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Integrated H5Part regression test and fixed numerous errors that it discovered.

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Finished integrating H5Block and the Fortran interface (untested).
Started adding an H5Block regression test with a few simple tests (all pass).
Added automatic detection of stripe information on lustre, and config option to compile against lustre API.
Moved buffers for H5Block ghost zone disolving out of the file handle and into the h5b_3d_set_view function.
Fixed bug with pointers in the H5Fed file data not being initialized to NULL.
This commit is contained in:
Marc Howison
2010-07-15 19:44:48 +00:00
parent 2c267f173a
commit 7ea00c38f8
50 changed files with 1404 additions and 747 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.gitattributes
+5 -2
View File
@@ -376,7 +376,6 @@ src/C/H5Fed_store.c -text
src/C/H5Fed_tags.c -text
src/C/H5Part.c -text
src/C/H5_attribs.c -text
src/C/H5_inquiry.c -text
src/C/Makefile.am -text
src/C/generate-h5b-readwrite.py -text
src/Fortran/H5.f90 -text
@@ -404,6 +403,8 @@ src/h5core/h5_hdf5.c -text
src/h5core/h5_hdf5_private.h -text
src/h5core/h5_hsearch.c -text
src/h5core/h5_hsearch_private.h -text
src/h5core/h5_lustre.c -text
src/h5core/h5_lustre_private.h -text
src/h5core/h5_maps.c -text
src/h5core/h5_model.c -text
src/h5core/h5_mpi.c -text
@@ -473,7 +474,6 @@ src/include/H5Fed_store.h -text
src/include/H5Fed_tags.h -text
src/include/H5Part.h -text
src/include/H5_attribs.h -text
src/include/H5_inquiry.h -text
src/include/H5hut.h -text
src/include/grephdr -text
src/include/h5core/h5_attribs.h -text
@@ -530,6 +530,9 @@ test/H5Part/H5testF.f -text
test/H5Part/H5testFpar.f90 -text
test/H5Part/Makefile.am -text
test/Makefile.am -text
test/h5b_read.c -text
test/h5b_test.c -text
test/h5b_write.c -text
test/h5u_read.c -text
test/h5u_test.c -text
test/h5u_write.c -text
Makefile.am
+3 -1
View File
@@ -1,5 +1,7 @@
SUBDIRS = \
src
src \
test \
tools
MAINTAINERCLEANFILES = \
config.h \
configure.ac
+46 -17
View File
@@ -18,6 +18,12 @@ AC_CONFIG_HEADER(config.h)
################# --enable-xxx and --with-xxx Argument ########################
###############################################################################
AC_ARG_ENABLE(
[debug],
[AC_HELP_STRING([--enable-debug],
[Compile with debug flags [default=no]])],
[USE_DEBUG=$enableval])
AC_ARG_ENABLE(
[64],
[AC_HELP_STRING([--enable-64],
@@ -54,6 +60,13 @@ AC_ARG_WITH(
[path to HDF5 installation [default=""]])],
[HDF5PATH=$withval], [HDF5PATH=""])
AC_ARG_WITH(
[lustre],
[AC_HELP_STRING([--with-lustre],
[path to lustre user API [default=""]])],
[LUSTREPATH=$withval], [LUSTREPATH=""])
###############################################################################
################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
###############################################################################
@@ -169,6 +182,15 @@ AC_DEFINE_UNQUOTED(MY_UNAME, "$uname", "")
######################## CONFIGURE LINE OPTIONS ###############################
###############################################################################
AC_MSG_CHECKING([if debug is enabled])
if test "X$USE_DEBUG" = "Xyes"; then
AC_MSG_RESULT([yes])
CFLAGS="$CFLAGS -g"
else
AC_MSG_RESULT([no])
fi
############################ fortran enabled ##################################
AC_MSG_CHECKING([if fortran interface enabled])
if test "X$USE_FORTRAN" = "Xyes"; then
@@ -361,23 +383,7 @@ else
P="$P /usr/local/hdf5"
P="$P /usr/local/packages/hdf5"
P="$P /apps/hdf5"
if test "X$USE_PARALLEL" = "Xyes"; then
P="$P /usr/local/phdf5"
P="$P /usr/local/hdf5/hdf5_par"
if test "X$USE_64" = "Xyes"; then
P="$P /usr/common/usg/hdf5/64/default/parallel"
else
P="$P /usr/common/usg/hdf5/32/default/parallel"
fi
else
P="$P /usr/local/hdf5/hdf5_serial"
if test "X$USE_64" = "Xyes"; then
P="$P /usr/common/usg/hdf5/64/default/serial"
else
P="$P /usr/common/usg/hdf5/32/default/serial"
fi
fi
P="$P /opt/hdf5"
fi
PATH_Search HDF5ROOT "$P" include/hdf5.h
if test -z "$HDF5ROOT"; then
@@ -403,6 +409,27 @@ if test -n "$ZLIBROOT"; then
LDFLAGS="$LDFLAGS -L$ZLIBROOT/lib"
fi
AC_MSG_CHECKING([for lustre API ])
AC_MSG_RESULT([])
if test -n "${LUSTREPATH}"; then
P=${LUSTREPATH}
elif test -n "${LUSTRE_DIR}" ; then
P=${LUSTRE_DIR}
else
P=''
P="$P /usr"
P="$P /usr/local"
P="$P /usr/local/lustre"
P="$P /opt/lustre"
fi
PATH_Search LUSTREROOT "$P" usr/include/lustre/liblustreapi.h
if test -z "$LUSTREROOT"; then
AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
else
CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
fi
###############################################################################
################# A SIMPLE WORK AROUND TO USE ENV. VARS #######################
###############################################################################
@@ -472,6 +499,7 @@ fi
# If value is given, in addition assign it to variable.
AC_SUBST(MPIROOT)
AC_SUBST(HDF5ROOT)
AC_SUBST(LUSTREROOT)
AC_SUBST(MPIINC)
AC_SUBST(MPILIB)
AC_SUBST(MPICC)
@@ -531,5 +559,6 @@ AC_MSG_RESULT([MPILIB = $MPILIB])
AC_MSG_RESULT([MPIINC = $MPIINC])
AC_MSG_RESULT([MPIROOT = $MPIROOT])
AC_MSG_RESULT([HDF5ROOT = $HDF5ROOT])
AC_MSG_RESULT([LUSTREROOT = $LUSTREROOT])
AC_MSG_RESULT([LDFLAGS = $LDFLAGS])
AC_MSG_RESULT([ ])
src/C/H5.c
+65 -3
View File
@@ -94,13 +94,13 @@ H5CheckFile (
Define format of the step names.
Example: ==H5FedDefineStepNameFormat( f, "Step", 6 )== defines step names
Example: ==H5SetStepNameFormat( f, "Step", 6 )== defines step names
like ==Step#000042==.
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5DefineStepNameFormat (
H5SetStepNameFormat (
h5_file_t* const f, /*!< Handle to file */
const char* name, /*!< Prefix */
const h5_int64_t width /*!< Width of the number */
@@ -140,7 +140,7 @@ H5GetStepNameFormat (
h5_err_t
H5SetStep (
h5_file_t* const f, /*!< [in] Handle to open file */
const h5_int64_t step /*!< [in] Step to set. */
const h5_id_t step /*!< [in] Step to set. */
) {
SET_FNAME (f, __func__);
@@ -163,6 +163,68 @@ H5GetStep (
return h5_get_step (f);
}
/*!
\ingroup h5_inquiry
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
) {
SET_FNAME (f, __func__);
return h5_get_num_procs(f);
}
/*!
\ingroup h5part_c_api_read
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_size_t
H5GetNumSteps (
h5_file_t* const f
) {
SET_FNAME (f, __func__);
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
) {
SET_FNAME (f, __func__);
return h5_has_step (f, stepno);
}
/*!
\ingroup h5_c_api_general
src/C/H5Block.c
+13 -9
View File
@@ -226,6 +226,9 @@ H5BlockGetNumFields (
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
@@ -239,22 +242,23 @@ H5BlockGetFieldInfo (
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 *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
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 */
) {
SET_FNAME( f, __func__ );
return h5b_get_field_info (
f, idx, name, len_name, grid_rank, grid_dims, field_rank, type);
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
*/
@@ -262,16 +266,16 @@ h5_err_t
H5BlockGetFieldInfoByName (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: field name */
h5_size_t *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
h5_size_t *field_rank, /*!< OUT: field rank */
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 */
) {
SET_FNAME( f, __func__ );
return h5b_get_field_info_by_name (
f, name, grid_rank, grid_dims, field_rank, type );
return h5b_get_field_info_by_name (f,
name, field_rank, field_dims, elem_rank, type );
}
/********************** reading and writing attribute ************************/
src/C/H5Part.c
+38 -44
View File
@@ -109,12 +109,12 @@ For further information contact: <a href="mailto:h5part@lists.psi.ch">h5part</a>
h5_err_t
H5PartSetNumParticles (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t nparticles /*!< [in] Number of particles */
h5_size_t nparticles /*!< [in] Number of particles */
) {
SET_FNAME( f, __func__ );
h5_int64_t stride = 1;
h5_size_t stride = 1;
return h5u_set_num_particles( f, nparticles, stride );
}
@@ -148,8 +148,8 @@ H5PartSetNumParticles (
h5_err_t
H5PartSetNumParticlesStrided (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t nparticles, /*!< [in] Number of particles */
h5_int64_t stride /*!< [in] Stride value (e.g. number of fields in the particle array) */
h5_size_t nparticles, /*!< [in] Number of particles */
h5_size_t stride /*!< [in] Stride value (e.g. number of fields in the particle array) */
) {
SET_FNAME( f, __func__ );
@@ -171,9 +171,9 @@ H5PartSetNumParticlesStrided (
\return \c H5_SUCCESS or error code
*/
h5_err_t
H5PartSetChunkSize (
H5PartSetChunk (
h5_file_t *f,
h5_int64_t size
h5_size_t size
) {
SET_FNAME( f, __func__ );
@@ -437,15 +437,13 @@ H5PartReadDataInt32 (
\return number of datasets in current timestep or error code
*/
h5_int64_t
h5_ssize_t
H5PartGetNumDatasets (
h5_file_t *f /*!< [in] Handle to open file */
) {
SET_FNAME( f, __func__ );
CHECK_FILEHANDLE( f );
return h5u_get_num_datasets(f);
}
@@ -459,19 +457,16 @@ H5PartGetNumDatasets (
\result \c H5_SUCCESS
*/
h5_int64_t
h5_err_t
H5PartGetDatasetName (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t idx, /*!< [in] Index of the dataset */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *name, /*!< [out] Name of dataset */
const h5_int64_t len /*!< [in] Size of buffer \c name */
const h5_size_t len /*!< [in] Size of buffer \c name */
) {
SET_FNAME( f, __func__ );
CHECK_FILEHANDLE ( f );
//CHECK_TIMEGROUP ( f );
return h5u_get_dataset_info(f, idx, name, len, NULL, NULL);
}
@@ -481,54 +476,53 @@ H5PartGetDatasetName (
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 macros:
Type is one of the following values:
- \c h5_float64 (for \c h5part_float64_t)
- \c h5_float32 (for \c h5part_float32_t)
- \c h5_int64 (for \c h5part_int64_t)
- \c h5_int32 (for \c h5part_int32_t)
- \c H5PART_CHAR (for \c char)
- \c H5PART_STRING (for \c char*)
- \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_int64_t
h5_err_t
H5PartGetDatasetInfo (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t idx,/*!< [in] Index of the dataset */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *dataset_name, /*!< [out] Name of dataset */
const h5_int64_t len_dataset_name,
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_int64_t *nelem /*!< [out] Number of elements. */
h5_size_t *nelem /*!< [out] Number of elements. */
) {
SET_FNAME( f, __func__ );
CHECK_FILEHANDLE ( f );
//CHECK_TIMEGROUP ( f );
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 the first dataset of
the current timestep (or in the first timestep if none has been set).
This function returns the number of particles in this processor's view,
if a view has been set.
If you have neither set the number of particles (read or write)
nor set a view (read-only), then this returns the total number of
elements on disk of the first dataset if is exists. Otherwise,
it returns 0.
If not, it returns the total number of particles across all processors
from the last \ref H5PartSetNumParticles call.
If you have set a view, this return the number of particles
in the view.
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_int64_t
h5_ssize_t
H5PartGetNumParticles (
h5_file_t *f /*!< [in] Handle to open file */
) {
@@ -556,7 +550,7 @@ H5PartResetView (
/*!
\ingroup h5part_model
*/
h5_int64_t
h5_err_t
H5PartHasView (
h5_file_t *f /*!< [in] Handle to open file */
) {
@@ -569,15 +563,15 @@ H5PartHasView (
/*!
\ingroup h5part_model
For parallel I/O or for subsetting operations on the datafile, the
\c H5PartSetView() function allows you to define a subset of the total
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, the \c H5PartGetNumParticles() will return the
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.
@@ -620,8 +614,8 @@ H5PartSetView (
h5_err_t
H5PartSetViewIndices (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t *indices, /*!< [in] List of indices */
h5_int64_t nelems /*!< [in] Size of list */
const h5_id_t *indices, /*!< [in] List of indices */
h5_size_t nelems /*!< [in] Size of list */
) {
SET_FNAME( f, __func__ );
src/C/H5_attribs.c
+1 -1
View File
@@ -161,7 +161,7 @@ H5WriteStepAttribFloat64 (
f,
H5_ATTRIB_STEP,
name,
H5T_NATIVE_FLOAT,
H5T_NATIVE_DOUBLE,
values,
nelems );
}
src/C/H5_inquiry.c
-89
View File
@@ -1,89 +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.
*/
/*!
\ingroup h5f_c_api
\defgroup h5_inquiry
*/
#include "h5core/h5_core.h"
#include "H5.h"
/*!
\ingroup h5_inquiry
Get the number of compute nodes.
\param[in] f File handle.
\return Number of compute notes.
\return \c -1 on error.
*/
int
H5GetNumNodes (
h5_file_t* const f
) {
SET_FNAME (f, __func__);
CHECK_FILEHANDLE (f);
return h5_get_num_procs(f);
}
/*!
