********************************/
/*!
\ingroup h5block_model
Tests whether a view has been set, either directly with
\ref H5Block3dSetView or indirectly with \ref H5Block3dSetGrid.
\return 0 on false, 1 on true
*/
h5_int64_t
H5Block3dHasView (
h5_file_t *const f /*!< IN: File handle */
) {
H5_API_ENTER (h5_int64_t, "f=%p", f);
H5_API_RETURN (h5b_3d_has_view (f));
}
/*!
\ingroup h5block_model
Defines the partition of the field that this processor owns, using
Fortran ordering: the fastest moving index is \c i.
This routine uses an MPI_Allgather, so at large concurrency it should
be called as infrequently as possible. For instance, if several timesteps
use the same field dimensions, set the layout only once before the
first timestep.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dSetView (
h5_file_t *const f, /*!< IN: File handle */
const h5_int64_t i_start, /*!< IN: start index of \c i */
const h5_int64_t i_end, /*!< IN: end index of \c i */
const h5_int64_t j_start, /*!< IN: start index of \c j */
const h5_int64_t j_end, /*!< IN: end index of \c j */
const h5_int64_t k_start, /*!< IN: start index of \c k */
const h5_int64_t k_end /*!< IN: end index of \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"i_start=%lld, i_end=%lld, "
"j_start=%lld, j_end=%lld, "
"k_start=%lld, k_end=%lld",
f,
(long long)i_start, (long long)i_end,
(long long)j_start, (long long)j_end,
(long long)k_start, (long long)k_end);
H5_API_RETURN (h5b_3d_set_view(f, i_start, i_end, j_start, j_end, k_start, k_end));
}
/*!
\ingroup h5block_model
Return the view of this processor.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dGetView (
h5_file_t *const f, /*!< IN: File handle */
h5_size_t *i_start, /*!< OUT: start index of \c i */
h5_size_t *i_end, /*!< OUT: end index of \c i */
h5_size_t *j_start, /*!< OUT: start index of \c j */
h5_size_t *j_end, /*!< OUT: end index of \c j */
h5_size_t *k_start, /*!< OUT: start index of \c k */
h5_size_t *k_end /*!< OUT: end index of \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"i_start=%p, i_end=%p, "
"j_start=%p, j_end=%p, "
"k_start=%p, k_end=%p",
f,
i_start, i_end,
j_start, j_end,
k_start, k_end);
H5_API_RETURN (h5b_3d_get_view (f, i_start, i_end, j_start, j_end, k_start, k_end));
}
/*!
\ingroup h5block_model
Return the reduced (ghost-zone free) view of this processor.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dGetReducedView (
h5_file_t *const f, /*!< IN: File handle */
h5_size_t *const i_start, /*!< OUT: start index of \c i */
h5_size_t *const i_end, /*!< OUT: end index of \c i */
h5_size_t *const j_start, /*!< OUT: start index of \c j */
h5_size_t *const j_end, /*!< OUT: end index of \c j */
h5_size_t *const k_start, /*!< OUT: start index of \c j */
h5_size_t *const k_end /*!< OUT: end index of \c j */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"i_start=%p, i_end=%p, "
"j_start=%p, j_end=%p, "
"k_start=%p, k_end=%p",
f,
i_start, i_end,
j_start, j_end,
k_start, k_end);
H5_API_RETURN (h5b_3d_get_reduced_view(f, i_start, i_end, j_start, j_end, k_start, k_end));
}
/*!
\ingroup h5block_model
Define the chunk dimensions and enable chunking in the underlying
HDF5 dataset.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dSetChunk (
h5_file_t *const f, /*!< IN: File handle */
const h5_size_t i, /*!< IN: size of \c i */
const h5_size_t j, /*!< IN: size of \c j */
const h5_size_t k /*!< IN: size of \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%llu, j=%llu, k=%llu",
f,
(long long unsigned)i,
(long long unsigned)j,
(long long unsigned)k);
H5_API_RETURN (h5b_3d_set_chunk(f, i, j, k));
}
/*!
\ingroup h5block_model
Lookup the chunk dimensions of the underlying HDF5 dataset.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dGetChunk (
h5_file_t *const f, /*!< IN: File handle */
const char *field_name, /*!< IN: name of dataset */
h5_size_t *const i, /*!< OUT: size of \c i */
h5_size_t *const j, /*!< OUT: size of \c j */
h5_size_t *const k /*!< OUT: size of \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%p, j=%p, k=%p",
f, i, j, k);
H5_API_RETURN (h5b_3d_get_chunk(f, field_name, i, j, k));
}
#ifdef PARALLEL_IO
/*!
\ingroup h5block_model
Define an underlying 3D Cartesian grid on the processors with dimensions
(\c i,\c j,\c k). You can look up a processor's index into the grid
using \ref H5Block3dGetGridCoords.
This function can be used in conjunction with \ref H5Block3dSetDims
to setup the view for a regular grid.
The product of the dimensions must equal the size of the MPI communicator.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dSetGrid (
h5_file_t *const f, /*!< IN: File handle */
const h5_size_t i, /*!< IN: dimension in \c i */
const h5_size_t j, /*!< IN: dimension in \c j */
const h5_size_t k /*!< IN: dimension in \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%llu, j=%llu, k=%llu",
f,
(long long unsigned)i,
(long long unsigned)j,
(long long unsigned)k);
H5_API_RETURN (h5b_3d_set_grid(f, i, j, k));
}
/*!
\ingroup h5block_model
Look up the index (\c i, \c j, \c k) in the grid belonging to MPI processor
\c proc.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dGetGridCoords (
h5_file_t *const f, /*!< IN: File handle */
const int proc, /*!< IN: MPI processor */
h5_int64_t *i, /*!< OUT: index in \c i */
h5_int64_t *j, /*!< OUT: index in \c j */
h5_int64_t *k /*!< OUT: index in \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, proc=%d, i=%p, j=%p, k=%p",
f, proc, i, j, k);
H5_API_RETURN (h5b_3d_get_grid_coords(f, proc, i, j, k));
}
/*!
\ingroup h5block_model
Set the dimensions of each processor's block when the field is a regular
grid.
A grid must be already set with \ref H5Block3dSetGrid, and all processors
must specify the same dimensions.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dSetDims (
h5_file_t *const f, /*!< IN: File handle */
const h5_size_t i, /*!< IN: dimension in \c i */
const h5_size_t j, /*!< IN: dimension in \c j */
const h5_size_t k /*!< IN: dimension in \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%llu, j=%llu, k=%llu",
f,
(long long unsigned)i,
(long long unsigned)j,
(long long unsigned)k);
H5_API_RETURN (h5b_3d_set_dims(f, i, j, k));
}
#endif
/*!
\ingroup h5block_model
Sets the additional cells (\c i, \c j, \c k) in each direction to use as
the `halo` region (or `ghost zone`) that overlaps between neighboring
processors on the grid.
A grid with dimensions must already be set with \ref H5Block3dSetGrid and
\ref H5Block3dSetDims, and all processors must specify the same halo radii.
\return \c H5_SUCCESS on success
*/
h5_err_t
H5Block3dSetHalo (
h5_file_t *const f, /*!< IN: File handle */
const h5_size_t i, /*!< IN: radius in \c i */
const h5_size_t j, /*!< IN: radius in \c j */
const h5_size_t k /*!< IN: radius in \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%llu, j=%llu, k=%llu",
f,
(long long unsigned)i,
(long long unsigned)j,
(long long unsigned)k);
H5_API_RETURN (h5b_3d_set_halo(f, i, j, k));
}
/*!
\ingroup h5block_model
Query number of fields in current time step.
\return \c H5_SUCCESS or error code
*/
h5_ssize_t
H5BlockGetNumFields (
h5_file_t *const f /*!< IN: file handle */
) {
H5_API_ENTER (h5_ssize_t, "f=%p", f);
H5_API_RETURN (h5b_get_num_fields(f));
}
/*!
\ingroup h5block_model
Get the name, rank and dimensions of the field specified by the
index \c idx.
\c elem_rank reports the rank of the elements in the field
(e.g. scalar or vector).
This function can be used to retrieve all fields bound to the
current time-step by looping from \c 0 to the number of fields
minus one. The number of fields bound to the current time-step
can be queried by calling the function \ref H5BlockGetNumFields.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockGetFieldInfo (
h5_file_t *const f, /*!< IN: file handle */
const h5_size_t idx, /*!< IN: index of field */
char *name, /*!< OUT: field name */
const h5_size_t len_name, /*!< IN: buffer size */
h5_size_t *field_rank, /*!< OUT: field rank */
h5_size_t *field_dims, /*!< OUT: field dimensions */
h5_size_t *elem_rank, /*!< OUT: element rank */
h5_int64_t *type /*!< OUT: datatype */
) {
H5_API_ENTER (h5_err_t,
"f=%p, idx=%llu, "
"name=%p, len_name=%llu, "
"field_rank=%p, field_dims=%p, elem_rank=%p, type=%p",
f, (long long unsigned)idx,
name, (long long unsigned)len_name,
field_rank, field_dims, elem_rank,
type);
H5_API_RETURN (
h5b_get_field_info (
f,
idx,
name,
len_name,
field_rank,
field_dims,
elem_rank,
type));
}
/*!
\ingroup h5block_model
Get the rank and dimensions of the field specified by its name.
See \ref H5BlockGetFieldInfo.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockGetFieldInfoByName (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: field name */
h5_size_t *field_rank, /*!< OUT: field rank */
h5_size_t *field_dims, /*!< OUT: field dimensions */
h5_size_t *elem_rank, /*!< OUT: element rank */
h5_int64_t *type /*!< OUT: datatype */
) {
H5_API_ENTER (h5_err_t,
"f=%p, name='%s', "
"field_rank=%p, field_dims=%p, elem_rank=%p, type=%p",
f, name, field_rank, field_dims, elem_rank, type);
H5_API_RETURN (
h5b_get_field_info_by_name (
f,
name,
field_rank,
field_dims,
elem_rank,
type));
}
/********************** reading and writing attribute ************************/
/*!
\ingroup h5block_attrib
Write the string \c value as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockWriteFieldAttribString (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const char *buffer /*!< IN: attribute value */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"field_name='%s', "
"attrib_name='%s', "
"buffer='%s'",
f,
field_name,
attrib_name,
buffer);
H5_API_RETURN (
h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_CHAR,
buffer,
strlen(buffer) + 1));
}
/*!
\ingroup h5block_attrib
Read the string value from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockReadFieldAttribString (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
char *buffer /*!< OUT: attribute value */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"field_name='%s', "
"attrib_name='%s', "
"buffer=%p",
f,
field_name,
attrib_name,
buffer);
H5_API_RETURN (
h5_read_field_attrib (
f,
field_name,
attrib_name,
H5_STRING_T,
(void*)buffer));
}
/*!
\ingroup h5block_attrib
Query the number of attributes of field \c field_name.
\return number of attributes or error code
*/
h5_ssize_t
H5BlockGetNumFieldAttribs (
h5_file_t *const f, /*<! IN: file handle */
const char *field_name /*<! IN: field name */
) {
H5_API_ENTER (h5_ssize_t, "f=%p, field_name='%s'", f, field_name);
H5_API_RETURN (h5b_get_num_field_attribs (f, field_name));
}
/*!
\ingroup h5block_attrib
Gets the name, type and number of elements of the field attribute
specified by its index.
This function can be used to retrieve all attributes bound to the
specified field by looping from \c 0 to the number of attribute
minus one. The number of attributes bound to the
field can be queried by calling \ref H5BlockGetNumFieldAttribs.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockGetFieldAttribInfo (
h5_file_t *const f, /*<! IN: Handle to open file */
const char *field_name, /*<! IN: field name */
const h5_size_t attrib_idx, /*<! IN: Index of attribute to
get infos about */
char *attrib_name, /*<! OUT: Name of attribute */
const h5_size_t len_attrib_name,
/*<! IN: length of buffer \c name */
h5_int64_t *attrib_type, /*<! OUT: Type of value. */
h5_size_t *attrib_nelem /*<! OUT: Number of elements */
) {
H5_API_ENTER (h5_err_t,
"f=%p field_name='%s', "
"attrib_idx=%llu, "
"attrib_name=%p, len_attrib_name=%llu, "
"attrib_type=%p, "
"attrib_nelem=%p",
f,
field_name,
(long long unsigned)attrib_idx,
attrib_name, (long long unsigned)len_attrib_name,
attrib_type,
attrib_nelem);
H5_API_RETURN (
h5b_get_field_attrib_info (
f,
field_name,
attrib_idx,
attrib_name,
len_attrib_name,
attrib_type,
attrib_nelem));
}
#define H5BLOCK_FIELD_ORIGIN_NAME "__Origin__"
#define H5BLOCK_FIELD_SPACING_NAME "__Spacing__"
/*!
\ingroup h5block_c_api
Get field origin.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dGetFieldOrigin (
h5_file_t *f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
h5_float64_t *x_origin, /*!< OUT: X origin */
h5_float64_t *y_origin, /*!< OUT: Y origin */
h5_float64_t *z_origin /*!< OUT: Z origin */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', x_origin=%p, y_origin=%p, z_origin=%p",
f, field_name, x_origin, y_origin, z_origin);
h5_float64_t origin[3];
TRY (h5_read_field_attrib (
f,
field_name,
H5BLOCK_FIELD_ORIGIN_NAME,
H5_FLOAT64_T,
origin));
*x_origin = origin[0];
*y_origin = origin[1];
*z_origin = origin[2];
H5_API_RETURN (H5_SUCCESS);
}
/*!
\ingroup h5block_c_api
Set field origin.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dSetFieldOrigin (
h5_file_t *f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const h5_float64_t x_origin, /*!< IN: X origin */
const h5_float64_t y_origin, /*!< IN: Y origin */
const h5_float64_t z_origin /*!< IN: Z origin */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', x_origin=%g, y_origin=%g, z_origin=%g",
f, field_name, x_origin, y_origin, z_origin);
h5_float64_t origin[3] = { x_origin, y_origin, z_origin };
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
H5BLOCK_FIELD_ORIGIN_NAME,
(hid_t)H5_FLOAT64_T,
origin,
3));
}
/*!
\ingroup h5block_c_api
Get field spacing for field \c field_name in the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dGetFieldSpacing (
h5_file_t *f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
h5_float64_t *x_spacing, /*!< OUT: X spacing */
h5_float64_t *y_spacing, /*!< OUT: Y spacing */
h5_float64_t *z_spacing /*!< OUT: Z spacing */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', x_spacing=%p, y_spacing=%p, z_spacing=%p",
f, field_name, x_spacing, y_spacing, z_spacing);
h5_float64_t spacing[3];
TRY (h5_read_field_attrib (
f,
field_name,
H5BLOCK_FIELD_SPACING_NAME,
H5_FLOAT64_T,
spacing));
*x_spacing = spacing[0];
*y_spacing = spacing[1];
*z_spacing = spacing[2];
H5_API_RETURN (H5_SUCCESS);
}
/*!
\ingroup h5block_c_api
Set field spacing for field \c field_name in the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dSetFieldSpacing (
h5_file_t *f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const h5_float64_t x_spacing, /*!< IN: X spacing */
const h5_float64_t y_spacing, /*!< IN: Y spacing */
const h5_float64_t z_spacing /*!< IN: Z spacing */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', x_spacing=%g, y_spacing=%g, z_spacing=%g",
f, field_name, x_spacing, y_spacing, z_spacing);
h5_float64_t spacing[3] = { x_spacing, y_spacing, z_spacing };
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
H5BLOCK_FIELD_SPACING_NAME,
(hid_t)H5_FLOAT64_T,
spacing,
3));
}
src/C/H5Block_readwrite.c
-625
View File
@@ -1,625 +0,0 @@
#include "h5core/h5_core.h"
#include "H5Block_readwrite.h"
/*!
\ingroup h5block_data
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
floating points (64-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dWriteScalarFieldFloat64 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_float64_t *buffer /*!< IN: pointer to write buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, (void*)buffer, H5T_NATIVE_DOUBLE ));
}
/*!
\ingroup h5block_data
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
floating points (64-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dReadScalarFieldFloat64 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_float64_t *buffer /*!< OUT: pointer to read buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, (void*)buffer, H5T_NATIVE_DOUBLE));
}
/*!
\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with floating points (64-bit) values.
You must use the Fortran indexing scheme to access items in \c x_buf.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dWriteVector3dFieldFloat64 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_float64_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_float64_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_float64_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_write_vector3d_data(f, name,
(void*)x_buf, (void*)y_buf, (void*)z_buf, H5T_NATIVE_DOUBLE));
}
/*!
\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with floating points (64-bit) values.
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dReadVector3dFieldFloat64 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
h5_float64_t *const x_buf, /*!< OUT: pointer to X axis buffer */
h5_float64_t *const y_buf, /*!< OUT: pointer to Y axis buffer */
h5_float64_t *const z_buf /*!< OUT: pointer to Z axis buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_read_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_DOUBLE));
}
/*!
\ingroup h5block_data
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
floating points (32-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dWriteScalarFieldFloat32 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_float32_t *buffer /*!< IN: pointer to write buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, buffer, H5T_NATIVE_FLOAT ));
}
/*!
\ingroup h5block_data
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
floating points (32-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dReadScalarFieldFloat32 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_float32_t *const buffer /*!< OUT: pointer to read buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, buffer, H5T_NATIVE_FLOAT));
}
/*!
\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with floating points (32-bit) values.
You must use the Fortran indexing scheme to access items in \c x_buf.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dWriteVector3dFieldFloat32 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_float32_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_float32_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_float32_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_write_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_FLOAT));
}
/*!
\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with floating points (32-bit) values.
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dReadVector3dFieldFloat32 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
h5_float32_t *const x_buf, /*!< OUT: pointer to X axis buffer */
h5_float32_t *const y_buf, /*!< OUT: pointer to Y axis buffer */
h5_float32_t *const z_buf /*!< OUT: pointer to Z axis buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_read_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_FLOAT));
}
/*!
