diff options
| -rw-r--r-- | perform/pio_engine.c | 3087 | ||||
| -rw-r--r-- | perform/pio_perf.c | 138 | ||||
| -rw-r--r-- | perform/pio_perf.h | 1 |
3 files changed, 2042 insertions, 1184 deletions
diff --git a/perform/pio_engine.c b/perform/pio_engine.c index 6bad358..8b0a7d0 100644 --- a/perform/pio_engine.c +++ b/perform/pio_engine.c @@ -54,20 +54,20 @@ #define ERRMSG(mesg) { \ fprintf(stderr, "Proc %d: ", pio_mpi_rank_g); \ fprintf(stderr, "*** Assertion failed (%s) at line %4d in %s\n", \ - mesg, (int)__LINE__, __FILE__); \ + mesg, (int)__LINE__, __FILE__); \ } #define MSG(mesg) { \ fprintf(stderr, "Proc %d: ", pio_mpi_rank_g); \ fprintf(stderr, "(%s) at line %4d in %s\n", \ - mesg, (int)__LINE__, __FILE__); \ + mesg, (int)__LINE__, __FILE__); \ } /* verify: if val is false (0), print mesg. */ #define VRFY(val, mesg) do { \ if (!val) { \ - ERRMSG(mesg); \ - GOTOERROR(FAIL); \ + ERRMSG(mesg); \ + GOTOERROR(FAIL); \ } \ } while(0) @@ -88,8 +88,8 @@ enum { /* Global variables */ static int clean_file_g = -1; /*whether to cleanup temporary test */ - /*files. -1 is not defined; */ - /*0 is no cleanup; 1 is do cleanup */ +/*files. -1 is not defined; */ +/*0 is no cleanup; 1 is do cleanup */ /* * In a parallel machine, the filesystem suitable for compiling is @@ -99,7 +99,7 @@ static int clean_file_g = -1; /*whether to cleanup temporary test */ */ #ifndef HDF5_PARAPREFIX # ifdef __PUMAGON__ - /* For the PFS of TFLOPS */ +/* For the PFS of TFLOPS */ # define HDF5_PARAPREFIX "pfs:/pfs_grande/multi/tmp_1" # else # define HDF5_PARAPREFIX "" @@ -119,13 +119,13 @@ typedef union _file_descr { /* local functions */ static char *pio_create_filename(iotype iot, const char *base_name, - char *fullname, size_t size); + char *fullname, size_t size); static herr_t do_write(results *res, file_descr *fd, parameters *parms, - long ndsets, off_t nelmts, size_t buf_size, void *buffer); + long ndsets, off_t nelmts, size_t buf_size, void *buffer); static herr_t do_read(results *res, file_descr *fd, parameters *parms, - long ndsets, off_t nelmts, size_t buf_size, void *buffer /*out*/); + long ndsets, off_t nelmts, size_t buf_size, void *buffer /*out*/); static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, - int flags); + int flags); static herr_t do_fclose(iotype iot, file_descr *fd); static void do_cleanupfile(iotype iot, char *fname); @@ -137,19 +137,20 @@ static void gpfs_clear_file_cache(int handle); static void gpfs_cancel_hints(int handle); static void gpfs_start_data_shipping(int handle, int num_insts); static void gpfs_start_data_ship_map(int handle, int partition_size, - int agent_count, int *agent_node_num); + int agent_count, int *agent_node_num); static void gpfs_stop_data_shipping(int handle); static void gpfs_invalidate_file_cache(const char *filename); #endif /* H5_HAVE_GPFS */ /* - * Function: do_pio - * Purpose: PIO Engine where Parallel IO are executed. - * Return: results - * Programmer: Albert Cheng, Bill Wendling 2001/12/12 + * Function: do_pio + * Purpose: PIO Engine where Parallel IO are executed. + * Return: results + * Programmer: Albert Cheng, Bill Wendling 2001/12/12 * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) */ -results + results do_pio(parameters param) { /* return codes */ @@ -160,12 +161,21 @@ do_pio(parameters param) iotype iot; char fname[FILENAME_MAX]; - long nf; + long nf; long ndsets; - off_t nbytes; /* Number of bytes per dataset */ + off_t nbytes; /*number of bytes per dataset */ + off_t snbytes; /*general dataset size */ + /*for 1D, it is the actual dataset size */ + /*for 2D, it is the size of a side of the dataset square */ + char *buffer = NULL; /*data buffer pointer */ - size_t buf_size; /*data buffer size in bytes */ + + size_t buf_size; /*general buffer size in bytes */ + /*for 1D, it is the actual buffer size */ + /*for 2D, it is the length of the buffer rectangle */ + size_t blk_size; /*data block size in bytes */ + size_t bsize; /*actual buffer size */ /* HDF5 variables */ herr_t hrc; /*HDF5 return code */ @@ -176,22 +186,22 @@ do_pio(parameters param) iot = param.io_type; switch (iot) { - case MPIO: - fd.mpifd = MPI_FILE_NULL; - res.timers = pio_time_new(MPI_TIMER); - break; - case POSIXIO: - fd.posixfd = -1; - res.timers = pio_time_new(MPI_TIMER); - break; - case PHDF5: - fd.h5fd = -1; - res.timers = pio_time_new(MPI_TIMER); - break; - default: - /* unknown request */ - fprintf(stderr, "Unknown IO type request (%d)\n", iot); - GOTOERROR(FAIL); + case MPIO: + fd.mpifd = MPI_FILE_NULL; + res.timers = pio_time_new(MPI_TIMER); + break; + case POSIXIO: + fd.posixfd = -1; + res.timers = pio_time_new(MPI_TIMER); + break; + case PHDF5: + fd.h5fd = -1; + res.timers = pio_time_new(MPI_TIMER); + break; + default: + /* unknown request */ + fprintf(stderr, "Unknown IO type request (%d)\n", iot); + GOTOERROR(FAIL); } ndsets = param.num_dsets; /* number