\ingroup h5part_c_api_read
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_size_t
H5GetNumSteps (
h5_file_t* const f
) {
SET_FNAME (f, __func__);
CHECK_FILEHANDLE (f);
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
) {
SET_FNAME (f, __func__);
CHECK_FILEHANDLE (f);
return h5_has_step (f, stepno);
}
src/C/Makefile.am
-2
View File
@@ -17,7 +17,6 @@ EXTRA_LIBRARIES = libH5hutC.a
include_HEADERS = \
../include/H5hut.h \
../include/H5.h \
../include/H5_inquiry.h \
../include/H5_attribs.h \
../include/H5Part.h \
../include/H5Block.h \
@@ -35,7 +34,6 @@ EXTRA_HEADERS =
libH5hutC_a_SOURCES = \
H5.c \
H5_attribs.c \
H5_inquiry.c \
H5Part.c \
H5Block.c \
H5Block_readwrite.c \
src/C/generate-h5b-readwrite.py
+2
View File
@@ -14,6 +14,8 @@ h_tail = """
"""
fc_head = """
#include <stdlib.h>
#include "H5hut.h"
#include "Underscore.h"
src/Fortran/H5Block_F.c
+1 -1
View File
@@ -277,7 +277,7 @@ h5bl_readfieldattrib_string (
char *field_name2 = h5_strdupfor2c ( field_name, l_field_name );
char *attrib_name2 = h5_strdupfor2c ( attrib_name, l_attrib_name );
h5_err_t herr = H5BlockReadFieldAttrib (
h5_err_t herr = H5BlockReadFieldAttribString (
filehandle, field_name2, attrib_name2, attrib_value );
h5_strc2for ( attrib_value, l_attrib_value );
src/Fortran/H5Block_readwrite_F.c
+2
View File
@@ -1,4 +1,6 @@
#include <stdlib.h>
#include "H5hut.h"
#include "Underscore.h"
src/Fortran/H5Part_F.c
+3 -11
View File
@@ -1,3 +1,5 @@
#include <stdlib.h>
#include "H5hut.h"
#include "Underscore.h"
@@ -97,16 +99,6 @@ h5pt_setnpoints_strided (
/*==============Reading Data Characteristics============*/
h5_err_t
h5pt_getnsteps (
const h5_int64_t *f
) {
h5_file_t *filehandle = (h5_file_t*)(size_t)*f;
return H5PartGetNumSteps ( filehandle );
}
h5_err_t
h5pt_getndatasets (
const h5_int64_t *f
@@ -140,7 +132,7 @@ h5pt_getdatasetname (
h5_int64_t herr = H5PartGetDatasetName (
filehandle, *index, name, l_name );
_h5_strc2for ( name, l_name );
h5_strc2for ( name, l_name );
return herr;
}
src/h5core/Makefile.am
+9 -7
View File
@@ -38,6 +38,7 @@ EXTRA_HEADERS = \
h5_qsort_private.h \
h5_readwrite_private.h \
h5_syscall_private.h \
h5_lustre_private.h \
h5u_errorhandling_private.h \
h5b_errorhandling_private.h \
h5b_model_private.h \
@@ -64,16 +65,16 @@ nodist_include_HEADERS =
#OBJEXT = o
# What to build... Will be determined by configure script.
lib_LIBRARIES = libH5Core.a
lib_LIBRARIES = libH5hut.a
# Listing of all possible targets that I may build.
EXTRA_LIBRARIES = libH5Core.a
EXTRA_LIBRARIES = libH5hut.a
# Header files that I wish to install in $(prefix)/include
include_HEADERS =
# Listing of sources
libH5Core_a_SOURCES = \
libH5hut_a_SOURCES = \
h5_attribs.c \
h5_errorhandling.c \
h5_fcmp.c \
@@ -86,6 +87,7 @@ libH5Core_a_SOURCES = \
h5_qsort_r.c \
h5_readwrite.c \
h5_syscall.c \
h5_lustre.c \
h5u_readwrite.c \
h5b_readwrite.c \
h5u_model.c \
@@ -110,12 +112,12 @@ libH5Core_a_SOURCES = \
h5t_store_trim.c \
h5t_tags.c
libH5Core_a_DEPENDENCIES = $(EXTRA_HEADERS)
libH5hut_a_DEPENDENCIES = $(EXTRA_HEADERS)
all: ../lib/libH5Core.a
all: ../lib/libH5hut.a
../lib/libH5Core.a: libH5Core.a
../lib/libH5hut.a: libH5hut.a
-cp $^ $@
$(libH5Core_a_OBJECTS): $(libH5Core_a_DEPENDENCIES)
$(libH5hut_a_OBJECTS): $(libH5hut_a_DEPENDENCIES)
src/h5core/h5_attribs.c
+12 -3
View File
@@ -31,10 +31,12 @@ h5_read_attrib (
const hid_t attrib_type, /*!< HDF5 type of attribute */
void* const attrib_value /*!< OUT: attribute value */
) {
if (mode != H5_ATTRIB_FILE) CHECK_TIMEGROUP( f );
hid_t attrib_id;
hid_t space_id;
hid_t type_id;
hid_t mytype;
hid_t id;
TRY( _get_hdf5_obj_id(f, mode, &id) );
@@ -56,7 +58,7 @@ h5_read_attrib (
TRY( space_id = h5priv_get_hdf5_attribute_dataspace (f, attrib_id) );
TRY( h5priv_read_hdf5_attribute (f, attrib_id, type_id, attrib_value) );
TRY( h5priv_close_hdf5_dataspace(f, space_id) );
TRY( h5priv_close_hdf5_type(f, mytype) );
TRY( h5priv_close_hdf5_type(f, type_id) );
TRY( h5priv_close_hdf5_attribute (f, attrib_id) );
return H5_SUCCESS;
@@ -78,6 +80,10 @@ h5_write_attrib (
const void* attrib_value, /*!< value of attribute */
const hsize_t attrib_nelem /*!< number of elements (dimension) */
) {
if (mode != H5_ATTRIB_FILE) CHECK_TIMEGROUP( f );
CHECK_WRITABLE_MODE( f );
hid_t space_id;
hid_t attrib_id;
hid_t type_id;
@@ -131,6 +137,9 @@ h5_get_attrib_info (
h5_int64_t* attrib_type, /*!< OUT: H5 type of attribute */
h5_size_t* attrib_nelem /*!< OUT: number of elements */
) {
if (mode != H5_ATTRIB_FILE) CHECK_TIMEGROUP( f );
hid_t attrib_id;
hid_t mytype;
hid_t space_id;
@@ -178,7 +187,7 @@ h5_get_num_attribs (
h5_file_t *const f, /*!< handle to open file */
const char mode /*!< FILE or STEP flag */
) {
CHECK_FILEHANDLE (f);
if (mode != H5_ATTRIB_FILE) CHECK_TIMEGROUP( f );
hid_t id;
TRY( _get_hdf5_obj_id(f, mode, &id) );
return h5priv_get_num_hdf5_attribute (f, id);
src/h5core/h5_core_private.h
+9 -4
View File
@@ -1,14 +1,16 @@
#ifndef __H5_CORE_PRIVATE_H
#define __H5_CORE_PRIVATE_H
#define H5_DATANAME_LEN 128
#define H5_STEPNAME_LEN 128
/* WARNING! Changing these values will alter the data model and introduce
* file incompatibilities with previous versions. */
#define H5_DATANAME_LEN 64
#define H5_STEPNAME_LEN 64
#define H5_STEPNAME "Step"
#define H5_STEPWIDTH 1
#define H5_BLOCKNAME "Block"
#define H5_BLOCKNAME_X "0"
#define H5_BLOCKNAME_Y "0"
#define H5_BLOCKNAME_Z "0"
#define H5_BLOCKNAME_Y "1"
#define H5_BLOCKNAME_Z "2"
#include "h5_types_private.h"
@@ -20,6 +22,9 @@
#include "h5_qsort_private.h"
#include "h5_readwrite_private.h"
#include "h5_syscall_private.h"
#ifdef H5_USE_LUSTRE
#include "h5_lustre_private.h"
#endif
#include "h5b_types_private.h"
#include "h5u_types_private.h"
src/h5core/h5_errorhandling.c
+1 -1
View File
@@ -6,7 +6,7 @@
#include "h5_core_private.h"
static h5_errorhandler_t h5priv_errhandler = h5_report_errorhandler;
static h5_int32_t h5priv_debug_level = 0;
static h5_int32_t h5priv_debug_level = 1;
/*!
\ingroup h5_core
src/h5core/h5_hdf5.c
+91 -28
View File
@@ -1,3 +1,4 @@
#include <stdlib.h>
#include <string.h>
#include <hdf5.h>
@@ -55,7 +56,6 @@ h5priv_open_group (
const char* const group_name
) {
hid_t group_id;
herr_t herr = H5Gget_objinfo (loc_id, group_name, 1, NULL);
/*
check access modes:
@@ -66,7 +66,9 @@ h5priv_open_group (
H5_O_APPEND x x (append datasets to an existing group)
*/
if (herr >= 0) {
h5_err_t exists;
TRY( exists = h5priv_hdf5_link_exists(f, loc_id, group_name) );
if (exists > 0) {
h5_info (
f,
"Opening group %s/%s.",
@@ -87,7 +89,7 @@ h5priv_open_group (
return h5_error (
f,
H5_ERR_HDF5,
"Cannot open group \"%s/%s\".",
"Cannot open or create group %s/%s.",
h5_get_objname (loc_id),
group_name);
@@ -574,7 +576,7 @@ h5priv_close_hdf5_dataspace (
h5_file_t* const f,
const hid_t dataspace_id
) {
if (dataspace_id == 0 || dataspace_id == -1 || dataspace_id == H5S_ALL)
if (dataspace_id <= 0 || dataspace_id == H5S_ALL)
return H5_SUCCESS;
herr_t herr = H5Sclose (dataspace_id);
@@ -582,8 +584,7 @@ h5priv_close_hdf5_dataspace (
return h5_error(
f,
H5_ERR_HDF5,
"Cannot terminate access to dataspace \"%s\".",
h5_get_objname (dataspace_id));
"Cannot terminate access to dataspace!");
return H5_SUCCESS;
}
@@ -1202,12 +1203,71 @@ h5priv_delete_hdf5_link (
typedef struct op_data {
int queried_idx;
int cnt;
H5L_type_t type;
H5O_type_t type;
char *name;
size_t len;
char *prefix;
h5_file_t *f;
} op_data_t;
static H5O_type_t
_iter_op_get_obj_type (
h5_file_t *const f,
const hid_t g_id,
const char* name,
const H5L_info_t* info
) {
herr_t herr;
H5O_info_t objinfo;
if ( info->type == H5L_TYPE_EXTERNAL ) {
char *buf;
TRY( buf = h5priv_alloc(f, NULL, info->u.val_size) );
herr = H5Lget_val(g_id, name, buf,
info->u.val_size, H5P_DEFAULT);
if ( herr < 0 )
return h5_error(f,
H5_ERR_HDF5,
"Can't get external link for object '%s'!",
name);
const char *filename;
const char *objname;
herr = H5Lunpack_elink_val(buf, info->u.val_size, 0,
&filename, &objname);
if ( herr < 0 )
return h5_error(f,
H5_ERR_HDF5,
"Can't unpack external link for object '%s'!",
name);
h5_debug(f,
"Followed external link to file '%s' / object '%s'.",
filename, objname);
free(buf);
hid_t obj_id = H5Oopen(g_id, name, H5P_DEFAULT);
if ( obj_id < 0 )
return h5_error(f,
H5_ERR_HDF5,
"Can't open external link for object '%s'!",
name);
herr = H5Oget_info(obj_id, &objinfo);
}
else { // H5L_TYPE_HARD
herr = H5Oget_info_by_name(g_id, name, &objinfo, H5P_DEFAULT);
}
if ( herr < 0 )
return h5_error(f,
H5_ERR_HDF5,
"Can't query object with name '%s'!", name);
return objinfo.type;
}
static herr_t
iter_op_count (
hid_t g_id,
@@ -1216,10 +1276,9 @@ iter_op_count (
void* _op_data
) {
op_data_t* op_data = (op_data_t*)_op_data;
if (info->type != op_data->type) {
return 0;
}
H5O_type_t type;
TRY( type = _iter_op_get_obj_type(op_data->f, g_id, name, info) );
if ( type != op_data->type ) return 0;
op_data->cnt++;
return 0;
}
@@ -1232,9 +1291,9 @@ iter_op_idx (
void* _op_data
) {
op_data_t* op_data = (op_data_t*)_op_data;
if (info->type != op_data->type) {
return 0;
}
H5O_type_t type;
TRY( type = _iter_op_get_obj_type(op_data->f, g_id, name, info) );
if ( type != op_data->type ) return 0;
op_data->cnt++;
/* stop iterating if index is equal cnt */
if (op_data->queried_idx == op_data->cnt) {
@@ -1253,14 +1312,13 @@ iter_op_count_match (
void* _op_data
) {
op_data_t* op_data = (op_data_t*)_op_data;
if (info->type != op_data->type) {
return 0;
}
H5O_type_t type;
TRY( type = _iter_op_get_obj_type(op_data->f, g_id, name, info) );
if ( type != op_data->type ) return 0;
/* count if prefix matches */
if (strncmp (name, op_data->prefix, strlen(op_data->prefix)) == 0) {
op_data->cnt++;
}
return 0;
}
@@ -1271,7 +1329,7 @@ h5_get_num_hdf5_groups (
) {
op_data_t op_data;
memset (&op_data, 0, sizeof (op_data));
op_data.type = (H5L_type_t)H5G_GROUP;
op_data.type = H5O_TYPE_GROUP;
hsize_t start_idx = 0;
herr_t herr = H5Literate (loc_id, H5_INDEX_NAME, H5_ITER_INC,
&start_idx,
@@ -1294,7 +1352,8 @@ h5_get_num_hdf5_groups_matching_prefix (
) {
op_data_t op_data;
memset (&op_data, 0, sizeof (op_data));
op_data.type = (H5L_type_t)H5G_GROUP;
op_data.f = f;
op_data.type = H5O_TYPE_GROUP;
op_data.prefix = prefix;
hsize_t start_idx = 0;
herr_t herr = H5Literate (loc_id, H5_INDEX_NAME, H5_ITER_INC,
@@ -1316,13 +1375,16 @@ h5_get_hdf5_groupname_by_idx (
hid_t loc_id,
hsize_t idx,
char *name,
size_t size
size_t len
) {
op_data_t op_data;
memset (&op_data, 0, sizeof (op_data));
op_data.type = (H5L_type_t)H5G_GROUP;
op_data.f = f;
op_data.type = H5O_TYPE_GROUP;
op_data.cnt = -1;
op_data.queried_idx = idx;
op_data.name = name;
op_data.len = len;
hsize_t start_idx = 0;
herr_t herr = H5Literate (loc_id, H5_INDEX_NAME, H5_ITER_INC,
&start_idx,
@@ -1334,7 +1396,6 @@ h5_get_hdf5_groupname_by_idx (
"Cannot get name of group with index \"%lu\" in \"%s\".",
