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Merge pull request #1167 in HDFFV/hdf5 from ~JHENDERSON/hdf5:bugfix/MPI2_only_fixes to develop

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* commit '9aa2eaeb9ed9c94f63973cb55f13de256558497c':
  Add Autotools and CMake checks for big I/O MPI-3 functions
  Add hdf5settings section for parallel compression status in CMake builds
  Switch to CheckSymbolExists in CMake
  Add configure check for MPI_Mprobe and MPI_Imrecv functions
This commit is contained in:
Jordan Henderson 2018-08-02 09:25:00 -05:00
commit 70de0b18e3
9 changed files with 195 additions and 39 deletions
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20
CMakeLists.txt
View File

@ -559,6 +559,26 @@ if (HDF5_ENABLE_PARALLEL)
# Used by Fortran + MPI
CHECK_SYMBOL_EXISTS (MPI_Comm_c2f "${MPI_C_INCLUDE_DIRS}/mpi.h" H5_HAVE_MPI_MULTI_LANG_Comm)
CHECK_SYMBOL_EXISTS (MPI_Info_c2f "${MPI_C_INCLUDE_DIRS}/mpi.h" H5_HAVE_MPI_MULTI_LANG_Info)
# Used by Parallel Compression feature
set (PARALLEL_FILTERED_WRITES ON)
CHECK_SYMBOL_EXISTS (MPI_Mprobe "${MPI_C_INCLUDE_DIRS}/mpi.h" H5_HAVE_MPI_Mprobe)
CHECK_SYMBOL_EXISTS (MPI_Imrecv "${MPI_C_INCLUDE_DIRS}/mpi.h" H5_HAVE_MPI_Imrecv)
if (NOT H5_HAVE_MPI_Mprobe OR NOT H5_HAVE_MPI_Imrecv)
message (WARNING "The MPI_Mprobe and/or MPI_Imrecv functions could not be located.
Parallel writes of filtered data will be disabled.")
set (PARALLEL_FILTERED_WRITES OFF)
endif ()
# Used by big I/O feature
set (LARGE_PARALLEL_IO ON)
CHECK_SYMBOL_EXISTS (MPI_Get_elements_x "${MPI_C_INCLUDE_DIRS}/mpi.h" H5_HAVE_MPI_Get_elements_x)
CHECK_SYMBOL_EXISTS (MPI_Type_size_x "${MPI_C_INCLUDE_DIRS}/mpi.h" H5_HAVE_MPI_Type_size_x)
if (NOT H5_HAVE_MPI_Get_elements_x OR NOT H5_HAVE_MPI_Type_size_x)
message (WARNING "The MPI_Get_elements_x and/or MPI_Type_size_x functions could not be located.
Reading/Writing >2GB of data in a single parallel I/O operation will be disabled.")
set (LARGE_PARALLEL_IO OFF)
endif ()
else ()
message (STATUS "Parallel libraries not found")
endif ()