of datasets per file */ @@ -199,142 +209,152 @@ do_pio(parameters param) buf_size = param.buf_size; blk_size = param.blk_size; + if (param.dim2d==0){ + snbytes = nbytes; /* General dataset size */ + bsize = buf_size; /* Actual buffer size */ + } + else { + snbytes = (off_t)sqrt(nbytes); /* General dataset size */ + bsize = buf_size * blk_size; /* Actual buffer size */ + } + if (param.num_files < 0 ) { - fprintf(stderr, - "number of files must be >= 0 (%ld)\n", - param.num_files); - GOTOERROR(FAIL); + fprintf(stderr, + "number of files must be >= 0 (%ld)\n", + param.num_files); + GOTOERROR(FAIL); } if (ndsets < 0 ) { - fprintf(stderr, - "number of datasets per file must be >= 0 (%ld)\n", - ndsets); - GOTOERROR(FAIL); + fprintf(stderr, + "number of datasets per file must be >= 0 (%ld)\n", + ndsets); + GOTOERROR(FAIL); } if (param.num_procs <= 0 ) { - fprintf(stderr, - "maximum number of process to use must be > 0 (%d)\n", - param.num_procs); - GOTOERROR(FAIL); + fprintf(stderr, + "maximum number of process to use must be > 0 (%d)\n", + param.num_procs); + GOTOERROR(FAIL); } /* Validate transfer buffer size & block size*/ if(blk_size<=0) { - HDfprintf(stderr, - "Transfer block size (%Hd) must be > 0\n", (long_long)blk_size); + HDfprintf(stderr, + "Transfer block size (%Hd) must be > 0\n", (long_long)blk_size); GOTOERROR(FAIL); } if(buf_size<=0) { - HDfprintf(stderr, - "Transfer buffer size (%Hd) must be > 0\n", (long_long)buf_size); + HDfprintf(stderr, + "Transfer buffer size (%Hd) must be > 0\n", (long_long)buf_size); GOTOERROR(FAIL); } if ((buf_size % blk_size) != 0){ - HDfprintf(stderr, - "Transfer buffer size (%Hd) must be a multiple of the " - "interleaved I/O block size (%Hd)\n", - (long_long)buf_size, (long_long)blk_size); - GOTOERROR(FAIL); + HDfprintf(stderr, + "Transfer buffer size (%Hd) must be a multiple of the " + "interleaved I/O block size (%Hd)\n", + (long_long)buf_size, (long_long)blk_size); + GOTOERROR(FAIL); } - if((nbytes%pio_mpi_nprocs_g)!=0) { - HDfprintf(stderr, - "Dataset size (%Hd) must be a multiple of the " - "number of processes (%d)\n", - (long_long)nbytes, pio_mpi_nprocs_g); + if((snbytes%pio_mpi_nprocs_g)!=0) { + HDfprintf(stderr, + "Dataset size (%Hd) must be a multiple of the " + "number of processes (%d)\n", + (long_long)nbytes, pio_mpi_nprocs_g); GOTOERROR(FAIL); } - if(((nbytes/pio_mpi_nprocs_g)%buf_size)!=0) { - HDfprintf(stderr, - "Dataset size/process (%Hd) must be a multiple of the " - "trasfer buffer size (%Hd)\n", - (long_long)(nbytes/pio_mpi_nprocs_g), (long_long)buf_size); + if(((snbytes/pio_mpi_nprocs_g)%buf_size)!=0) { + HDfprintf(stderr, + "Dataset size/process (%Hd) must be a multiple of the " + "trasfer buffer size (%Hd)\n", + (long_long)(nbytes/pio_mpi_nprocs_g), (long_long)buf_size); GOTOERROR(FAIL); } /* Allocate transfer buffer */ - if ((buffer = malloc(buf_size)) == NULL){ - HDfprintf(stderr, "malloc for transfer buffer size (%Hd) failed\n", - (long_long)(buf_size)); - GOTOERROR(FAIL); + if ((buffer = malloc(bsize)) == NULL){ + HDfprintf(stderr, "malloc for transfer buffer size (%Hd) failed\n", + (long_long)(bsize)); + GOTOERROR(FAIL); } if (pio_debug_level >= 4) { - int myrank; + int myrank; - MPI_Comm_rank(pio_comm_g, &myrank); + MPI_Comm_rank(pio_comm_g, &myrank); - /* output all of the times for all iterations */ - if (myrank == 0) - fprintf(output, "Timer details:\n"); + /* output all of the times for all iterations */ + if (myrank == 0) + fprintf(output, "Timer details:\n"); } for (nf = 1; nf <= param.num_files; nf++) { /* * Write performance measurement */ - /* Open file for write */ - char base_name[256]; + /* Open file for write */ + char base_name[256]; - sprintf(base_name, "#pio_tmp_%lu", nf); - pio_create_filename(iot, base_name, fname, sizeof(fname)); + sprintf(base_name, "#pio_tmp_%lu", nf); + pio_create_filename(iot, base_name, fname, sizeof(fname)); if (pio_debug_level > 0) HDfprintf(output, "rank %d: data filename=%s\n", - pio_mpi_rank_g, fname); + pio_mpi_rank_g, fname); /* Need barrier to make sure everyone starts at the same time */ - MPI_Barrier(pio_comm_g); + MPI_Barrier(pio_comm_g); - set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, START); - hrc = do_fopen(¶m, fname, &fd, PIO_CREATE | PIO_WRITE); + set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, START); + hrc = do_fopen(¶m, fname, &fd, PIO_CREATE | PIO_WRITE); - VRFY((hrc == SUCCESS), "do_fopen failed"); + VRFY((hrc == SUCCESS), "do_fopen failed"); - set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, START); - hrc = do_write(&res, &fd, ¶m, ndsets, nbytes, buf_size, buffer); - set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, STOP); + set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, START); + hrc = do_write(&res, &fd, ¶m, ndsets, nbytes, buf_size, buffer); + hrc == SUCCESS; + set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, STOP); - VRFY((hrc == SUCCESS), "do_write failed"); + VRFY((hrc == SUCCESS), "do_write failed"); - /* Close file for write */ - hrc = do_fclose(iot, &fd); + /* Close file for write */ + hrc = do_fclose(iot, &fd); - set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, STOP); - VRFY((hrc == SUCCESS), "do_fclose failed"); + set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, STOP); + VRFY((hrc == SUCCESS), "do_fclose failed"); - if (!param.h5_write_only) { - /* - * Read performance measurement - */ + if (!param.h5_write_only) { + /* + * Read performance measurement + */ /* Need barrier to make sure everyone is done writing and has * closed the file. Also to make sure everyone starts reading * at the same time. */ - MPI_Barrier(pio_comm_g); + MPI_Barrier(pio_comm_g); - /* Open file for read */ - set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, START); - hrc = do_fopen(¶m, fname, &fd, PIO_READ); + /* Open file for read */ + set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, START); + hrc = do_fopen(¶m, fname, &fd, PIO_READ); - VRFY((hrc == SUCCESS), "do_fopen failed"); + VRFY((hrc == SUCCESS), "do_fopen failed"); - set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, START); - hrc = do_read(&res, &fd, ¶m, ndsets, nbytes, buf_size, buffer); - set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, STOP); - VRFY((hrc == SUCCESS), "do_read failed"); + set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, START); + hrc = do_read(&res, &fd, ¶m, ndsets, nbytes, buf_size, buffer); + set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, STOP); + VRFY((hrc == SUCCESS), "do_read failed"); - /* Close file for read */ - hrc = do_fclose(iot, &fd); + /* Close file for read */ + hrc = do_fclose(iot, &fd); - set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, STOP); - VRFY((hrc == SUCCESS), "do_fclose failed"); - } + set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, STOP); + VRFY((hrc == SUCCESS), "do_fclose failed"); + } /* Need barrier to make sure everyone is done with the file */ /* before it may be removed by do_cleanupfile */ - MPI_Barrier(pio_comm_g); - do_cleanupfile(iot, fname); + MPI_Barrier(pio_comm_g); + do_cleanupfile(iot, fname); } done: @@ -344,23 +364,23 @@ done: /* close any opened files */ /* no remove(fname) because that should have happened normally. */ switch (iot) { - case POSIXIO: - if (fd.posixfd != -1) - hrc = do_fclose(iot, &fd); - break; - case MPIO: - if (fd.mpifd != MPI_FILE_NULL) - hrc = do_fclose(iot, &fd); - break; - case PHDF5: - if (fd.h5fd != -1) - hrc = do_fclose(iot, &fd); - break; + case POSIXIO: + if (fd.posixfd != -1) + hrc = do_fclose(iot, &fd); + break; + case MPIO: + if (fd.mpifd != MPI_FILE_NULL) + hrc = do_fclose(iot, &fd); + break; + case PHDF5: + if (fd.h5fd != -1) + hrc = do_fclose(iot, &fd); + break; } /* release generic resources */ if(buffer) - free(buffer); + free(buffer); res.ret_code = ret_code; return res; } @@ -375,7 +395,7 @@ done: * Programmer: Bill Wendling, 21. November 2001 * Modifications: */ -static char * + static char * pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size) { const char *prefix, *suffix=""; @@ -383,20 +403,20 @@ pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t si size_t i, j; if (!base_name || !fullname || size < 1) - return NULL; + return NULL; memset(fullname, 0, size); switch (iot) { - case POSIXIO: - suffix = ".posix"; - break; - case MPIO: - suffix = ".mpio"; - break; - case PHDF5: - suffix = ".h5"; - break; + case POSIXIO: + suffix = ".posix"; + break; + case MPIO: + suffix = ".mpio"; + break; + case PHDF5: + suffix = ".h5"; + break; } /* First use the environment variable and then try the constant */ @@ -404,88 +424,89 @@ pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t si #ifdef HDF5_PARAPREFIX if (!prefix) - prefix = HDF5_PARAPREFIX; + prefix = HDF5_PARAPREFIX; #endif /* HDF5_PARAPREFIX */ /* Prepend the prefix value to the base name */ if (prefix && *prefix) { - /* If the prefix specifies the HDF5_PARAPREFIX directory, then - * default to using the "/tmp/$USER" or "/tmp/$LOGIN" - * directory instead. */ - register char *user, *login, *subdir; - - user = getenv("USER"); - login = getenv("LOGIN"); - subdir = (user ? user : login); - - if (subdir) { - for (i = 0; i < size && prefix[i]; i++) - fullname[i] = prefix[i]; - - fullname[i++] = '/'; - - for (j = 0; i < size && subdir[j]; i++, j++) - fullname[i] = subdir[j]; - } else { - /* We didn't append the prefix yet */ - strncpy(fullname, prefix, MIN(strlen(prefix), size)); - } - - if ((strlen(fullname) + strlen(base_name) + 1) < size) { - /* Append the base_name with a slash first. Multiple slashes are - * handled below. */ - h5_stat_t buf; - - if (HDstat(fullname, &buf) < 0) - /* The directory doesn't exist just yet */ - if (mkdir(fullname, (mode_t)0755) < 0 && errno != EEXIST) { - /* We couldn't make the "/tmp/${USER,LOGIN}" subdirectory. - * Default to PREFIX's original prefix value. */ - strcpy(fullname, prefix); - } - - strcat(fullname, "/"); - strcat(fullname, base_name); - } else { - /* Buffer is too small */ - return NULL; - } + /* If the prefix specifies the HDF5_PARAPREFIX directory, then + * default to using the "/tmp/$USER" or "/tmp/$LOGIN" + * directory instead. */ + register char *user, *login, *subdir; + + user = getenv("USER"); + login = getenv("LOGIN"); + subdir = (user ? user : login); + + if (subdir) { + for (i = 0; i < size && prefix[i]; i++) + fullname[i] = prefix[i]; + + fullname[i++] = '/'; + + for (j = 0; i < size && subdir[j]; i++, j++) + fullname[i] = subdir[j]; + } else { + /* We didn't append the prefix yet */ + strncpy(fullname, prefix, MIN(strlen(prefix), size)); + } + + if ((strlen(fullname) + strlen(base_name) + 1) < size) { + /* Append the base_name with a slash first. Multiple slashes are + * handled below. */ + h5_stat_t buf; + + if (HDstat(fullname, &buf) < 0) + /* The directory doesn't exist just yet */ + if (mkdir(fullname, (mode_t)0755) < 0 && errno != EEXIST) { + /* We couldn't make the "/tmp/${USER,LOGIN}" subdirectory. + * Default to PREFIX's original prefix value. */ + strcpy(fullname, prefix); + } + + strcat(fullname, "/"); + strcat(fullname, base_name); + } else { + /* Buffer is too small */ + return NULL; + } } else if (strlen(base_name) >= size) { - /* Buffer is too small */ - return NULL; + /* Buffer is too small */ + return NULL; } else { - strcpy(fullname, base_name); + strcpy(fullname, base_name); } /* Append a suffix */ if (suffix) { - if (strlen(fullname) + strlen(suffix) >= size) - return NULL; + if (strlen(fullname) + strlen(suffix) >= size) + return NULL; - strcat(fullname, suffix); + strcat(fullname, suffix); } /* Remove any double slashes in the filename */ for (ptr = fullname, i = j = 0; ptr && i < size; i++, ptr++) { - if (*ptr != '/' || last != '/') - fullname[j++] = *ptr; + if (*ptr != '/' || last != '/') + fullname[j++] = *ptr; - last = *ptr; + last = *ptr; } return fullname; } /* - * Function: do_write - * Purpose: Write the required amount of data to the file. - * Return: SUCCESS or FAIL - * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 + * Function: do_write + * Purpose: Write the required amount of data to the file. + * Return: SUCCESS or FAIL + * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) */ -static herr_t + static herr_t do_write(results *res, file_descr *fd, parameters *parms, long ndsets, - off_t nbytes, size_t buf_size, void *buffer) + off_t nbytes, size_t buf_size, void *buffer) { int ret_code = SUCCESS; int rc; /*routine return code */ @@ -495,8 +516,9 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets, size_t nbytes_toxfer; /* Number of bytes to transfer a particular time */ char dname[64]; off_t dset_offset=0; /*dataset offset in a file */ - off_t bytes_begin; /*first elmt this process transfer */ + off_t bytes_begin[2]; /*first elmt this process transfer */ off_t bytes_count; /*number of elmts this process transfer */ + off_t snbytes=0; /*size of a side of the dataset square */ unsigned char *buf_p; /* Current buffer pointer */ /* POSIX variables */ @@ -506,32 +528,32 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets, /* MPI variables */ MPI_Offset mpi_file_offset;/* Base file offset of the next transfer*/ MPI_Offset mpi_offset; /* Offset in MPI file */ - MPI_Datatype mpi_file_type; /* MPI derived type for file */ - MPI_Datatype mpi_blk_type; /* MPI derived type for buffer */ + MPI_Datatype mpi_file_type; /* MPI derived type for 1D file */ + MPI_Datatype mpi_blk_type; /* MPI derived type for 1D buffer */ + MPI_Datatype mpi_cont_type; /* MPI derived type for 2D contiguous file */ + MPI_Datatype contig_cont; /* MPI derived type for 2D contiguous buffer */ + MPI_Datatype mpi_inter_type;/* MPI derived type for 2D interleaved file */ + MPI_Datatype contig_inter; /* MPI derived type for 2D interleaved buffer*/ MPI_Status mpi_status; int mrc; /* MPI return code */ /* HDF5 variables */ herr_t hrc; /*HDF5 return code */ - hsize_t h5dims[1]; /*dataset dim sizes */ + hsize_t h5dims[2]; /*dataset dim sizes */ hid_t h5dset_space_id = -1; /*dataset space ID */ hid_t h5mem_space_id = -1; /*memory dataspace ID */ hid_t h5ds_id = -1; /*dataset handle */ - hsize_t h5block[1]; /*dataspace selection */ - hsize_t h5stride[1]; - hsize_t h5count[1]; - hsize_t h5start[1]; - hssize_t h5offset[1]; /* Selection offset within dataspace */ + hsize_t h5block[2]; /*dataspace selection */ + hsize_t h5stride[2]; + hsize_t h5count[2]; + hsize_t h5start[2]; + hssize_t h5offset[2]; /* Selection offset within dataspace */ hid_t h5dcpl = -1; /* Dataset creation property list */ hid_t h5dxpl = -1; /* Dataset transfer property list */ /* Get the parameters from the parameter block */ blk_size=parms->blk_size; - /* Prepare buffer for verifying data */ - if (parms->verify) - memset(buffer,pio_mpi_rank_g,buf_size); - /* There are two kinds of transfer patterns, contiguous and interleaved. * Let 0,1,2,...,n be data accessed by process 0,1,2,...,n * where n is rank of the last process. @@ -541,14 +563,43 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets, * 012...n012...n... * These are all in the scope of one dataset. */ - if (parms->interleaved==0) { - /* Contiguous Pattern: */ - bytes_begin = (off_t)(((double)nbytes*pio_mpi_rank_g)/pio_mpi_nprocs_g); - } /* end if */ + + /* 1D dataspace */ + if (parms->dim2d==0){ + if (parms->interleaved==0) { + /* Contiguous Pattern: */ + bytes_begin[0] = (off_t)(((double)nbytes*pio_mpi_rank_g)/pio_mpi_nprocs_g); + } /* end if */ + else { + /* Interleaved Pattern: */ + bytes_begin[0] = (off_t)(blk_size*pio_mpi_rank_g); + } /* end else */ + /* Prepare buffer for verifying data */ + if (parms->verify) + memset(buffer,pio_mpi_rank_g+1,buf_size); + }/* end if */ + /* 2D dataspace */ else { - /* Interleaved Pattern: */ - bytes_begin = (off_t)(blk_size*pio_mpi_rank_g); - } /* end else */ + snbytes = (off_t)sqrt(nbytes); + /* nbytes is always the number of bytes per dataset (1D or 2D). If the + dataspace is 2D, snbytes is the size of a side of the dataset square. + */ + if (parms->interleaved==0) { + /* Contiguous Pattern: */ + bytes_begin[0] = (off_t)((double)snbytes*pio_mpi_rank_g / pio_mpi_nprocs_g); + bytes_begin[1] = 0; + } /* end if */ + else { + /* Interleaved Pattern: */ + bytes_begin[0] = 0; + bytes_begin[1] = (off_t)(blk_size*pio_mpi_rank_g); + } /* end else */ + /* Prepare buffer for verifying data */ + if (parms->verify) + memset(buffer,pio_mpi_rank_g+1,buf_size*blk_size); + } + + /* end else */ /* Calculate the total number of bytes (bytes_count) to be * transferred by this process. It may be different for different @@ -561,151 +612,258 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets, * (This is tricky, don't mess with the formula, rounding errors * can easily get introduced) */ bytes_count = (off_t)(((double)nbytes*(pio_mpi_rank_g+1)) / pio_mpi_nprocs_g) - - (off_t)(((double)nbytes*pio_mpi_rank_g) / pio_mpi_nprocs_g); + - (off_t)(((double)nbytes*pio_mpi_rank_g) / pio_mpi_nprocs_g); /* debug */ if (pio_debug_level >= 4) { - HDprint_rank(output); - HDfprintf(output, "Debug(do_write): " - "buf_size=%Hd, bytes_begin=%Hd, bytes_count=%Hd\n", - (long_long)buf_size, (long_long)bytes_begin, - (long_long)bytes_count); + HDprint_rank(output); + HDfprintf(output, "Debug(do_write): " + "buf_size=%Hd, bytes_begin=%Hd, bytes_count=%Hd\n", + (long_long)buf_size, (long_long)bytes_begin, + (long_long)bytes_count); } /* I/O Access specific setup */ switch (parms->io_type) { - case POSIXIO: - /* No extra setup */ - break; - - case MPIO: /* MPI-I/O setup */ - /* Build block's derived type */ - mrc = MPI_Type_contiguous((int)blk_size, - MPI_BYTE, &mpi_blk_type); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); - - /* Build file's derived type */ - mrc = MPI_Type_vector((int)(buf_size/blk_size), (int)1, - (int)pio_mpi_nprocs_g, mpi_blk_type, &mpi_file_type); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); - - /* Commit file type */ - mrc = MPI_Type_commit( &mpi_file_type ); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); - - /* Commit buffer type */ - mrc = MPI_Type_commit( &mpi_blk_type ); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); - break; - - case PHDF5: /* HDF5 setup */ - if(nbytes>0) { - /* define a contiquous dataset of nbytes native bytes */ - h5dims[0] = nbytes; - h5dset_space_id = H5Screate_simple(1, h5dims, NULL); - VRFY((h5dset_space_id >= 0), "H5Screate_simple"); - - /* Set up the file dset space id to select the pattern to access */ - if (parms->interleaved==0){ - /* Contiguous pattern */ - h5start[0] = bytes_begin; - h5stride[0] = h5block[0] = blk_size; - h5count[0] = buf_size/blk_size; - } /* end if */ - else { - /* Interleaved access pattern */ - /* Skip offset over blocks of other processes */ - h5start[0] = bytes_begin; - h5stride[0] = blk_size*pio_mpi_nprocs_g; - h5block[0] = blk_size; - h5count[0] = buf_size/blk_size; - } /* end else */ - hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, - h5start, h5stride, h5count, h5block); - VRFY((hrc >= 0), "H5Sselect_hyperslab"); - } /* end if */ - else { - h5dset_space_id = H5Screate(H5S_SCALAR); - VRFY((h5dset_space_id >= 0), "H5Screate"); - } /* end else */ - - /* Create the memory dataspace that corresponds to the xfer buffer */ - if(buf_size>0) { - h5dims[0] = buf_size; - h5mem_space_id = H5Screate_simple(1, h5dims, NULL); - VRFY((h5mem_space_id >= 0), "H5Screate_simple"); - } /* end if */ - else { - h5mem_space_id = H5Screate(H5S_SCALAR); - VRFY((h5mem_space_id >= 0), "H5Screate"); - } /* end else */ - - /* Create the dataset