(long unsigned int)idx, h5_get_objname (loc_id));
}
strncpy (name, op_data.name, size);
return H5_SUCCESS;
}
@@ -1345,7 +1406,8 @@ h5_get_num_hdf5_datasets (
) {
op_data_t op_data;
memset (&op_data, 0, sizeof (op_data));
op_data.type = (H5L_type_t)H5G_DATASET;
op_data.f = f;
op_data.type = H5O_TYPE_DATASET;
hsize_t start_idx = 0;
herr_t herr = H5Literate (loc_id, H5_INDEX_NAME, H5_ITER_INC,
&start_idx,
@@ -1369,14 +1431,16 @@ h5_get_hdf5_datasetname_by_idx (
hid_t loc_id,
hsize_t idx,
char *name,
size_t size
size_t len
) {
return H5_SUCCESS;
op_data_t op_data;
memset (&op_data, 0, sizeof (op_data));
op_data.type = (H5L_type_t)H5G_DATASET;
op_data.f = f;
op_data.type = H5O_TYPE_DATASET;
op_data.cnt = -1;
op_data.queried_idx = idx;
op_data.name = name;
op_data.len = len;
hsize_t start_idx = 0;
herr_t herr = H5Literate (loc_id, H5_INDEX_NAME, H5_ITER_INC,
&start_idx,
@@ -1388,7 +1452,6 @@ h5_get_hdf5_datasetname_by_idx (
"Cannot get name of dataset with index \"%lu\" in \"%s\".",
(long unsigned int)idx, h5_get_objname (loc_id));
}
strncpy (name, op_data.name, size);
return H5_SUCCESS;
}
src/h5core/h5_lustre.c
+155
View File
@@ -0,0 +1,155 @@
#ifdef H5_USE_LUSTRE
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <sys/ioctl.h>
#define __USE_GNU
#include <fcntl.h>
#undef __USE_GNU
#include <lustre/liblustreapi.h>
#include "h5core/h5_core.h"
#include "h5_core_private.h"
#define MSG_HEADER "optimize for lustre: "
static void
_print_stripe_info(struct lov_user_md *lum)
{
fprintf (stderr, "lmm_magic: %u\n", (unsigned)lum->lmm_magic);
fprintf (stderr, "lmm_pattern: %u\n", (unsigned)lum->lmm_pattern);
fprintf (stderr, "lmm_object_id: %lu\n", (unsigned long)lum->lmm_object_id);
fprintf (stderr, "lmm_object_gr: %lu\n", (unsigned long)lum->lmm_object_gr);
fprintf (stderr, "lmm_stripe_size: %u\n", (unsigned)lum->lmm_stripe_size);
fprintf (stderr, "lmm_stripe_count: %u\n", (unsigned)lum->lmm_stripe_count);
fprintf (stderr, "lmm_stripe_offset: %u\n", (unsigned)lum->lmm_stripe_offset);
}
static ssize_t
_get_lustre_stripe_size ( const char *path )
{
size_t nbytes = sizeof(struct lov_user_md) +
INIT_ALLOC_NUM_OSTS * sizeof(struct lov_user_ost_data);
struct lov_user_md *lum;
TRY( lum = h5priv_alloc(f, NULL, nbytes) );
lum->lmm_magic = LOV_USER_MAGIC;
int fd = open64(path, O_RDONLY);
if (fd < 0) {
extern int errno;
if (errno == EINVAL)
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"open64: a flag is invalid!");
else if (errno == EACCES)
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"open64: access denied or file does not exist!");
else if (errno == ENAMETOOLONG)
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"open64: path is too long!");
else
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"open64: unspecific error!");
return -1;
}
int ret = ioctl(fd, LL_IOC_LOV_GETSTRIPE, lum);
if (ret == -1) {
extern int errno;
if (errno == EBADF)
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"ioctl: bad file handle!");
else if (errno == EINVAL)
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"ioctl: invalid argument!");
else if (errno == EIO)
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"ioctl: physical I/O problem!");
else if (errno == ENOTTY)
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"ioctl: file handle does not accept control functions!");
else if (errno == ENODEV)
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"ioctl: driver doesn't support control functions!");
else
h5_error(f, H5_ERR_INTERNAL, MSG_HEADER
"ioctl: unspecific error!");
return -1;
}
close(fd);
if ( f->myproc == 0 && h5_get_debuglevel() >= 5 )
_print_stripe_info(lum);
ssize_t stripe_size = (ssize_t)lum->lmm_stripe_size;
free(lum);
return stripe_size;
}
herr_t
h5_optimize_for_lustre (
h5_file_t *const f,
const char *filename
) {
ssize_t stripe_size;
if ( f->myproc == 0 )
{
char *path = malloc(strlen(filename)+4);
strcpy(path, filename);
/* check for existing file */
FILE *test = fopen(path, "r");
if (!test) {
/* use directory as path */
int i = strlen(path)-1;
while (i >= 0) {
if (path[i] != '/') path[i] = '\0';
else break;
i--;
}
if (strlen(path) == 0) sprintf(path, ".");
}
else fclose(test);
stripe_size = _get_lustre_stripe_size(path);
free(path);
}
TRY( h5priv_mpi_bcast(f, &stripe_size, 1, MPI_LONG_LONG, 0, f->comm) );
h5_info(f, "Found lustre stripe size of %lld bytes", (long long)stripe_size);
hsize_t btree_ik = (stripe_size - 4096) / 96;
hsize_t btree_bytes = 64 + 96*btree_ik;
h5_info(f,
"Setting HDF5 btree ik to %lld (= %lld bytes at rank 3)",
(long long)btree_ik, (long long)btree_bytes);
TRY( h5priv_set_hdf5_btree_ik_property(f, f->create_prop, btree_ik) );
/* set alignment to lustre stripe size */
TRY( h5priv_set_hdf5_alignment_property(f,
f->access_prop, 0, stripe_size) );
if (_verbose) {
fprintf(MSG_STREAM, MSG_HEADER "disabling metadata cache flushes.\n");
}
/* disable metadata cache flushes */
/* defer metadata writes */
H5AC_cache_config_t config;
config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
TRY( H5Pget_mdc_config( fapl_id, &config ) );
config.set_initial_size = 1;
config.initial_size = 16 * 1024 * 1024;
config.evictions_enabled = 0;
config.incr_mode = H5C_incr__off;
config.decr_mode = H5C_decr__off;
config.flash_incr_mode = H5C_flash_incr__off;
TRY( H5Pset_mdc_config( fapl_id, &config ) );
return H5_SUCCESS;
}
#endif // H5_USE_LUSTRE
src/h5core/h5_lustre_private.h
+10
View File
@@ -0,0 +1,10 @@
#ifndef __H5_LUSTRE_PRIVATE_H
#define __H5_LUSTRE_PRIVATE_H
h5_err_t
h5_optimize_for_lustre (
h5_file_t *const f,
const char *filename
);
#endif
src/h5core/h5_mpi.c
+23
View File
@@ -50,6 +50,29 @@ h5priv_mpi_send(
return H5_SUCCESS;
}
h5_err_t
h5priv_mpi_bcast (
h5_file_t* const f,
void* buf,
const int count,
const MPI_Datatype type,
const int root,
const MPI_Comm comm
) {
int err = MPI_Bcast(
buf,
count,
type,
root,
comm
);
if (err != MPI_SUCCESS)
return h5_error (f, H5_ERR_MPI, "Cannot perform broadcast");
return H5_SUCCESS;
}
h5_err_t
h5priv_mpi_sum (
h5_file_t* const f,
src/h5core/h5_mpi_private.h
+10
View File
@@ -24,6 +24,16 @@ h5priv_mpi_send(
const MPI_Comm comm
);
h5_err_t
h5priv_mpi_bcast (
h5_file_t* const f,
void* buf,
const int count,
const MPI_Datatype type,
const int root,
const MPI_Comm comm
);
h5_err_t
h5priv_mpi_sum (
h5_file_t* const f,
src/h5core/h5_openclose.c
+16 -70
View File
@@ -3,9 +3,6 @@
#include <string.h>
#include <errno.h>
#include <fcntl.h>
#if H5_LUSTRE
#include <lustre/liblustreapi.h>
#endif
#include "h5core/h5_core.h"
#include "h5_core_private.h"
@@ -27,7 +24,7 @@ h5_check_filehandle (
h5_file_t* const f /*!< filehandle to check validity of */
) {
if (f == NULL || f->file == 0 || f->u == NULL || f->b == NULL || f->t == NULL) {
if (f == NULL || f->file < 0 || f->u == NULL || f->b == NULL || f->t == NULL) {
return h5_error (
f,
H5_ERR_BADFD,
@@ -59,13 +56,14 @@ h5priv_error_handler (
\return H5_SUCCESS or error code
*/
static h5_int64_t
static h5_err_t
h5upriv_open_file (
h5_file_t* const f /*!< IN: file handle */
) {
TRY( f->u = (h5u_fdata_t*)h5priv_alloc (f, NULL, sizeof (*f->u)) );
h5u_fdata_t *u = f->u;
u->shape = -1;
u->diskshape = H5S_ALL;
u->memshape = H5S_ALL;
u->viewstart = -1;
@@ -86,7 +84,7 @@ h5upriv_open_file (
\return H5_SUCCESS or error code
*/
static h5_int64_t
static h5_err_t
h5bpriv_open_file (
h5_file_t * const f /*!< IN: file handle */
) {
@@ -99,15 +97,13 @@ h5bpriv_open_file (
b = f->b;
memset (b, 0, sizeof (*b));
size_t size = f->nprocs * sizeof (b->user_layout[0]);
TRY( b->user_layout = h5priv_alloc (f, NULL, size) );
size = f->nprocs * sizeof (b->write_layout[0]);
TRY( b->write_layout = h5priv_alloc (f, NULL, size) );
size_t n = sizeof (struct h5b_partition) / sizeof (h5_int64_t);
TRY( h5priv_mpi_type_contiguous(f,
n, MPI_LONG_LONG, &b->partition_mpi_t) );
memset (b->user_layout, 0, sizeof(*b->user_layout));
memset (b->write_layout, 0, sizeof(*b->write_layout));
b->shape = -1;
b->diskshape = -1;
b->memshape = -1;
@@ -177,33 +173,10 @@ h5priv_open_file (
f->xfer_prop, H5FD_MPIO_COLLECTIVE) );
}
}
/* defer metadata writes */
H5AC_cache_config_t config;
config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
TRY( h5priv_get_hdf5_mdc_property(f, f->access_prop, &config) );
config.set_initial_size = 1;
config.initial_size = 16 * 1024 * 1024;
config.evictions_enabled = 0;
config.incr_mode = H5C_incr__off;
config.decr_mode = H5C_decr__off;
config.flash_incr_mode = H5C_flash_incr__off;
TRY( h5priv_set_hdf5_mdc_property(f, f->access_prop, &config) );
#endif /* PARALLEL_IO */
#if H5_LUSTRE
// set alignment
lov_user_md lum;
llapi_file_get_stripe(filename, &lum);
hsize_t stripe_size = (hsize_t)lum.lmm_stripe_size;
h5info(f, "Found lustre stripe size of %lld bytes", (long long)stripe_size);
TRY( h5priv_set_hdf5_alignment_property(f,
f->access_prop, 0, stripe_size) );
hsize_t btree_ik = (stripe_size - 4096) / 96;
hsize_t btree_bytes = 64 + 96*btree_ik;
h5info(f, "Using %lld bytes for HDF5 btree", (long long)btree_bytes);
TRY( h5priv_set_hdf5_btree_ik_property(f, f->create_prop, btree_ik) );
#ifdef H5_USE_LUSTRE
TRY( h5_optimize_for_lustre(f, filename) );
#endif
if (flags & H5_O_RDONLY) {
@@ -240,7 +213,7 @@ h5priv_open_file (
H5_ERR_HDF5,
"Cannot open file \"%s\" with mode \"%d\"",
filename, flags);
TRY( f->root_gid = h5priv_open_group (f, f->file, "/" ));
TRY( f->root_gid = h5priv_open_hdf5_group (f, f->file, "/" ) );
f->mode = flags;
f->step_gid = -1;
f->throttle = 0;
@@ -300,25 +273,16 @@ h5_open_file (
\return H5_SUCCESS or error code
*/
static h5_int64_t
static h5_err_t
h5upriv_close_file (
h5_file_t* const f /*!< file handle */
) {
struct h5u_fdata* u = f->u;
f->__errno = H5_SUCCESS;
if(u->shape != H5S_ALL) {
TRY( h5priv_close_hdf5_dataspace (f, u->shape) );
u->shape = 0;
}
if(u->diskshape != H5S_ALL) {
TRY( h5priv_close_hdf5_dataspace (f, u->diskshape) );
u->diskshape = 0;
}
if(u->memshape != H5S_ALL) {
TRY( h5priv_close_hdf5_dataspace (f, u->memshape) );
u->memshape = 0;
}
TRY( h5priv_close_hdf5_dataspace (f, u->shape) );
TRY( h5priv_close_hdf5_dataspace (f, u->diskshape) );
TRY( h5priv_close_hdf5_dataspace (f, u->memshape) );
TRY( h5priv_close_hdf5_property (f, u->dcreate_prop) );
free (f->u);
f->u = NULL;
@@ -336,13 +300,14 @@ h5upriv_close_file (
\return H5_SUCCESS or error code
*/
static h5_int64_t
static h5_err_t
h5bpriv_close_file (
h5_file_t* const f /*!< IN: file handle */
) {
struct h5b_fdata* b = f->b;
TRY( h5priv_close_hdf5_group (f, b->block_gid) );
TRY( h5priv_close_hdf5_group (f, b->field_gid) );
TRY( h5priv_close_hdf5_dataspace (f, b->shape) );
TRY( h5priv_close_hdf5_dataspace (f, b->diskshape) );
TRY( h5priv_close_hdf5_dataspace (f, b->memshape) );
@@ -490,25 +455,6 @@ h5_get_num_steps(
f->prefix_step_name);
}
/*!