36
config/cmake/libhdf5.settings.cmake.in
View File

@ -64,20 +64,22 @@ Languages:
Features:
---------
Parallel HDF5: @HDF5_ENABLE_PARALLEL@
High-level library: @HDF5_BUILD_HL_LIB@
Threadsafety: @HDF5_ENABLE_THREADSAFE@
Default API mapping: @DEFAULT_API_VERSION@
With deprecated public symbols: @HDF5_ENABLE_DEPRECATED_SYMBOLS@
I/O filters (external): @EXTERNAL_FILTERS@
MPE: @H5_HAVE_LIBLMPE@
Direct VFD: @H5_HAVE_DIRECT@
dmalloc: @H5_HAVE_LIBDMALLOC@
Packages w/ extra debug output: @INTERNAL_DEBUG_OUTPUT@
API Tracing: @HDF5_ENABLE_TRACE@
Using memory checker: @HDF5_ENABLE_USING_MEMCHECKER@
Memory allocation sanity checks: @HDF5_MEMORY_ALLOC_SANITY_CHECK@
Metadata trace file: @METADATATRACEFILE@
Function Stack Tracing: @HDF5_ENABLE_CODESTACK@
Strict File Format Checks: @HDF5_STRICT_FORMAT_CHECKS@
Optimization Instrumentation: @HDF5_Enable_Instrument@
Parallel HDF5: @HDF5_ENABLE_PARALLEL@
Parallel Filtered Dataset Writes: @PARALLEL_FILTERED_WRITES@
Large Parallel I/O: @LARGE_PARALLEL_IO@
High-level library: @HDF5_BUILD_HL_LIB@
Threadsafety: @HDF5_ENABLE_THREADSAFE@
Default API mapping: @DEFAULT_API_VERSION@
With deprecated public symbols: @HDF5_ENABLE_DEPRECATED_SYMBOLS@
I/O filters (external): @EXTERNAL_FILTERS@
MPE: @H5_HAVE_LIBLMPE@
Direct VFD: @H5_HAVE_DIRECT@
dmalloc: @H5_HAVE_LIBDMALLOC@
Packages w/ extra debug output: @INTERNAL_DEBUG_OUTPUT@
API Tracing: @HDF5_ENABLE_TRACE@
Using memory checker: @HDF5_ENABLE_USING_MEMCHECKER@
Memory allocation sanity checks: @HDF5_MEMORY_ALLOC_SANITY_CHECK@
Metadata trace file: @METADATATRACEFILE@
Function Stack Tracing: @HDF5_ENABLE_CODESTACK@
Strict File Format Checks: @HDF5_STRICT_FORMAT_CHECKS@
Optimization Instrumentation: @HDF5_Enable_Instrument@

63
configure.ac
View File

@ -2531,6 +2531,8 @@ esac
AC_SUBST([ADD_PARALLEL_FILES]) ADD_PARALLEL_FILES="no"
AC_SUBST([MPE]) MPE=no
AC_SUBST([INSTRUMENT_LIBRARY]) INSTRUMENT_LIBRARY=no
AC_SUBST([PARALLEL_FILTERED_WRITES])
AC_SUBST([LARGE_PARALLEL_IO])
if test -n "$PARALLEL"; then
## The 'testpar' directory should participate in the build
@ -2686,6 +2688,61 @@ if test -n "$PARALLEL"; then
if test "X-$MPE" = "X-yes"; then
AC_DEFINE([HAVE_MPE], [1], [Define if we have MPE support])
fi
## ----------------------------------------------------------------------
## Check for the MPI-3 functions necessary for the Parallel Compression
## feature. If these are not present, issue a warning that Parallel
## Compression will be disabled.
##
AC_MSG_CHECKING([for MPI_Mprobe and MPI_Imrecv functions])
AC_LINK_IFELSE(
[AC_LANG_PROGRAM(
[[
#include <mpi.h>
]],
[[
MPI_Message message;
MPI_Init(0, (void *) 0);
MPI_Mprobe(0, 0, 0, &message, (void *) 0);
MPI_Imrecv((void *) 0, 0, 0, (void *) 0, (void *) 0);
]]
)],
[AC_MSG_RESULT([yes])
PARALLEL_FILTERED_WRITES=yes],
[AC_MSG_RESULT([no])
AC_MSG_WARN([A simple MPI program using the MPI_Mprobe and MPI_Imrecv functions could not be compiled and linked.
Parallel writes of filtered data will be disabled.])
PARALLEL_FILTERED_WRITES=no]
)
## ----------------------------------------------------------------------
## Check for the MPI-3 functions necessary for the big I/O feature.
## If these are not present, issue a warning that the big I/O feature
## will be disabled.
##
AC_MSG_CHECKING([for MPI_Get_elements_x and MPI_Type_size_x functions])
AC_LINK_IFELSE(
[AC_LANG_PROGRAM(
[[
#include <mpi.h>
]],
[[
MPI_Count count;
MPI_Init(0, (void *) 0);
MPI_Get_elements_x(0, 0, &count);
MPI_Type_size_x(0, &count);
]]
)],
[AC_MSG_RESULT([yes])
LARGE_PARALLEL_IO=yes],
[AC_MSG_RESULT([no])
AC_MSG_WARN([A simple MPI program using the MPI_Get_elements_x and MPI_Type_size_x functions could not be compiled and linked.
Reading/Writing >2GB of data in a single parallel I/O operation will be disabled.])
LARGE_PARALLEL_IO=no]
)
fi
## ----------------------------------------------------------------------
@ -2976,6 +3033,12 @@ AC_SUBST([WORDS_BIGENDIAN])
## Parallel support? (set above except empty if none)
PARALLEL=${PARALLEL:-no}
## Parallel writes to filtered datasets support?
PARALLEL_FILTERED_WRITES=${PARALLEL_FILTERED_WRITES:-no}
## >2GB writes in parallel support?
LARGE_PARALLEL_IO=${LARGE_PARALLEL_IO:-no}
## Compiler with version information. This consists of the full path
## name of the compiler and the reported version number.
AC_SUBST([CC_VERSION])

