mirror/hdf5
2
0
Fork 0
mirror of https://github.com/HDFGroup/hdf5.git synced 2025-01-18 15:15:56 +08:00
Code Issues Packages Projects Releases Wiki Activity

[svn-r26279] re-commit 26260 that Dana moved out fixing the versioning of functions to work with v16 default API.

Browse Source
This commit is contained in:
Mohamad Chaarawi 2015-02-23 10:14:43 -05:00
parent f175fd25c8
commit 0c29ac42cd
11 changed files with 363 additions and 45 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
MANIFEST
View File

@ -1146,6 +1146,8 @@
./testpar/t_pflush2.c
./testpar/t_prop.c
./testpar/t_shapesame.c
./testpar/t_pshutdown.c
./testpar/t_prestart.c
./testpar/t_span_tree.c
./testpar/testpar.h
./testpar/testphdf5.c

80
src/H5.c
View File

@ -52,7 +52,9 @@
/* Local Prototypes */
/********************/
static void H5_debug_mask(const char*);
#ifdef H5_HAVE_PARALLEL
static int H5_mpi_delete_cb(MPI_Comm comm, int keyval, void *attr_val, int *flag);
#endif /*H5_HAVE_PARALLEL*/
/*********************/
/* Package Variables */
@ -109,6 +111,43 @@ H5_init_library(void)
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI(FAIL)
#ifdef H5_HAVE_PARALLEL
{
int mpi_initialized;
int mpi_code;
MPI_Initialized(&mpi_initialized);
#ifdef H5_HAVE_MPE
/* Initialize MPE instrumentation library. */
if (!H5_MPEinit_g)
{
int mpe_code;
if (mpi_initialized){
mpe_code = MPE_Init_log();
HDassert(mpe_code >=0);
H5_MPEinit_g = TRUE;
}
}
#endif /*H5_HAVE_MPE*/
/* add an attribute on MPI_COMM_SELF to call H5_term_library
when it is destroyed, i.e. on MPI_Finalize */
if (mpi_initialized) {
int key_val;
if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN,
(MPI_Comm_delete_attr_function *)H5_mpi_delete_cb,
&key_val, NULL)))
HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code)
if(MPI_SUCCESS != (mpi_code = MPI_Comm_set_attr(MPI_COMM_SELF, key_val, NULL)))
HMPI_GOTO_ERROR(FAIL, "MPI_Comm_set_attr failed", mpi_code)
}
}
#endif /*H5_HAVE_PARALLEL*/
/*
* Make sure the package information is updated.
*/
@ -132,24 +171,6 @@ H5_init_library(void)
H5_debug_g.pkg[H5_PKG_V].name = "v";
H5_debug_g.pkg[H5_PKG_Z].name = "z";
#ifdef H5_HAVE_MPE
/* Initialize MPE instrumentation library. May need to move this
* up earlier if any of the above initialization involves using
* the instrumentation code.
*/
if (!H5_MPEinit_g)
{
int mpe_code;
int mpi_initialized;
MPI_Initialized(&mpi_initialized);
if (mpi_initialized){
mpe_code = MPE_Init_log();
HDassert(mpe_code >=0);
H5_MPEinit_g = TRUE;
}
}
#endif
/*
* Install atexit() library cleanup routines unless the H5dont_atexit()
* has been called. Once we add something to the atexit() list it stays
@ -580,6 +601,27 @@ H5_debug_mask(const char *s)
}
} /* end H5_debug_mask() */
#ifdef H5_HAVE_PARALLEL
/*-------------------------------------------------------------------------
* Function: H5_mpi_delete_cb
*
* Purpose: Callback attribute on MPI_COMM_SELF to terminate the HDF5
* library when the communicator is destroyed, i.e. on MPI_Finalize.
*
* Return: MPI_SUCCESS
*
* Programmer: Mohamad Chaarawi, February 2015
*
*-------------------------------------------------------------------------
*/
static int H5_mpi_delete_cb(MPI_Comm UNUSED comm, int UNUSED keyval, void UNUSED *attr_val, int UNUSED *flag)
{
H5_term_library();
return MPI_SUCCESS;
}
#endif /*H5_HAVE_PARALLEL*/
/*-------------------------------------------------------------------------
* Function: H5get_libversion