\ingroup h5_core_filehandling
Check whether step with number \c stepno exists.
\return True (value != 0) if step with \c stepno exists.
\return False (0) otherwise
*/
h5_err_t
h5_has_step (
h5_file_t* const f, /*!< file handle */
h5_id_t stepno /*!< step number to check */
) {
char name[128];
sprintf (name, "%s#%0*ld",
f->prefix_step_name, f->width_step_idx, (long)stepno);
return (H5Gget_info_by_name (f->file, name, NULL, H5P_DEFAULT) >= 0);
}
/*!
\ingroup h5_core_filehandling
src/h5core/h5_readwrite.c
+11 -10
View File
@@ -200,7 +200,7 @@ h5priv_close_step (
static h5_err_t
_set_step (
h5_file_t* const f,
const h5_int64_t step_idx /*!< [in] Step to set. */
const h5_id_t step_idx /*!< [in] Step to set. */
) {
f->step_idx = step_idx;
@@ -219,10 +219,10 @@ _set_step (
return H5_SUCCESS;
}
h5_int64_t
h5_err_t
h5_set_step (
h5_file_t* const f, /*!< [in] Handle to open file */
const h5_int64_t step_idx /*!< [in] Step to set. */
h5_file_t* const f, /*!< [in] Handle to open file */
const h5_id_t step_idx /*!< [in] Step to set. */
) {
TRY( h5priv_close_step (f) );
@@ -290,15 +290,15 @@ h5_get_dataset_type(
}
h5_err_t
h5_has_index (
h5_has_step (
h5_file_t* const f, /*!< [in] Handle to open file */
const h5_int64_t step /*!< [in] Step number to query */
const h5_id_t step /*!< [in] Step number to query */
) {
char name[2*H5_STEPNAME_LEN];
sprintf (name,
"%s#%0*lld",
f->prefix_step_name, f->width_step_idx, (long long)step);
return (H5Gget_objinfo(f->file, name, 1, NULL) >= 0);
return h5priv_hdf5_link_exists(f, f->file, name);
}
h5_err_t
@@ -309,8 +309,9 @@ h5_normalize_dataset_name (
) {
if ( strlen(name) > H5_DATANAME_LEN ) {
strncpy ( name2, name, H5_DATANAME_LEN - 1 );
strncpy ( name2, name, H5_DATANAME_LEN-1 );
name2[H5_DATANAME_LEN-1] = '\0';
h5_warn (f, "Truncated name '%s' to '%s'.", name, name2);
} else {
strcpy ( name2, name );
}
@@ -318,8 +319,8 @@ h5_normalize_dataset_name (
if ( strcmp( name2, H5_BLOCKNAME ) == 0 ) {
h5_error (f,
H5_ERR_INVAL,
"Can't create dataset or field with name '%s' because it is "
"reserved by H5Block.",
"Can't create dataset or field with name '%s' because "
"it is reserved by H5Block.",
H5_BLOCKNAME);
}
src/h5core/h5_types_private.h
+1 -1
View File
@@ -29,7 +29,7 @@ struct h5_file {
hid_t xfer_prop; /* dataset transfer properties */
hid_t access_prop; /* file access properties */
hid_t create_prop; /* file create properties */
hid_t root_gid; /* id of root group */
hid_t root_gid; /* id of root */
hid_t step_gid; /* id of current step */
/* step internal data */
src/h5core/h5b_attribs.c
+1 -1
View File
@@ -11,7 +11,7 @@ h5_write_field_attrib (
const h5_int64_t attrib_nelem /*!< IN: number of elements */
) {
TRY( h5bpriv_open_field_group(f, field_name) );
TRY( h5bpriv_create_field_group(f, field_name) );
TRY( h5_write_attrib (
f,
src/h5core/h5b_errorhandling_private.h
+2 -2
View File
@@ -6,12 +6,12 @@
return h5_error( \
f, \
H5_ERR_LAYOUT, \
"No layout defined.")
"No view has been defined!")
#define HANDLE_H5_LAYOUT_ERR( f ) \
h5_error( \
f, \
H5_ERR_LAYOUT, \
"Bad layout.");
"Bad view!");
#endif
src/h5core/h5b_model.c
+176 -157
View File
@@ -17,75 +17,46 @@
static void
_normalize_partition (
struct h5b_partition *p /*!< IN/OUT: partition */
h5b_partition_t *const p /*!< IN/OUT: partition */
) {
h5_int64_t x;
h5_size_t tmp;
if ( p->i_start > p->i_end ) {
x = p->i_start;
tmp = p->i_start;
p->i_start = p->i_end;
p->i_end = x;
p->i_end = tmp;
}
if ( p->j_start > p->j_end ) {
x = p->j_start;
tmp = p->j_start;
p->j_start = p->j_end;
p->j_end = x;
p->j_end = tmp;
}
if ( p->k_start > p->k_end ) {
x = p->k_start;
tmp = p->k_start;
p->k_start = p->k_end;
p->k_end = x;
p->k_end = tmp;
}
}
/*!
\ingroup h5block_private
\internal
Gather layout to all processors
\return H5_SUCCESS or error code
*/
static h5_err_t
_allgather (
h5_file_t *const f /*!< IN: file handle */
) {
#ifdef PARALLEL_IO
struct h5b_partition *partition = &f->b->user_layout[f->myproc];
struct h5b_partition *layout = f->b->user_layout;
TRY( h5priv_mpi_allgather(f,
partition, 1, f->b->partition_mpi_t,
layout, 1, f->b->partition_mpi_t, f->comm) );
#endif
return H5_SUCCESS;
}
/*!
\ingroup h5block_private
\internal
Get dimension sizes of block. These informations are stored inside the
block structure.
*/
/* MLH: this could be improved with an MPI_Reduce and MAX operator...
* but the user_layout array-of-structs would need to be a struct-of-arrays */
static void
_get_dimension_sizes (
h5_file_t *const f /*!< IN: file handle */
_get_max_dimensions (
h5_file_t *const f,
h5b_partition_t *const user_layout
) {
int proc;
struct h5b_fdata *b = f->b;
struct h5b_partition *partition = b->user_layout;
h5b_fdata_t *b = f->b;
h5b_partition_t *p = user_layout;
b->i_max = 0;
b->j_max = 0;
b->k_max = 0;
for ( proc = 0; proc < f->nprocs; proc++, partition++ ) {
if ( partition->i_end > b->i_max ) b->i_max = partition->i_end;
if ( partition->j_end > b->j_max ) b->j_max = partition->j_end;
if ( partition->k_end > b->k_max ) b->k_max = partition->k_end;
for ( proc = 0; proc < f->nprocs; proc++, p++ ) {
if ( p->i_end > b->i_max ) b->i_max = p->i_end;
if ( p->j_end > b->j_max ) b->j_max = p->j_end;
if ( p->k_end > b->k_max ) b->k_max = p->k_end;
}
}
@@ -105,8 +76,8 @@ _get_dimension_sizes (
*/
static int
_have_ghostzone (
const struct h5b_partition *p, /*!< IN: partition \c p */
const struct h5b_partition *q /*!< IN: partition \c q */
const h5b_partition_t *const p, /*!< IN: partition \c p */
const h5b_partition_t *const q /*!< IN: partition \c q */
) {
return ( ! ( _NO_GHOSTZONE ( p, q ) || _NO_GHOSTZONE ( q, p ) ) );
}
@@ -122,7 +93,7 @@ _have_ghostzone (
*/
static h5_int64_t
_volume_of_partition (
const struct h5b_partition *p /*!< IN: partition */
const h5b_partition_t *const p /*!< IN: partition */
) {
return (p->i_end - p->i_start)
* (p->j_end - p->j_start)
@@ -144,8 +115,8 @@ _volume_of_partition (
*/
static h5_int64_t
_volume_of_ghostzone (
const struct h5b_partition *p, /*!< IN: ptr to first partition */
const struct h5b_partition *q /*!< IN: ptr to second partition */
const h5b_partition_t *const p, /*!< IN: ptr to first partition */
const h5b_partition_t *const q /*!< IN: ptr to second partition */
) {
h5_int64_t dx = MIN ( p->i_end, q->i_end )
@@ -171,8 +142,8 @@ _volume_of_ghostzone (
*/
static h5_int64_t
_dissolve_X_ghostzone (
struct h5b_partition *p, /*!< IN/OUT: ptr to first partition */
struct h5b_partition *q /*!< IN/OUT: ptr to second partition */
h5b_partition_t *const p, /*!< IN/OUT: ptr to first partition */
h5b_partition_t *const q /*!< IN/OUT: ptr to second partition */
) {
if ( p->i_start > q->i_start )
@@ -199,8 +170,8 @@ _dissolve_X_ghostzone (
*/
static h5_int64_t
_dissolve_Y_ghostzone (
struct h5b_partition *p, /*!< IN/OUT: ptr to first partition */
struct h5b_partition *q /*!< IN/OUT: ptr to second partition */
h5b_partition_t *const p, /*!< IN/OUT: ptr to first partition */
h5b_partition_t *const q /*!< IN/OUT: ptr to second partition */
) {
if ( p->j_start > q->j_start )
@@ -227,8 +198,8 @@ _dissolve_Y_ghostzone (
*/
static h5_int64_t
_dissolve_Z_ghostzone (
struct h5b_partition *p, /*!< IN/OUT: ptr to first partition */
struct h5b_partition *q /*!< IN/OUT: ptr to second partition */
h5b_partition_t *const p, /*!< IN/OUT: ptr to first partition */
h5b_partition_t *const q /*!< IN/OUT: ptr to second partition */
) {
if ( p->k_start > q->k_start )
@@ -256,17 +227,17 @@ _dissolve_Z_ghostzone (
\return H5_SUCCESS or error code.
*/
static h5_int64_t
static h5_err_t
_dissolve_ghostzone (
h5_file_t *const f,
struct h5b_partition *p, /*!< IN/OUT: ptr to first partition */
struct h5b_partition *q /*!< IN/OUT: ptr to second partition */
h5b_partition_t *const p, /*!< IN/OUT: ptr to first partition */
h5b_partition_t *const q /*!< IN/OUT: ptr to second partition */
) {
struct h5b_partition p_;
struct h5b_partition q_;
struct h5b_partition p_best;
struct h5b_partition q_best;
h5b_partition_t p_;
h5b_partition_t q_;
h5b_partition_t p_best;
h5b_partition_t q_best;
h5_int64_t vol;
h5_int64_t max_vol = 0;
@@ -338,36 +309,36 @@ _dissolve_ghostzone (
\return H5_SUCCESS or error code.