\ingroup h5block_data
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
integers (64-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dWriteScalarFieldInt64 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_int64_t *buffer /*!< IN: pointer to write buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, buffer, H5T_NATIVE_INT64 ));
}
/*!
\ingroup h5block_data
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
integers (64-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dReadScalarFieldInt64 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_int64_t *const buffer /*!< OUT: pointer to read buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, buffer, H5T_NATIVE_INT64));
}
/*!
\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with integers (64-bit) values.
You must use the Fortran indexing scheme to access items in \c x_buf.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dWriteVector3dFieldInt64 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_int64_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_int64_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_int64_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN (h5b_write_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_INT64));
}
/*!
\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with integers (64-bit) values.
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dReadVector3dFieldInt64 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
h5_int64_t *const x_buf, /*!< OUT: pointer to X axis buffer */
h5_int64_t *const y_buf, /*!< OUT: pointer to Y axis buffer */
h5_int64_t *const z_buf /*!< OUT: pointer to Z axis buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN (h5b_read_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_INT64));
}
/*!
\ingroup h5block_data
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
integers (32-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dWriteScalarFieldInt32 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_int32_t *buffer /*!< IN: pointer to write buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, buffer, H5T_NATIVE_INT32 ));
}
/*!
\ingroup h5block_data
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
integers (32-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dReadScalarFieldInt32 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_int32_t *const buffer /*!< OUT: pointer to read buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, buffer, H5T_NATIVE_INT32));
}
/*!
\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with integers (32-bit) values.
You must use the Fortran indexing scheme to access items in \c x_buf.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dWriteVector3dFieldInt32 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_int32_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_int32_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_int32_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_write_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_INT32));
}
/*!
\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with integers (32-bit) values.
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5Block3dReadVector3dFieldInt32 (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
h5_int32_t *const x_buf, /*!< OUT: pointer to X axis buffer */
h5_int32_t *const y_buf, /*!< OUT: pointer to Y axis buffer */
h5_int32_t *const z_buf /*!< OUT: pointer to Z axis buffer */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_read_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_INT32));
}
/*!
\ingroup h5block_attrib
Write float64 \c values as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockWriteFieldAttribFloat64 (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_float64_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', attrib_name='%s', "
"buffer=%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_DOUBLE,
buffer,
nelems ));
}
/*!
\ingroup h5block_attrib
Read float64 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockReadFieldAttribFloat64 (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_float64_t *buffer /*!< OUT: attribute values */
) {
H5_API_ENTER (h5_err_t, "f=%p, field_name='%s', attrib_name='%s', buffer=%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN (h5_read_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_DOUBLE,
(void*)buffer ));
}
/*!
\ingroup h5block_attrib
Write float32 \c values as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockWriteFieldAttribFloat32 (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_float32_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', attrib_name='%s', "
"buffer=%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_FLOAT,
buffer,
nelems ));
}
/*!
\ingroup h5block_attrib
Read float32 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockReadFieldAttribFloat32 (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_float32_t *const buffer /*!< OUT: attribute values */
) {
H5_API_ENTER (h5_err_t, "f=%p, field_name='%s', attrib_name='%s', buffer=%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN (h5_read_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_FLOAT,
buffer ));
}
/*!
\ingroup h5block_attrib
Write int64 \c values as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockWriteFieldAttribInt64 (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_int64_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', attrib_name='%s', buffer=%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_INT64,
buffer,
nelems ));
}
/*!
\ingroup h5block_attrib
Read int64 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockReadFieldAttribInt64 (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_int64_t *const buffer /*!< OUT: attribute values */
) {
H5_API_ENTER (h5_err_t, "f=%p, field_name='%s', attrib_name='%s', buffer=%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN (h5_read_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_INT64,
buffer ));
}
/*!
\ingroup h5block_attrib
Write int32 \c values as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockWriteFieldAttribInt32 (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_int32_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', attrib_name='%s', "
"buffer=%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_INT32,
buffer,
nelems ));
}
/*!
\ingroup h5block_attrib
Read int32 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5BlockReadFieldAttribInt32 (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_int32_t *buffer /*!< OUT: attribute values */
) {
H5_API_ENTER (h5_err_t, "f=%p, field_name='%s', attrib_name='%s', buffer=%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN (h5_read_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_INT32,
(void*)buffer ));
}
src/C/H5Part.c
-604
View File
@@ -1,604 +0,0 @@
#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h> /* va_arg - System dependent ?! */
#include <string.h>
#include <errno.h>
#include <fcntl.h>
#include <hdf5.h>
#ifndef WIN32
#include <unistd.h>
#else /* WIN32 */
#include <io.h>
#define open _open
#define close _close
#endif /* WIN32 */
#include "h5core/h5_core.h"
#include "H5Part.h"
/*!
\ingroup h5part_model
Set the number of particles for the current time-step.
After you call this subroutine, all subsequent
operations will assume this number of particles will be written.
For the parallel library, the \c nparticles value is the number of
particles that the \e individual task will write. You can use
a different value on different tasks.
This function uses an \c MPI_Allgather
call to aggregate each tasks number of particles and determine
the appropiate offsets. Because of the use of this MPI collective,
it is advisable to call this function as
few times as possible when running at large concurrency.
This function assumes that your particles' data fields are in stored in
contiguous 1D arrays.
For instance, the fields \e x and \e y for your particles are stored
in separate arrays \c x[] and \c y[].
If instead you store your particles as tuples, so that the values
are arranged \f$ x_1,y_1,x_2,y_2\f$... than you need to setup striding
(in this case with value 2) using \ref H5PartSetNumParticlesStrided.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartSetNumParticles (
h5_file_t *f, /*!< [in] Handle to open file */
h5_size_t nparticles /*!< [in] Number of particles */
) {
H5_API_ENTER (h5_err_t,
"f=%p, nparticles=%llu",
f, (long long unsigned)nparticles);
h5_size_t stride = 1;
H5_API_RETURN (h5u_set_num_particles(f, nparticles, stride));
}
/*!
\ingroup h5part_model
Set the number of particles for the current time-step.
After you call this subroutine, all subsequent
operations will assume this number of particles will be written.
For the parallel library, the \c nparticles value is the number of
particles that the \e individual task will write. You can use
a different value on different tasks.
This function uses an \c MPI_Allgather
call to aggregate each tasks number of particles and determine
the appropiate offsets. Because of the use of this MPI collective,
it is advisable to call this function as
few times as possible when running at large concurrency.
This function assumes that your particles' data fields are
stored tuples. For instance, the fields \e x and \e y of your
particles are arranged \f$x_1,y_1,x_2,y_2\f$... in a single data
array. In this example, the stride value would be 2.
If you instead have a separate array for each fields,
such as \c x[] and \c y[],
use \ref H5PartSetNumParticles.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartSetNumParticlesStrided (
h5_file_t *f, /*!< [in] Handle to open file */
h5_size_t nparticles, /*!< [in] Number of particles */
h5_size_t stride /*!< [in] Stride value (e.g. number of fields in the particle array) */
) {
H5_API_ENTER (h5_err_t,
"f=%p, nparticles=%llu, stride=%llu",
f, (long long unsigned)nparticles,
(long long unsigned)stride);
H5_API_RETURN (h5u_set_num_particles (f, nparticles, stride));
}
/*!
\ingroup h5part_model
Define the chunk \c size and enables chunking in the underlying
HDF5 layer.
Note that this policy wastes disk space, but can improve write
bandwidth on parallel filesystems that are sensitive to write alignment
(e.g. lustre). It is only recommended when using the MPI-POSIX or MPI-IO
independent VFDs (see \ref H5OpenFile).
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartSetChunk (
h5_file_t *f,
h5_size_t size
) {
H5_API_ENTER (h5_err_t, "f=%p, size=%llu", f, (long long unsigned)size);
H5_API_RETURN (h5u_set_chunk (f, size));
}
/*!
\ingroup h5part_data
Write array of 64 bit floating point data to file.
After setting the number of particles with \c H5PartSetNumParticles() and
the current timestep using \c H5SetStep(), you can start writing datasets
into the file. Each dataset has a name associated with it (chosen by the
user) in order to facilitate later retrieval. The name of the dataset is
specified in the parameter \c name, which must be a null-terminated string.
There are no restrictions on naming of datasets, but it is useful to arrive
at some common naming convention when sharing data with other groups.
The writing routines also implicitly store the datatype of the array so that
the array can be reconstructed properly on other systems with incompatible
type representations.
All data that is written after setting the timestep is associated with that
timestep. While the number of particles can change for each timestep, you
cannot change the number of particles in the middle of a given timestep.
The data is committed to disk before the routine returns.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartWriteDataFloat64 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate array with */
const h5_float64_t *data /*!< [in] Array to commit to disk */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_DOUBLE));
}
/*!
\ingroup h5part_data
Write array of 32 bit floating point data to file.
After setting the number of particles with \c H5PartSetNumParticles() and
the current timestep using \c H5SetStep(), you can start writing datasets
into the file. Each dataset has a name associated with it (chosen by the
user) in order to facilitate later retrieval. The name of the dataset is
specified in the parameter \c name, which must be a null-terminated string.
There are no restrictions on naming of datasets, but it is useful to arrive
at some common naming convention when sharing data with other groups.
The writing routines also implicitly store the datatype of the array so that
the array can be reconstructed properly on other systems with incompatible
type representations.
All data that is written after setting the timestep is associated with that
timestep. While the number of particles can change for each timestep, you
cannot change the number of particles in the middle of a given timestep.
The data is committed to disk before the routine returns.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartWriteDataFloat32 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate array with */
const h5_float32_t *data /*!< [in] Array to commit to disk */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
h5_err_t h5err = h5u_write_data( f, name, (void*)data, H5T_NATIVE_FLOAT );
H5_API_RETURN (h5err);
}
/*!
\ingroup h5part_data
Write array of 64 bit integer data to file.
After setting the number of particles with \c H5PartSetNumParticles() and
the current timestep using \c H5SetStep(), you can start writing datasets
into the file. Each dataset has a name associated with it (chosen by the
user) in order to facilitate later retrieval. The name of the dataset is
specified in the parameter \c name, which must be a null-terminated string.
There are no restrictions on naming of datasets, but it is useful to arrive
at some common naming convention when sharing data with other groups.
The writing routines also implicitly store the datatype of the array so that
the array can be reconstructed properly on other systems with incompatible
type representations.
All data that is written after setting the timestep is associated with that
timestep. While the number of particles can change for each timestep, you
cannot change the number of particles in the middle of a given timestep.
The data is committed to disk before the routine returns.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartWriteDataInt64 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate array with */
const h5_int64_t *data /*!< [in] Array to commit to disk */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_INT64));
}
/*!
\ingroup h5part_data
Write array of 32 bit integer data to file.
After setting the number of particles with \c H5PartSetNumParticles() and
the current timestep using \c H5SetStep(), you can start writing datasets
into the file. Each dataset has a name associated with it (chosen by the
user) in order to facilitate later retrieval. The name of the dataset is
specified in the parameter \c name, which must be a null-terminated string.
There are no restrictions on naming of datasets, but it is useful to arrive
at some common naming convention when sharing data with other groups.
The writing routines also implicitly store the datatype of the array so that
the array can be reconstructed properly on other systems with incompatible
type representations.
All data that is written after setting the timestep is associated with that
timestep. While the number of particles can change for each timestep, you
cannot change the number of particles in the middle of a given timestep.
The data is committed to disk before the routine returns.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartWriteDataInt32 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate array with */
const h5_int32_t *data /*!< [in] Array to commit to disk */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_INT32));
}
/*!
\ingroup h5part_data
Read array of 64 bit floating point data from file.
When retrieving datasets from disk, you ask for them
by name. There are no restrictions on naming of arrays,
but it is useful to arrive at some common naming
convention when sharing data with other groups.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartReadDataFloat64 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate dataset with */
h5_float64_t *data /*!< [out] Array of data */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_DOUBLE));
}
/*!
\ingroup h5part_data
Read array of 32 bit floating point data from file.
When retrieving datasets from disk, you ask for them
by name. There are no restrictions on naming of arrays,
but it is useful to arrive at some common naming
convention when sharing data with other groups.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartReadDataFloat32 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate dataset with */
h5_float32_t *data /*!< [out] Array of data */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_FLOAT));
}
/*!
\ingroup h5part_data
Read array of 64 bit integer data from file.
When retrieving datasets from disk, you ask for them
by name. There are no restrictions on naming of arrays,
but it is useful to arrive at some common naming
convention when sharing data with other groups.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartReadDataInt64 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate dataset with */
h5_int64_t *data /*!< [out] Array of data */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_INT64));
}
/*!
\ingroup h5part_data
Read array of 32 bit integer data from file.
When retrieving datasets from disk, you ask for them
by name. There are no restrictions on naming of arrays,
but it is useful to arrive at some common naming
convention when sharing data with other groups.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartReadDataInt32 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate dataset with */
h5_int32_t *data /*!< [out] Array of data */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_INT32));
}
/*!
\ingroup h5part_model
Get the number of datasets that are stored at the current time-step.
\return number of datasets in current timestep or error code
*/
h5_ssize_t
H5PartGetNumDatasets (
h5_file_t *f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5u_get_num_datasets(f));
}
/*!
\ingroup h5part_model
This reads the name of a dataset specified by it's index in the current
time-step.
If the number of datasets is \c n, the range of \c _index is \c 0 to \c n-1.
\result \c H5_SUCCESS
*/
h5_err_t
H5PartGetDatasetName (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *name, /*!< [out] Name of dataset */
const h5_size_t len /*!< [in] Size of buffer \c name */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"idx=%lld, "
"name='%p', len=%llu, ",
f,
(long long)idx,
name, (unsigned long long)len);
H5_API_RETURN (h5u_get_dataset_info(f, idx, name, len, NULL, NULL));
}
/*!
\ingroup h5part_model
Gets the name, type and number of elements of a dataset based on its
index in the current timestep.
Type is one of the following values:
- \c H5_FLOAT64_T (for \c h5_float64_t)
- \c H5_FLOAT32_T (for \c h5_float32_t)
- \c H5_INT64_T (for \c h5_int64_t)
- \c H5_INT32_T (for \c h5_int32_t)
\return \c H5_SUCCESS
*/
h5_err_t
H5PartGetDatasetInfo (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *dataset_name, /*!< [out] Name of dataset */
const h5_size_t len_dataset_name,
/*!< [in] Size of buffer \c dataset_name */
h5_int64_t *type, /*!< [out] Type of data in dataset */
h5_size_t *nelem /*!< [out] Number of elements. */
) {
H5_API_ENTER (h5_int64_t,
"f=%p, "
"idx=%lld, "
"dataset_name='%p', len_dataset_name=%llu, "
"type=%p, nelem=%p",
f,
(long long)idx,
dataset_name, (long long unsigned)len_dataset_name,
type, nelem);
H5_API_RETURN (h5u_get_dataset_info (
f, idx, dataset_name, len_dataset_name, type, nelem));
}
/*!
\ingroup h5part_model
This function returns the number of particles in this processor's view,
if a view has been set.
If not, it returns the total number of particles across all processors
from the last \ref H5PartSetNumParticles call.
If you have neither set the number of particles
nor set a view, then this returns the total number of
particles in the first data set of the current time step.
Note that H5Part assumes that all data sets within a given time step
have the same number of particles (although the number particles can
vary across time steps).
If none of these conditions are met, an error is thrown.
\return number of particles in current timestep or an error
code.
*/
h5_ssize_t
H5PartGetNumParticles (
h5_file_t *f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_ssize_t, "f=%p", f);
CHECK_FILEHANDLE( f );
H5_API_RETURN (h5u_get_num_particles (f));
}
/*!
\ingroup h5part_model
Reset the view.
\return \c H5_SUCCESS
*/
h5_err_t
H5PartResetView (
h5_file_t *f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_ssize_t, "f=%p", f);
H5_API_RETURN (h5u_reset_view (f));
}
/*!
\ingroup h5part_model
Check whether a view has been set, either automatically with
\ref H5PartSetNumParticles or manually with \ref H5PartSetView
or \ref H5PartSetViewIndices.
\return 0 for false or 1 for true
*/
h5_err_t
H5PartHasView (
h5_file_t *f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5u_has_view (f));
}
/*!
\ingroup h5part_model
For parallel I/O or for subsetting operations on the datafile,
this function allows you to define a subset of the total
particle dataset to operate on.
The concept of "view" works for both serial
and for parallel I/O. The "view" will remain in effect until a new view
is set, or the number of particles in a dataset changes, or the view is
"unset" by calling \c H5PartSetView(file,-1,-1);
Before you set a view, \ref H5PartGetNumParticles will return the
total number of particles in the current time-step (even for the parallel
reads). However, after you set a view, it will return the number of
particles contained in the view.
The range is \e inclusive: the end value is the last index of the
data.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartSetView (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t start, /*!< [in] Start particle */
h5_int64_t end /*!< [in] End particle */
) {
H5_API_ENTER (h5_err_t,
"f=%p, start=%lld, end=%lld",
f, (long long)start, (long long)end);
H5_API_RETURN (h5u_set_view (f, start, end));
}
/*!
\ingroup h5part_model
For parallel I/O or for subsetting operations on the datafile,
this function allows you to define a subset of the total
dataset to operate on by specifying a list of indices.
The concept of "view" works for both serial
and for parallel I/O. The "view" will remain in effect until a new view
is set, or the number of particles in a dataset changes, or the view is
"unset" by calling \c H5PartSetViewIndices(NULL,0);
When you perform a read or write on a view consisting of indices, it
is assumed that your buffer is \b unpacked, meaning that there is room
for all the intermediate values (which will not be touched by the read
or write).