2
testpar/CMakeLists.txt
View File

@ -46,6 +46,8 @@ set (H5P_TESTS
t_cache
t_pflush1
t_pflush2
t_pshutdown
t_prestart
t_shapesame
)

5
testpar/Makefile.am
View File

@ -25,7 +25,7 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test
# Test programs. These are our main targets.
#
TEST_PROG_PARA=t_mpi testphdf5 t_cache t_pflush1 t_pflush2 t_shapesame
TEST_PROG_PARA=t_mpi testphdf5 t_cache t_pflush1 t_pflush2 t_pshutdown t_prestart t_shapesame
check_PROGRAMS = $(TEST_PROG_PARA)
@ -39,7 +39,8 @@ LDADD = $(LIBH5TEST) $(LIBHDF5)
# Temporary files
# MPItest.h5 is from t_mpi
# Para*.h5 are from testphdf
# shutdown.h5 is from t_pshutdown
# go is used for debugging. See testphdf5.c.
CHECK_CLEANFILES+=MPItest.h5 Para*.h5 CacheTestDummy.h5 go
CHECK_CLEANFILES+=MPItest.h5 Para*.h5 CacheTestDummy.h5 shutdown.h5 go
include $(top_srcdir)/config/conclude.am

34
testpar/Makefile.in
View File

@ -112,7 +112,8 @@ CONFIG_HEADER = $(top_builddir)/src/H5config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
am__EXEEXT_1 = t_mpi$(EXEEXT) testphdf5$(EXEEXT) t_cache$(EXEEXT) \
t_pflush1$(EXEEXT) t_pflush2$(EXEEXT) t_shapesame$(EXEEXT)
t_pflush1$(EXEEXT) t_pflush2$(EXEEXT) t_pshutdown$(EXEEXT) \
t_prestart$(EXEEXT) t_shapesame$(EXEEXT)
t_cache_SOURCES = t_cache.c
t_cache_OBJECTS = t_cache.$(OBJEXT)
t_cache_LDADD = $(LDADD)
@ -133,6 +134,14 @@ t_pflush2_SOURCES = t_pflush2.c
t_pflush2_OBJECTS = t_pflush2.$(OBJEXT)
t_pflush2_LDADD = $(LDADD)
t_pflush2_DEPENDENCIES = $(LIBH5TEST) $(LIBHDF5)
t_prestart_SOURCES = t_prestart.c
t_prestart_OBJECTS = t_prestart.$(OBJEXT)
t_prestart_LDADD = $(LDADD)
t_prestart_DEPENDENCIES = $(LIBH5TEST) $(LIBHDF5)
t_pshutdown_SOURCES = t_pshutdown.c
t_pshutdown_OBJECTS = t_pshutdown.$(OBJEXT)
t_pshutdown_LDADD = $(LDADD)
t_pshutdown_DEPENDENCIES = $(LIBH5TEST) $(LIBHDF5)
t_shapesame_SOURCES = t_shapesame.c
t_shapesame_OBJECTS = t_shapesame.$(OBJEXT)
t_shapesame_LDADD = $(LDADD)
@ -179,10 +188,10 @@ AM_V_CCLD = $(am__v_CCLD_@AM_V@)
am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@)
am__v_CCLD_0 = @echo " CCLD " $@;
am__v_CCLD_1 =
SOURCES = t_cache.c t_mpi.c t_pflush1.c t_pflush2.c t_shapesame.c \
$(testphdf5_SOURCES)
DIST_SOURCES = t_cache.c t_mpi.c t_pflush1.c t_pflush2.c t_shapesame.c \
$(testphdf5_SOURCES)
SOURCES = t_cache.c t_mpi.c t_pflush1.c t_pflush2.c t_prestart.c \
t_pshutdown.c t_shapesame.c $(testphdf5_SOURCES)
DIST_SOURCES = t_cache.c t_mpi.c t_pflush1.c t_pflush2.c t_prestart.c \
t_pshutdown.c t_shapesame.c $(testphdf5_SOURCES)
am__can_run_installinfo = \
case $$AM_UPDATE_INFO_DIR in \
n|no|NO) false;; \
@ -687,13 +696,14 @@ TRACE = perl $(top_srcdir)/bin/trace
# Temporary files
# MPItest.h5 is from t_mpi
# Para*.h5 are from testphdf
# shutdown.h5 is from t_pshutdown
# go is used for debugging. See testphdf5.c.
CHECK_CLEANFILES = *.chkexe *.chklog *.clog MPItest.h5 Para*.h5 \
CacheTestDummy.h5 go
CacheTestDummy.h5 shutdown.h5 go