*/
static h5_int64_t
static h5_err_t
_dissolve_ghostzones (
h5_file_t *const f /*!< IN: file handle */
h5_file_t *const f,
const h5b_partition_t *const user_layout,
h5b_partition_t *const write_layout
) {
struct h5b_fdata *b = f->b;
struct h5b_partition *p;
struct h5b_partition *q;
h5b_partition_t *p;
h5b_partition_t *q;
int proc_p, proc_q;
struct list {
struct list *prev;
struct list *next;
struct h5b_partition *p;
struct h5b_partition *q;
h5b_partition_t *p;
h5b_partition_t *q;
h5_int64_t vol;
} *p_begin, *p_el, *p_max, *p_end, *p_save;
memcpy ( b->write_layout, b->user_layout,
f->nprocs * sizeof (*f->b->user_layout) );
memcpy( write_layout, user_layout, f->nprocs*sizeof(h5b_partition_t) );
TRY( p_begin = (struct list*)h5priv_alloc(f, NULL, sizeof(*p_begin)) );
p_max = p_end = p_begin;
memset ( p_begin, 0, sizeof ( *p_begin ) );
memset( p_begin, 0, sizeof ( *p_begin ) );
for ( proc_p = 0, p = b->write_layout;
for ( proc_p = 0, p = write_layout;
proc_p < f->nprocs-1;
proc_p++, p++ ) {
for ( proc_q = proc_p+1, q = &b->write_layout[proc_q];
for ( proc_q = proc_p+1, q = &write_layout[proc_q];
proc_q < f->nprocs;
proc_q++, q++ ) {
@@ -416,45 +387,6 @@ _dissolve_ghostzones (
}
free ( p_begin );
p = &b->user_layout[f->myproc];
h5_debug (f,
"PROC[%d]: User layout: %lld:%lld, %lld:%lld, %lld:%lld",
f->myproc,
(long long)p->i_start, (long long)p->i_end,
(long long)p->j_start, (long long)p->j_end,
(long long)p->k_start, (long long)p->k_end );
/* more detailed debug output: all procs report their view
of all other procs */
for ( proc_p = 0, p = b->user_layout;
proc_p < f->nprocs;
proc_p++, p++ ) {
h5_debug (f,
"PROC[%d]: proc[%d]: User layout: %lld:%lld, %lld:%lld, %lld:%lld ",
f->myproc, proc_p,
(long long)p->i_start, (long long)p->i_end,
(long long)p->j_start, (long long)p->j_end,
(long long)p->k_start, (long long)p->k_end );
}
p = &b->write_layout[f->myproc];
h5_debug (f,
"PROC[%d]: Ghost-zone layout: %lld:%lld, %lld:%lld, %lld:%lld",
f->myproc,
(long long)p->i_start, (long long)p->i_end,
(long long)p->j_start, (long long)p->j_end,
(long long)p->k_start, (long long)p->k_end );
/* more detailed debug output: all procs report their view
of all other procs */
for ( proc_p = 0, p = b->write_layout;
proc_p < f->nprocs;
proc_p++, p++ ) {
h5_debug (f,
"PROC[%d]: proc[%d]: Ghost-zone layout: %lld:%lld, %lld:%lld, %lld:%lld ",
f->myproc, proc_p,
(long long)p->i_start, (long long)p->i_end,
(long long)p->j_start, (long long)p->j_end,
(long long)p->k_start, (long long)p->k_end );
}
return H5_SUCCESS;
}
@@ -482,15 +414,31 @@ h5bpriv_open_block_group (
h5_file_t *const f /*!< IN: file handle */
) {
struct h5b_fdata *b = f->b;
h5b_fdata_t *b = f->b;
if ( b->block_gid >= 0) {
TRY( h5priv_close_hdf5_group(f, b->block_gid) );
b->block_gid = -1;
}
TRY( h5priv_close_hdf5_group(f, b->block_gid) );
b->block_gid = h5priv_open_hdf5_group(f, f->step_gid, H5_BLOCKNAME);
if (f->b->block_gid < 0)
return h5_error(f,
H5_ERR_INVAL,
"Time step does not contain H5Block data!");
if ( b->block_gid < 0 ) {
TRY( b->block_gid = h5priv_open_hdf5_group(f,
return H5_SUCCESS;
}
static h5_err_t
_create_block_group (
h5_file_t *const f /*!< IN: file handle */
) {
h5_err_t exists;
TRY( exists = h5priv_hdf5_link_exists(f, f->step_gid, H5_BLOCKNAME) );
if (exists > 0) {
TRY( h5bpriv_open_block_group(f) );
} else {
TRY( h5priv_close_hdf5_group(f, f->b->block_gid) );
TRY( f->b->block_gid = h5priv_create_hdf5_group(f,
f->step_gid, H5_BLOCKNAME) );
}
@@ -506,10 +454,10 @@ h5bpriv_have_field_group (
char name2[H5_DATANAME_LEN];
h5_normalize_dataset_name(f, name, name2);
TRY( h5bpriv_open_block_group ( f ) );
TRY( h5bpriv_open_block_group(f) );
h5_err_t exists;
TRY( exists = h5priv_hdf5_have_link(f, f->b->block_gid, name2) );
TRY( exists = h5priv_hdf5_link_exists(f, f->b->block_gid, name2) );
return exists;
}
@@ -523,16 +471,44 @@ h5bpriv_open_field_group (
char name2[H5_DATANAME_LEN];
h5_normalize_dataset_name(f, name, name2);
if ( f->b->field_gid >= 0 ) {
TRY( h5priv_close_hdf5_group(f, f->b->field_gid) );
}
TRY( h5bpriv_open_block_group ( f ) );
TRY( f->b->field_gid = h5priv_open_hdf5_group(f, f->b->block_gid, name2) );
TRY( h5priv_close_hdf5_group(f, f->b->field_gid) );
TRY( h5bpriv_open_block_group(f) );
f->b->field_gid = h5priv_open_hdf5_group(f, f->b->block_gid, name2);
if (f->b->field_gid < 0)
return h5_error(f,
H5_ERR_INVAL,
"Field '%s' does not exist!", name2);
return H5_SUCCESS;
}
h5_err_t
h5bpriv_create_field_group (
h5_file_t *const f, /*!< IN: file handle */
const char *name /*!< IN: name of field group to create */
) {
h5b_fdata_t *b = f->b;
TRY( _create_block_group(f) );
char name2[H5_DATANAME_LEN];
h5_normalize_dataset_name(f, name, name2);
h5_err_t exists;
TRY( exists = h5priv_hdf5_link_exists(f, b->block_gid, name2) );
if (exists > 0) {
TRY( h5bpriv_open_field_group(f, name2) );
} else {
TRY( h5priv_close_hdf5_group(f, f->b->field_gid) );
TRY( b->field_gid = h5priv_create_hdf5_group(f,
b->block_gid, name2) );
}
return H5_SUCCESS;
}
h5_err_t
h5b_3d_set_view (
h5_file_t *const f, /*!< IN: File handle */
@@ -544,22 +520,59 @@ h5b_3d_set_view (
const h5_size_t k_end /*!< IN: end index of \c k */
) {
struct h5b_fdata *b = f->b;
struct h5b_partition *p = &b->user_layout[f->myproc];
h5b_partition_t *p = f->b->user_layout;
p->i_start = i_start;
p->i_end = i_end;
p->j_start = j_start;
p->j_end = j_end;
p->k_start = k_start;
p->k_end = k_end;
_normalize_partition(p);
_normalize_partition ( p );
TRY( _allgather( f ) );
_get_dimension_sizes ( f );
TRY( _dissolve_ghostzones ( f ) );
TRY( _release_hyperslab ( f ) );
#ifdef PARALLEL_IO
h5b_fdata_t *b = f->b;
h5b_partition_t *user_layout;
h5b_partition_t *write_layout;
size_t size = f->nprocs * sizeof (h5b_partition_t);
TRY( user_layout = h5priv_alloc (f, NULL, size) );
TRY( write_layout = h5priv_alloc (f, NULL, size) );
TRY( h5priv_mpi_allgather(f,
p, 1, f->b->partition_mpi_t,
user_layout, 1, f->b->partition_mpi_t, f->comm) );
_get_max_dimensions(f, user_layout);
TRY( _dissolve_ghostzones(f, user_layout, write_layout) );
b->user_layout[0] = user_layout[f->myproc];
b->write_layout[0] = write_layout[f->myproc];
b->have_layout = 1;
p = b->user_layout;
h5_debug (f,
"[%d] User layout: %lld:%lld, %lld:%lld, %lld:%lld",
f->myproc,
(long long)p->i_start, (long long)p->i_end,
(long long)p->j_start, (long long)p->j_end,
(long long)p->k_start, (long long)p->k_end );
p = b->write_layout;
h5_debug (f,
"[%d] Ghost-zone layout: %lld:%lld, %lld:%lld, %lld:%lld",
f->myproc,
(long long)p->i_start, (long long)p->i_end,
(long long)p->j_start, (long long)p->j_end,
(long long)p->k_start, (long long)p->k_end );
free(user_layout);
free(write_layout);
TRY( h5bpriv_release_hyperslab(f) );
#endif
return H5_SUCCESS;
}
@@ -597,7 +610,7 @@ h5b_3d_get_chunk (
CHECK_TIMEGROUP ( f );
struct h5b_fdata *b = f->b;
h5b_fdata_t *b = f->b;
TRY( h5bpriv_open_field_group ( f, field_name ) );
@@ -639,7 +652,7 @@ h5b_3d_get_view (
if ( ( proc < 0 ) || ( proc >= f->nprocs ) )
return h5_error(f, H5_ERR_INVAL, "Invalid processor id %d!", proc);
struct h5b_partition *p = &f->b->user_layout[(size_t)proc];
h5b_partition_t *p = &f->b->user_layout[(size_t)proc];
*i_start = p->i_start;
*i_end = p->i_end;
@@ -666,7 +679,7 @@ h5b_3d_get_reduced_view (
if ( ( proc < 0 ) || ( proc >= f->nprocs ) )
return h5_error(f, H5_ERR_INVAL, "Invalid processor id %d!", proc);
struct h5b_partition *p = &f->b->write_layout[(size_t)proc];
h5b_partition_t *p = &f->b->write_layout[(size_t)proc];
*i_start = p->i_start;
*i_end = p->i_end;
@@ -686,7 +699,7 @@ h5b_3d_get_proc (
const h5_int64_t k /*!< IN: \c k coordinate */
) {
struct h5b_partition *layout = f->b->write_layout;
h5b_partition_t *layout = f->b->write_layout;
int proc;
for ( proc = 0; proc < f->nprocs; proc++, layout++ ) {
@@ -704,6 +717,8 @@ h5b_get_num_fields (
h5_file_t *const f /*!< IN: File handle */
) {
CHECK_TIMEGROUP( f );
TRY( h5bpriv_open_block_group(f) );
return h5priv_get_num_objs_in_hdf5_group( f, f->b->block_gid );
}
@@ -712,14 +727,16 @@ h5_err_t
h5b_get_field_info_by_name (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< OUT: field name */
h5_size_t *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
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 */
) {
CHECK_TIMEGROUP( f );
hsize_t dims[16]; /* give it plenty of space even though we don't expect rank > 3 */
hsize_t _grid_rank, _field_rank;
hsize_t _field_rank, _elem_rank;
h5_size_t i, j;
TRY( h5bpriv_open_field_group(f, name) );
@@ -731,18 +748,18 @@ h5b_get_field_info_by_name (
f->b->field_gid, H5_BLOCKNAME_X) );
TRY( dataspace_id = h5priv_get_hdf5_dataset_space(f, dataset_id) );
TRY( _grid_rank = h5priv_get_dims_of_hdf5_dataspace(f,
TRY( _field_rank = h5priv_get_dims_of_hdf5_dataspace(f,
dataspace_id, dims, NULL) );
if ( grid_rank ) *grid_rank = (h5_size_t) _grid_rank;
if ( field_rank ) *field_rank = (h5_size_t) _field_rank;
if ( grid_dims ) {
for ( i = 0, j = _grid_rank-1; i < _grid_rank; i++, j-- )
grid_dims[i] = (h5_size_t)dims[j];
if ( field_dims ) {
for ( i = 0, j = _field_rank-1; i < _field_rank; i++, j-- )
field_dims[i] = (h5_size_t)dims[j];
}
TRY( _field_rank = h5priv_get_num_objs_in_hdf5_group(f,
f->b->block_gid) );
if ( field_rank ) *field_rank = (h5_size_t) _field_rank;
TRY( _elem_rank = h5priv_get_num_objs_in_hdf5_group(f,
f->b->field_gid) );
if ( elem_rank ) *elem_rank = (h5_size_t) _elem_rank;
hid_t h5type;
TRY( h5type = h5priv_get_hdf5_dataset_type(f, dataset_id) );
@@ -762,12 +779,14 @@ h5b_get_field_info (
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 *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
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 */
) {
CHECK_TIMEGROUP( f );
TRY( h5bpriv_open_block_group(f) );
TRY( h5priv_get_hdf5_objname_by_idx(
f,
@@ -777,6 +796,6 @@ h5b_get_field_info (
(size_t)len_name) );
return h5b_get_field_info_by_name(f,
name, grid_rank, grid_dims, field_rank, type);
name, field_rank, field_dims, elem_rank, type);
}
src/h5core/h5b_model_private.h
+6
View File
@@ -13,6 +13,12 @@ h5bpriv_open_field_group (
const char *name
);
h5_err_t
h5bpriv_create_field_group (
h5_file_t *const f, /*!< IN: file handle */
const char *name /*!< IN: name of field group to create */
);
h5_err_t
h5bpriv_open_block_group (
h5_file_t *const f /*!< IN: file handle */
src/h5core/h5b_readwrite.c
+19 -53
View File
@@ -1,50 +1,6 @@
#include "h5core/h5_core.h"
#include "h5_core_private.h"
static h5_err_t
_create_block_group (
h5_file_t *const f /*!< IN: file handle */
) {
h5_err_t exists;
TRY( exists = h5priv_hdf5_link_exists(f, f->step_gid, H5_BLOCKNAME) );
if (exists > 0) {
TRY( h5bpriv_open_block_group(f) );
} else {
TRY( f->b->block_gid = h5priv_create_hdf5_group(f,
f->step_gid, H5_BLOCKNAME) );
}
return H5_SUCCESS;
}
static h5_err_t
_create_field_group (
h5_file_t *const f, /*!< IN: file handle */
const char *name /*!< IN: name of field group to create */
) {
struct h5b_fdata *b = f->b;
TRY( _create_block_group(f) );
char name2[H5_DATANAME_LEN];
h5_normalize_dataset_name(f, name, name2);
h5_err_t exists;
TRY( exists = h5priv_hdf5_link_exists(f, b->block_gid, name2) );
if (exists > 0) {
TRY( h5bpriv_open_field_group(f, name2) );
} else {
TRY( b->field_gid = h5priv_create_hdf5_group(f,
b->block_gid, name2) );
}
return H5_SUCCESS;
}
static h5_err_t
_select_hyperslab_for_writing (
h5_file_t *const f /*!< IN: file handle */
@@ -55,9 +11,9 @@ _select_hyperslab_for_writing (
*/
if ( f->b->shape >= 0 ) return H5_SUCCESS;
struct h5b_fdata *b = f->b;
struct h5b_partition *p = &b->write_layout[f->myproc];
struct h5b_partition *q = &b->user_layout[f->myproc];
h5b_fdata_t *b = f->b;
h5b_partition_t *p = b->write_layout;
h5b_partition_t *q = b->user_layout;
int rank = 3;
@@ -156,7 +112,7 @@ _write_data (
) {
hid_t dataset;
struct h5b_fdata *b = f->b;
h5b_fdata_t *b = f->b;
h5_err_t exists;
TRY( exists = h5priv_hdf5_link_exists (f, b->field_gid, data_name) );
@@ -203,7 +159,10 @@ h5b_write_scalar_data (
const void *data, /*!< IN: data to write */
const hid_t type /*!< IN: data type */
) {
TRY( _create_field_group(f, field_name) );
CHECK_TIMEGROUP( f );
CHECK_WRITABLE_MODE( f );
CHECK_LAYOUT( f );
TRY( h5bpriv_create_field_group(f, field_name) );
TRY( _select_hyperslab_for_writing(f) );
TRY( _write_data(f, field_name, H5_BLOCKNAME_X, data, type) );
return H5_SUCCESS;
@@ -218,7 +177,10 @@ h5b_write_vector3d_data (
const void *zdata, /*!< IN: z data to write */
const hid_t type /*!< IN: data type */
) {
TRY( _create_field_group(f, field_name) );
CHECK_TIMEGROUP( f );
CHECK_WRITABLE_MODE( f );
CHECK_LAYOUT( f );
TRY( h5bpriv_create_field_group(f, field_name) );
TRY( _select_hyperslab_for_writing(f) );
TRY( _write_data(f, field_name, H5_BLOCKNAME_X, xdata, type) );
TRY( _write_data(f, field_name, H5_BLOCKNAME_Y, ydata, type) );
@@ -232,8 +194,8 @@ _select_hyperslab_for_reading (
const hid_t dataset
) {
struct h5b_fdata *b = f->b;
struct h5b_partition *p = &b->user_layout[f->myproc];
h5b_fdata_t *b = f->b;
h5b_partition_t *p = b->user_layout;
int rank;
hsize_t field_dims[3];
hsize_t start[3] = {
@@ -314,7 +276,7 @@ _read_data (
) {
hid_t dataset;
struct h5b_fdata *b = f->b;
h5b_fdata_t *b = f->b;
TRY( dataset = h5priv_open_hdf5_dataset(f, b->field_gid, data_name) );
TRY( _select_hyperslab_for_reading(f, dataset) );
@@ -337,6 +299,8 @@ h5b_read_scalar_data (
void *data, /*!< OUT: read bufer */
const hid_t type /*!< IN: data type */
) {
CHECK_TIMEGROUP( f );
CHECK_LAYOUT( f );
TRY( h5bpriv_open_field_group(f, field_name) );
TRY( _read_data(f, field_name, H5_BLOCKNAME_X, data, type) );
return H5_SUCCESS;
@@ -351,6 +315,8 @@ h5b_read_vector3d_data (
void *zdata, /*!< IN: z data to write */
const hid_t type /*!< IN: data type */
) {
CHECK_TIMEGROUP( f );
CHECK_LAYOUT( f );
TRY( h5bpriv_open_field_group(f, field_name) );
TRY( _read_data(f, field_name, H5_BLOCKNAME_X, xdata, type) );
TRY( _read_data(f, field_name, H5_BLOCKNAME_Y, ydata, type) );
src/h5core/h5b_types_private.h
+3 -2
View File
@@ -15,8 +15,8 @@ struct h5b_fdata {
h5_size_t i_max;
h5_size_t j_max;
h5_size_t k_max;
struct h5b_partition* user_layout;
struct h5b_partition* write_layout;
struct h5b_partition user_layout[1];
struct h5b_partition write_layout[1];
int have_layout;
hid_t shape;
@@ -29,4 +29,5 @@ struct h5b_fdata {
MPI_Datatype partition_mpi_t;
};
typedef struct h5b_fdata h5b_fdata_t;
typedef struct h5b_partition h5b_partition_t;
#endif
src/h5core/h5t_openclose.c
+37 -20
View File
@@ -313,6 +313,18 @@ init_fdata (
t->dsinfo_num_elems_on_level.chunk_dims) );
t->dsinfo_num_elems_on_level.access_prop = H5P_DEFAULT;
/* initialize pointers */
t->elems.data = NULL;
t->num_elems = NULL;
t->elems_ldta = NULL;
t->num_elems_on_level = NULL;
t->map_elem_g2l.items = NULL;
t->vertices = NULL;
t->vertices_data = NULL;
t->num_vertices = NULL;
t->map_vertex_g2l.items = NULL;
t->mtags.names = NULL;
return H5_SUCCESS;
}
@@ -348,25 +360,6 @@ h5tpriv_open_file (
return H5_SUCCESS;
}
/*!
