diff options
| -rw-r--r-- | src/H5FDmpio.h | 21 | ||||
| -rw-r--r-- | src/H5Fsuper.c | 30 | ||||
| -rw-r--r-- | testpar/CMakeLists.txt | 1 | ||||
| -rw-r--r-- | testpar/Makefile.am | 2 | ||||
| -rw-r--r-- | testpar/t_pread.c | 196 |
5 files changed, 247 insertions, 3 deletions
diff --git a/src/H5FDmpio.h b/src/H5FDmpio.h index 6ee0a1a..9bcc182 100644 --- a/src/H5FDmpio.h +++ b/src/H5FDmpio.h @@ -29,6 +29,27 @@ #endif /* H5_HAVE_PARALLEL */ #ifdef H5_HAVE_PARALLEL +#define H5FD_GET_MPI_RANK_AND_SIZE(rank,size, f) { \ + (rank) = 0; (size) = 1; \ + if (H5F_HAS_FEATURE((f), H5FD_FEAT_HAS_MPI)) { \ + (rank) = H5F_mpi_get_rank((f)); \ + (size) = H5F_mpi_get_size((f)); \ + } else { \ + int mpi_initialized = 0, mpi_finalized = 0; \ + MPI_Initialized(&mpi_initialized); \ + MPI_Finalized(&mpi_finalized); \ + if (mpi_initialized && !mpi_finalized) { \ + MPI_Comm_rank(MPI_COMM_WORLD, &(rank)); \ + MPI_Comm_size(MPI_COMM_WORLD, &(size)); \ + } \ + }} + +#define H5FD_GET_MPI_COMM(comm, f) { \ + if (H5F_HAS_FEATURE((f), H5FD_FEAT_HAS_MPI)) \ + (comm) = H5F_mpi_get_comm((f)); \ + else (comm) = MPI_COMM_WORLD; \ + } + /*Turn on H5FDmpio_debug if H5F_DEBUG is on */ #ifdef H5F_DEBUG #ifndef H5FDmpio_DEBUG diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c index 7c70a64..32051f3 100644 --- a/src/H5Fsuper.c +++ b/src/H5Fsuper.c @@ -333,6 +333,7 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial unsigned rw_flags; /* Read/write permissions for file */ hbool_t skip_eof_check = FALSE; /* Whether to skip checking the EOF value */ herr_t ret_value = SUCCEED; /* Return value */ + int mpi_rank = 0, mpi_size = 1; FUNC_ENTER_PACKAGE_TAG(meta_dxpl_id, H5AC__SUPERBLOCK_TAG, FAIL) @@ -354,8 +355,33 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list") /* Find the superblock */ - if(H5FD_locate_signature(&fdio_info, &super_addr) < 0) - HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "unable to locate file signature") +#ifdef H5_HAVE_PARALLEL + H5FD_GET_MPI_RANK_AND_SIZE(mpi_rank, mpi_size, f); + /* If we are an MPI application with at least two processes, the + * following superblock signature location optimization is applicable. + */ + if ( mpi_size > 1 ) { + MPI_Comm this_comm = MPI_COMM_NULL; + + if ( mpi_rank == 0 ) { + if(H5FD_locate_signature(&fdio_info, &super_addr) < 0) + HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "unable to locate file signature") + } + H5FD_GET_MPI_COMM(this_comm, f); + if (( this_comm == MPI_COMM_NULL ) || + ( MPI_Bcast(&super_addr,sizeof(super_addr), MPI_BYTE, 0, this_comm) != MPI_SUCCESS)) + HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "unable to locate file signature") + } + else { + /* Locate the signature as per per the serial library */ +#endif /* H5_HAVE_PARALLEL */ + + if(H5FD_locate_signature(&fdio_info, &super_addr) < 0) + HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "unable to locate file signature") + +#ifdef H5_HAVE_PARALLEL + } +#endif if(HADDR_UNDEF == super_addr) HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "file signature not found") diff --git a/testpar/CMakeLists.txt b/testpar/CMakeLists.txt index 39d23a9..0c9f70e 100644 --- a/testpar/CMakeLists.txt +++ b/testpar/CMakeLists.txt @@ -47,6 +47,7 @@ set (H5P_TESTS t_cache t_pflush1 t_pflush2 + t_pread t_pshutdown t_prestart t_init_term diff --git a/testpar/Makefile.am b/testpar/Makefile.am index b0fe0cd..1f15830 100644 --- a/testpar/Makefile.am +++ b/testpar/Makefile.am @@ -23,7 +23,7 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test # Test programs. These are our main targets. # -TEST_PROG_PARA=t_mpi t_bigio testphdf5 t_cache t_cache_image t_pflush1 t_pflush2 t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel +TEST_PROG_PARA=t_mpi t_bigio testphdf5 t_cache t_cache_image t_pflush1 t_pflush2 t_pread t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel check_PROGRAMS = $(TEST_PROG_PARA) diff --git a/testpar/t_pread.c b/testpar/t_pread.c new file mode 100644 index 0000000..4512185 --- /dev/null +++ b/testpar/t_pread.c @@ -0,0 +1,196 @@ +#include <stdio.h> +#include <stdlib.h> +#include <string.h> + +#include "mpi.h" +#include "hdf5.h" + +static char *random_hdf5_text = + "Now is the time for all first-time-users of HDF5 to read their manual or go thru the tutorials!\n\ +While you\'re at it, now is also the time to read up on MPI-IO."; + +static char *datafile_relocated = "relocated_super.h5"; +hbool_t pass = true; + + +static void +generate_test_file( int mpi_rank, int mpi_size ) +{ + FILE *header; + char *datafile_base = "mytestfile.h5"; + char *prologue_file = "hdf5_readme.txt"; + hid_t file_id, memspace, filespace, attr_id, fapl_id, dxpl_id, dset_id; + hsize_t i, offset, count = 1000; + hsize_t dims[1] = {0}; + float nextValue, data_slice[count]; + + pass = true; + + nextValue = (float)(mpi_rank * count); + for(i=0; i<count; i++) { + data_slice[i] = nextValue; + nextValue += 1; + } + + /* create the file (parallel) */ + fapl_id = H5Pcreate(H5P_FILE_ACCESS); + H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL); + file_id = H5Fcreate(datafile_base, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + if ( file_id < 0 ) { + pass = false; + HDfprintf(stderr, "FATAL: H5Fcreate failed!\n"); + } + + if ( pass ) { + dxpl_id = H5Pcreate(H5P_DATASET_XFER); + H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE); + } + + dims[0] = count; + memspace = H5Screate_simple(1, dims, NULL); + dims[0] *= mpi_size; + filespace = H5Screate_simple(1, dims, NULL); + offset = mpi_rank * count; + H5Sselect_hyperslab(filespace, H5S_SELECT_SET, &offset, NULL, &count, NULL); + + dset_id = H5Dcreate2(file_id, "dataset0", H5T_NATIVE_FLOAT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + if ( dset_id < 0 ) { + pass = false; + HDfprintf(stderr, "FATAL: H5Dcreate2 failed!\n"); + } + + if ( pass ) { + H5Dwrite(dset_id, H5T_NATIVE_FLOAT, memspace, filespace, dxpl_id, data_slice); + } + H5Dclose(dset_id); + H5Sclose(memspace); + H5Sclose(filespace); + + /* finished creating a data file */ + H5Fclose(file_id); + H5Pclose(dxpl_id); + + if ( mpi_rank > 0 ) return; + + /* ---- mpi_rank 0 ------*/ + header = fopen( prologue_file, "w+"); + if (header == NULL) { + pass = false; + HDfprintf(stderr, "FATAL: Unable to create a simple txt file\n"); + return; + } + else { + size_t bytes_written, bytes_to_write = strlen(random_hdf5_text); + bytes_written = fwrite( random_hdf5_text, 1, bytes_to_write , header); + if (bytes_written == 0) { + pass = false; + HDfprintf(stderr, "FATAL: Unable to write a simple txt file\n"); + } + fclose(header); + } + + if ( pass ) { + char cmd[256]; + sprintf(cmd, "../tools/src/h5jam/h5jam -i %s -u %s -o %s", + datafile_base, prologue_file, datafile_relocated); + system(cmd); + unlink(datafile_base); + unlink(prologue_file); + } +} + + +static void +test_parallel_read( int mpi_rank, int mpi_size ) +{ + int status, errors = 0; + hid_t access_plist = -1, dataset = -1; + hid_t file_id = -1, memspace = -1, dataspace = -1; + hsize_t i, offset, count = 1000; + hsize_t dims[1] = {0}; + float nextValue, data_slice[count]; + herr_t ret; + + access_plist = H5Pcreate(H5P_FILE_ACCESS); + if (access_plist >= 0) { + ret = H5Pset_fapl_mpio(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL); + } else pass = false; + if (ret >= 0) { + file_id = H5Fopen(datafile_relocated,H5F_ACC_RDONLY,access_plist); + } else pass = false; + if (file_id >= 0) { + dataset = H5Dopen2(file_id, "dataset0", H5P_DEFAULT); + } else pass = false; + if (dataset >= 0) { + dims[0] = count; + memspace = H5Screate_simple(1, dims, NULL); + } else pass = false; + if ( memspace >= 0 ) { + dataspace = H5Dget_space(dataset); + } else pass = false; + if ( dataspace >= 0 ) { + offset = mpi_rank * count; + ret = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, &offset, NULL, &count, NULL); + } else pass = false; + if ( ret >= 0 ) { + ret = H5Dread(dataset, H5T_NATIVE_FLOAT, memspace, dataspace, H5P_DEFAULT, data_slice); + } else pass = false; + if (ret >= 0) { + nextValue = (float)(mpi_rank * count); + for (i=0; i < count; i++) { + if (data_slice[i] != nextValue) pass = false; + nextValue += 1; + } + } else pass = false; + + status = ( pass ? 0 : -1 ); + MPI_Allreduce( &status, &errors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD ); + + if ( mpi_rank == 0) + HDfprintf(stderr, "H5Fopen/H5Dread/data_validation %s\n", ((errors == 0) ? "succeeded" : "FAILED")); + + H5Pclose(access_plist); + H5Dclose(dataset); + H5Fclose(file_id); + + /* Cleanup */ + unlink(datafile_relocated); + + return; +} + + +int +main( int argc, char **argv) +{ + int status, errors, mpi_rank, mpi_size; + + if ((status = MPI_Init(&argc, &argv)) != MPI_SUCCESS) { + HDfprintf(stderr, "FATAL: Unable to initialize MPI\n"); + exit(1); + } + if ((status = MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank)) != MPI_SUCCESS) { + HDfprintf(stderr, "FATAL: MPI_Comm_rank returned an error\n"); + exit(2); + } + if ((status = MPI_Comm_size(MPI_COMM_WORLD, &mpi_size)) != MPI_SUCCESS) { + HDfprintf(stderr, "FATAL: MPI_Comm_size returned an error\n"); + exit(2); + } + + generate_test_file( mpi_rank, mpi_size ); + status = ( pass ? 0 : -1 ); + + /* Synch all ranks before attempting the parallel read */ + if ( MPI_Allreduce( &status, &errors, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD ) != MPI_SUCCESS) { + pass = false; + if (mpi_rank == 0) HDfprintf(stderr, "FATAL: MPI_Allreduce returned an error\n"); + } + + if ( errors == 0 ) { + test_parallel_read( mpi_rank, mpi_size ); + } + + MPI_Finalize(); + return 0; +} |