# Test programs. These are our main targets.
#
TEST_PROG_PARA = t_mpi testphdf5 t_cache t_pflush1 t_pflush2 t_shapesame
TEST_PROG_PARA = t_mpi testphdf5 t_cache t_pflush1 t_pflush2 t_pshutdown t_prestart t_shapesame
testphdf5_SOURCES = testphdf5.c t_dset.c t_file.c t_file_image.c t_mdset.c \
t_ph5basic.c t_coll_chunk.c t_span_tree.c t_chunk_alloc.c t_filter_read.c \
t_prop.c
@ -782,6 +792,14 @@ t_pflush2$(EXEEXT): $(t_pflush2_OBJECTS) $(t_pflush2_DEPENDENCIES) $(EXTRA_t_pfl
@rm -f t_pflush2$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(t_pflush2_OBJECTS) $(t_pflush2_LDADD) $(LIBS)
t_prestart$(EXEEXT): $(t_prestart_OBJECTS) $(t_prestart_DEPENDENCIES) $(EXTRA_t_prestart_DEPENDENCIES)
@rm -f t_prestart$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(t_prestart_OBJECTS) $(t_prestart_LDADD) $(LIBS)
t_pshutdown$(EXEEXT): $(t_pshutdown_OBJECTS) $(t_pshutdown_DEPENDENCIES) $(EXTRA_t_pshutdown_DEPENDENCIES)
@rm -f t_pshutdown$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(t_pshutdown_OBJECTS) $(t_pshutdown_LDADD) $(LIBS)
t_shapesame$(EXEEXT): $(t_shapesame_OBJECTS) $(t_shapesame_DEPENDENCIES) $(EXTRA_t_shapesame_DEPENDENCIES)
@rm -f t_shapesame$(EXEEXT)
$(AM_V_CCLD)$(LINK) $(t_shapesame_OBJECTS) $(t_shapesame_LDADD) $(LIBS)
@ -808,7 +826,9 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/t_pflush1.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/t_pflush2.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/t_ph5basic.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/t_prestart.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/t_prop.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/t_pshutdown.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/t_shapesame.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/t_span_tree.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/testphdf5.Po@am__quote@

11
testpar/t_pflush1.c
View File

@ -164,12 +164,9 @@ main(int argc, char* argv[])
} /* end else */
/*
* Some systems like Linux with mpich, if you just _exit without MPI_Finalize
* called, it would terminate but left the launching process waiting forever.
* OTHO, some systems like AIX do not like files not closed when MPI_Finalize
* is called. So, we need to get the MPI file handles, close them by hand,
* then MPI_Finalize. Then the _exit is still needed to stop at_exit from
* happening in some systems.
* Some systems like AIX do not like files not closed when MPI_Finalize
* is called. So, we need to get the MPI file handles, close them by hand.
* Then the _exit is still needed to stop at_exit from happening in some systems.
* Note that MPIO VFD returns the address of the file-handle in the VFD struct
* because MPI_File_close wants to modify the file-handle variable.
*/
@ -195,13 +192,11 @@ main(int argc, char* argv[])
fflush(stdout);
fflush(stderr);
MPI_Finalize();
HD_exit(0);
error:
fflush(stdout);
fflush(stderr);
MPI_Finalize();
HD_exit(1);
}