Before you set a view, the \c H5PartGetNumParticles() will return the
total number of particles in the current time-step (even for the parallel
reads). However, after you set a view, it will return the number of
particles contained in the view.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartSetViewIndices (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_size_t *indices, /*!< [in] List of indices */
h5_size_t nelems /*!< [in] Size of list */
) {
H5_API_ENTER (h5_err_t,
"f=%p, indices=%p, nelems=%llu",
f, indices, (long long unsigned)nelems);
H5_API_RETURN (h5u_set_view_indices (f, indices, nelems));
}
/*!
\ingroup h5part_model
Allows you to query the current view. Start and End
will be \c -1 if there is no current view established.
Use \c H5PartHasView() to see if the view is smaller than the
total dataset.
\return number of elements in the view or error code
*/
h5_err_t
H5PartGetView (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t *start, /*!< [out] Start particle */
h5_int64_t *end /*!< [out] End particle */
) {
H5_API_ENTER (h5_err_t,
"f=%p, start=%p, end=%p",
f, start, end);
H5_API_RETURN (h5u_get_view (f, start, end));
}
/*!
\ingroup h5part_model
If it is too tedious to manually set the start and end coordinates
for a view, the \c H5SetCanonicalView() will automatically select an
appropriate domain decomposition of the data arrays for the degree
of parallelism and set the "view" accordingly.
\return H5_SUCCESS or error code
*/
h5_err_t
H5PartSetCanonicalView (
h5_file_t *f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5u_set_canonical_view (f));
}
src/C/H5_attachments.c
-65
View File
@@ -1,65 +0,0 @@
#include "h5core/h5_core.h"
#include "H5hut.h"
h5_ssize_t
H5GetNumAttachments (
h5_file_t* const f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_ssize_t, "f=%p", f);
H5_API_RETURN (h5_get_num_attachments (f));
}
h5_err_t
H5GetAttachmentInfoByIdx (
h5_file_t* const f,
const h5_size_t idx, // IN
char* const fname, // OUT
h5_size_t len_fname, // IN
h5_size_t* const fsize // OUT
) {
H5_API_ENTER (h5_err_t,
"idx=%llu, fname=%p, len_fname=%llu, fsize=%p",
(long long unsigned)idx,
fname, (long long unsigned)len_fname,
fsize);
H5_API_RETURN (h5_get_attachment_info_by_idx (
f, idx, fname, len_fname, fsize));
}
h5_err_t
H5GetAttachmentInfoByName (
h5_file_t* const f,
char* const fname, // OUT
h5_size_t* const fsize // OUT
) {
H5_API_ENTER (h5_err_t, "fname='%s', fsize=%p", fname, fsize);
H5_API_RETURN (h5_get_attachment_info_by_name (
f, fname, fsize));
}
h5_err_t
H5AddAttachment (
h5_file_t* const f, /*!< [in] Handle to open file */
const char* fname /*!< [in] Name of file to attach */
) {
H5_API_ENTER (h5_err_t, "fname='%s'", fname);
H5_API_RETURN (h5_add_attachment (f, fname));
}
h5_err_t
H5GetAttachment (
h5_file_t* const f, /*!< [in] Handle to open file */
const char* fname /*!< [in] Name of attachment */
) {
H5_API_ENTER (h5_err_t, "fname='%s'", fname);
H5_API_RETURN (h5_get_attachment (f, fname));
}
h5_err_t
H5DeleteAttachment (
h5_file_t* const f,
const char* const fname
) {
H5_API_ENTER (h5_err_t, "fname='%s'", fname);
H5_API_RETURN (h5_delete_attachment (f, fname));
}
src/C/H5_attribs.c
-629
View File
@@ -1,629 +0,0 @@
#include <string.h>
#include "h5core/h5_core.h"
#include "H5hut.h"
/*** WRITE ***/
/*!
\ingroup h5hut_attrib
Write an attribute \c name with the string \c value to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteFileAttribString (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const char *value /*!< [in] Value of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', value='%s'", f, name, value);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_CHAR,
value,
strlen(value) + 1 ));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with the string \c value to
the current timestep.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteStepAttribString (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const char *value /*!< [in] Value of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', value='%s'", f, name, value);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_CHAR,
value,
strlen(value) + 1 ));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with float32 \c values to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteFileAttribFloat32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_float32_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_FLOAT,
values,
nelems ));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with float32 \c values to
the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteStepAttribFloat32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_float32_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_FLOAT,
values,
nelems ));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with float64 \c values to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteFileAttribFloat64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_float64_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_DOUBLE,
values,
nelems));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with float64 \c values to
the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteStepAttribFloat64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_float64_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_DOUBLE,
values,
nelems));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with int32 \c values to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteFileAttribInt32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_int32_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_INT32,
values,
nelems));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with int32 \c values to
the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteStepAttribInt32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_int32_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_INT32,
values,
nelems));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with int64 \c values to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteFileAttribInt64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_int64_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_INT64,
values,
nelems));
}
/*!
\ingroup h5hut_attrib
Write an attribute \c name with int64 \c values to
the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5WriteStepAttribInt64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_int64_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_INT64,
values,
nelems));
}
/*** READ ***/
/*!
\ingroup h5hut_attrib
Read a string into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadFileAttribString (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
char *buffer /*!< [out] Value of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', value='%s'", f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_STRING_T,
(void*)buffer));
}
/*!
\ingroup h5hut_attrib
Read a string into a \c buffer from an attribute \c name
in the current timestep.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadStepAttribString (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
char *buffer /*!< [out] Value of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', value='%s'",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_STRING_T,
(void*)buffer));
}
/*!
\ingroup h5hut_attrib
Read int32 values into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadFileAttribInt32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_int32_t *buffer /*!< [out] Values of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_INT32_T,
(void*)buffer));
}
/*!
\ingroup h5hut_attrib
Read int32 values into a \c buffer from an attribute \c name
in the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadStepAttribInt32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_int32_t *buffer /*!< [out] Values of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_INT32_T,
(void*)buffer));
}
/*!
\ingroup h5hut_attrib
Read int64 values into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadFileAttribInt64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_int64_t *buffer /*!< [out] Values of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_INT64_T,
(void*)buffer));
}
/*!
\ingroup h5hut_attrib
Read int64 values into a \c buffer from an attribute \c name
in the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadStepAttribInt64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_int64_t *buffer /*!< [out] Values of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
h5_err_t h5err = h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_INT64_T,
(void*)buffer);
H5_API_RETURN (h5err);
}
/*!
\ingroup h5hut_attrib
Read float32 values into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadFileAttribFloat32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_float32_t *buffer /*!< [out] Values of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_FLOAT32_T,
(void*)buffer));
}
/*!
\ingroup h5hut_attrib
Read float32 values into a \c buffer from an attribute \c name
in the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadStepAttribFloat32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_float32_t *buffer /*!< [out] Values of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_FLOAT32_T,
(void*)buffer));
}
/*!
\ingroup h5hut_attrib
Read float64 values into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadFileAttribFloat64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_float64_t *buffer /*!< [out] Values of attribute */
) {
H5_API_ENTER (h5_err_t,
"f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_FLOAT64_T,
(void*)buffer));
}
/*!
\ingroup h5hut_attrib
Read float64 values into a \c buffer from an attribute \c name
in the current time step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5ReadStepAttribFloat64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_float64_t *buffer /*!< [out] Values of attribute */
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_FLOAT64_T,
(void*)buffer));
}
/*** QUERY ***/
/*!
\ingroup h5hut_attrib
Gets the number of attributes in the file's root ("/").
\return Number of attributes or error code.
*/
h5_int64_t
H5GetNumFileAttribs (
h5_file_t *const f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_int64_t, "f=%p", f);
H5_API_RETURN (h5_get_num_attribs (f, H5_ATTRIB_FILE));
}
/*!
\ingroup h5hut_attrib
Gets the number of attributes bound to the current step.
\h5_err_t h5err = Number of attributes or error code.
*/
h5_int64_t
H5GetNumStepAttribs (
h5_file_t *const f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_int64_t, "f=%p", f);
H5_API_RETURN (h5_get_num_attribs (f, H5_ATTRIB_STEP));
}
/*!
\ingroup h5hut_attrib
Gets the name, type and number of elements of the file attribute
specified by its index.
This function can be used to retrieve all attributes bound to the
file \c f by looping from \c 0 to the number of attribute minus
one. The number of attributes bound to file \c f can be queried
by calling \ref H5GetNumFileAttribs.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5GetFileAttribInfo (
h5_file_t *const f, /*!< [in] Handle to open file */
const h5_size_t attrib_idx, /*!< [in] Index of attribute to get
infos about */
char *attrib_name, /*!< [out] Name of attribute */
const h5_size_t len_of_attrib_name,
/*!< [in] length of buffer \c name */
h5_int64_t *attrib_type, /*!< [out] Type of value. */
h5_size_t *attrib_nelem /*!< [out] Number of elements */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"attrib_idx=%llu, attrib_name=%p, len_attrib_name=%llu, "
"attrib_type=%p, attrib_nelem=%p",
f,
(long long unsigned)attrib_idx,
attrib_name,
(long long unsigned)len_of_attrib_name,
attrib_type,
attrib_nelem);
H5_API_RETURN (h5_get_attrib_info (
f,
H5_ATTRIB_FILE,
attrib_idx,
attrib_name,
len_of_attrib_name,
attrib_type,
attrib_nelem));
}
/*!
\ingroup h5hut_attrib
Gets the name, type and number of elements of the step attribute
specified by its index.
This function can be used to retrieve all attributes bound to the
current time-step by looping from \c 0 to the number of attribute
minus one. The number of attributes bound to the current
time-step can be queried by calling \ref H5GetNumStepAttribs.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5GetStepAttribInfo (
h5_file_t *const f, /*!< [in] Handle to open file */
const h5_size_t attrib_idx, /*!< [in] Index of attribute to
get infos about */
char *attrib_name, /*!< [out] Name of attribute */
const h5_size_t len_of_attrib_name,
/*!< [in] length of buffer \c name */
h5_int64_t *attrib_type, /*!< [out] Type of value. */
h5_size_t *attrib_nelem /*!< [out] Number of elements */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"attrib_idx=%llu, attrib_name=%p, len_attrib_name=%llu, "
"attrib_type=%p, attrib_nelem=%p",
f,
(unsigned long long)attrib_idx,
attrib_name,
(unsigned long long)len_of_attrib_name,
attrib_type,
attrib_nelem);
H5_API_RETURN (h5_get_attrib_info (
f,
H5_ATTRIB_STEP,
attrib_idx,
attrib_name,
len_of_attrib_name,
attrib_type,
attrib_nelem));
}
src/C/Makefile.am
+3 -26
View File
@@ -1,15 +1,5 @@
# src/C level Makefile.am
OBJEXT=o
AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
# What to build... Will be determined by configure script.
lib_LTLIBRARIES = @LIB_C@
# Listing of all possible targets that I may build.
EXTRA_LTLIBRARIES = libH5hutC.la
if ENABLE_C
# Header files that I wish to install in $(prefix)/include
include_HEADERS = \
../include/H5hut.h \
@@ -28,20 +18,7 @@ include_HEADERS = \
# Listing of all possible headers that I may include
EXTRA_HEADERS =
# Listing of sources
libH5hutC_la_SOURCES = \
H5.c \
H5_attribs.c \
H5_attachments.c \
H5Part.c \
H5Block.c \
H5Block_readwrite.c
libH5hutC_la_LDFLAGS = -version-info 2:0:0 -rpath '$(libdir)'
all-local:
$(INSTALL) -m644 .libs/libH5hutC.a ../lib
endif
clean-local:
$(RM) ../lib/libH5hutC.a
$(RM) *~
src/C/generate-h5b-readwrite.py
-580
View File
@@ -1,580 +0,0 @@
#!/usr/bin/python
c_head = """
#include "h5core/h5_core.h"
"""
h_head = """
#ifndef __H5BLOCK_READWRITE_H
#define __H5BLOCK_READWRITE_H
"""
h_tail = """
#endif
"""
fc_head = """
#include <stdlib.h>
#include "h5core/h5_core.h"
#include "Underscore.h"
#if defined(F77_SINGLE_UNDERSCORE)
#define F77NAME(a,b) a
#elif defined(F77_CRAY_UNDERSCORE)
#define F77NAME(a,b) b
#elif defined(F77_NO_UNDERSCORE)
#else
#error Error, no way to determine how to construct fortran bindings
#endif
"""
write_scalar_h = """
h5_err_t
H5Block#DIM#dWriteScalarField#TYPE_ABV# (
h5_file_t *const f,
const char *name,
const h5_#TYPE_H5P#_t *buffer
);
"""
read_scalar_h = """
h5_err_t
H5Block#DIM#dReadScalarField#TYPE_ABV# (
h5_file_t *const f,
const char *name,
h5_#TYPE_H5P#_t *buffer
);
"""
write_scalar_c = """
/*!
\\ingroup h5block_data
Write a 3-dimensional field \\c name from the buffer starting at \\c data
to the current time-step using the defined field layout. Values are
#TYPE_FULL#.
You must use the Fortran indexing scheme to access items in \\c data.
\\return \\c H5_SUCCESS or error code
*/
h5_err_t
H5Block#DIM#dWriteScalarField#TYPE_ABV# (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_#TYPE_H5P#_t *buffer /*!< IN: pointer to write buffer */
) {
H5_API_ENTER3 (h5_err_t, "f=0x%p, name=\\"%s\\", buffer=0x%p",
f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, (void*)buffer, #TYPE_HDF5# ));
}
"""
read_scalar_c = """
/*!
\\ingroup h5block_data
Read a 3-dimensional field \\c name into the buffer starting at \\c data from
the current time-step using the defined field layout. Values are
#TYPE_FULL#.
You must use the Fortran indexing scheme to access items in \\c data.
\\return \\c H5_SUCCESS or error code
*/
h5_err_t
H5Block#DIM#dReadScalarField#TYPE_ABV# (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_#TYPE_H5P#_t *buffer /*!< OUT: pointer to read buffer */
) {
H5_API_ENTER3 (h5_err_t, "f=0x%p, name=\\"%s\\", buffer=0x%p",
f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, (void*)buffer, #TYPE_HDF5#));
}
"""
write_scalar_fi = """
!> \\ingroup h5block_data_f
!! See \\ref H5Block#DIM#dWriteScalarField#TYPE_ABV#
!! \\return 0 on success or error code
!<
INTEGER*8 FUNCTION h5bl_#DIM#d_write_scalar_field_#TYPE_F90_ABV# ( filehandle, name, buffer )
INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open
CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
#TYPE_F90#, INTENT(IN) :: buffer(*) !< the array of data
END FUNCTION
"""
read_scalar_fi = """
!> \\ingroup h5block_data_f
!! See \\ref H5Block#DIM#dReadScalarField#TYPE_ABV#
!! \\return 0 on success or error code
!<
INTEGER*8 FUNCTION h5bl_#DIM#d_read_scalar_field_#TYPE_F90_ABV# ( filehandle, name, buffer )
INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open
CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
#TYPE_F90#, INTENT(OUT) :: buffer(*) !< buffer to read the data into
END FUNCTION
"""
write_scalar_fc = """
#if ! defined(F77_NO_UNDERSCORE)
#define h5bl_#DIM#d_write_scalar_field_#TYPE_F90_ABV# F77NAME ( \\
h5bl_#DIM#d_write_scalar_field_#TYPE_F90_ABV#_, \\
H5BL_#DIM#D_WRITE_SCALAR_FIELD_#TYPE_F90_ABVC# )
#endif
h5_err_t
h5bl_#DIM#d_write_scalar_field_#TYPE_F90_ABV# (
h5_int64_t *const f,
const char *name,
const h5_#TYPE_H5P#_t *buffer,
const int l_name
) {
h5_file_t *fh = h5_filehandlefor2c(f);
H5_API_ENTER4 (h5_err_t, "f=0x%p, name=\\"%s\\", buffer=0x%p, l_name=%d",
fh, name, buffer, l_name);
char *name2 = h5_strdupfor2c ( name, l_name );
h5_err_t herr = h5b_write_scalar_data (
fh, name2, (void*)buffer, #TYPE_HDF5# );
free ( name2 );
H5_API_RETURN(herr);
}
"""
read_scalar_fc = """
#if ! defined(F77_NO_UNDERSCORE)
#define h5bl_3d_read_scalar_field_#TYPE_F90_ABV# F77NAME ( \\
h5bl_3d_read_scalar_field_#TYPE_F90_ABV#_, \\
H5BL_#DIM#D_READ_SCALAR_FIELD_#TYPE_F90_ABVC# )
#endif
h5_err_t
h5bl_#DIM#d_read_scalar_field_#TYPE_F90_ABV# (
h5_int64_t *const f,
const char *name,
h5_#TYPE_H5P#_t *buffer,
const int l_name
) {
h5_file_t *fh = h5_filehandlefor2c(f);
H5_API_ENTER4 (h5_err_t, "f=0x%p, name=\\"%s\\", buffer=0x%p, l_name=%d",
fh, name, buffer, l_name);
char *name2 = h5_strdupfor2c ( name, l_name );
h5_err_t herr = h5b_read_scalar_data (
fh, name2, buffer, #TYPE_HDF5# );
free ( name2 );
H5_API_RETURN(herr);
}
"""
write_vector_h = """
h5_err_t
H5Block#DIM#dWriteVector3dField#TYPE_ABV# (
h5_file_t *const f,
const char *name,
const h5_#TYPE_H5P#_t *x_buf,
const h5_#TYPE_H5P#_t *y_buf,
const h5_#TYPE_H5P#_t *z_buf
);
"""
read_vector_h = """
h5_err_t
H5Block#DIM#dReadVector3dField#TYPE_ABV# (
h5_file_t *const f,
const char *name,
h5_#TYPE_H5P#_t *x_buf,
h5_#TYPE_H5P#_t *y_buf,
h5_#TYPE_H5P#_t *z_buf
);
"""
write_vector_c = """
/*!