\ingroup h5_private
\internal
De-initialize topological internal structure. Open HDF5 objects are
closed and allocated memory freed.
\return H5_SUCCESS or error code
*/
h5_err_t
h5tpriv_close_file (
h5_file_t* const f /*!< IN: file handle */
) {
TRY( h5t_close_mesh (f) );
return H5_SUCCESS;
}
h5_err_t
h5tpriv_init_step (
h5_file_t* const f
@@ -533,7 +526,9 @@ h5_err_t
h5t_close_mesh (
h5_file_t* const f
) {
TRY( h5tpriv_write_mesh (f) );
if (!(f->mode & H5_O_RDONLY)) {
TRY( h5tpriv_write_mesh (f) );
}
TRY( release_memory (f) );
TRY( init_fdata (f) );
@@ -575,3 +570,25 @@ h5tpriv_alloc_num_vertices (
return H5_SUCCESS;
}
/*!
\ingroup h5_private
\internal
De-initialize topological internal structure. Open HDF5 objects are
closed and allocated memory freed.
\return H5_SUCCESS or error code
*/
h5_err_t
h5tpriv_close_file (
h5_file_t* const f /*!< IN: file handle */
) {
TRY( release_memory (f) );
TRY( h5t_close_mesh (f) );
return H5_SUCCESS;
}
src/h5core/h5u_model.c
+64 -102
View File
@@ -1,45 +1,11 @@
#include "h5core/h5_core.h"
#include "h5_core_private.h"
h5_int64_t
h5_ssize_t
h5u_get_num_particles (
h5_file_t *const f /*!< [in] Handle to open file */
) {
h5_int64_t nparticles;
ssize_t exists;
/* returns 0 if there are no datasets on disk */
TRY ( exists = h5_get_num_hdf5_datasets(f, f->step_gid ) );
if ( exists == 0 )
{
/* try to recover number of particles from a previous
* H5PartSetNumParticles call. */
#ifdef PARALLEL_IO
hsize_t total;
TRY( h5priv_mpi_sum(f,
&(f->u->nparticles), &total,
1, MPI_LONG_LONG, f->comm) );
nparticles = (h5_int64_t)total;
#else
nparticles = (h5_int64_t)f->u->nparticles;
#endif
if ( nparticles > 0 ) {
h5_debug (
f,
"Using existing view to report "
"nparticles = %lld", (long long)nparticles );
return nparticles;
}
else {
h5_warn (
f,
"There are no datasets in the current timestep "
"nor existing views: "
"reporting 0 particles.");
return 0;
}
}
/* if a view exists, use its size as the number of particles */
if ( h5u_has_view ( f ) )
@@ -47,38 +13,52 @@ h5u_get_num_particles (
TRY( nparticles = h5priv_get_selected_npoints_of_hdf5_dataspace(
f,
f->u->diskshape) );
h5_debug(
f,
"Found %lld points with H5Sget_select_npoints",
(long long)nparticles );
h5_debug(f,
"Found %lld particles in existing view.",
(long long)nparticles );
}
/* otherwise, report all particles on disk in the first dataset
* for this timestep */
else
{
else if ( f->u->shape > 0 ) {
TRY( nparticles = h5priv_get_npoints_of_hdf5_dataspace(f, f->u->shape) );
h5_debug(f,
"Found %lld particles from previous H5PartSetNumParticles call.",
(long long)nparticles );
}
else {
/* otherwise, report all particles on disk in the first dataset
* for this timestep */
char dataset_name[H5_DATANAME_LEN];
TRY( h5priv_get_hdf5_objname_by_idx(
dataset_name[0] = '\0';
h5_err_t exists = h5_get_hdf5_datasetname_by_idx(
f,
f->step_gid,
0,
dataset_name,
H5_DATANAME_LEN) );
TRY( nparticles = h5priv_get_npoints_of_hdf5_dataset_by_name (
H5_DATANAME_LEN);
if ( exists < 0 )
return h5_error(f,
H5_ERR_INVAL,
"Cannot determine the number of particles: "
"H5PartSetNumParticles has not been called, "
"no view has been set, and there are no "
"data sets for this time step!");
TRY( nparticles = h5priv_get_npoints_of_hdf5_dataset_by_name(
f,
f->step_gid,
dataset_name ) );
dataset_name) );
h5_debug(f,
"Found %lld particles in the first data set of this time step.",
(long long)nparticles );
}
return nparticles;
}
h5_int64_t
h5_err_t
h5u_set_num_particles (
h5_file_t *const f, /*!< [in] Handle to open file */
const h5_int64_t nparticles, /*!< [in] Number of particles */
const h5_int64_t stride /*!< [in] Stride of particles in memory */
const h5_size_t nparticles, /*!< [in] Number of particles */
const h5_size_t stride /*!< [in] Stride of particles in memory */
) {
CHECK_FILEHANDLE( f );
struct h5u_fdata *u = f->u;
hsize_t hstride;
@@ -88,22 +68,14 @@ h5u_set_num_particles (
hsize_t dmax = H5S_UNLIMITED;
if ( nparticles <= 0 )
return h5_error(
f,
return h5_error(f,
H5_ERR_INVAL,
"Invalid number particles: %lld!\n",
(long long)nparticles);
/* prevent invalid stride value */
if (stride < 1)
{
h5_warn (
f,
"Stride < 1 was specified: changing to 1." );
hstride = 1;
} else {
hstride = (hsize_t)stride;
}
hstride = (hsize_t)stride;
if ( hstride > 1 )
h5_debug( f, "Striding by %lld elements.", (long long)hstride);
#ifndef PARALLEL_IO
/*
@@ -135,22 +107,16 @@ h5u_set_num_particles (
{
start = 0;
count = u->nparticles;
TRY( h5priv_select_hyperslab_of_hdf5_dataspace(
f,
TRY( h5priv_select_hyperslab_of_hdf5_dataspace(f,
u->memshape,
H5S_SELECT_SET,
&start,
&hstride,
&count, NULL ) );
&start, &hstride, &count,
NULL) );
}
#ifndef PARALLEL_IO
count = u->nparticles;
TRY( u->shape = h5priv_create_hdf5_dataspace (
f,
1,
&count,
NULL ) );
TRY( u->shape = h5priv_create_hdf5_dataspace(f, 1, &count, NULL) );
u->viewstart = 0;
u->viewend = nparticles - 1; // view range is *inclusive*
#else /* PARALLEL_IO */
@@ -173,30 +139,33 @@ h5u_set_num_particles (
&(u->nparticles), &total, 1, MPI_LONG_LONG, f->comm ) );
TRY( h5priv_mpi_prefix_sum(f,
&(u->nparticles), &start, 1, MPI_LONG_LONG, f->comm ) );
start -= u->nparticles;
h5_debug(f, "Total particles across all processors: %lld.",
(long long)total);
u->viewstart = start;
u->viewend = start + u->nparticles - 1; // view range is *inclusive*
/* declare overall datasize */
count = total;
TRY ( u->shape = h5priv_create_hdf5_dataspace (f, 1, &count, NULL) );
TRY( u->shape = h5priv_create_hdf5_dataspace(f, 1, &count, NULL) );
/* declare overall data size but then will select a subset */
TRY ( u->diskshape = h5priv_create_hdf5_dataspace (f, 1, &count, NULL) );
TRY( u->diskshape = h5priv_create_hdf5_dataspace(f, 1, &count, NULL) );
count = nparticles;
hstride = 1;
TRY ( h5priv_select_hyperslab_of_hdf5_dataspace (
f,
TRY( h5priv_select_hyperslab_of_hdf5_dataspace(f,
u->diskshape,
H5S_SELECT_SET,
&start, &hstride, &count,
NULL ) );
NULL) );
#endif
return H5_SUCCESS;
}
h5_int64_t
h5_err_t
h5u_has_view (
const h5_file_t *const f
) {
@@ -264,8 +233,6 @@ h5u_set_view (
if ( start == -1 ) start = 0;
if ( end == -1 ) end = total - 1; // range is *inclusive*
h5_debug ( f, "Total nparticles=%lld", (long long)total );
/* so, is this selection inclusive or exclusive?
it appears to be inclusive for both ends of the range.
*/
@@ -282,7 +249,9 @@ h5u_set_view (
u->viewend = end;
u->nparticles = end - start + 1;
h5_debug ( f, "nparticles=%lld", (long long)u->nparticles );
h5_debug (f,
"This view selected %lld particles.",
(long long)u->nparticles );
/* declare overall data size but then will select a subset */
TRY ( u->diskshape = h5priv_create_hdf5_dataspace ( f, 1, &total, NULL ) );
@@ -304,11 +273,11 @@ h5u_set_view (
return H5_SUCCESS;
}
h5_int64_t
h5_err_t
h5u_set_view_indices (
h5_file_t *const f, /*!< [in] Handle to open file */
const h5_int64_t *const indices, /*!< [in] List of indices */
const h5_int64_t nelems /*!< [in] Size of list */
const h5_id_t *const indices, /*!< [in] List of indices */
const h5_size_t nelems /*!< [in] Size of list */
) {
hsize_t total;
@@ -338,19 +307,12 @@ h5u_set_view_indices (
return H5_SUCCESS;
}
h5_debug ( f, "Total nparticles=%lld", (long long)total );
if ( total == 0 ) return H5_SUCCESS;
/* check length of list */
if ( nelems < 0 ) {
h5_warn (f,
"Array of view indices has length < 0: "
"resetting view.");
u->nparticles = 0;
} else {
u->nparticles = (hsize_t) nelems;
}
u->nparticles = (hsize_t) nelems;
h5_debug (f,
"This view selected %lld particles.",
(long long)u->nparticles );
/* declare overall data size but then will select a subset */
TRY ( u->diskshape = h5priv_create_hdf5_dataspace ( f, 1, &total, NULL ) );
@@ -371,7 +333,7 @@ h5u_set_view_indices (
return H5_SUCCESS;
}
h5_int64_t
h5_err_t
h5u_get_view (
h5_file_t *const f,
h5_int64_t *start,
@@ -444,7 +406,7 @@ h5u_set_canonical_view (
return H5_SUCCESS;
}
h5_int64_t
h5_ssize_t
h5u_get_num_datasets (
h5_file_t *const f /*!< [in] Handle to open file */
) {
@@ -456,15 +418,15 @@ h5u_get_num_datasets (
/*!