3
testpar/t_pflush2.c
View File

@ -209,9 +209,6 @@ main(int argc, char* argv[])
puts(" Test not compatible with current Virtual File Driver");
}
/* close HDF5 library */
H5close();
MPI_Finalize();
return 0;

138
testpar/t_prestart.c Normal file
View File

@ -0,0 +1,138 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Mohamad Chaarawi
* February 2015
*
* Purpose: This test opens a file created by the t_pshutdown program
* and makes sure the objects created are there.
*/
#include "testphdf5.h"
int nerrors = 0; /* errors count */
const char *FILENAME[] = {
"shutdown",
NULL
};
int
main (int argc, char **argv)
{
hid_t file_id, dset_id, grp_id;
hid_t fapl, sid, mem_dataspace;
herr_t ret;
char filename[1024];
int mpi_size, mpi_rank, ndims, i, j;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
hsize_t dims[RANK];
hsize_t start[RANK];
hsize_t count[RANK];
hsize_t stride[RANK];
hsize_t block[RANK];
DATATYPE *data_array = NULL, *dataptr; /* data buffer */
MPI_Init(&argc, &argv);
MPI_Comm_size(comm, &mpi_size);
MPI_Comm_rank(comm, &mpi_rank);
if(MAINPROCESS)
TESTING("proper shutdown of HDF5 library");
/* Set up file access property list with parallel I/O access */
fapl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_fapl_mpio(fapl, comm, info);
VRFY((ret >= 0), "");
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
file_id = H5Fopen(filename, H5F_ACC_RDONLY, fapl);
VRFY((file_id >= 0), "H5Fopen succeeded");
grp_id = H5Gopen2(file_id, "Group", H5P_DEFAULT);
VRFY((grp_id >= 0), "H5Gopen succeeded");
dset_id = H5Dopen2(grp_id, "Dataset", H5P_DEFAULT);
VRFY((dset_id >= 0), "H5Dopen succeeded");
sid = H5Dget_space(dset_id);
VRFY((dset_id >= 0), "H5Dget_space succeeded");
ndims = H5Sget_simple_extent_dims(sid, dims, NULL);
VRFY((ndims == 2), "H5Sget_simple_extent_dims succeeded");
VRFY(dims[0] == ROW_FACTOR*mpi_size, "Wrong dataset dimensions");
VRFY(dims[1] == COL_FACTOR*mpi_size, "Wrong dataset dimensions");
/* allocate memory for data buffer */
data_array = (DATATYPE *)HDmalloc(dims[0]*dims[1]*sizeof(DATATYPE));
VRFY((data_array != NULL), "data_array HDmalloc succeeded");
/* Each process takes a slabs of rows. */
block[0] = dims[0]/mpi_size;
block[1] = dims[1];
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = mpi_rank*block[0];
start[1] = 0;
ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* write data independently */
ret = H5Dread(dset_id, H5T_NATIVE_INT, mem_dataspace, sid,
H5P_DEFAULT, data_array);
VRFY((ret >= 0), "H5Dwrite succeeded");
dataptr = data_array;
for (i=0; i < block[0]; i++){
for (j=0; j < block[1]; j++){
if(*dataptr != mpi_rank+1) {
printf("Dataset Verify failed at [%lu][%lu](row %lu, col %lu): expect %d, got %d\n",
(unsigned long)i, (unsigned long)j,
(unsigned long)(i+start[0]), (unsigned long)(j+start[1]),
mpi_rank+1, *(dataptr));
nerrors ++;
}
dataptr++;
}
}
MPI_Finalize();
HDremove(filename);
/* release data buffers */
if(data_array)
HDfree(data_array);
nerrors += GetTestNumErrs();
if(MAINPROCESS) {
if(0 == nerrors)
PASSED()
else
H5_FAILED()
}
return (nerrors!=0);
}