\\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \\c name with 3-dimensional vectors as values
from the buffers starting at \\c x_buf, \\c y_buf and \\c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with #TYPE_FULL# values.
You must use the Fortran indexing scheme to access items in \\c x_buf.
\\return \\c H5_SUCCESS or error code
*/
h5_err_t
H5Block#DIM#dWriteVector3dField#TYPE_ABV# (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_#TYPE_H5P#_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_#TYPE_H5P#_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_#TYPE_H5P#_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
H5_API_ENTER5 (h5_err_t, "f=0x%p, name=\\"%s\\", x_buf=0x%p, y_buf=0x%p, z_buf=0x%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_write_vector3d_data(f, name,
(void*)x_buf, (void*)y_buf, (void*)z_buf, #TYPE_HDF5#));
}
"""
read_vector_c = """
/*!
\\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \\c name with 3-dimensional vectors as values
from the buffers starting at \\c x_buf, \\c y_buf and \\c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with #TYPE_FULL# values.
You must use the Fortran indexing scheme to access items in \\c data.
\\return \\c H5_SUCCESS or error code
*/
h5_err_t
H5Block#DIM#dReadVector3dField#TYPE_ABV# (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_#TYPE_H5P#_t *x_buf, /*!< OUT: pointer to X axis buffer */
const h5_#TYPE_H5P#_t *y_buf, /*!< OUT: pointer to Y axis buffer */
const h5_#TYPE_H5P#_t *z_buf /*!< OUT: pointer to Z axis buffer */
) {
H5_API_ENTER5 (h5_err_t, "f=0x%p, name=\\"%s\\", x_buf=0x%p, y_buf=0x%p, z_buf=0x%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_read_vector3d_data(f, name,
(void*)x_buf, (void*)y_buf, (void*)z_buf, #TYPE_HDF5#));
}
"""
write_vector_fi = """
!> \\ingroup h5block_data_f
!! See \\ref H5Block#DIM#dWriteVector3dField#TYPE_ABV#
!! \\return 0 on success or error code
!<
INTEGER*8 FUNCTION h5bl_#DIM#d_write_vector3d_field_#TYPE_F90_ABV# ( filehandle, name, x, y, z )
INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open
CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
#TYPE_F90#, INTENT(IN) :: x(*) !< the array of x data to write
#TYPE_F90#, INTENT(IN) :: y(*) !< the array of y data to write
#TYPE_F90#, INTENT(IN) :: z(*) !< the array of z data to write
END FUNCTION
"""
read_vector_fi = """
!> \\ingroup h5block_data_f
!! See \\ref H5Block#DIM#dReadVector3dField#TYPE_ABV#
!! \\return 0 on success or error code
!<
INTEGER*8 FUNCTION h5bl_#DIM#d_read_vector3d_field_#TYPE_F90_ABV# ( filehandle, name, x, y, z )
INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open
CHARACTER(LEN=*), INTENT(IN) :: name !< the name of the dataset
#TYPE_F90#, INTENT(OUT) :: x(*) !< buffer to read the x data into
#TYPE_F90#, INTENT(OUT) :: y(*) !< buffer to read the y data into
#TYPE_F90#, INTENT(OUT) :: z(*) !< buffer to read the z data into
END FUNCTION
"""
write_vector_fc = """
#if ! defined(F77_NO_UNDERSCORE)
#define h5bl_#DIM#d_write_vector3d_field_#TYPE_F90_ABV# F77NAME ( \\
h5bl_#DIM#d_write_vector3d_field_#TYPE_F90_ABV#_, \\
H5BL_#DIM#D_WRITE_VECTOR3D_FIELD_#TYPE_F90_ABVC# )
#endif
h5_err_t
h5bl_#DIM#d_write_vector3d_field_#TYPE_F90_ABV# (
h5_int64_t *const f,
const char *name,
const h5_#TYPE_H5P#_t *x_buf,
const h5_#TYPE_H5P#_t *y_buf,
const h5_#TYPE_H5P#_t *z_buf,
const int l_name
) {
h5_file_t *fh = h5_filehandlefor2c(f);
H5_API_ENTER6 (h5_err_t, "f=0x%p, name=\\"%s\\", x_buf=0x%p, y_buf=0x%p, z_buf=0x%p, l_name=%d",
fh, name, x_buf, y_buf, z_buf, l_name);
char *name2 = h5_strdupfor2c ( name, l_name );
h5_err_t herr = h5b_write_vector3d_data (
fh, name2,
(void*)x_buf, (void*)y_buf, (void*)z_buf, #TYPE_HDF5# );
free ( name2 );
H5_API_RETURN(herr);
}
"""
read_vector_fc = """
#if ! defined(F77_NO_UNDERSCORE)
#define h5bl_#DIM#d_read_vector3d_field_#TYPE_F90_ABV# F77NAME ( \\
h5bl_#DIM#d_read_vector3d_field_#TYPE_F90_ABV#_, \\
H5BL_#DIM#D_READ_VECTOR3D_FIELD_#TYPE_F90_ABVC# )
#endif
h5_err_t
h5bl_#DIM#d_read_vector3d_field_#TYPE_F90_ABV# (
h5_int64_t *const f,
const char *name,
h5_#TYPE_H5P#_t *x_buf,
h5_#TYPE_H5P#_t *y_buf,
h5_#TYPE_H5P#_t *z_buf,
const int l_name
) {
h5_file_t *fh = h5_filehandlefor2c(f);
H5_API_ENTER6 (h5_err_t, "f=0x%p, name=\\"%s\\", x_buf=0x%p, y_buf=0x%p, z_buf=0x%p, l_name=%d",
fh, name, x_buf, y_buf, z_buf, l_name);
char *name2 = h5_strdupfor2c ( name, l_name );
h5_err_t herr = h5b_read_vector3d_data (
fh, name2,
(void*)x_buf, (void*)y_buf, (void*)z_buf, #TYPE_HDF5# );
free ( name2 );
H5_API_RETURN(herr);
}
"""
write_attr_h = """
h5_err_t
H5BlockWriteFieldAttrib#TYPE_ABV# (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
const h5_#TYPE_H5P#_t *buffer,
const h5_size_t nelems
);
"""
write_attr_c = """
/*!
\\ingroup h5block_attrib
Write #TYPE_H5P# \\c values as attribute \\c attrib_name of field
\\c field_name.
\\return \\c H5_SUCCESS or error code
*/
h5_err_t
H5BlockWriteFieldAttrib#TYPE_ABV# (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_#TYPE_H5P#_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
H5_API_ENTER5 (h5_err_t, "f=0x%p, field_name=\\"%s\\", attrib_name=\\"%s\\", "
"buffer=0x%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN(h5_write_field_attrib (
f,
field_name,
attrib_name,
#TYPE_HDF5#,
buffer,
nelems ));
}
"""
write_attr_fi = """
!> \\ingroup h5block_attrib_f
!! See \\ref H5BlockWriteFieldAttrib#TYPE_ABV#
!! \\return 0 on success or error code
!<
INTEGER*8 FUNCTION h5bl_writefieldattrib_#TYPE_F90_ABV# ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem)
INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open
CHARACTER(LEN=*), INTENT(IN) :: field_name !< the name of the field
CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute
#TYPE_F90#, INTENT(IN) :: buffer(*) !< the array of data to write into the attribute
INTEGER*8, INTENT(IN) :: nelems !< the number of elements in the array
END FUNCTION
"""
write_attr_fc = """
#if ! defined(F77_NO_UNDERSCORE)
#define h5bl_writefieldattrib_#TYPE_F90_ABV# F77NAME ( \\
h5bl_writefieldattrib_#TYPE_F90_ABV#_, \\
H5BL_WRITEFIELDATTRIB_#TYPE_F90_ABVC# )
#endif
h5_err_t
h5bl_writefieldattrib_#TYPE_F90_ABV# (
h5_int64_t *const f,
const char *field_name,
const char *attrib_name,
const h5_#TYPE_H5P#_t *buffer,
const h5_size_t *nelems,
const int l_field_name,
const int l_attrib_name
) {
h5_file_t *fh = h5_filehandlefor2c(f);
H5_API_ENTER7 (h5_err_t, "f=0x%p, field_name=\\"%s\\", attrib_name=\\"%s\\", "
"buffer=0x%p, nelems=%lld, l_field_name=%d, l_attrib_name=%d",
fh, field_name, attrib_name, buffer, (long long)*nelems,
l_field_name, l_attrib_name);
char *field_name2 = h5_strdupfor2c ( field_name, l_field_name );
char *attrib_name2 = h5_strdupfor2c ( attrib_name, l_attrib_name );
h5_err_t herr = h5_write_field_attrib (
fh, field_name2, attrib_name2,
#TYPE_HDF5#, buffer, *nelems );
free ( field_name2 );
free ( attrib_name2 );
H5_API_RETURN(herr);
}
"""
read_attr_h = """
h5_err_t
H5BlockReadFieldAttrib#TYPE_ABV# (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
h5_#TYPE_H5P#_t *buffer
);
"""
read_attr_c = """
/*!
\\ingroup h5block_attrib
Read #TYPE_H5P# values from attribute \\c attrib_name of field
\\c field_name into a \\c buffer.
\\return \\c H5_SUCCESS or error code
*/
h5_err_t
H5BlockReadFieldAttrib#TYPE_ABV# (
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_#TYPE_H5P#_t *buffer /*!< OUT: attribute values */
) {
H5_API_ENTER4 (h5_err_t, "f=%p, field_name=\\\"%s\\", attrib_name=\\"%s\\", buffer=0x%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN(h5_read_field_attrib (
f,
field_name,
attrib_name,
#TYPE_HDF5#,
(void*)buffer ));
}
"""
read_attr_fi = """
!> \\ingroup h5block_attrib_f
!! See \\ref H5BlockReadFieldAttrib#TYPE_ABV#
!! \\return 0 on success or error code
!<
INTEGER*8 FUNCTION h5bl_readfieldattrib_#TYPE_F90_ABV# ( filehandle, field_name, attrib_name, attrib_value, attrib_nelem)
INTEGER*8, INTENT(IN) :: filehandle !< the handle returned at file open
CHARACTER(LEN=*), INTENT(IN) :: field_name !< the name of the field
CHARACTER(LEN=*), INTENT(IN) :: attrib_name !< the name of the attribute
#TYPE_F90#, INTENT(IN) :: buffer(*) !< the buffer to read into
END FUNCTION
"""
read_attr_fc = """
#if ! defined(F77_NO_UNDERSCORE)
#define h5bl_readfieldattrib_#TYPE_F90_ABV# F77NAME ( \\
h5bl_readfieldattrib_#TYPE_F90_ABV#_, \\
H5BL_READFIELDATTRIB_#TYPE_F90_ABVC# )
#endif
h5_err_t
h5bl_readfieldattrib_#TYPE_F90_ABV# (
h5_int64_t *const f,
const char *field_name,
const char *attrib_name,
h5_#TYPE_H5P#_t *buffer,
const int l_field_name,
const int l_attrib_name
) {
h5_file_t *fh = h5_filehandlefor2c(f);
H5_API_ENTER6 (h5_err_t, "f=0x%p, field_name=\\"%s\\", attrib_name=\\"%s\\", "
"values=0x%p, l_field_name=%d, l_attrib_name=%d",
fh, field_name, attrib_name, buffer,
l_field_name, l_attrib_name);
char *field_name2 = h5_strdupfor2c ( field_name, l_field_name );
char *attrib_name2 = h5_strdupfor2c ( attrib_name, l_attrib_name );
h5_err_t herr = h5_read_field_attrib (
fh, field_name2, attrib_name2, #TYPE_HDF5#, buffer );
free ( field_name2 );
free ( attrib_name2 );
H5_API_RETURN(herr);
}
"""
dims = ["3"]
types = [
["floating points (64-bit)", "Float64", "float64", "H5T_NATIVE_DOUBLE", "REAL*8", "r8", "R8"],
["floating points (32-bit)", "Float32", "float32", "H5T_NATIVE_FLOAT", "REAL*4", "r4", "R4"],
["integers (64-bit)", "Int64", "int64", "H5T_NATIVE_INT64", "INTEGER*8", "i8", "I8"],
["integers (32-bit)", "Int32", "int32", "H5T_NATIVE_INT32", "INTEGER*4", "i4", "I4"]
]
def create_call(template, type, dim):
fcn = template
fcn = fcn.replace('#DIM#',dim)\
.replace('#TYPE_FULL#',type[0])\
.replace('#TYPE_ABV#',type[1])\
.replace('#TYPE_H5P#',type[2])\
.replace('#TYPE_HDF5#',type[3])\
.replace('#TYPE_F90#',type[4])\
.replace('#TYPE_F90_ABV#',type[5])\
.replace('#TYPE_F90_ABVC#',type[6])
return fcn
def write_calls():
cfile = file('H5Block_readwrite.c','w')
cfile.write(c_head)
hfile = file('../include/H5Block_readwrite.h','w')
hfile.write(h_head)
fcfile = file('../Fortran/H5Block_readwrite_F.c','w')
fcfile.write(fc_head)
fifile = file('../Fortran/H5Block_readwrite.f90','w')
for dim in dims:
for type in types:
cfile.write(create_call(write_scalar_c,type,dim));
cfile.write(create_call(read_scalar_c,type,dim));
hfile.write(create_call(write_scalar_h,type,dim));
hfile.write(create_call(read_scalar_h,type,dim));
fcfile.write(create_call(write_scalar_fc,type,dim));
fcfile.write(create_call(read_scalar_fc,type,dim));
fifile.write(create_call(write_scalar_fi,type,dim));
fifile.write(create_call(read_scalar_fi,type,dim));
cfile.write(create_call(write_vector_c,type,dim));
cfile.write(create_call(read_vector_c,type,dim));
hfile.write(create_call(write_vector_h,type,dim));
hfile.write(create_call(read_vector_h,type,dim));
fcfile.write(create_call(write_vector_fc,type,dim));
fcfile.write(create_call(read_vector_fc,type,dim));
fifile.write(create_call(write_vector_fi,type,dim));
fifile.write(create_call(read_vector_fi,type,dim));
for type in types:
cfile.write(create_call(write_attr_c,type,""));
hfile.write(create_call(write_attr_h,type,""));
fifile.write(create_call(write_attr_fi,type,""));
fcfile.write(create_call(write_attr_fc,type,""));
cfile.write(create_call(read_attr_c,type,""));
hfile.write(create_call(read_attr_h,type,""));
fifile.write(create_call(read_attr_fi,type,""));
fcfile.write(create_call(read_attr_fc,type,""));
cfile.close()
hfile.write(h_tail)
hfile.close()
fcfile.close()
fifile.close()
write_calls()
src/Fortran/Makefile.am
+17 -13
View File
@@ -1,8 +1,6 @@
# src/Fortran level Makefile.am
OBJEXT=o
AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
if ENABLE_FORTRAN
AM_CPPFLAGS += -I$(top_srcdir)/src/include
F90_FILES = H5.f90 \
H5_attribs.f90 \
@@ -10,7 +8,7 @@ F90_FILES = H5.f90 \
H5Block.f90 \
H5Block_readwrite.f90
EXTRA_HEADERS = ../include/H5hut.h
EXTRA_HEADERS =
# Extra files that I wish to include in the dist tar ball.
EXTRA_DIST = TestUnderscoreC.c \
@@ -19,13 +17,13 @@ EXTRA_DIST = TestUnderscoreC.c \
# Files that I don't want to include in the dist tar ball
#nodist_include_HEADERS = ../include/H5hutF.h @UNDERSCORE_H@
nodist_include_HEADERS = ../include/H5hutF.h
nodist_include_HEADERS = $(top_srcdir)/src/include/H5hutF.h
# What to build... Will be determined by configure script.
lib_LTLIBRARIES = @LIB_FORTRAN@
lib_LTLIBRARIES = libH5hutF.la
# Listing of all possible targets that I may build.
EXTRA_LTLIBRARIES = libH5hutF.la
include_HEADERS = \
$(top_srcdir)/src/include/H5hutF.h
libH5hutF_la_SOURCES = \
H5_F.c \
@@ -34,13 +32,19 @@ libH5hutF_la_SOURCES = \
H5Block_F.c \
H5Block_readwrite_F.c
libH5hutF_la_DEPENDENCIES = ../include/H5hutF.h
libH5hutF_la_DEPENDENCIES = $(top_srcdir)/src/include/H5hutF.h
libH5hutF_la_LDFLAGS = -version-info 2:0:0 -rpath '$(libdir)'
../include/H5hutF.h: $(F90_FILES)
$(top_srcdir)/src/include/H5hutF.h: $(F90_FILES)
awk '/INTEGER\*8 FUNCTION/{print "\t" $$1 " " $$3}' $^ >$@
clean: clean-am
$(RM) ../include/H5hutF.h
all-local:
$(INSTALL) -m755 -d ../lib
$(INSTALL) -m644 .libs/libH5hutF.a ../lib
endif
clean: clean-am
clean-local:
$(RM) -f *~
src/Makefile.am
+1 -1
View File
@@ -1,4 +1,4 @@
# test level Makefile.am
SUBDIRS = h5core @BINDINGS@
SUBDIRS = h5core C Fortran
src/h5core/Makefile.am
+7 -35
View File
@@ -1,36 +1,6 @@
# src level Makefile.am
OBJEXT=o
AM_CPPFLAGS = -I../include @AM_CPPFLAGS@
AM_CPPFLAGS += -I$(top_srcdir)/src/include
EXTRA_HEADERS = \
../include/h5core/h5_attach.h \
../include/h5core/h5_attribs.h \
../include/h5core/h5_core.h \
../include/h5core/h5_errno.h \
../include/h5core/h5_errorhandling.h \
../include/h5core/h5_hdf5.h \
../include/h5core/h5_maps.h \
../include/h5core/h5_openclose.h \
../include/h5core/h5_readwrite.h \
../include/h5core/h5_syscall.h \
../include/h5core/h5_types.h \
../include/h5core/h5u_readwrite.h \
../include/h5core/h5b_readwrite.h \
../include/h5core/h5u_model.h \
../include/h5core/h5b_model.h \
../include/h5core/h5b_attribs.h \
../include/h5core/h5t_adjacencies.h \
../include/h5core/h5t_core.h \
../include/h5core/h5t_inquiry.h \
../include/h5core/h5t_map.h \
../include/h5core/h5t_model.h \
../include/h5core/h5t_readwrite.h \
../include/h5core/h5t_ref_elements.h \
../include/h5core/h5t_retrieve.h \
../include/h5core/h5t_storemesh.h \
../include/h5core/h5t_tags.h \
h5_attribs_private.h \
h5_core_private.h \
h5_errorhandling_private.h \
@@ -72,7 +42,7 @@ EXTRA_DIST = $(EXTRA_HEADERS)
lib_LTLIBRARIES = libH5hut.la
# Listing of sources
libH5hut_la_SOURCES = \
libH5hut_la_SOURCES = \
h5_attach.c \
h5_attribs.c \
h5_errorhandling.c \
@@ -120,12 +90,14 @@ libH5hut_la_DEPENDENCIES = $(EXTRA_HEADERS)
libH5hut_la_LDFLAGS = -version-info 2:0:0
all-local:
$(INSTALL) -m644 .libs/libH5hut.a ../lib
$(INSTALL) -m0755 -d $(top_builddir)/src/lib
$(INSTALL) -m644 .libs/libH5hut.a $(top_builddir)/src/lib
install-exec-local:
@$(INSTALL) -d $(DESTDIR)$(includedir)/h5core
@$(INSTALL) -m644 ../include/h5core/*.h $(DESTDIR)$(includedir)/h5core/
@$(INSTALL) -m644 $(top_srcdir)/src/include/h5core/*.h $(DESTDIR)$(includedir)/h5core/
clean-local:
$(RM) -f ../lib/libH5hut.*
$(RM) -f $(top_srcdir)/src/lib/libH5hut.*
$(RM) -f *~
src/h5core/h5_openclose.c
-30
View File
@@ -495,36 +495,6 @@ h5_get_num_steps(
f->prefix_step_name);
}
/*!