Get information about dataset in current index given by its index
*/
h5_int64_t
h5_err_t
h5u_get_dataset_info (
h5_file_t *const f, /*!< [in] Handle to open file */
const h5_int64_t idx, /*!< [in] Index of the dataset */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *dataset_name, /*!< [out] Name of dataset */
const h5_int64_t len_dataset_name,
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_int64_t *nelem /*!< [out] Number of elements. */
h5_size_t *nelem /*!< [out] Number of elements. */
) {
TRY( h5_get_hdf5_datasetname_by_idx (
src/h5core/h5u_readwrite.c
+4 -8
View File
@@ -9,6 +9,8 @@ h5u_read_data (
const hid_t type
) {
CHECK_TIMEGROUP( f );
struct h5u_fdata *u = f->u;
hid_t dataset_id;
hid_t space_id;
@@ -107,9 +109,9 @@ h5u_write_data (
const hid_t type /*!< IN: Type of data */
) {
CHECK_FILEHANDLE ( f );
CHECK_WRITABLE_MODE( f );
CHECK_TIMEGROUP( f );
CHECK_WRITABLE_MODE( f );
struct h5u_fdata *u = f->u;
hid_t dset_id;
@@ -138,9 +140,6 @@ h5u_write_data (
H5P_DEFAULT) );
}
#ifdef PARALLEL_IO
TRY( h5_start_throttle(f) );
#endif
h5_info (f,
"Writing dataset %s/%s.",
h5_get_objname(f->step_gid), name2);
@@ -153,9 +152,6 @@ h5u_write_data (
f->xfer_prop,
data) );
TRY( h5priv_close_hdf5_dataset (f, dset_id) );
#ifdef PARALLEL_IO
TRY( h5_end_throttle(f) );
#endif
f->empty = 0;
src/include/H5.h
+17 -2
View File
@@ -16,7 +16,6 @@
#ifndef __H5_H
#define __H5_H
#include "H5_inquiry.h"
#include "H5_attribs.h"
h5_file_t *
@@ -54,7 +53,7 @@ H5GetStepNameFormat (
h5_err_t
H5SetStep (
h5_file_t *f,
const h5_int64_t step
const h5_id_t step
);
h5_int64_t
@@ -62,6 +61,22 @@ H5GetStep (
h5_file_t *f
);
int
H5GetNumProcs (
h5_file_t * const f
);
h5_size_t
H5GetNumSteps (
h5_file_t * const f
);
h5_err_t
H5HasStep (
h5_file_t * const f,
h5_id_t step
);
h5_err_t
H5StartTraverseSteps (
h5_file_t *f
src/include/H5Block.h
+5 -5
View File
@@ -73,9 +73,9 @@ H5BlockGetFieldInfo (
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 *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
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 */
);
@@ -83,9 +83,9 @@ h5_err_t
H5BlockGetFieldInfoByName (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< IN: field name */
h5_size_t *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
h5_size_t *field_rank, /*!< OUT: field rank */
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 */
);
src/include/H5Part.h
+19 -18
View File
@@ -4,20 +4,20 @@
h5_err_t
H5PartSetNumParticles (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t nparticles /*!< [in] Number of particles */
h5_size_t nparticles /*!< [in] Number of particles */
);
h5_err_t
H5PartSetNumParticlesStrided (
h5_file_t *f, /*!< [in] Handle to open file */
h5_int64_t nparticles, /*!< [in] Number of particles */
h5_int64_t stride /*!< [in] Stride value (e.g. number of fields in the particle array) */
);
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_err_t
H5PartSetChunkSize (
H5PartSetChunk (
h5_file_t *f,
h5_int64_t size
h5_size_t size
);
h5_err_t
@@ -76,31 +76,31 @@ H5PartReadDataInt32 (
h5_int32_t *data /*!< [out] Array of data */
);
h5_int64_t
h5_ssize_t
H5PartGetNumDatasets (
h5_file_t *f /*!< [in] Handle to open file */
);
h5_int64_t
h5_err_t
H5PartGetDatasetName (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t idx, /*!< [in] Index of the dataset */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *name, /*!< [out] Name of dataset */
const h5_int64_t len /*!< [in] Size of buffer \c name */
const h5_size_t len /*!< [in] Size of buffer \c name */
);
h5_int64_t
h5_err_t
H5PartGetDatasetInfo (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t idx,/*!< [in] Index of the dataset */
const h5_id_t idx, /*!< [in] Index of the dataset */
char *dataset_name, /*!< [out] Name of dataset */
const h5_int64_t len_dataset_name,
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_int64_t *nelem /*!< [out] Number of elements. */
h5_size_t *nelem /*!< [out] Number of elements. */
);
h5_int64_t
h5_ssize_t
H5PartGetNumParticles (
h5_file_t *f /*!< [in] Handle to open file */
);
@@ -110,7 +110,7 @@ H5PartResetView (
h5_file_t *f /*!< [in] Handle to open file */
);
h5_int64_t
h5_err_t
H5PartHasView (
h5_file_t *f /*!< [in] Handle to open file */
);
@@ -125,8 +125,8 @@ H5PartSetView (
h5_err_t
H5PartSetViewIndices (
h5_file_t *f, /*!< [in] Handle to open file */
const h5_int64_t *indices, /*!< [in] List of indices */
h5_int64_t nelems /*!< [in] Size of list */
const h5_id_t *indices, /*!< [in] List of indices */
h5_size_t nelems /*!< [in] Size of list */
);
h5_err_t
@@ -146,4 +146,5 @@ H5PartSetCanonicalView (
h5_file_t *f /*!< [in] Handle to open file */
);
#endif
src/include/H5_inquiry.h
-21
View File
@@ -1,21 +0,0 @@
#ifndef __H5_INQUIRY_H
#define __H5_INQUIRY_H
int
H5GetNumNodes (
h5_file_t * const f
);
h5_size_t
H5GetNumSteps (
h5_file_t * const f
);
h5_err_t
H5HasStep (
h5_file_t * const f,
h5_id_t step
);
#endif
src/include/h5core/h5_attribs.h
+2 -2
View File
@@ -1,5 +1,5 @@
#ifndef __H5_ATTRIBS_H
#define __H5_ATTRIBS_H
#ifndef __H5CORE_ATTRIBS_H
#define __H5CORE_ATTRIBS_H
#define H5_ATTRIB_FILE 0
#define H5_ATTRIB_STEP 1
src/include/h5core/h5_errorhandling.h
+1 -1
View File
@@ -26,7 +26,7 @@
return h5_error ( \
f, \
H5_ERR_INVAL, \
"Internal error: step_gid <= 0.");
"Time step is invalid! Have you set the time step?");
#define h5_error_not_implemented( f, file, func, lino ) \
h5_error( \
src/include/h5core/h5_hdf5.h
+2 -2
View File
@@ -20,7 +20,7 @@ h5_get_hdf5_groupname_by_idx (
hid_t loc_id,
hsize_t idx,
char *name,
size_t size
size_t len
);
ssize_t
@@ -35,7 +35,7 @@ h5_get_hdf5_datasetname_by_idx (
hid_t loc_id,
hsize_t idx,
char *name,
size_t size
size_t len
);
const char *
src/include/h5core/h5b_model.h
+4 -4
View File
@@ -68,9 +68,9 @@ h5_err_t
h5b_get_field_info_by_name (
h5_file_t *const f, /*!< IN: file handle */
const char *name, /*!< OUT: field name */
h5_size_t *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
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 */
);
@@ -80,9 +80,9 @@ h5b_get_field_info (
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 *grid_rank, /*!< OUT: grid rank */
h5_size_t *grid_dims, /*!< OUT: grid dimensions */
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 */
);
src/include/h5core/h5u_model.h
+17 -17
View File
@@ -1,67 +1,67 @@
#ifndef __H5U_MODEL_H
#define __H5U_MODEL_H
h5_int64_t
h5_ssize_t
h5u_get_num_particles (
h5_file_t *const f
);
h5_int64_t
h5_err_t
h5u_set_num_particles (
h5_file_t *const f,
const h5_int64_t nparticles,
const h5_int64_t stride
const h5_size_t nparticles,
const h5_size_t stride
);
h5_int64_t
h5_err_t
h5u_has_view (
const h5_file_t *const f
);
h5_int64_t
h5_err_t
h5u_reset_view (
h5_file_t *const f
);
h5_int64_t
h5_err_t
h5u_set_view (
h5_file_t *const f,
h5_int64_t start,
h5_int64_t end
);
h5_int64_t
h5_err_t
h5u_set_view_indices (
h5_file_t *const f,
const h5_int64_t *const indices,
const h5_int64_t nelems
const h5_id_t *const indices,
const h5_size_t nelems
);
h5_int64_t
h5_err_t
h5u_get_view (
h5_file_t *const f,
h5_int64_t *start,
h5_int64_t *end
);
h5_int64_t
h5_err_t
h5u_set_canonical_view (
h5_file_t *const f
);
h5_int64_t
h5_ssize_t
h5u_get_num_datasets (
h5_file_t *const f
);
h5_int64_t
h5_err_t
h5u_get_dataset_info (
h5_file_t *const f,
const h5_int64_t idx,
const h5_id_t idx,
char *dataset_name,
const h5_int64_t len_dataset_name,
const h5_size_t len_dataset_name,
h5_int64_t *type,
h5_int64_t *nelem
h5_size_t *nelem
);
h5_err_t
test/Makefile.am
+21 -5
View File
@@ -4,18 +4,18 @@
OBJEXT=o
HDFLIB = -L@HDF5ROOT@/lib -lhdf5 -lz @SZLIB@
H5LIB = -L../src/lib -lH5hutC -lH5core
HDFLIB = -L@HDF5ROOT@/lib -lhdf5 -lz @SZLIB@ -lm
H5LIB = -L../src/lib -lH5hutC -lH5hut
LIBS = $(H5LIB) $(HDFLIB) @MPILIB@
INCLUDES = -I../src/include -I@HDF5ROOT@/include @MPIINC@
noinst_PROGRAMS = h5u_test
noinst_PROGRAMS = h5u_test h5b_test
TESTS_ENVIRONMENT = env LD_LIBRARY_PATH=@HDF5ROOT@/lib:$(LD_LIBRARY_PATH)
TESTS = h5u_test
TESTS = h5u_test h5b_test
EXTRA_PROGRAMS = h5u_test
EXTRA_PROGRAMS = h5u_test h5b_test
h5u_test_SOURCES = \
h5u_test.c \
@@ -25,6 +25,22 @@ h5u_test_SOURCES = \
testframe.h \
params.h
h5u_test_DEPENDENCIES = \
../src/lib/libH5hut.a \
../src/lib/libH5hutC.a
h5b_test_SOURCES = \
h5b_test.c \
h5b_write.c \
h5b_read.c \
testframe.c \
testframe.h \
params.h
h5b_test_DEPENDENCIES = \
../src/lib/libH5hut.a \
../src/lib/libH5hutC.a
clean: clean-am
rm -f *.h5
test/h5b_read.c
+197
View File
@@ -0,0 +1,197 @@
#include <stdlib.h>
#include <string.h>
#include "testframe.h"
#include "params.h"
static void
test_read_field_attribs(
h5_file_t *file,
const char *field_name,
int position)
{
h5_err_t status;
char name[ATTR_NAME_SIZE];
char str[ATTR_NAME_SIZE];
h5_int32_t i32;
h5_int64_t i64;
h5_float32_t f32;
h5_float64_t f64;
TEST("Reading field attributes");
i64 = H5BlockGetNumFieldAttribs(file, field_name);
VALUE(i64 % 5, 0, "file attribute count");
get_attr_name(name, "str", position);
status = H5BlockReadFieldAttribString(
file, field_name, name, str);
RETURN(status, H5_SUCCESS, "H5BlockReadFieldAttribString");
SVALUE(str, ATTR_STR_VAL, "string attribute");
get_attr_name(name, "i32", position);
status = H5BlockReadFieldAttribInt32(
file, field_name, name, &i32);
RETURN(status, H5_SUCCESS, "H5BlockReadFieldAttribInt32");
IVALUE(i32, ATTR_INT32_VAL, "int32 attribute");
get_attr_name(name, "i64", position);
status = H5BlockReadFieldAttribInt64(
file, field_name, name, &i64);
RETURN(status, H5_SUCCESS, "H5BlockReadFieldAttribInt64");
IVALUE(i64, ATTR_INT64_VAL, "int64 attribute");
get_attr_name(name, "f32", position);
status = H5BlockReadFieldAttribFloat32(
file, field_name, name, &f32);
RETURN(status, H5_SUCCESS, "H5BlockReadFieldAttribFloat32");
FVALUE(f32, ATTR_FLOAT_VAL, "float32 attribute");
get_attr_name(name, "f64", position);
status = H5BlockReadFieldAttribFloat64(
file, field_name, name, &f64);
RETURN(status, H5_SUCCESS, "H5BlockReadFieldAttribFloat64");
FVALUE(f64, ATTR_FLOAT_VAL, "float64 attribute");
}
static void
test_read_data64(h5_file_t *file, int step)
{
extern h5_size_t layout[6];
int i,t;
int rank, nprocs;
h5_err_t status;
h5_int64_t val, type[2];
char name[4];
h5_size_t field_rank[2], field_dims[6], elem_rank[2];
double *e;
double *ex,*ey,*ez;
h5_int64_t *id;
const size_t nelems =
(layout[1] - layout[0] + 1) *
(layout[3] - layout[2] + 1) *
(layout[5] - layout[4] + 1);
e=(double*)malloc(nelems*sizeof(double));
ex=(double*)malloc(nelems*sizeof(double));
ey=(double*)malloc(nelems*sizeof(double));
ez=(double*)malloc(nelems*sizeof(double));
id=(h5_int64_t*)malloc(nelems*sizeof(h5_int64_t));
TEST("Verifying dataset info");
#if PARALLEL_IO
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
#else
nprocs = 1;
rank = 2;
#endif
status = H5SetStep(file, step);
RETURN(status, H5_SUCCESS, "H5SetStep");
val = H5BlockGetNumFields(file);
IVALUE(val, 3, "field count");
for (i=0; i<3; i++) {
status = H5BlockGetFieldInfo(
file, i, name, 4,
field_rank, field_dims, elem_rank, type);
RETURN(status, H5_SUCCESS, "H5BlockGetFieldInfo");
status = H5BlockGetFieldInfoByName(
file, name,
field_rank+1, field_dims+3, elem_rank+1, type+1);
RETURN(status, H5_SUCCESS, "H5BlockGetFieldInfoByName");
IVALUE(field_rank[0], field_rank[1], "field rank");
IVALUE(field_dims[0], field_dims[3], "field dims x");
IVALUE(field_dims[1], field_dims[4], "field dims y");
IVALUE(field_dims[2], field_dims[5], "field dims z");
IVALUE(elem_rank[0], elem_rank[1], "elem rank");
IVALUE(type[0], type[1], "field type");
IVALUE(field_rank[0], 3, "field rank");
IVALUE(field_dims[0], NBLOCKX, "field dims x");
IVALUE(field_dims[1], NBLOCKY, "field dims y");