3
src/H5Dio.c
View File

@ -1189,7 +1189,8 @@ H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset,
"data transforms needed to be applied",
"optimized MPI types flag wasn't set",
"one of the dataspaces was neither simple nor scalar",
"dataset was not contiguous or chunked" };
"dataset was not contiguous or chunked",
"parallel writes to filtered datasets are disabled" };
if(H5CX_get_mpio_local_no_coll_cause(&local_no_collective_cause) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get local no collective cause value")

24
src/H5Dmpio.c
View File

@ -229,9 +229,11 @@ static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info,
static herr_t H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info,
const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm,
H5D_filtered_collective_io_info_t **chunk_list, size_t *num_entries);
#if MPI_VERSION >= 3
static herr_t H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info,
const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm,
H5D_filtered_collective_io_info_t *local_chunk_array, size_t *local_chunk_array_num_entries);
#endif
static herr_t H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries,
size_t array_entry_size, void **gathered_array, size_t *gathered_array_num_entries,
hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *));
@ -244,8 +246,10 @@ static herr_t H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io
static int H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2);
static int H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1,
const void *filtered_collective_io_info_entry2);
#if MPI_VERSION >= 3
static int H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective_io_info_entry1,
const void *filtered_collective_io_info_entry2);
#endif
/*********************/
@ -330,6 +334,18 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space,
* use collective IO will defer until each chunk IO is reached.
*/
#if MPI_VERSION < 3
/*
* Don't allow parallel writes to filtered datasets if the MPI version
* is less than 3. The functions needed (MPI_Mprobe and MPI_Imrecv) will
* not be available.
*/
if (io_info->op_type == H5D_IO_OP_WRITE &&
io_info->dset->shared->layout.type == H5D_CHUNKED &&
io_info->dset->shared->dcpl_cache.pline.nused > 0)
local_cause |= H5D_MPIO_PARALLEL_FILTERED_WRITES_DISABLED;
#endif
/* Check for independent I/O */
if(local_cause & H5D_MPIO_SET_INDEPENDENT)
global_cause = local_cause;
@ -2127,6 +2143,7 @@ H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_in
FUNC_LEAVE_NOAPI(H5F_addr_cmp(addr1, addr2))
} /* end H5D__cmp_filtered_collective_io_info_entry() */
#if MPI_VERSION >= 3
/*-------------------------------------------------------------------------
* Function: H5D__cmp_filtered_collective_io_info_entry_owner
@ -2157,6 +2174,7 @@ H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective
FUNC_LEAVE_NOAPI(owner1 - owner2)
} /* end H5D__cmp_filtered_collective_io_info_entry_owner() */
#endif
/*-------------------------------------------------------------------------
@ -2585,8 +2603,12 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ
/* Redistribute shared chunks to new owners as necessary */
if (io_info->op_type == H5D_IO_OP_WRITE)
#if MPI_VERSION >= 3
if (H5D__chunk_redistribute_shared_chunks(io_info, type_info, fm, local_info_array, &num_chunks_selected) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks")
#else
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks - MPI version < 3 (MPI_Mprobe and MPI_Imrecv missing)")
#endif
*chunk_list = local_info_array;
*num_entries = num_chunks_selected;
@ -2595,6 +2617,7 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__construct_filtered_io_info_list() */
#if MPI_VERSION >= 3
/*-------------------------------------------------------------------------
* Function: H5D__chunk_redistribute_shared_chunks
@ -2893,6 +2916,7 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__chunk_redistribute_shared_chunks() */
#endif
/*-------------------------------------------------------------------------