\ingroup h5_core_filehandling
Start traversing steps.
\return \c H5_SUCCESS or error code
*/
h5_err_t
h5_start_traverse_steps (
h5_file_t* const f /*!< file handle */
) {
UNUSED_ARGUMENT (f);
return h5_error_not_implemented ();
}
/*!
\ingroup h5_core_filehandling
Go to next step.
\return \c H5_SUCCESS or error code
*/
h5_err_t
h5_traverse_steps (
h5_file_t* const f /*!< file handle */
) {
UNUSED_ARGUMENT (f);
return h5_error_not_implemented ();
}
char *
h5_strdupfor2c (
const char *s,
src/h5core/h5t_adjacencies_trim.c
+4 -4
View File
@@ -559,14 +559,14 @@ update_internal_structs (
"m=%p, from_lvl=%u",
m, (unsigned)from_lvl);
h5_debug ("%s (%lld)", __func__, (long long)from_lvl);
clock_t t1 = clock();
// clock_t t1 = clock();
TRY( compute_elems_of_vertices (m, from_lvl) );
clock_t t2 = clock();
// clock_t t2 = clock();
// fprintf (stderr, "compute_elems_of_vertices(): %f\n",
// (float)(t2-t1)/CLOCKS_PER_SEC);
t1 = clock();
// t1 = clock();
TRY( compute_elems_of_edges (m, from_lvl ) );
t2 = clock();
// t2 = clock();
// fprintf (stderr, "compute_elems_of_edge(): %f\n",
// (float)(t2-t1)/CLOCKS_PER_SEC);
h5_debug ("%s (%lld): done", __func__, (long long)from_lvl);
src/include/H5.h
+270 -83
View File
@@ -1,17 +1,11 @@
/*
Copyright 2007-2008
Paul Scherrer Institut, Villigen, Switzerland;
Benedikt Oswald;
Achim Gsell
All rights reserved.
Authors
Achim Gsell
Warning
This code is under development.
*/
Copyright (c) 2006-2013, 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.
License: see file COPYING in top level of source distribution.
*/
#ifndef __H5_H
#define __H5_H
@@ -20,121 +14,314 @@
extern "C" {
#endif
h5_file_t *
/*!
\ingroup h5hut_file
Open file with name \c filbename. This function is available in the parallel
and serial version. In the serial case \c comm may have any value.
File mode flags are:
- H5_O_RDONLY: only reading allowed
- H5_O_WRONLY: create new file, dataset must not exist
- H5_O_APPEND: allows to append a new datasets to an existing file
- H5_O_RDWR: dataset may exist
You can also select a "virtual file driver" in the HDF5 layer using:
- H5_VFD_INDEPENDENT: MPI-IO in independent (asynchronous) mode
- H5_VFD_MPIPOSIX: parallel I/O implemented directly by HDF5, bypassing MPI-IO
\return File handle.
\return NULL on error.
*/
static inline h5_file_p
H5OpenFile (
const char * filename,
h5_int32_t flag,
MPI_Comm comm
);
const char* filename, /*!< file name */
h5_int32_t flags, /*!< file open flags */
MPI_Comm comm /*!< MPI communicator */
) {
H5_API_ENTER (h5_file_p, "filename='%s', flags=%d, ...",filename,flags);
H5_API_RETURN (h5_open_file (filename, flags, comm, 0));
}
/*!
\ingroup h5hut_file
h5_err_t
Close file and free all memory associated with the file handle.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5CloseFile (
h5_file_t * f
);
h5_file_t* const f /*!< file handle */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_close_file (f));
}
h5_err_t
/*!
\ingroup h5hut_file
Verify that the file handle points to a valid H5hut file structure.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5CheckFile (
h5_file_t * f
);
h5_file_t* const f /*!< file handle */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_check_filehandle (f));
}
/*!
\ingroup h5hut_model
h5_err_t
Define format of the step names.
Example: ==H5SetStepNameFormat( f, "Step", 6 )== defines step names
like ==Step#000042==.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5SetStepNameFormat (
h5_file_t *f,
const char *name,
const h5_int64_t width
);
h5_file_t* const f, /*!< Handle to file */
const char* name, /*!< Prefix */
const h5_int64_t width /*!< Width of the number */
) {
H5_API_ENTER (h5_err_t,
"f=%p, name='%s', width=%lld",
f, name, (long long) width);
H5_API_RETURN (h5_set_stepname_fmt (f, name, width));
}
h5_err_t
/*!
\ingroup h5hut_model
Get format of the step names.
\return value \c >=0 on success
\return -1 on error
*/
static inline h5_err_t
H5GetStepNameFormat (
h5_file_t *f,
char *name,
const h5_size_t l_name,
int *width
);
h5_file_t* const f, /*!< Handle to file */
char* name, /*!< OUT: Prefix */
const h5_size_t l_name, /*!< length of buffer name */
int* width /*!< OUT: Width of the number */
) {
H5_API_ENTER (h5_err_t,
"f=%p, name=%p, l_name=%llu, width=%p",
f, name, (unsigned long long)l_name, width);
H5_API_RETURN (h5_get_stepname_fmt (f, name, l_name, width));
}
h5_err_t
/*!
\ingroup h5hut_model
Set the current step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5SetStep (
h5_file_t *f,
const h5_id_t step
);
h5_file_t* const f, /*!< [in] Handle to open file */
const h5_id_t step /*!< [in] Step to set. */
) {
H5_API_ENTER (h5_err_t, "f=%p, step=%lld", f, (long long)step);
H5_API_RETURN (h5_set_step (f, step));
}
h5_int64_t
/*!
\ingroup h5hut_model
Get current step.
\return \c H5_SUCCESS or error code
*/
static inline h5_id_t
H5GetStep (
h5_file_t *f
);
h5_file_t* const f /*!< Handle to open file */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_get_step (f));
}
int
/*!
\ingroup h5hut_file
Get the number of processors.
\param[in] f File handle.
\return Number of processors.
\return \c -1 on error.
*/
static inline int
H5GetNumProcs (
h5_file_t * const f
);
h5_file_t* const f
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_get_num_procs(f));
}
h5_ssize_t
/*!
\ingroup h5hut_model
Get the number of time-steps that are currently stored in the file
\c f.
It works for both reading and writing of files, but is probably
only typically used when you are reading.
\param[in] f File handle.
\return number of time-steps or error code
*/
static inline h5_ssize_t
H5GetNumSteps (
h5_file_t * const f
);
h5_file_t* const f
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_get_num_steps(f));
}
h5_err_t
/*!
\ingroup h5_inquiry
Query whether a particular step already exists in the file.
\param[in] f File handle.
\param[in] stepno Step number to query for existence
\return true or false
*/
static inline h5_err_t
H5HasStep (
h5_file_t * const f,
h5_id_t step
);
h5_file_t* const f,
h5_id_t stepno
) {
H5_API_ENTER (h5_err_t,
"f=%p, stepno=%lld",
f, (long long)stepno);
H5_API_RETURN (h5_has_step (f, stepno));
}
h5_err_t
H5StartTraverseSteps (
h5_file_t *f
);
h5_id_t
H5TraverseSteps (
h5_file_t *f
);
/*!
\ingroup h5hut_error
h5_err_t
H5EndTraverseSteps (
h5_file_t *f
);
Set verbosity level to \c level.
h5_err_t
\return \c H5_SUCCESS
*/
static inline h5_err_t
H5SetVerbosityLevel (
const h5_id_t level
);
) {
return h5_set_debuglevel (level);
}
h5_err_t
/*!
\ingroup h5hut_error
Set error handler to \c handler.
\return \c H5_SUCCESS
*/
static inline h5_err_t
H5SetErrorHandler (
h5_errorhandler_t handler
);
) {
H5_API_ENTER (h5_err_t, "handler=%p", handler);
H5_API_RETURN (h5_set_errorhandler (handler));
}
h5_errorhandler_t
/*!
\ingroup h5hut_error
Get current error handler.
\return Pointer to error handler.
*/
static inline h5_errorhandler_t
H5GetErrorHandler (
void
);
) {
H5_API_ENTER (h5_errorhandler_t, "%s", "void");
H5_API_RETURN (h5_get_errorhandler());
}
h5_err_t
static inline h5_err_t
H5ReportErrorhandler (
const char *fmt,
const char* fmt,
va_list ap
);
) {
return h5_report_errorhandler (fmt, ap);
}
h5_err_t
static inline h5_err_t
H5AbortErrorhandler (
const char *fmt,
const char* fmt,
va_list ap
);
) {
return h5_abort_errorhandler (fmt, ap);
}
h5_err_t
/*!
\ingroup h5hut_error
Get last error code.
\return error code
*/
static inline h5_err_t
H5GetErrno (
void
);
) {
return h5_get_errno ();
}
static inline h5_err_t
H5FlushStep (
h5_file_t* const f /*!< file handle */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_flush_step (f));
}
static inline h5_err_t
H5FlushFile (
h5_file_t* const f /*!< file handle */
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5_flush_file (f));
}
/*!
\ingroup h5hut_file
Set the `throttle` factor, which causes HDF5 write and read
calls to be issued in that number of batches.
This can prevent large concurrency parallel applications that
use independent writes from overwhelming the underlying
parallel file system.
Throttling only works with the H5_VFD_MPIPOSIX or
H5_VFD_INDEPENDENT drivers and is only available in
the parallel library.
\return \c H5_SUCCESS
*/
#ifdef PARALLEL_IO
h5_err_t
static inline h5_err_t
H5SetThrottle (
h5_file_t* f,
int factor
);
#endif
#ifdef __cplusplus
) {
H5_API_ENTER (h5_err_t, "f=%p, factor=%d", f, factor);
H5_API_RETURN (h5_set_throttle(f, factor));
}
#endif
#endif // PARALLEL_IO
#endif
src/include/H5Block.h
+585 -103
View File
@@ -1,16 +1,96 @@
#ifndef __H5BLOCK_H
#define __H5BLOCK_H
/*!
\defgroup h5block_c_api H5Block C API
*/
/*!
\internal
\defgroup h5block_kernel H5Block Kernel
*/
/*!
\internal
\defgroup h5block_private H5Block Private
*/
/*!
\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
*/
/*!
\note
Different field sizes are allowed in the same time-step.
\note
The same layout can be used, if the size of the field matches the
size of the layout. If the size of the layout doesn't match the
size of the field, an error will be indicated.
\note
In write mode partitions are shrinked to make them non-overlaping. This
process may shrink the partitions more than required.
\note
In read-mode partitions may not cross boundaries. This means, if the grid
size is (X, Y, Z), all partitions must fit into this grid.
\todo
check whether layout is reasonable
API function names
*/
#ifdef __cplusplus
extern "C" {
#endif
h5_int64_t
/********************** defining the layout **********************************/
/*!
\ingroup h5block_model
Tests whether a view has been set, either directly with
\ref H5Block3dSetView or indirectly with \ref H5Block3dSetGrid.
\return 0 on false, 1 on true
*/
static inline h5_int64_t
H5Block3dHasView (
h5_file_t *const f /*!< IN: File handle */
);
) {
H5_API_ENTER (h5_int64_t, "f=%p", f);
H5_API_RETURN (h5b_3d_has_view (f));
}
h5_err_t
/*!
\ingroup h5block_model
Defines the partition of the field that this processor owns, using
Fortran ordering: the fastest moving index is \c i.
This routine uses an MPI_Allgather, so at large concurrency it should
be called as infrequently as possible. For instance, if several timesteps
use the same field dimensions, set the layout only once before the
first timestep.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dSetView (
h5_file_t *const f, /*!< IN: File handle */
const h5_int64_t i_start, /*!< IN: start index of \c i */
@@ -19,20 +99,56 @@ H5Block3dSetView (
const h5_int64_t j_end, /*!< IN: end index of \c j */
const h5_int64_t k_start, /*!< IN: start index of \c k */
const h5_int64_t k_end /*!< IN: end index of \c k */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"i_start=%lld, i_end=%lld, "
"j_start=%lld, j_end=%lld, "
"k_start=%lld, k_end=%lld",
f,
(long long)i_start, (long long)i_end,
(long long)j_start, (long long)j_end,
(long long)k_start, (long long)k_end);
H5_API_RETURN (h5b_3d_set_view(f, i_start, i_end, j_start, j_end, k_start, k_end));
}
h5_err_t
/*!
\ingroup h5block_model
Return the view of this processor.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dGetView (
h5_file_t *const f, /*!< IN: File handle */
h5_size_t *const i_start, /*!< OUT: start index of \c i */
h5_size_t *const i_end, /*!< OUT: end index of \c i */
h5_size_t *const j_start, /*!< OUT: start index of \c j */
h5_size_t *const j_end, /*!< OUT: end index of \c j */
h5_size_t *const k_start, /*!< OUT: start index of \c k */
h5_size_t *const k_end /*!< OUT: end index of \c k */
);
h5_file_t *const f, /*!< IN: File handle */
h5_size_t *i_start, /*!< OUT: start index of \c i */
h5_size_t *i_end, /*!< OUT: end index of \c i */
h5_size_t *j_start, /*!< OUT: start index of \c j */
h5_size_t *j_end, /*!< OUT: end index of \c j */
h5_size_t *k_start, /*!< OUT: start index of \c k */
h5_size_t *k_end /*!< OUT: end index of \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"i_start=%p, i_end=%p, "
"j_start=%p, j_end=%p, "
"k_start=%p, k_end=%p",
f,
i_start, i_end,
j_start, j_end,
k_start, k_end);
H5_API_RETURN (h5b_3d_get_view (f, i_start, i_end, j_start, j_end, k_start, k_end));
}
h5_err_t
/*!
\ingroup h5block_model
Return the reduced (ghost-zone free) view of this processor.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dGetReducedView (
h5_file_t *const f, /*!< IN: File handle */
h5_size_t *const i_start, /*!< OUT: start index of \c i */
@@ -41,157 +157,523 @@ H5Block3dGetReducedView (
h5_size_t *const j_end, /*!< OUT: end index of \c j */
h5_size_t *const k_start, /*!< OUT: start index of \c j */
h5_size_t *const k_end /*!< OUT: end index of \c j */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"i_start=%p, i_end=%p, "
"j_start=%p, j_end=%p, "
"k_start=%p, k_end=%p",
f,
i_start, i_end,
j_start, j_end,
k_start, k_end);
H5_API_RETURN (h5b_3d_get_reduced_view(f, i_start, i_end, j_start, j_end, k_start, k_end));
}
h5_err_t
/*!
\ingroup h5block_model
Define the chunk dimensions and enable chunking in the underlying
HDF5 dataset.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dSetChunk (
h5_file_t *const f, /*!< IN: File handle */
const h5_size_t i, /*!< IN: size of \c i */
const h5_size_t j, /*!< IN: size of \c j */
const h5_size_t k /*!< IN: size of \c k */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%llu, j=%llu, k=%llu",
f,
(long long unsigned)i,
(long long unsigned)j,
(long long unsigned)k);
H5_API_RETURN (h5b_3d_set_chunk(f, i, j, k));
}
h5_err_t
/*!
\ingroup h5block_model
Lookup the chunk dimensions of the underlying HDF5 dataset.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dGetChunk (
h5_file_t *const f, /*!< IN: File handle */
const char *field_name, /*!< IN: name of dataset */
h5_size_t *const i, /*!< OUT: size of i */
h5_size_t *const j, /*!< OUT: size of j */
h5_size_t *const k /*!< OUT: size of k */
);
h5_size_t *const i, /*!< OUT: size of \c i */
h5_size_t *const j, /*!< OUT: size of \c j */
h5_size_t *const k /*!< OUT: size of \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%p, j=%p, k=%p",
f, i, j, k);
H5_API_RETURN (h5b_3d_get_chunk(f, field_name, i, j, k));
}
#if defined(PARALLEL_IO)
h5_err_t
#ifdef PARALLEL_IO
/*!