127
testpar/t_pshutdown.c Normal file
View File

@ -0,0 +1,127 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: Mohamad Chaarawi
* February 2015
*
* Purpose: This test creates a file and a bunch of objects in the
* file and then calls MPI_Finalize without closing anything. The
* library should exercise the attribute callback destroy attached to
* MPI_COMM_SELF and terminate the HDF5 library closing all open
* objects. The t_prestart test will read back the file and make sure
* all created objects are there.
*/
#include "testphdf5.h"
int nerrors = 0; /* errors count */
const char *FILENAME[] = {
"shutdown",
NULL
};
int
main (int argc, char **argv)
{
hid_t file_id, dset_id, grp_id;
hid_t fapl, sid, mem_dataspace;
hsize_t dims[RANK], i;
herr_t ret;
char filename[1024];
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
hsize_t start[RANK];
hsize_t count[RANK];
hsize_t stride[RANK];
hsize_t block[RANK];
DATATYPE *data_array = NULL; /* data buffer */
MPI_Init(&argc, &argv);
MPI_Comm_size(comm, &mpi_size);
MPI_Comm_rank(comm, &mpi_rank);
if(MAINPROCESS)
TESTING("proper shutdown of HDF5 library");
/* Set up file access property list with parallel I/O access */
fapl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_fapl_mpio(fapl, comm, info);
VRFY((ret >= 0), "");
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
VRFY((file_id >= 0), "H5Fcreate succeeded");
grp_id = H5Gcreate2(file_id, "Group", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((grp_id >= 0), "H5Gcreate succeeded");
dims[0] = ROW_FACTOR*mpi_size;
dims[1] = COL_FACTOR*mpi_size;
sid = H5Screate_simple (RANK, dims, NULL);
VRFY((sid >= 0), "H5Screate_simple succeeded");
dset_id = H5Dcreate2(grp_id, "Dataset", H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dset_id >= 0), "H5Dcreate succeeded");
/* allocate memory for data buffer */
data_array = (DATATYPE *)HDmalloc(dims[0]*dims[1]*sizeof(DATATYPE));
VRFY((data_array != NULL), "data_array HDmalloc succeeded");
/* Each process takes a slabs of rows. */
block[0] = dims[0]/mpi_size;
block[1] = dims[1];
stride[0] = block[0];
stride[1] = block[1];
count[0] = 1;
count[1] = 1;
start[0] = mpi_rank*block[0];
start[1] = 0;
/* put some trivial data in the data_array */
for(i=0 ; i<dims[0]*dims[1]; i++)
data_array[i] = mpi_rank + 1;
ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");
/* create a memory dataspace independently */
mem_dataspace = H5Screate_simple (RANK, block, NULL);
VRFY((mem_dataspace >= 0), "");
/* write data independently */
ret = H5Dwrite(dset_id, H5T_NATIVE_INT, mem_dataspace, sid,
H5P_DEFAULT, data_array);
VRFY((ret >= 0), "H5Dwrite succeeded");
/* release data buffers */
if(data_array)
HDfree(data_array);
MPI_Finalize();
nerrors += GetTestNumErrs();
if(MAINPROCESS) {
if(0 == nerrors)
PASSED()
else
H5_FAILED()
}
return (nerrors!=0);
}

3
testpar/t_shapesame.c
View File

@ -5142,10 +5142,7 @@ int main(int argc, char **argv)
printf("Shape Same tests finished with no errors\n");
printf("===================================\n");
}
/* close HDF5 library */
H5close();
/* MPI_Finalize must be called AFTER H5close which may use MPI calls */
MPI_Finalize();
/* cannot just return (nerrors) because exit code is limited to 1byte */

3
tools/perform/perf.c
View File

@ -391,9 +391,6 @@ die_jar_jar_die:
free(tmp);
if (opt_correct) free(tmp2);
/* close HDF5 library */
H5close();
MPI_Finalize();
return(0);