3
src/H5Ppublic.h
View File

@ -166,7 +166,8 @@ typedef enum H5D_mpio_no_collective_cause_t {
H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED = 0x08,
H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES = 0x10,
H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET = 0x20,
H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE = 0x40
H5D_MPIO_PARALLEL_FILTERED_WRITES_DISABLED = 0x40,
H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE = 0x80
} H5D_mpio_no_collective_cause_t;
/********************/

35
src/H5Smpio.c
View File

@ -271,29 +271,58 @@ H5S_mpio_create_point_datatype (size_t elmt_size, hsize_t num_points,
if(NULL == (inner_disps = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * (size_t)total_types)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks")
#if MPI_VERSION < 3
/* Allocate block sizes for MPI datatype call */
if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * bigio_count)))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks")
for(u = 0; u < bigio_count; u++)
blocks[u] = 1;
#endif
for(i=0 ; i<num_big_types ; i++) {
#if MPI_VERSION >= 3
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block(bigio_count,
1,
&disp[i*bigio_count],
elmt_type,
&inner_types[i]))) {
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code);
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code);
}
#else
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)bigio_count,
blocks,
&disp[i*bigio_count],
elmt_type,
&inner_types[i]))) {
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
}
#endif
inner_blocks[i] = 1;
inner_disps[i] = 0;
}
if(remaining_points) {
#if MPI_VERSION >= 3
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block(remaining_points,
1,
&disp[num_big_types*bigio_count],
elmt_type,
&inner_types[num_big_types]))) {
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code);
}
}
#else
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)remaining_points,
blocks,
&disp[num_big_types*bigio_count],
elmt_type,
&inner_types[num_big_types]))) {
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
}
#endif
inner_blocks[num_big_types] = 1;
inner_disps[num_big_types] = 0;
}
}
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct(total_types,
inner_blocks,

36
src/libhdf5.settings.in
View File

@ -67,20 +67,22 @@ Languages:
Features:
---------
Parallel HDF5: @PARALLEL@
High-level library: @HDF5_HL@
Threadsafety: @THREADSAFE@
Default API mapping: @DEFAULT_API_VERSION@
With deprecated public symbols: @DEPRECATED_SYMBOLS@
I/O filters (external): @EXTERNAL_FILTERS@
MPE: @MPE@
Direct VFD: @DIRECT_VFD@
dmalloc: @HAVE_DMALLOC@
Packages w/ extra debug output: @INTERNAL_DEBUG_OUTPUT@
API tracing: @TRACE_API@
Using memory checker: @USINGMEMCHECKER@
Memory allocation sanity checks: @MEMORYALLOCSANITYCHECK@
Metadata trace file: @METADATATRACEFILE@
Function stack tracing: @CODESTACK@
Strict file format checks: @STRICT_FORMAT_CHECKS@
Optimization instrumentation: @INSTRUMENT_LIBRARY@
Parallel HDF5: @PARALLEL@
Parallel Filtered Dataset Writes: @PARALLEL_FILTERED_WRITES@
Large Parallel I/O: @LARGE_PARALLEL_IO@
High-level library: @HDF5_HL@
Threadsafety: @THREADSAFE@
Default API mapping: @DEFAULT_API_VERSION@
With deprecated public symbols: @DEPRECATED_SYMBOLS@
I/O filters (external): @EXTERNAL_FILTERS@
MPE: @MPE@
Direct VFD: @DIRECT_VFD@
dmalloc: @HAVE_DMALLOC@
Packages w/ extra debug output: @INTERNAL_DEBUG_OUTPUT@
API tracing: @TRACE_API@
Using memory checker: @USINGMEMCHECKER@
Memory allocation sanity checks: @MEMORYALLOCSANITYCHECK@
Metadata trace file: @METADATATRACEFILE@
Function stack tracing: @CODESTACK@
Strict file format checks: @STRICT_FORMAT_CHECKS@
Optimization instrumentation: @INSTRUMENT_LIBRARY@