\ingroup h5block_model
Define an underlying 3D Cartesian grid on the processors with dimensions
(\c i,\c j,\c k). You can look up a processor's index into the grid
using \ref H5Block3dGetGridCoords.
This function can be used in conjunction with \ref H5Block3dSetDims
to setup the view for a regular grid.
The product of the dimensions must equal the size of the MPI communicator.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dSetGrid (
h5_file_t *const f, /*!< IN: File handle */
const h5_size_t i, /*!< IN: dimension in \c i */
const h5_size_t j, /*!< IN: dimension in \c j */
const h5_size_t k /*!< IN: dimension in \c k */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%llu, j=%llu, k=%llu",
f,
(long long unsigned)i,
(long long unsigned)j,
(long long unsigned)k);
H5_API_RETURN (h5b_3d_set_grid(f, i, j, k));
}
h5_err_t
/*!
\ingroup h5block_model
Look up the index (\c i, \c j, \c k) in the grid belonging to MPI processor
\c proc.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dGetGridCoords (
h5_file_t *const f, /*!< IN: File handle */
const int proc, /*!< IN: MPI processor */
h5_int64_t *const i, /*!< OUT: index in \c i */
h5_int64_t *const j, /*!< OUT: index in \c j */
h5_int64_t *const k /*!< OUT: index in \c k */
);
h5_int64_t *i, /*!< OUT: index in \c i */
h5_int64_t *j, /*!< OUT: index in \c j */
h5_int64_t *k /*!< OUT: index in \c k */
) {
H5_API_ENTER (h5_err_t,
"f=%p, proc=%d, i=%p, j=%p, k=%p",
f, proc, i, j, k);
H5_API_RETURN (h5b_3d_get_grid_coords(f, proc, i, j, k));
}
h5_err_t
/*!
\ingroup h5block_model
Set the dimensions of each processor's block when the field is a regular
grid.
A grid must be already set with \ref H5Block3dSetGrid, and all processors
must specify the same dimensions.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dSetDims (
h5_file_t *const f, /*!< IN: File handle */
const h5_size_t i, /*!< IN: dimension in \c i */
const h5_size_t j, /*!< IN: dimension in \c j */
const h5_size_t k /*!< IN: dimension in \c k */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%llu, j=%llu, k=%llu",
f,
(long long unsigned)i,
(long long unsigned)j,
(long long unsigned)k);
H5_API_RETURN (h5b_3d_set_dims(f, i, j, k));
}
#endif
h5_err_t
/*!
\ingroup h5block_model
Sets the additional cells (\c i, \c j, \c k) in each direction to use as
the `halo` region (or `ghost zone`) that overlaps between neighboring
processors on the grid.
A grid with dimensions must already be set with \ref H5Block3dSetGrid and
\ref H5Block3dSetDims, and all processors must specify the same halo radii.
\return \c H5_SUCCESS on success
*/
static inline h5_err_t
H5Block3dSetHalo (
h5_file_t *const f, /*!< IN: File handle */
const h5_size_t i, /*!< IN: radius in \c i */
const h5_size_t j, /*!< IN: radius in \c j */
const h5_size_t k /*!< IN: radius in \c k */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, i=%llu, j=%llu, k=%llu",
f,
(long long unsigned)i,
(long long unsigned)j,
(long long unsigned)k);
H5_API_RETURN (h5b_3d_set_halo(f, i, j, k));
}
h5_ssize_t
/*!
\ingroup h5block_model
Query number of fields in current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_ssize_t
H5BlockGetNumFields (
h5_file_t *const f /*!< IN: file handle */
);
) {
H5_API_ENTER (h5_ssize_t, "f=%p", f);
H5_API_RETURN (h5b_get_num_fields(f));
}
h5_err_t
/*!
\ingroup h5block_model
Get the name, rank and dimensions of the field specified by the
index \c idx.
\c elem_rank reports the rank of the elements in the field
(e.g. scalar or vector).
This function can be used to retrieve all fields bound to the
current time-step by looping from \c 0 to the number of fields
minus one. The number of fields bound to the current time-step
can be queried by calling the function \ref H5BlockGetNumFields.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockGetFieldInfo (
h5_file_t *const f, /*!< IN: file handle */
const h5_size_t idx, /*!< IN: index of field */
char *name, /*!< OUT: field name */
const h5_size_t len_name, /*!< IN: buffer size */
h5_size_t *const field_rank, /*!< OUT: field rank */
h5_size_t *const field_dims, /*!< OUT: field dimensions */
h5_size_t *const elem_rank, /*!< OUT: element rank */
h5_int64_t *const type /*!< OUT: datatype */
);
h5_file_t *const f, /*!< IN: file handle */
const h5_size_t idx, /*!< IN: index of field */
char *name, /*!< OUT: field name */
const h5_size_t len_name, /*!< IN: buffer size */
h5_size_t *field_rank, /*!< OUT: field rank */
h5_size_t *field_dims, /*!< OUT: field dimensions */
h5_size_t *elem_rank, /*!< OUT: element rank */
h5_int64_t *type /*!< OUT: datatype */
) {
H5_API_ENTER (h5_err_t,
"f=%p, idx=%llu, "
"name=%p, len_name=%llu, "
"field_rank=%p, field_dims=%p, elem_rank=%p, type=%p",
f, (long long unsigned)idx,
name, (long long unsigned)len_name,
field_rank, field_dims, elem_rank,
type);
H5_API_RETURN (
h5b_get_field_info (
f,
idx,
name,
len_name,
field_rank,
field_dims,
elem_rank,
type));
}
h5_err_t
/*!
\ingroup h5block_model
Get the rank and dimensions of the field specified by its name.
See \ref H5BlockGetFieldInfo.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockGetFieldInfoByName (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: field name */
h5_size_t *const field_rank, /*!< OUT: field rank */
h5_size_t *const field_dims, /*!< OUT: field dimensions */
h5_size_t *const elem_rank, /*!< OUT: element rank */
h5_int64_t *const type /*!< OUT: datatype */
);
h5_size_t *field_rank, /*!< OUT: field rank */
h5_size_t *field_dims, /*!< OUT: field dimensions */
h5_size_t *elem_rank, /*!< OUT: element rank */
h5_int64_t *type /*!< OUT: datatype */
) {
H5_API_ENTER (h5_err_t,
"f=%p, name='%s', "
"field_rank=%p, field_dims=%p, elem_rank=%p, type=%p",
f, name, field_rank, field_dims, elem_rank, type);
H5_API_RETURN (
h5b_get_field_info_by_name (
f,
name,
field_rank,
field_dims,
elem_rank,
type));
}
h5_err_t
/********************** reading and writing attribute ************************/
/*!
\ingroup h5block_attrib
Write the string \c value as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockWriteFieldAttribString (
h5_file_t *const f, /*!< IN: file handle */
const char *const field_name, /*!< IN: field name */
const char *const attrib_name, /*!< IN: attribute name */
const char *const value /*!< IN: attribute value */
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const char *buffer /*!< IN: attribute value */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"field_name='%s', "
"attrib_name='%s', "
"buffer='%s'",
f,
field_name,
attrib_name,
buffer);
H5_API_RETURN (
h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_CHAR,
buffer,
strlen(buffer) + 1));
}
h5_err_t
/*!
\ingroup h5block_attrib
Read the string value from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockReadFieldAttribString (
h5_file_t *const f, /*!< IN: file handle */
const char *const field_name, /*!< IN: field name */
const char *const attrib_name, /*!< IN: attribute name */
char *const buffer /*!< OUT: attribute value */
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
char *buffer /*!< OUT: attribute value */
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"field_name='%s', "
"attrib_name='%s', "
"buffer=%p",
f,
field_name,
attrib_name,
buffer);
H5_API_RETURN (
h5_read_field_attrib (
f,
field_name,
attrib_name,
H5_STRING_T,
(void*)buffer));
}
h5_ssize_t
/*!
\ingroup h5block_attrib
Query the number of attributes of field \c field_name.
\return number of attributes or error code
*/
static inline h5_ssize_t
H5BlockGetNumFieldAttribs (
h5_file_t *const f, /*<! IN: file handle */
const char *const field_name /*<! IN: field name */
);
h5_file_t *const f, /*<! IN: file handle */
const char *field_name /*<! IN: field name */
) {
H5_API_ENTER (h5_ssize_t, "f=%p, field_name='%s'", f, field_name);
H5_API_RETURN (h5b_get_num_field_attribs (f, field_name));
}
h5_int64_t
/*!
\ingroup h5block_attrib
Gets the name, type and number of elements of the field attribute
specified by its index.
This function can be used to retrieve all attributes bound to the
specified field by looping from \c 0 to the number of attribute
minus one. The number of attributes bound to the
field can be queried by calling \ref H5BlockGetNumFieldAttribs.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockGetFieldAttribInfo (
h5_file_t *const f, /*<! IN: Handle to open file */
const char *const field_name, /*<! IN: field name */
const char *field_name, /*<! IN: field name */
const h5_size_t attrib_idx, /*<! IN: Index of attribute to
get infos about */
char *const attrib_name, /*<! OUT: Name of attribute */
const h5_size_t len_of_attrib_name,
char *attrib_name, /*<! OUT: Name of attribute */
const h5_size_t len_attrib_name,
/*<! IN: length of buffer \c name */
h5_int64_t *const attrib_type, /*<! OUT: Type of value. */
h5_size_t *const attrib_nelem /*<! OUT: Number of elements */
);
h5_int64_t *attrib_type, /*<! OUT: Type of value. */
h5_size_t *attrib_nelem /*<! OUT: Number of elements */
) {
H5_API_ENTER (h5_err_t,
"f=%p field_name='%s', "
"attrib_idx=%llu, "
"attrib_name=%p, len_attrib_name=%llu, "
"attrib_type=%p, "
"attrib_nelem=%p",
f,
field_name,
(long long unsigned)attrib_idx,
attrib_name, (long long unsigned)len_attrib_name,
attrib_type,
attrib_nelem);
H5_API_RETURN (
h5b_get_field_attrib_info (
f,
field_name,
attrib_idx,
attrib_name,
len_attrib_name,
attrib_type,
attrib_nelem));
}
h5_err_t
#define H5BLOCK_FIELD_ORIGIN_NAME "__Origin__"
#define H5BLOCK_FIELD_SPACING_NAME "__Spacing__"
/*!
\ingroup h5block_c_api
Get field origin.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dGetFieldOrigin (
h5_file_t *f,
const char *field_name,
h5_float64_t *x_origin,
h5_float64_t *y_origin,
h5_float64_t *z_origin
);
h5_file_t *f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
h5_float64_t *x_origin, /*!< OUT: X origin */
h5_float64_t *y_origin, /*!< OUT: Y origin */
h5_float64_t *z_origin /*!< OUT: Z origin */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', x_origin=%p, y_origin=%p, z_origin=%p",
f, field_name, x_origin, y_origin, z_origin);
h5_float64_t origin[3];
h5_err_t
TRY (h5_read_field_attrib (
f,
field_name,
H5BLOCK_FIELD_ORIGIN_NAME,
H5_FLOAT64_T,
origin));
*x_origin = origin[0];
*y_origin = origin[1];
*z_origin = origin[2];
H5_API_RETURN (H5_SUCCESS);
}
/*!
\ingroup h5block_c_api
Set field origin.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dSetFieldOrigin (
h5_file_t *f,
const char *field_name,
const h5_float64_t x_origin,
const h5_float64_t y_origin,
const h5_float64_t z_origin
);
h5_file_t *f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const h5_float64_t x_origin, /*!< IN: X origin */
const h5_float64_t y_origin, /*!< IN: Y origin */
const h5_float64_t z_origin /*!< IN: Z origin */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', x_origin=%g, y_origin=%g, z_origin=%g",
f, field_name, x_origin, y_origin, z_origin);
h5_float64_t origin[3] = { x_origin, y_origin, z_origin };
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
H5BLOCK_FIELD_ORIGIN_NAME,
(hid_t)H5_FLOAT64_T,
origin,
3));
}
h5_err_t
/*!
\ingroup h5block_c_api
Get field spacing for field \c field_name in the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dGetFieldSpacing (
h5_file_t *f,
const char *field_name,
h5_float64_t *x_spacing,
h5_float64_t *y_spacing,
h5_float64_t *z_spacing
);
h5_file_t *f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
h5_float64_t *x_spacing, /*!< OUT: X spacing */
h5_float64_t *y_spacing, /*!< OUT: Y spacing */
h5_float64_t *z_spacing /*!< OUT: Z spacing */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', x_spacing=%p, y_spacing=%p, z_spacing=%p",
f, field_name, x_spacing, y_spacing, z_spacing);
h5_float64_t spacing[3];
TRY (h5_read_field_attrib (
f,
field_name,
H5BLOCK_FIELD_SPACING_NAME,
H5_FLOAT64_T,
spacing));
*x_spacing = spacing[0];
*y_spacing = spacing[1];
*z_spacing = spacing[2];
H5_API_RETURN (H5_SUCCESS);
}
h5_err_t
/*!
\ingroup h5block_c_api
Set field spacing for field \c field_name in the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dSetFieldSpacing (
h5_file_t *f,
const char *field_name,
const h5_float64_t x_spacing,
const h5_float64_t y_spacing,
const h5_float64_t z_spacing
);
h5_file_t *f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const h5_float64_t x_spacing, /*!< IN: X spacing */
const h5_float64_t y_spacing, /*!< IN: Y spacing */
const h5_float64_t z_spacing /*!< IN: Z spacing */
) {
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', x_spacing=%g, y_spacing=%g, z_spacing=%g",
f, field_name, x_spacing, y_spacing, z_spacing);
h5_float64_t spacing[3] = { x_spacing, y_spacing, z_spacing };
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
H5BLOCK_FIELD_SPACING_NAME,
(hid_t)H5_FLOAT64_T,
spacing,
3));
}
#ifdef __cplusplus
}
src/include/H5Block_readwrite.h
+575 -148
View File
@@ -5,201 +5,628 @@
extern "C" {
#endif
h5_err_t
/*!
\ingroup h5block_data
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
floating points (64-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dWriteScalarFieldFloat64 (
h5_file_t *const f,
const char *name,
const h5_float64_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_float64_t *buffer /*!< IN: pointer to write buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, (void*)buffer, H5T_NATIVE_DOUBLE ));
}
/*!
\ingroup h5block_data
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
floating points (64-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dReadScalarFieldFloat64 (
h5_file_t *const f,
const char *name,
h5_float64_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_float64_t *buffer /*!< OUT: pointer to read buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, (void*)buffer, H5T_NATIVE_DOUBLE));
}
/*!
\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with floating points (64-bit) values.
You must use the Fortran indexing scheme to access items in \c x_buf.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dWriteVector3dFieldFloat64 (
h5_file_t *const f,
const char *name,
const h5_float64_t *x_buf,
const h5_float64_t *y_buf,
const h5_float64_t *z_buf
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_float64_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_float64_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_float64_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_write_vector3d_data(f, name,
(void*)x_buf, (void*)y_buf, (void*)z_buf, H5T_NATIVE_DOUBLE));
}
/*!
\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with floating points (64-bit) values.
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dReadVector3dFieldFloat64 (
h5_file_t *const f,
const char *name,
h5_float64_t *x_buf,
h5_float64_t *y_buf,
h5_float64_t *z_buf
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
h5_float64_t *const x_buf, /*!< OUT: pointer to X axis buffer */
h5_float64_t *const y_buf, /*!< OUT: pointer to Y axis buffer */
h5_float64_t *const z_buf /*!< OUT: pointer to Z axis buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_read_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_DOUBLE));
}
/*!
\ingroup h5block_data
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
floating points (32-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dWriteScalarFieldFloat32 (
h5_file_t *const f,
const char *name,
const h5_float32_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_float32_t *buffer /*!< IN: pointer to write buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, buffer, H5T_NATIVE_FLOAT ));
}
/*!
\ingroup h5block_data
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
floating points (32-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dReadScalarFieldFloat32 (
h5_file_t *const f,
const char *name,
h5_float32_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_float32_t *const buffer /*!< OUT: pointer to read buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, buffer, H5T_NATIVE_FLOAT));
}
/*!
\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with floating points (32-bit) values.
You must use the Fortran indexing scheme to access items in \c x_buf.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dWriteVector3dFieldFloat32 (
h5_file_t *const f,
const char *name,
const h5_float32_t *x_buf,
const h5_float32_t *y_buf,
const h5_float32_t *z_buf
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_float32_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_float32_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_float32_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_write_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_FLOAT));
}
/*!
\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with floating points (32-bit) values.
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dReadVector3dFieldFloat32 (
h5_file_t *const f,
const char *name,
h5_float32_t *x_buf,
h5_float32_t *y_buf,
h5_float32_t *z_buf
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
h5_float32_t *const x_buf, /*!< OUT: pointer to X axis buffer */
h5_float32_t *const y_buf, /*!< OUT: pointer to Y axis buffer */
h5_float32_t *const z_buf /*!< OUT: pointer to Z axis buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_read_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_FLOAT));
}
/*!
\ingroup h5block_data
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
integers (64-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dWriteScalarFieldInt64 (
h5_file_t *const f,
const char *name,
const h5_int64_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_int64_t *buffer /*!< IN: pointer to write buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, buffer, H5T_NATIVE_INT64 ));
}
/*!
\ingroup h5block_data
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
integers (64-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dReadScalarFieldInt64 (
h5_file_t *const f,
const char *name,
h5_int64_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_int64_t *const buffer /*!< OUT: pointer to read buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, buffer, H5T_NATIVE_INT64));
}
/*!
\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with integers (64-bit) values.