IVALUE(field_dims[2], NBLOCKZ, "field dims z");
if (i==1) {
CVALUE(name[0], 'e', "field name");
IVALUE(elem_rank[0], 1, "elem rank");
IVALUE(type[0], H5_FLOAT64_T, "field type");
} else if (i==0) {
CVALUE(name[0], 'E', "field name");
IVALUE(elem_rank[0], 3, "elem rank");
IVALUE(type[1], H5_FLOAT64_T, "field type");
} else if (i==2) {
CVALUE(name[0], 'i', "field name");
IVALUE(elem_rank[0], 1, "elem rank");
IVALUE(type[1], H5_INT64_T, "field type");
}
}
#if PARALLEL_IO
TEST("Setting throttle");
status = H5SetThrottle(file, 3);
RETURN(status, H5_SUCCESS, "H5SetThrottle");
#endif
TEST("Reading 64-bit data");
for (t=step; t<step+NTIMESTEPS; t++)
{
val = H5HasStep(file, t);
IVALUE(val, 1, "has step");
status = H5SetStep(file, t);
RETURN(status, H5_SUCCESS, "H5SetStep");
test_read_field_attribs(file, "e", t);
status = H5Block3dSetView(file,
layout[0], layout[1],
layout[2], layout[3],
layout[4], layout[5]);
RETURN(status, H5_SUCCESS, "H5Block3dSetView");
status = H5Block3dReadScalarFieldFloat64(file, "e", e);
RETURN(status, H5_SUCCESS, "H5Block3dReadScalarFieldFloat64");
status = H5Block3dReadVector3dFieldFloat64(file,
"E", ex, ey, ez);
RETURN(status, H5_SUCCESS,
"H5Block3dReadVector3dFieldFloat64");
status = H5Block3dReadScalarFieldInt64(file, "id", id);
RETURN(status, H5_SUCCESS, "H5Block3dReadScalarFieldInt64");
for (i=0; i<nelems; i++)
{
FVALUE(e[i] , 0.0 + (double)(i+nelems*t), " e data");
FVALUE(ex[i], 0.1 + (double)(i+nelems*t), " ex data");
FVALUE(ey[i], 0.2 + (double)(i+nelems*t), " ey data");
FVALUE(ez[i], 0.3 + (double)(i+nelems*t), " ez data");
IVALUE(id[i], (i+nelems*t), " id data");
}
}
}
void h5b_test_read1(void)
{
h5_file_t *file1;
h5_err_t status;
TEST("Opening file once, read-only");
file1 = H5OpenFile(FILENAME, H5_O_RDONLY, MPI_COMM_WORLD);
status = H5CheckFile(file1);
RETURN(status, H5_SUCCESS, "H5CheckFile");
test_read_data64(file1, 1);
status = H5CloseFile(file1);
RETURN(status, H5_SUCCESS, "H5CloseFile");
}
test/h5b_test.c
+109
View File
@@ -0,0 +1,109 @@
#include <math.h>
#include <stdlib.h>
#include <H5hut.h>
#include "testframe.h"
#include "params.h"
/* global */
h5_size_t layout[6];
/* from write.c */
void h5b_test_write1(void);
/* from read.c */
void h5b_test_read1(void);
static int
_nth_root_int_divisor (const int m, const int n)
{
int i, root;
double p;
p = 1.0 / (double)n;
root = (int) ceil ( pow ( (double)m, p ) );
for (i=root; i<=m; i++)
{
if (m % i == 0) return i;
}
return i;
}
int main(int argc, char **argv)
{
extern h5_size_t layout[6];
#ifdef PARALLEL_IO
MPI_Init(&argc, &argv);
int procs, rank;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &procs);
if (procs > MAX_MPI_TASKS) {
fprintf(stderr,
"ERROR: please use <= %d MPI tasks for the test.\n",
MAX_MPI_TASKS);
exit(EXIT_FAILURE);
}
/* make up a 3D layout */
h5_size_t decomp[3];
decomp[0] = _nth_root_int_divisor (procs, 3);
decomp[1] = _nth_root_int_divisor (procs / decomp[0], 2);
decomp[2] = procs / decomp[0] / decomp[1];
h5_size_t i,j,k;
k = rank % decomp[2];
j = (rank / decomp[2]) % decomp[1];
i = rank / (decomp[2] * decomp[1]);
layout[0] = i*NBLOCKX;
layout[1] = (i+1)*NBLOCKX - 1;
layout[2] = j*NBLOCKY;
layout[3] = (j+1)*NBLOCKY - 1;
layout[4] = k*NBLOCKZ;
layout[5] = (k+1)*NBLOCKZ - 1;
#else // PARALLEL_IO
layout[0] = 0;
layout[1] = NBLOCKX - 1;
layout[2] = 0;
layout[3] = NBLOCKY - 1;
layout[4] = 0;
layout[5] = NBLOCKZ - 1;
#endif
/* Initialize testing framework */
TestInit(argv[0], NULL, NULL);
/* Tests are generally arranged from least to most complexity... */
AddTest("write1", h5b_test_write1, NULL, "Write 64-bit data", NULL);
AddTest("read1", h5b_test_read1, NULL, "Read 64-bit data", NULL);
/* Display testing information */
TestInfo(argv[0]);
/* Parse command line arguments */
TestParseCmdLine(argc, argv);
H5SetVerbosityLevel(GetTestVerbosity());
/* Perform requested testing */
PerformTests();
/* Display test summary, if requested */
if (GetTestSummary())
TestSummary();
/* Clean up test files, if allowed */
//if (GetTestCleanup() && !getenv("HDF5_NOCLEANUP"))
// TestCleanup();
#ifdef PARALLEL_IO
TestPrintf ("reached end\n");
fflush(stdout);
MPI_Finalize();
#endif
return GetTestNumErrs();
}
test/h5b_write.c
+131
View File
@@ -0,0 +1,131 @@
#include <stdlib.h>
#include "testframe.h"
#include "params.h"
static void
test_write_field_attribs(
h5_file_t *file,
const char *field_name,
int position)
{
h5_err_t status;
char name[ATTR_NAME_SIZE];
TEST("Writing field attributes");
get_attr_name(name, "str", position);
status = H5BlockWriteFieldAttribString(
file, field_name, name, ATTR_STR_VAL);
RETURN(status, H5_SUCCESS, "H5BlockWriteFieldAttribString");
get_attr_name(name, "i32", position);
h5_int32_t i32 = ATTR_INT32_VAL;
status = H5BlockWriteFieldAttribInt32(
file, field_name, name, &i32, 1);
RETURN(status, H5_SUCCESS, "H5BlockWriteFieldAttribInt32");
get_attr_name(name, "i64", position);
h5_int64_t i64 = ATTR_INT64_VAL;
status = H5BlockWriteFieldAttribInt64(
file, field_name, name, &i64, 1);
RETURN(status, H5_SUCCESS, "H5BlockWriteFieldAttribInt64");
get_attr_name(name, "f32", position);
h5_float32_t f32 = ATTR_FLOAT_VAL;
status = H5BlockWriteFieldAttribFloat32(
file, field_name, name, &f32, 1);
RETURN(status, H5_SUCCESS, "H5BlockWriteFieldAttribFloat32");
get_attr_name(name, "f64", position);
h5_float64_t f64 = ATTR_FLOAT_VAL;
status = H5BlockWriteFieldAttribFloat64(
file, field_name, name, &f64, 1);
RETURN(status, H5_SUCCESS, "H5BlockWriteFieldAttribFloat64");
}
static void
test_write_data64(h5_file_t *file, int step)
{
extern h5_size_t layout[6];
int i,t;
h5_int64_t status, val;
double *e;
double *ex,*ey,*ez;
h5_int64_t *id;
const size_t nelems =
(layout[1] - layout[0] + 1) *
(layout[3] - layout[2] + 1) *
(layout[5] - layout[4] + 1);
e=(double*)malloc(nelems*sizeof(double));
ex=(double*)malloc(nelems*sizeof(double));
ey=(double*)malloc(nelems*sizeof(double));
ez=(double*)malloc(nelems*sizeof(double));
id=(h5_int64_t*)malloc(nelems*sizeof(h5_int64_t));
#if PARALLEL_IO
TEST("Setting throttle");
status = H5SetThrottle(file, 2);
RETURN(status, H5_SUCCESS, "H5SetThrottle");
#endif
TEST("Writing 64-bit data");
for (t=step; t<step+NTIMESTEPS; t++)
{
for (i=0; i<nelems; i++)
{
e[i] = 0.0 + (double)(i+nelems*t);
ex[i] = 0.1 + (double)(i+nelems*t);
ey[i] = 0.2 + (double)(i+nelems*t);
ez[i] = 0.3 + (double)(i+nelems*t);
id[i] = i + nelems*t;
}
val = H5HasStep(file, t);
status = H5SetStep(file, t);
RETURN(status, H5_SUCCESS, "H5SetStep");
if (val == 0) test_write_field_attribs(file, "e", t);
status = H5Block3dSetView(file,
layout[0], layout[1],
layout[2], layout[3],
layout[4], layout[5]);
RETURN(status, H5_SUCCESS, "H5Block3dSetView");
status = H5Block3dWriteScalarFieldFloat64(file, "e", e);
RETURN(status, H5_SUCCESS, "H5Block3dWriteScalarFieldFloat64");
status = H5Block3dWriteVector3dFieldFloat64(file,
"E", ex, ey, ez);
RETURN(status, H5_SUCCESS,
"H5Block3dWriteVector3dFieldFloat64");
status = H5Block3dWriteScalarFieldInt64(file, "id", id);
RETURN(status, H5_SUCCESS, "H5Block3dWriteScalarFieldInt64");
}
}
void h5b_test_write1(void)
{
h5_file_t *file1;
h5_err_t status;
TEST("Opening file once, write-truncate");
file1 = H5OpenFile(FILENAME, H5_O_WRONLY, MPI_COMM_WORLD);
status = H5CheckFile(file1);
RETURN(status, H5_SUCCESS, "H5CheckFile");
test_write_data64(file1, 1);
status = H5CloseFile(file1);
RETURN(status, H5_SUCCESS, "H5CloseFile");
}
test/h5u_read.c
+25 -6
View File
@@ -92,10 +92,12 @@ test_read_data64(h5_file_t *file, int nparticles, int step)
{
int i,t;
int rank, nprocs;
h5_int64_t status, val, start, end, type, size;
h5_err_t status;
h5_int64_t val, start, end, type;
char name1[4];
char name2[8];
h5_int64_t indices[8];
h5_id_t indices[8];
h5_size_t size;
double *x,*y,*z;
double *px,*py,*pz;
@@ -194,7 +196,7 @@ test_read_data64(h5_file_t *file, int nparticles, int step)
indices[2] = rank*2 + 9;
indices[3] = rank*2 + 7;
status = H5PartSetViewIndices(file, indices, -1);
status = H5PartSetViewIndices(file, indices, 0);
RETURN(status, H5_SUCCESS, "H5PartSetViewIndices");
status = H5PartReadDataFloat64(file, "x", x);
@@ -226,9 +228,26 @@ test_read_data64(h5_file_t *file, int nparticles, int step)
status = H5PartSetCanonicalView(file);
RETURN(status, H5_SUCCESS, "H5PartSetCanonicalView");
status = H5PartReadParticleStep (
file, t, x, y, z, px, py, pz, id);
RETURN(status, H5_SUCCESS, "H5PartReadParticleStep");
status = H5PartReadDataFloat64(file, "x", x);
RETURN(status, H5_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "y", y);
RETURN(status, H5_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "z", z);
RETURN(status, H5_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "px", px);
RETURN(status, H5_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "py", py);
RETURN(status, H5_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataFloat64(file, "pz", pz);
RETURN(status, H5_SUCCESS, "H5PartReadDataFloat64");
status = H5PartReadDataInt64(file, "id", id);
RETURN(status, H5_SUCCESS, "H5PartReadDataInt64");
for (i=0; i<nparticles; i++)
{
test/h5u_write.c
+11 -15
View File
@@ -41,26 +41,30 @@ test_write_step_attribs(h5_file_t *file, int position)
h5_err_t status;
char name[ATTR_NAME_SIZE];
TEST("Writing step attributes");
TEST("Writing file attributes");
get_attr_name(name, "str", position);
status = H5WriteStepAttribString(file, name, ATTR_STR_VAL);
RETURN(status, H5_SUCCESS, "H5WriteStepAttribString");
get_attr_name(name, "i32", position);
status = H5WriteStepAttribInt32(file, name, ATTR_INT32_VAL, 1);
h5_int32_t i32 = ATTR_INT32_VAL;
status = H5WriteStepAttribInt32(file, name, &i32, 1);
RETURN(status, H5_SUCCESS, "H5WriteStepAttribInt32");
get_attr_name(name, "i64", position);
status = H5WriteStepAttribInt64(file, name, ATTR_INT64_VAL, 1);
h5_int64_t i64 = ATTR_INT64_VAL;
status = H5WriteStepAttribInt64(file, name, &i64, 1);
RETURN(status, H5_SUCCESS, "H5WriteStepAttribInt64");
get_attr_name(name, "f32", position);
status = H5WriteStepAttribFloat32(file, name, ATTR_FLOAT_VAL, 1);
h5_float32_t f32 = ATTR_FLOAT_VAL;
status = H5WriteStepAttribFloat32(file, name, &f32, 1);
RETURN(status, H5_SUCCESS, "H5WriteStepAttribFloat32");
get_attr_name(name, "f64", position);
status = H5WriteStepAttribFloat64(file, name, ATTR_FLOAT_VAL, 1);
h5_float64_t f64 = ATTR_FLOAT_VAL;
status = H5WriteStepAttribFloat64(file, name, &f64, 1);
RETURN(status, H5_SUCCESS, "H5WriteStepAttribFloat64");
}
@@ -82,14 +86,6 @@ test_write_data64(h5_file_t *file, int nparticles, int step)
pz=(double*)malloc(nparticles*sizeof(double));
id=(h5_int64_t*)malloc(nparticles*sizeof(h5_int64_t));
/* invalid stride will produce a warning */
status = H5PartSetNumParticlesStrided(file, nparticles, -1);
RETURN(status, H5_SUCCESS, "H5PartSetNumParticlesStrided");
/* invalid nparticles will produce an error */
status = H5PartSetNumParticlesStrided(file, -1, 2);
RETURN(status, H5_ERR_INVAL, "H5PartSetNumParticlesStrided");
#if PARALLEL_IO
TEST("Setting throttle");
status = H5SetThrottle(file, 2);
@@ -458,8 +454,8 @@ void h5u_test_write4(void)
status = H5SetStepNameFormat(file2, LONGNAME, 16);
RETURN(status, H5_SUCCESS, "H5SetStepNameFormat");
status = H5PartSetChunkSize(file1, NPARTICLES);
RETURN(status, H5_SUCCESS, "H5PartSetChunkSize");
status = H5PartSetChunk(file1, NPARTICLES);
RETURN(status, H5_SUCCESS, "H5PartSetChunk");
test_write_data64(file1, NPARTICLES, NTIMESTEPS-2);
test_write_file_attribs(file1, 1);
test/params.h
+4
View File
@@ -9,6 +9,10 @@
* made in the read tests! */
#define NPARTICLES 99
#define NBLOCKX 16
#define NBLOCKY 12
#define NBLOCKZ 18
/* do not increase this value past 32! */
#define MAX_MPI_TASKS 32