14
testpar/t_filters_parallel.c
View File

@ -37,6 +37,7 @@ size_t cur_filter_idx = 0;
static herr_t set_dcpl_filter(hid_t dcpl);
#if MPI_VERSION >= 3
/* Tests for writing data in parallel */
static void test_write_one_chunk_filtered_dataset(void);
static void test_write_filtered_dataset_no_overlap(void);
@ -52,6 +53,7 @@ static void test_write_cmpd_filtered_dataset_no_conversion_unshared(void);
static void test_write_cmpd_filtered_dataset_no_conversion_shared(void);
static void test_write_cmpd_filtered_dataset_type_conversion_unshared(void);
static void test_write_cmpd_filtered_dataset_type_conversion_shared(void);
#endif
/* Tests for reading data in parallel */
static void test_read_one_chunk_filtered_dataset(void);
@ -69,8 +71,10 @@ static void test_read_cmpd_filtered_dataset_no_conversion_shared(void);
static void test_read_cmpd_filtered_dataset_type_conversion_unshared(void);
static void test_read_cmpd_filtered_dataset_type_conversion_shared(void);
#if MPI_VERSION >= 3
/* Other miscellaneous tests */
static void test_shrinking_growing_chunks(void);
#endif
/*
* Tests for attempting to round-trip the data going from
@ -82,7 +86,9 @@ static void test_shrinking_growing_chunks(void);
* written in parallel -> read serially
*/
static void test_write_serial_read_parallel(void);
#if MPI_VERSION >= 3
static void test_write_parallel_read_serial(void);
#endif
static MPI_Comm comm = MPI_COMM_WORLD;
static MPI_Info info = MPI_INFO_NULL;
@ -90,6 +96,7 @@ static int mpi_rank;
static int mpi_size;
static void (*tests[])(void) = {
#if MPI_VERSION >= 3
test_write_one_chunk_filtered_dataset,
test_write_filtered_dataset_no_overlap,
test_write_filtered_dataset_overlap,
@ -104,6 +111,7 @@ static void (*tests[])(void) = {
test_write_cmpd_filtered_dataset_no_conversion_shared,
test_write_cmpd_filtered_dataset_type_conversion_unshared,
test_write_cmpd_filtered_dataset_type_conversion_shared,
#endif
test_read_one_chunk_filtered_dataset,
test_read_filtered_dataset_no_overlap,
test_read_filtered_dataset_overlap,
@ -119,8 +127,10 @@ static void (*tests[])(void) = {
test_read_cmpd_filtered_dataset_type_conversion_unshared,
test_read_cmpd_filtered_dataset_type_conversion_shared,
test_write_serial_read_parallel,
#if MPI_VERSION >= 3
test_write_parallel_read_serial,
test_shrinking_growing_chunks,
#endif
};
/*
@ -143,6 +153,7 @@ set_dcpl_filter(hid_t dcpl)
}
}
#if MPI_VERSION >= 3
/*
* Tests parallel write of filtered data in the special
* case where a dataset is composed of a single chunk.
@ -2458,6 +2469,7 @@ test_write_cmpd_filtered_dataset_type_conversion_shared(void)
return;
}
#endif
/*
* Tests parallel read of filtered data in the special
@ -5528,6 +5540,7 @@ test_write_serial_read_parallel(void)
return;
}
#if MPI_VERSION >= 3
/*
* Tests parallel write of filtered data
* to a dataset. After the write has
@ -5839,6 +5852,7 @@ test_shrinking_growing_chunks(void)
return;
}
#endif
int
main(int argc, char** argv)