You must use the Fortran indexing scheme to access items in \c x_buf.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dWriteVector3dFieldInt64 (
h5_file_t *const f,
const char *name,
const h5_int64_t *x_buf,
const h5_int64_t *y_buf,
const h5_int64_t *z_buf
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_int64_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_int64_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_int64_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN (h5b_write_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_INT64));
}
/*!
\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with integers (64-bit) values.
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dReadVector3dFieldInt64 (
h5_file_t *const f,
const char *name,
h5_int64_t *x_buf,
h5_int64_t *y_buf,
h5_int64_t *z_buf
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
h5_int64_t *const x_buf, /*!< OUT: pointer to X axis buffer */
h5_int64_t *const y_buf, /*!< OUT: pointer to Y axis buffer */
h5_int64_t *const z_buf /*!< OUT: pointer to Z axis buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN (h5b_read_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_INT64));
}
/*!
\ingroup h5block_data
Write a 3-dimensional field \c name from the buffer starting at \c data
to the current time-step using the defined field layout. Values are
integers (32-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dWriteScalarFieldInt32 (
h5_file_t *const f,
const char *name,
const h5_int32_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_int32_t *buffer /*!< IN: pointer to write buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_write_scalar_data(f, name, buffer, H5T_NATIVE_INT32 ));
}
/*!
\ingroup h5block_data
Read a 3-dimensional field \c name into the buffer starting at \c data from
the current time-step using the defined field layout. Values are
integers (32-bit).
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dReadScalarFieldInt32 (
h5_file_t *const f,
const char *name,
h5_int32_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to read */
h5_int32_t *const buffer /*!< OUT: pointer to read buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p", f, name, buffer);
H5_API_RETURN (h5b_read_scalar_data(f, name, buffer, H5T_NATIVE_INT32));
}
/*!
\ingroup h5block_data
*/
/*!
Write a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with integers (32-bit) values.
You must use the Fortran indexing scheme to access items in \c x_buf.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dWriteVector3dFieldInt32 (
h5_file_t *const f,
const char *name,
const h5_int32_t *x_buf,
const h5_int32_t *y_buf,
const h5_int32_t *z_buf
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
const h5_int32_t *x_buf, /*!< IN: pointer to X axis buffer */
const h5_int32_t *y_buf, /*!< IN: pointer to Y axis buffer */
const h5_int32_t *z_buf /*!< IN: pointer to Z axis buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_write_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_INT32));
}
/*!
\ingroup h5block_data
*/
/*!
Read a 3-dimensional field \c name with 3-dimensional vectors as values
from the buffers starting at \c x_buf, \c y_buf and \c z_buf to the
current time-step using the defined field layout. Values are 3-dimensional
vectors with integers (32-bit) values.
You must use the Fortran indexing scheme to access items in \c data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5Block3dReadVector3dFieldInt32 (
h5_file_t *const f,
const char *name,
h5_int32_t *x_buf,
h5_int32_t *y_buf,
h5_int32_t *z_buf
);
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: name of dataset to write */
h5_int32_t *const x_buf, /*!< OUT: pointer to X axis buffer */
h5_int32_t *const y_buf, /*!< OUT: pointer to Y axis buffer */
h5_int32_t *const z_buf /*!< OUT: pointer to Z axis buffer */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, name='%s', x_buf=%p, y_buf=%p, z_buf=%p",
f, name, x_buf, y_buf, z_buf);
H5_API_RETURN(h5b_read_vector3d_data(f, name,
x_buf, y_buf, z_buf, H5T_NATIVE_INT32));
}
/*!
\ingroup h5block_attrib
Write float64 \c values as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockWriteFieldAttribFloat64 (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
const h5_float64_t *buffer,
const h5_size_t nelems
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_float64_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
h5_err_t
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', attrib_name='%s', "
"buffer=%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_DOUBLE,
buffer,
nelems ));
}
/*!
\ingroup h5block_attrib
Read float64 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockReadFieldAttribFloat64 (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
h5_float64_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_float64_t *buffer /*!< OUT: attribute values */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, field_name='%s', attrib_name='%s', buffer=%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN (h5_read_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_DOUBLE,
(void*)buffer ));
}
/*!
\ingroup h5block_attrib
Write float32 \c values as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockWriteFieldAttribFloat32 (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
const h5_float32_t *buffer,
const h5_size_t nelems
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_float32_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
h5_err_t
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', attrib_name='%s', "
"buffer=%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_FLOAT,
buffer,
nelems ));
}
/*!
\ingroup h5block_attrib
Read float32 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockReadFieldAttribFloat32 (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
h5_float32_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_float32_t *const buffer /*!< OUT: attribute values */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, field_name='%s', attrib_name='%s', buffer=%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN (h5_read_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_FLOAT,
buffer ));
}
/*!
\ingroup h5block_attrib
Write int64 \c values as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockWriteFieldAttribInt64 (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
const h5_int64_t *buffer,
const h5_size_t nelems
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_int64_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
h5_err_t
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', attrib_name='%s', buffer=%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_INT64,
buffer,
nelems ));
}
/*!
\ingroup h5block_attrib
Read int64 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockReadFieldAttribInt64 (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
h5_int64_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_int64_t *const buffer /*!< OUT: attribute values */
) {
h5_err_t
H5_API_ENTER (h5_err_t, "f=%p, field_name='%s', attrib_name='%s', buffer=%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN (h5_read_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_INT64,
buffer ));
}
/*!
\ingroup h5block_attrib
Write int32 \c values as attribute \c attrib_name of field
\c field_name.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockWriteFieldAttribInt32 (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
const h5_int32_t *buffer,
const h5_size_t nelems
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
const h5_int32_t *buffer, /*!< IN: attribute values */
const h5_size_t nelems /*!< IN: number of elements */
) {
h5_err_t
H5_API_ENTER (h5_err_t,
"f=%p, field_name='%s', attrib_name='%s', "
"buffer=%p, nelems=%lld",
f, field_name, attrib_name, buffer, (long long)nelems);
H5_API_RETURN (h5_write_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_INT32,
buffer,
nelems ));
}
/*!
\ingroup h5block_attrib
Read int32 values from attribute \c attrib_name of field
\c field_name into a \c buffer.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5BlockReadFieldAttribInt32 (
h5_file_t *const f,
const char *field_name,
const char *attrib_name,
h5_int32_t *buffer
);
h5_file_t *const f, /*!< IN: file handle */
const char *field_name, /*!< IN: field name */
const char *attrib_name, /*!< IN: attribute name */
h5_int32_t *buffer /*!< OUT: attribute values */
) {
H5_API_ENTER (h5_err_t, "f=%p, field_name='%s', attrib_name='%s', buffer=%p",
f, field_name, attrib_name, buffer);
H5_API_RETURN (h5_read_field_attrib (
f,
field_name,
attrib_name,
H5T_NATIVE_INT32,
(void*)buffer ));
}
#ifdef __cplusplus
}
src/include/H5Part.h
+491 -42
View File
@@ -5,95 +5,402 @@
extern "C" {
#endif
h5_err_t
/*!
\ingroup h5part_model
Set the number of particles for the current time-step.
After you call this subroutine, all subsequent
operations will assume this number of particles will be written.
For the parallel library, the \c nparticles value is the number of
particles that the \e individual task will write. You can use
a different value on different tasks.
This function uses an \c MPI_Allgather
call to aggregate each tasks number of particles and determine
the appropiate offsets. Because of the use of this MPI collective,
it is advisable to call this function as
few times as possible when running at large concurrency.
This function assumes that your particles' data fields are in stored in
contiguous 1D arrays.
For instance, the fields \e x and \e y for your particles are stored
in separate arrays \c x[] and \c y[].
If instead you store your particles as tuples, so that the values
are arranged \f$ x_1,y_1,x_2,y_2\f$... than you need to setup striding
(in this case with value 2) using \ref H5PartSetNumParticlesStrided.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartSetNumParticles (
h5_file_t *f, /*!< [in] Handle to open file */
h5_size_t nparticles /*!< [in] Number of particles */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, nparticles=%llu",
f, (long long unsigned)nparticles);
h5_size_t stride = 1;
H5_API_RETURN (h5u_set_num_particles(f, nparticles, stride));
}
h5_err_t
/*!
\ingroup h5part_model
Set the number of particles for the current time-step.
After you call this subroutine, all subsequent
operations will assume this number of particles will be written.
For the parallel library, the \c nparticles value is the number of
particles that the \e individual task will write. You can use
a different value on different tasks.
This function uses an \c MPI_Allgather
call to aggregate each tasks number of particles and determine
the appropiate offsets. Because of the use of this MPI collective,
it is advisable to call this function as
few times as possible when running at large concurrency.
This function assumes that your particles' data fields are
stored tuples. For instance, the fields \e x and \e y of your
particles are arranged \f$x_1,y_1,x_2,y_2\f$... in a single data
array. In this example, the stride value would be 2.
If you instead have a separate array for each fields,
such as \c x[] and \c y[],
use \ref H5PartSetNumParticles.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartSetNumParticlesStrided (
h5_file_t *f, /*!< [in] Handle to open file */
h5_size_t nparticles, /*!< [in] Number of particles */
h5_size_t stride /*!< [in] Stride value (e.g. number of fields in the particle array) */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, nparticles=%llu, stride=%llu",
f, (long long unsigned)nparticles,
(long long unsigned)stride);
H5_API_RETURN (h5u_set_num_particles (f, nparticles, stride));
}
h5_err_t
/*!
\ingroup h5part_model
Define the chunk \c size and enables chunking in the underlying
HDF5 layer.
Note that this policy wastes disk space, but can improve write
bandwidth on parallel filesystems that are sensitive to write alignment
(e.g. lustre). It is only recommended when using the MPI-POSIX or MPI-IO
independent VFDs (see \ref H5OpenFile).
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartSetChunk (
h5_file_t *f,
h5_size_t size
);
) {
H5_API_ENTER (h5_err_t, "f=%p, size=%llu", f, (long long unsigned)size);
H5_API_RETURN (h5u_set_chunk (f, size));
}
h5_err_t
/*!
\ingroup h5part_data
Write array of 64 bit floating point data to file.
After setting the number of particles with \c H5PartSetNumParticles() and
the current timestep using \c H5SetStep(), you can start writing datasets
into the file. Each dataset has a name associated with it (chosen by the
user) in order to facilitate later retrieval. The name of the dataset is
specified in the parameter \c name, which must be a null-terminated string.
There are no restrictions on naming of datasets, but it is useful to arrive
at some common naming convention when sharing data with other groups.
The writing routines also implicitly store the datatype of the array so that
the array can be reconstructed properly on other systems with incompatible
type representations.
All data that is written after setting the timestep is associated with that
timestep. While the number of particles can change for each timestep, you
cannot change the number of particles in the middle of a given timestep.
The data is committed to disk before the routine returns.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartWriteDataFloat64 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate array with */
const h5_float64_t *data /*!< [in] Array to commit to disk */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_DOUBLE));
}
h5_err_t
/*!
\ingroup h5part_data
Write array of 32 bit floating point data to file.
After setting the number of particles with \c H5PartSetNumParticles() and
the current timestep using \c H5SetStep(), you can start writing datasets
into the file. Each dataset has a name associated with it (chosen by the
user) in order to facilitate later retrieval. The name of the dataset is
specified in the parameter \c name, which must be a null-terminated string.
There are no restrictions on naming of datasets, but it is useful to arrive
at some common naming convention when sharing data with other groups.
The writing routines also implicitly store the datatype of the array so that
the array can be reconstructed properly on other systems with incompatible
type representations.
All data that is written after setting the timestep is associated with that
timestep. While the number of particles can change for each timestep, you
cannot change the number of particles in the middle of a given timestep.
The data is committed to disk before the routine returns.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartWriteDataFloat32 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate array with */
const h5_float32_t *data /*!< [in] Array to commit to disk */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
h5_err_t h5err = h5u_write_data( f, name, (void*)data, H5T_NATIVE_FLOAT );
H5_API_RETURN (h5err);
}
h5_err_t
/*!
\ingroup h5part_data
Write array of 64 bit integer data to file.
After setting the number of particles with \c H5PartSetNumParticles() and
the current timestep using \c H5SetStep(), you can start writing datasets
into the file. Each dataset has a name associated with it (chosen by the
user) in order to facilitate later retrieval. The name of the dataset is
specified in the parameter \c name, which must be a null-terminated string.
There are no restrictions on naming of datasets, but it is useful to arrive
at some common naming convention when sharing data with other groups.
The writing routines also implicitly store the datatype of the array so that
the array can be reconstructed properly on other systems with incompatible
type representations.
All data that is written after setting the timestep is associated with that
timestep. While the number of particles can change for each timestep, you
cannot change the number of particles in the middle of a given timestep.
The data is committed to disk before the routine returns.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartWriteDataInt64 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate array with */
const h5_int64_t *data /*!< [in] Array to commit to disk */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_INT64));
}
h5_err_t
/*!
\ingroup h5part_data
Write array of 32 bit integer data to file.
After setting the number of particles with \c H5PartSetNumParticles() and
the current timestep using \c H5SetStep(), you can start writing datasets
into the file. Each dataset has a name associated with it (chosen by the
user) in order to facilitate later retrieval. The name of the dataset is
specified in the parameter \c name, which must be a null-terminated string.
There are no restrictions on naming of datasets, but it is useful to arrive
at some common naming convention when sharing data with other groups.
The writing routines also implicitly store the datatype of the array so that
the array can be reconstructed properly on other systems with incompatible
type representations.
All data that is written after setting the timestep is associated with that
timestep. While the number of particles can change for each timestep, you
cannot change the number of particles in the middle of a given timestep.
The data is committed to disk before the routine returns.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartWriteDataInt32 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate array with */
const h5_int32_t *data /*!< [in] Array to commit to disk */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_write_data (f, name, (void*)data, H5T_NATIVE_INT32));
}
h5_err_t
/*!
\ingroup h5part_data
Read array of 64 bit floating point data from file.
When retrieving datasets from disk, you ask for them
by name. There are no restrictions on naming of arrays,
but it is useful to arrive at some common naming
convention when sharing data with other groups.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartReadDataFloat64 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate dataset with */
h5_float64_t *data /*!< [out] Array of data */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_DOUBLE));
}
h5_err_t
/*!
\ingroup h5part_data
Read array of 32 bit floating point data from file.
When retrieving datasets from disk, you ask for them
by name. There are no restrictions on naming of arrays,
but it is useful to arrive at some common naming
convention when sharing data with other groups.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartReadDataFloat32 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate dataset with */
h5_float32_t *data /*!< [out] Array of data */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_FLOAT));
}
h5_err_t
/*!
\ingroup h5part_data
Read array of 64 bit integer data from file.
When retrieving datasets from disk, you ask for them
by name. There are no restrictions on naming of arrays,
but it is useful to arrive at some common naming
convention when sharing data with other groups.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartReadDataInt64 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate dataset with */
h5_int64_t *data /*!< [out] Array of data */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_INT64));
}
h5_err_t
/*!
\ingroup h5part_data
Read array of 32 bit integer data from file.
When retrieving datasets from disk, you ask for them
by name. There are no restrictions on naming of arrays,
but it is useful to arrive at some common naming
convention when sharing data with other groups.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartReadDataInt32 (
h5_file_t *f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name to associate dataset with */
h5_int32_t *data /*!< [out] Array of data */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', date=%p", f,name,data);
H5_API_RETURN (h5u_read_data (f, name, data, H5T_NATIVE_INT32));
}
h5_ssize_t
/*!
\ingroup h5part_model
Get the number of datasets that are stored at the current time-step.
\return number of datasets in current timestep or error code
*/
static inline h5_ssize_t
H5PartGetNumDatasets (
h5_file_t *f /*!< [in] Handle to open file */
);
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5u_get_num_datasets(f));
}
h5_err_t
/*!
\ingroup h5part_model
This reads the name of a dataset specified by it's index in the current
time-step.
If the number of datasets is \c n, the range of \c _index is \c 0 to \c n-1.
\result \c H5_SUCCESS
*/
static inline h5_err_t
H5PartGetDatasetName (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *name, /*!< [out] Name of dataset */
const h5_size_t len /*!< [in] Size of buffer \c name */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"idx=%lld, "
"name='%p', len=%llu, ",
f,
(long long)idx,
name, (unsigned long long)len);
H5_API_RETURN (h5u_get_dataset_info(f, idx, name, len, NULL, NULL));
}
h5_err_t
/*!
\ingroup h5part_model
Gets the name, type and number of elements of a dataset based on its
index in the current timestep.
Type is one of the following values:
- \c H5_FLOAT64_T (for \c h5_float64_t)
- \c H5_FLOAT32_T (for \c h5_float32_t)
- \c H5_INT64_T (for \c h5_int64_t)
- \c H5_INT32_T (for \c h5_int32_t)
\return \c H5_SUCCESS
*/
static inline h5_err_t
H5PartGetDatasetInfo (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_id_t idx, /*!< [in] Index of the dataset */
@@ -102,48 +409,190 @@ H5PartGetDatasetInfo (
/*!< [in] Size of buffer \c dataset_name */
h5_int64_t *type, /*!< [out] Type of data in dataset */
h5_size_t *nelem /*!< [out] Number of elements. */
);
) {
H5_API_ENTER (h5_int64_t,
"f=%p, "
"idx=%lld, "
"dataset_name='%p', len_dataset_name=%llu, "
"type=%p, nelem=%p",
f,
(long long)idx,
dataset_name, (long long unsigned)len_dataset_name,
type, nelem);
H5_API_RETURN (h5u_get_dataset_info (
f, idx, dataset_name, len_dataset_name, type, nelem));
}
h5_ssize_t
/*!
\ingroup h5part_model
This function returns the number of particles in this processor's view,
if a view has been set.
If not, it returns the total number of particles across all processors
from the last \ref H5PartSetNumParticles call.
If you have neither set the number of particles
nor set a view, then this returns the total number of
particles in the first data set of the current time step.
Note that H5Part assumes that all data sets within a given time step
have the same number of particles (although the number particles can
vary across time steps).
If none of these conditions are met, an error is thrown.
\return number of particles in current timestep or an error
code.
*/
static inline h5_ssize_t
H5PartGetNumParticles (
h5_file_t *f /*!< [in] Handle to open file */
);
) {
H5_API_ENTER (h5_ssize_t, "f=%p", f);
CHECK_FILEHANDLE( f );
H5_API_RETURN (h5u_get_num_particles (f));
}
h5_err_t
/*!
\ingroup h5part_model
Reset the view.
\return \c H5_SUCCESS
*/
static inline h5_err_t
H5PartResetView (
h5_file_t *f /*!< [in] Handle to open file */
);
) {
H5_API_ENTER (h5_ssize_t, "f=%p", f);
H5_API_RETURN (h5u_reset_view (f));
}
h5_err_t
/*!
\ingroup h5part_model
Check whether a view has been set, either automatically with
\ref H5PartSetNumParticles or manually with \ref H5PartSetView
or \ref H5PartSetViewIndices.
\return 0 for false or 1 for true
*/
static inline h5_err_t
H5PartHasView (
h5_file_t *f /*!< [in] Handle to open file */
);
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5u_has_view (f));
}
h5_err_t
/*!
\ingroup h5part_model
For parallel I/O or for subsetting operations on the datafile,
this function allows you to define a subset of the total
particle dataset to operate on.
The concept of "view" works for both serial
and for parallel I/O. The "view" will remain in effect until a new view
is set, or the number of particles in a dataset changes, or the view is
"unset" by calling \c H5PartSetView(file,-1,-1);
Before you set a view, \ref H5PartGetNumParticles will return the
total number of particles in the current time-step (even for the parallel
reads). However, after you set a view, it will return the number of
particles contained in the view.
The range is \e inclusive: the end value is the last index of the
data.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartSetView (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t start, /*!< [in] Start particle */
h5_int64_t end /*!< [in] End particle */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, start=%lld, end=%lld",
f, (long long)start, (long long)end);
H5_API_RETURN (h5u_set_view (f, start, end));
}
h5_err_t
/*!
\ingroup h5part_model
For parallel I/O or for subsetting operations on the datafile,
this function allows you to define a subset of the total
dataset to operate on by specifying a list of indices.
The concept of "view" works for both serial
and for parallel I/O. The "view" will remain in effect until a new view
is set, or the number of particles in a dataset changes, or the view is
"unset" by calling \c H5PartSetViewIndices(NULL,0);
When you perform a read or write on a view consisting of indices, it
is assumed that your buffer is \b unpacked, meaning that there is room
for all the intermediate values (which will not be touched by the read
or write).
Before you set a view, the \c H5PartGetNumParticles() will return the
total number of particles in the current time-step (even for the parallel
reads). However, after you set a view, it will return the number of
particles contained in the view.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartSetViewIndices (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_size_t *indices, /*!< [in] List of indices */
h5_size_t nelems /*!< [in] Size of list */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, indices=%p, nelems=%llu",
f, indices, (long long unsigned)nelems);
H5_API_RETURN (h5u_set_view_indices (f, indices, nelems));
}
h5_err_t
/*!
\ingroup h5part_model
Allows you to query the current view. Start and End
will be \c -1 if there is no current view established.
Use \c H5PartHasView() to see if the view is smaller than the
total dataset.
\return number of elements in the view or error code
*/
static inline h5_err_t
H5PartGetView (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t *start, /*!< [out] Start particle */
h5_int64_t *end /*!< [out] End particle */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, start=%p, end=%p",
f, start, end);
H5_API_RETURN (h5u_get_view (f, start, end));
}
h5_err_t
/*!
\ingroup h5part_model
If it is too tedious to manually set the start and end coordinates
for a view, the \c H5SetCanonicalView() will automatically select an
appropriate domain decomposition of the data arrays for the degree
of parallelism and set the "view" accordingly.
\return H5_SUCCESS or error code
*/
static inline h5_err_t
H5PartSetCanonicalView (
h5_file_t *f /*!< [in] Handle to open file */
);
) {
H5_API_ENTER (h5_err_t, "f=%p", f);
H5_API_RETURN (h5u_set_canonical_view (f));
}
#ifdef __cplusplus
}
src/include/H5_attachments.h
+44 -20
View File
@@ -5,44 +5,68 @@
extern "C" {
#endif
h5_ssize_t
static inline h5_ssize_t
H5GetNumAttachments (
h5_file_t* const f
);
h5_file_t* const f /*!< [in] Handle to open file */
) {
H5_API_ENTER (h5_ssize_t, "f=%p", f);
H5_API_RETURN (h5_get_num_attachments (f));
}
h5_err_t
static inline h5_err_t
H5GetAttachmentInfoByIdx (
h5_file_t* const f,
const h5_size_t idx, // IN
char* const fname, // OUT
h5_size_t len_fname, // IN
h5_size_t* const fsize // OUT
);
) {
H5_API_ENTER (h5_err_t,
"idx=%llu, fname=%p, len_fname=%llu, fsize=%p",
(long long unsigned)idx,
fname, (long long unsigned)len_fname,
fsize);
H5_API_RETURN (h5_get_attachment_info_by_idx (
f, idx, fname, len_fname, fsize));
}
h5_err_t
static inline h5_err_t
H5GetAttachmentInfoByName (
h5_file_t* const f,
char* const fname,
h5_size_t* const fsize
);
char* const fname, // OUT
h5_size_t* const fsize // OUT
) {
H5_API_ENTER (h5_err_t, "fname='%s', fsize=%p", fname, fsize);
H5_API_RETURN (h5_get_attachment_info_by_name (
f, fname, fsize));
}
h5_err_t
static inline h5_err_t
H5AddAttachment (
h5_file_t* const f,
const char* fname
);
h5_file_t* const f, /*!< [in] Handle to open file */
const char* fname /*!< [in] Name of file to attach */
) {
H5_API_ENTER (h5_err_t, "fname='%s'", fname);
H5_API_RETURN (h5_add_attachment (f, fname));
}
h5_err_t
static inline h5_err_t
H5GetAttachment (
h5_file_t* const f,
const char* name
);
h5_file_t* const f, /*!< [in] Handle to open file */
const char* fname /*!< [in] Name of attachment */
) {
H5_API_ENTER (h5_err_t, "fname='%s'", fname);
H5_API_RETURN (h5_get_attachment (f, fname));
}
h5_err_t
static inline h5_err_t
H5DeleteAttachment (
h5_file_t* const f,
const char* const name
);
const char* const fname
) {
H5_API_ENTER (h5_err_t, "fname='%s'", fname);
H5_API_RETURN (h5_delete_attachment (f, fname));
}
#ifdef __cplusplus
}
src/include/H5_attribs.h
+489 -48
View File
@@ -5,165 +5,555 @@
extern "C" {
#endif
h5_err_t
/*** WRITE ***/
/*!
\ingroup h5hut_attrib
Write an attribute \c name with the string \c value to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteFileAttribString (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const char *value /*!< [in] Value of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', value='%s'", f, name, value);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_CHAR,
value,
strlen(value) + 1 ));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with the string \c value to
the current timestep.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteStepAttribString (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const char *value /*!< [in] Value of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', value='%s'", f, name, value);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_CHAR,
value,
strlen(value) + 1 ));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with float32 \c values to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteFileAttribFloat32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_float32_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_FLOAT,
values,
nelems ));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with float32 \c values to
the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteStepAttribFloat32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_float32_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_FLOAT,
values,
nelems ));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with float64 \c values to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteFileAttribFloat64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_float64_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_DOUBLE,
values,
nelems));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with float64 \c values to
the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteStepAttribFloat64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_float64_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_DOUBLE,
values,
nelems));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with int32 \c values to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteFileAttribInt32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_int32_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_INT32,
values,
nelems));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with int32 \c values to
the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteStepAttribInt32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_int32_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_INT32,
values,
nelems));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with int64 \c values to
the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteFileAttribInt64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_int64_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_FILE,
name,
H5T_NATIVE_INT64,
values,
nelems));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Write an attribute \c name with int64 \c values to
the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5WriteStepAttribInt64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
const h5_int64_t *values, /*!< [in] Values of attribute */
const h5_size_t nelems /*!< [in] Number of values */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', values=%p, nelems=%llu",
f, name, values, (long long unsigned)nelems);
H5_API_RETURN (h5_write_attrib (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_INT64,
values,
nelems));
}
h5_err_t
/*** READ ***/
/*!
\ingroup h5hut_attrib
Read a string into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadFileAttribString (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
char *buffer /*!< [out] Value of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', value='%s'", f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_STRING_T,
(void*)buffer));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read a string into a \c buffer from an attribute \c name
in the current timestep.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadStepAttribString (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
char *buffer /*!< [out] Value of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', value='%s'",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_STRING_T,
(void*)buffer));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read int32 values into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadFileAttribInt32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_int32_t *buffer /*!< [out] Values of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_INT32_T,
(void*)buffer));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read int32 values into a \c buffer from an attribute \c name
in the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadStepAttribInt32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_int32_t *buffer /*!< [out] Values of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_INT32_T,
(void*)buffer));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read int64 values into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadFileAttribInt64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_int64_t *buffer /*!< [out] Values of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_INT64_T,
(void*)buffer));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read int64 values into a \c buffer from an attribute \c name
in the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadStepAttribInt64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_int64_t *buffer /*!< [out] Values of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
h5_err_t h5err = h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_INT64_T,
(void*)buffer);
H5_API_RETURN (h5err);
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read float32 values into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadFileAttribFloat32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_float32_t *buffer /*!< [out] Values of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_FLOAT32_T,
(void*)buffer));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read float32 values into a \c buffer from an attribute \c name
in the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadStepAttribFloat32 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_float32_t *buffer /*!< [out] Values of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_FLOAT32_T,
(void*)buffer));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read float64 values into a \c buffer from an attribute \c name
in the file root ("/").
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadFileAttribFloat64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_float64_t *buffer /*!< [out] Values of attribute */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_FILE,
name,
H5_FLOAT64_T,
(void*)buffer));
}
h5_err_t
/*!
\ingroup h5hut_attrib
Read float64 values into a \c buffer from an attribute \c name
in the current time step.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5ReadStepAttribFloat64 (
h5_file_t *const f, /*!< [in] Handle to open file */
const char *name, /*!< [in] Name of attribute to create */
h5_float64_t *buffer /*!< [out] Values of attribute */
);
) {
H5_API_ENTER (h5_err_t, "f=%p, name='%s', buffer=%p",
f, name, buffer);
H5_API_RETURN (h5_read_attrib (
f,
H5_ATTRIB_STEP,
name,
H5_FLOAT64_T,
(void*)buffer));
}
h5_int64_t
/*** QUERY ***/
/*!
\ingroup h5hut_attrib
Gets the number of attributes in the file's root ("/").
\return Number of attributes or error code.
*/
static inline h5_int64_t
H5GetNumFileAttribs (
h5_file_t *const f /*!< [in] Handle to open file */
);
) {
H5_API_ENTER (h5_int64_t, "f=%p", f);
H5_API_RETURN (h5_get_num_attribs (f, H5_ATTRIB_FILE));
}
h5_int64_t
/*!
\ingroup h5hut_attrib
Gets the number of attributes bound to the current step.
\h5_err_t h5err = Number of attributes or error code.
*/
static inline h5_int64_t
H5GetNumStepAttribs (
h5_file_t *const f /*!< [in] Handle to open file */
);
) {
H5_API_ENTER (h5_int64_t, "f=%p", f);
H5_API_RETURN (h5_get_num_attribs (f, H5_ATTRIB_STEP));
}
h5_int64_t
/*!
\ingroup h5hut_attrib
Gets the name, type and number of elements of the file attribute
specified by its index.
This function can be used to retrieve all attributes bound to the
file \c f by looping from \c 0 to the number of attribute minus
one. The number of attributes bound to file \c f can be queried
by calling \ref H5GetNumFileAttribs.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5GetFileAttribInfo (
h5_file_t *const f, /*!< [in] Handle to open file */
const h5_size_t attrib_idx, /*!< [in] Index of attribute to get
@@ -173,9 +563,41 @@ H5GetFileAttribInfo (
/*!< [in] length of buffer \c name */
h5_int64_t *attrib_type, /*!< [out] Type of value. */
h5_size_t *attrib_nelem /*!< [out] Number of elements */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"attrib_idx=%llu, attrib_name=%p, len_attrib_name=%llu, "
"attrib_type=%p, attrib_nelem=%p",
f,
(long long unsigned)attrib_idx,
attrib_name,
(long long unsigned)len_of_attrib_name,
attrib_type,
attrib_nelem);
H5_API_RETURN (h5_get_attrib_info (
f,
H5_ATTRIB_FILE,
attrib_idx,
attrib_name,
len_of_attrib_name,
attrib_type,
attrib_nelem));
}
h5_int64_t
/*!
\ingroup h5hut_attrib
Gets the name, type and number of elements of the step attribute
specified by its index.
This function can be used to retrieve all attributes bound to the
current time-step by looping from \c 0 to the number of attribute
minus one. The number of attributes bound to the current
time-step can be queried by calling \ref H5GetNumStepAttribs.
\return \c H5_SUCCESS or error code
*/
static inline h5_err_t
H5GetStepAttribInfo (
h5_file_t *const f, /*!< [in] Handle to open file */
const h5_size_t attrib_idx, /*!< [in] Index of attribute to
@@ -185,7 +607,26 @@ H5GetStepAttribInfo (
/*!< [in] length of buffer \c name */
h5_int64_t *attrib_type, /*!< [out] Type of value. */
h5_size_t *attrib_nelem /*!< [out] Number of elements */
);
) {
H5_API_ENTER (h5_err_t,
"f=%p, "
"attrib_idx=%llu, attrib_name=%p, len_attrib_name=%llu, "
"attrib_type=%p, attrib_nelem=%p",
f,
(unsigned long long)attrib_idx,
attrib_name,
(unsigned long long)len_of_attrib_name,
attrib_type,
attrib_nelem);
H5_API_RETURN (h5_get_attrib_info (
f,
H5_ATTRIB_STEP,
attrib_idx,
attrib_name,
len_of_attrib_name,
attrib_type,
attrib_nelem));
}
#ifdef __cplusplus
}
test/Makefile.am
+9 -19
View File
@@ -1,16 +1,17 @@
# test level Makefile.am
#SUBDIRS = H5Block H5Fed H5Part
SUBDIRS = H5Fed
AM_CPPFLAGS += -I$(top_srcdir)/src/include
AM_LDFLAGS += -L${abs_top_builddir}/src/lib
OBJEXT=o
LDADD =
LDADD += -lH5hut
AM_CPPFLAGS = -I../src/include @AM_CPPFLAGS@
noinst_PROGRAMS =
noinst_PROGRAMS = @BUILD_TESTS@
if ENABLE_C
noinst_PROGRAMS += h5u_test h5b_test h5_attach_test
TESTS_ENVIRONMENT = env LD_LIBRARY_PATH=@HDF5ROOT@/lib:$(LD_LIBRARY_PATH)
TESTS = @BUILD_TESTS@
TESTS_ENVIRONMENT = env LD_LIBRARY_PATH=@HDF5_PREFIX@/lib:$(LD_LIBRARY_PATH)
EXTRA_PROGRAMS = h5u_test h5b_test h5_attach_test
@@ -22,10 +23,6 @@ h5u_test_SOURCES = \
testframe.h \
params.h
h5u_test_LDADD = \
../src/C/libH5hutC.la \
../src/h5core/libH5hut.la
h5b_test_SOURCES = \
h5b_test.c \
h5b_write.c \
@@ -34,16 +31,9 @@ h5b_test_SOURCES = \
testframe.h \
params.h
h5b_test_LDADD = \
../src/C/libH5hutC.la \
../src/h5core/libH5hut.la
h5_attach_test_SOURCES = \
h5_attach_test.c
h5_attach_test_LDADD = \
../src/C/libH5hutC.la \
../src/h5core/libH5hut.la
endif
clean-local:
${RM} -f *.h5
tools/Makefile.am
+9 -17
View File
@@ -6,31 +6,23 @@ if ENABLE_VTKCONVERTER
SUBDIRS += vtk2h5grid
endif
AM_LDFLAGS = -L../src/lib @LDFLAGS@
LIBS = -lH5hutC -lH5hut @LIBS@
AM_CPPFLAGS += -I${abs_top_builddir}/src/include -Wno-deprecated
FFLAGS += -cpp $(AM_CPPFLAGS)
AM_LDFLAGS += -L${abs_top_builddir}/src/lib
AM_CPPFLAGS = -I../src/include @AM_CPPFLAGS@
LDADD =
LDADD += -lH5hut
# What to build... make install will place these files in the $(prefix)/bin directory.
bin_PROGRAMS = @BUILD_TOOLS@
EXTRA_PROGRAMS = h5pAttrib h5PartDcToVtk h5PartSurfaceToVtk
if ENABLE_C
EXTRA_SCRIPTS = # h5hutcc
EXTRA_PROGRAMS = h5pAttrib
endif
# Listing of all programs that maybe built. (Has to know statically...)
EXTRA_SCRIPTS = h5hutcc
# Extra files that I wish to include in the dist tar ball.
#EXTRA_DIST = h5pAttrib.cc h5pToGNUplot.cc## TO BE TAILORED LATER...
# Listing of sources
h5pAttrib_SOURCES = h5pAttrib.cc
#h5pToGNUplot_SOURCES = h5pToGNUplot.cc
#homdynToH5p_SOURCES = homdynToH5p.cc
h5PartDcToVtk_SOURCES = h5PartDcToVtk.cc
h5PartSurfaceToVtk_SOURCES = h5PartSurfaceToVtk.cc
clean: clean-am