transfer property list */ - h5dxpl = H5Pcreate(H5P_DATASET_XFER); - if (h5dxpl < 0) { - fprintf(stderr, "HDF5 Property List Create failed\n"); - GOTOERROR(FAIL); - } - - /* Change to collective I/O, if asked */ - if(parms->collective) { - hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE); - if (hrc < 0) { - fprintf(stderr, "HDF5 Property List Set failed\n"); - GOTOERROR(FAIL); - } /* end if */ - } /* end if */ - break; + case POSIXIO: + /* No extra setup */ + break; + + case MPIO: /* MPI-I/O setup */ + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Build block's derived type */ + mrc = MPI_Type_contiguous((int)blk_size, + MPI_BYTE, &mpi_blk_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Build file's derived type */ + mrc = MPI_Type_vector((int)(buf_size/blk_size), (int)1, + (int)pio_mpi_nprocs_g, mpi_blk_type, &mpi_file_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit file type */ + mrc = MPI_Type_commit( &mpi_file_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Commit buffer type */ + mrc = MPI_Type_commit( &mpi_blk_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + } /* end if */ + /* 2D dataspace */ + else { + /* Build partial buffer derived type for contiguous access */ + mrc = MPI_Type_contiguous((int)buf_size, MPI_BYTE, + &contig_cont); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Build contiguous file's derived type */ + mrc = MPI_Type_vector((int)blk_size, (int)1, (int)(snbytes/buf_size), + contig_cont, &mpi_cont_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit contiguous file type */ + mrc = MPI_Type_commit(&mpi_cont_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build partial buffer derived type for interleaved access */ + mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, + &contig_inter); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Build interleaved file's derived type */ + mrc = MPI_Type_vector((int)buf_size, (int)1, (int)(snbytes/blk_size), + contig_inter, &mpi_inter_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit interleaved file type */ + mrc = MPI_Type_commit(&mpi_inter_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + } /* end else */ + break; + + case PHDF5: /* HDF5 setup */ + /* 1D dataspace */ + if (parms->dim2d==0){ + if(nbytes>0) { + /* define a contiguous dataset of nbytes native bytes */ + h5dims[0] = nbytes; + h5dset_space_id = H5Screate_simple(1, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + /* Set up the file dset space id to select the pattern to access */ + if (parms->interleaved==0){ + /* Contiguous pattern */ + h5start[0] = bytes_begin[0]; + h5stride[0] = h5block[0] = blk_size; + h5count[0] = buf_size/blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5start[0] = bytes_begin[0]; + h5stride[0] = blk_size*pio_mpi_nprocs_g; + h5block[0] = blk_size; + h5count[0] = buf_size/blk_size; + } /* end else */ + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, + h5start, h5stride, h5count, h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + } /* end if */ + else { + h5dset_space_id = H5Screate(H5S_SCALAR); + VRFY((h5dset_space_id >= 0), "H5Screate"); + } /* end else */ + + /* Create the memory dataspace that corresponds to the xfer buffer */ + if(buf_size>0) { + h5dims[0] = buf_size; + h5mem_space_id = H5Screate_simple(1, h5dims, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + } /* end if */ + else { + h5mem_space_id = H5Screate(H5S_SCALAR); + VRFY((h5mem_space_id >= 0), "H5Screate"); + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + if(nbytes>0) { + /* define a contiguous dataset of nbytes native bytes */ + h5dims[0] = snbytes; + h5dims[1] = snbytes; + h5dset_space_id = H5Screate_simple(2, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + /* Set up the file dset space id to select the pattern to access */ + if (parms->interleaved==0){ + /* Contiguous pattern */ + h5start[0] = bytes_begin[0]; + h5start[1] = bytes_begin[1]; + h5stride[0] = 1; + h5stride[1] = h5block[0] = h5block[1] = blk_size; + h5count[0] = 1; + h5count[1] = buf_size/blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5start[0] = bytes_begin[0]; + h5start[1] = bytes_begin[1]; + h5stride[0] = blk_size; + h5stride[1] = blk_size*pio_mpi_nprocs_g; + h5block[0] = h5block[1] = blk_size; + h5count[0] = buf_size/blk_size; + h5count[1] = 1; + } /* end else */ + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, + h5start, h5stride, h5count, h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + } /* end if */ + else { + h5dset_space_id = H5Screate(H5S_SCALAR); + VRFY((h5dset_space_id >= 0), "H5Screate"); + } /* end else */ + + /* Create the memory dataspace that corresponds to the xfer buffer */ + if(buf_size>0) { + if (parms->interleaved==0){ + h5dims[0] = blk_size; + h5dims[1] = buf_size; + }else{ + h5dims[0] = buf_size; + h5dims[1] = blk_size; + } + h5mem_space_id = H5Screate_simple(2, h5dims, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + } /* end if */ + else { + h5mem_space_id = H5Screate(H5S_SCALAR); + VRFY((h5mem_space_id >= 0), "H5Screate"); + } /* end else */ + } /* end else */ + + /* Create the dataset transfer property list */ + h5dxpl = H5Pcreate(H5P_DATASET_XFER); + if (h5dxpl < 0) { + fprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + /* Change to collective I/O, if asked */ + if(parms->collective) { + hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE); + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + break; } /* end switch */ for (ndset = 1; ndset <= ndsets; ++ndset) { - /* Calculate dataset offset within a file */ - - /* create dataset */ - switch (parms->io_type) { - case POSIXIO: - case MPIO: - /* both posix and mpi io just need dataset offset in file*/ - dset_offset = (ndset - 1) * nbytes; - break; - - case PHDF5: - h5dcpl = H5Pcreate(H5P_DATASET_CREATE); - if (h5dcpl < 0) { - fprintf(stderr, "HDF5 Property List Create failed\n"); - GOTOERROR(FAIL); - } - - /* Make the dataset chunked if asked */ - if(parms->h5_use_chunks) { - /* Set the chunk size to be the same as the buffer size */ - h5dims[0] = buf_size; - hrc = H5Pset_chunk(h5dcpl, 1, h5dims); - if (hrc < 0) { - fprintf(stderr, "HDF5 Property List Set failed\n"); - GOTOERROR(FAIL); - } /* end if */ - } /* end if */ - - sprintf(dname, "Dataset_%ld", ndset); - h5ds_id = H5Dcreate(fd->h5fd, dname, ELMT_H5_TYPE, - h5dset_space_id, h5dcpl); - - if (h5ds_id < 0) { - fprintf(stderr, "HDF5 Dataset Create failed\n"); - GOTOERROR(FAIL); - } - - hrc = H5Pclose(h5dcpl); - /* verifying the close of the dcpl */ - if (hrc < 0) { - fprintf(stderr, "HDF5 Property List Close failed\n"); - GOTOERROR(FAIL); - } - - break; - } + /* Calculate dataset offset within a file */ + + /* create dataset */ + switch (parms->io_type) { + case POSIXIO: + case MPIO: + /* both posix and mpi io just need dataset offset in file*/ + dset_offset = (ndset - 1) * nbytes; + break; + + case PHDF5: + h5dcpl = H5Pcreate(H5P_DATASET_CREATE); + if (h5dcpl < 0) { + fprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Make the dataset chunked if asked */ + if(parms->h5_use_chunks) { + /* Set the chunk size to be the same as the buffer size */ + h5dims[0] = blk_size; + hrc = H5Pset_chunk(h5dcpl, 1, h5dims); + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + }/* end if */ + else{ + /* 2D dataspace */ + if(parms->h5_use_chunks) { + /* Set the chunk size to be the same as the block size */ + h5dims[0] = blk_size; + h5dims[1] = blk_size; + hrc = H5Pset_chunk(h5dcpl, 2, h5dims); + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + }/* end else */ + + sprintf(dname, "Dataset_%ld", ndset); + h5ds_id = H5Dcreate(fd->h5fd, dname, ELMT_H5_TYPE, + h5dset_space_id, h5dcpl); + + if (h5ds_id < 0) { + fprintf(stderr, "HDF5 Dataset Create failed\n"); + GOTOERROR(FAIL); + } + + hrc = H5Pclose(h5dcpl); + /* verifying the close of the dcpl */ + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Close failed\n"); + GOTOERROR(FAIL); + } + + break; + } /* The task is to transfer bytes_count bytes, starting at * bytes_begin position, using transfer buffer of buf_size bytes. @@ -713,271 +871,523 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets, * fashion, according to number of process. Otherwise, select * all bytes_count in contiguous. */ - nbytes_xfer = 0 ; - - /* Set base file offset for all I/O patterns and POSIX access */ - posix_file_offset = dset_offset + bytes_begin; - - /* Set base file offset for all I/O patterns and MPI access */ - mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin); - - /* Start "raw data" write timer */ - set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, START); - - while (nbytes_xfer < bytes_count){ - /* Write */ - /* Calculate offset of write within a dataset/file */ - switch (parms->io_type) { - case POSIXIO: - /* Contiguous pattern */ - if (parms->interleaved==0) { - /* Compute file offset */ - file_offset = posix_file_offset + (off_t)nbytes_xfer; - - /* only care if seek returns error */ - rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; - VRFY((rc==0), "POSIXSEEK"); - - /* check if all bytes are written */ - rc = ((ssize_t)buf_size == - POSIXWRITE(fd->posixfd, buffer, buf_size)); - VRFY((rc != 0), "POSIXWRITE"); - - /* Advance global offset in dataset */ - nbytes_xfer+=buf_size; - } /* end if */ - /* Interleaved access pattern */ - else { - /* Set the base of user's buffer */ - buf_p=(unsigned char *)buffer; - - /* Set the number of bytes to transfer this time */ - nbytes_toxfer = buf_size; - - /* Loop over the buffers to write */ - while(nbytes_toxfer>0) { - /* Skip offset over blocks of other processes */ - file_offset = posix_file_offset + - (off_t)(nbytes_xfer*pio_mpi_nprocs_g); - - /* only care if seek returns error */ - rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; - VRFY((rc==0), "POSIXSEEK"); - - /* check if all bytes are written */ - rc = ((ssize_t)blk_size == - POSIXWRITE(fd->posixfd, buf_p, blk_size)); - VRFY((rc != 0), "POSIXWRITE"); - - /* Advance location in buffer */ - buf_p+=blk_size; - - /* Advance global offset in dataset */ - nbytes_xfer+=blk_size; - - /* Decrement number of bytes left this time */ - nbytes_toxfer-=blk_size; - } /* end while */ - } /* end else */ - break; - - case MPIO: - /* Independent file access */ - if(parms->collective==0) { - /* Contiguous pattern */ - if (parms->interleaved==0){ - /* Compute offset in file */ - mpi_offset = mpi_file_offset + - nbytes_xfer; - - /* Perform independent write */ - mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buffer, - (int)(buf_size/blk_size), mpi_blk_type, - &mpi_status); - VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); - - /* Advance global offset in dataset */ - nbytes_xfer+=buf_size; - } /* end if */ - /* Interleaved access pattern */ - else { - /* Set the base of user's buffer */ - buf_p=(unsigned char *)buffer; - - /* Set the number of bytes to transfer this time */ - nbytes_toxfer = buf_size; - - /* Loop over the buffers to write */ - while(nbytes_toxfer>0) { - /* Skip offset over blocks of other processes */ - mpi_offset = mpi_file_offset + - (nbytes_xfer*pio_mpi_nprocs_g); - - /* Perform independent write */ - mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buf_p, - (int)1, mpi_blk_type, &mpi_status); - VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); - - /* Advance location in buffer */ - buf_p+=blk_size; - - /* Advance global offset in dataset */ - nbytes_xfer+=blk_size; - - /* Decrement number of bytes left this time */ - nbytes_toxfer-=blk_size; - } /* end while */ - } /* end else */ - } /* end if */ - /* Collective file access */ - else { - /* Contiguous access pattern */ - if (parms->interleaved==0){ - /* Compute offset in file */ - mpi_offset = mpi_file_offset + - nbytes_xfer; - - /* Perform independent write */ - mrc = MPI_File_write_at_all(fd->mpifd, mpi_offset, buffer, - (int)(buf_size/blk_size), mpi_blk_type, &mpi_status); - VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); - - /* Advance global offset in dataset */ - nbytes_xfer+=buf_size; - } /* end if */ - /* Interleaved access pattern */ - else { - /* Compute offset in file */ - mpi_offset = mpi_file_offset + - (nbytes_xfer*pio_mpi_nprocs_g); - - /* Set the file view */ - mrc = MPI_File_set_view(fd->mpifd, mpi_offset, mpi_blk_type, - mpi_file_type, (char*)"native", h5_io_info_g); - VRFY((mrc==MPI_SUCCESS), "MPIO_VIEW"); - - /* Perform write */ - mrc = MPI_File_write_at_all(fd->mpifd, 0, buffer, - (int)(buf_size/blk_size), mpi_blk_type, &mpi_status); - VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); - - /* Advance global offset in dataset */ - nbytes_xfer+=buf_size; - } /* end else */ - } /* end else */ - break; - - case PHDF5: - /* Set up the file dset space id to move the selection to process */ - if (parms->interleaved==0){ - /* Contiguous pattern */ - h5offset[0] = nbytes_xfer; - } /* end if */ - else { - /* Interleaved access pattern */ - /* Skip offset over blocks of other processes */ - h5offset[0] = (nbytes_xfer*pio_mpi_nprocs_g); - } /* end else */ - hrc = H5Soffset_simple(h5dset_space_id, h5offset); - VRFY((hrc >= 0), "H5Soffset_simple"); - - /* Write the buffer out */ - hrc = H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, - h5dset_space_id, h5dxpl, buffer); - VRFY((hrc >= 0), "H5Dwrite"); - - /* Increment number of bytes transferred */ - nbytes_xfer += buf_size; - - break; - } /* switch (parms->io_type) */ - } /* end while */ - - /* Stop "raw data" write timer */ - set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, STOP); - - /* Calculate write time */ - - /* Close dataset. Only HDF5 needs to do an explicit close. */ - if (parms->io_type == PHDF5) { - hrc = H5Dclose(h5ds_id); - - if (hrc < 0) { - fprintf(stderr, "HDF5 Dataset Close failed\n"); - GOTOERROR(FAIL); - } - - h5ds_id = -1; - } /* end if */ + nbytes_xfer = 0 ; + + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Set base file offset for all I/O patterns and POSIX access */ + posix_file_offset = dset_offset + bytes_begin[0]; + + /* Set base file offset for all I/O patterns and MPI access */ + mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0]); + } /* end if */ + else { + /* Set base file offset for all I/O patterns and POSIX access */ + posix_file_offset=dset_offset + bytes_begin[0]*snbytes+ + bytes_begin[1]; + + /* Set base file offset for all I/O patterns and MPI access */ + mpi_file_offset=(MPI_Offset)(dset_offset + bytes_begin[0]*snbytes+ + bytes_begin[1]); + } /* end else */ + + /* Start "raw data" write timer */ + set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, START); + + while (nbytes_xfer < bytes_count){ + /* Write */ + /* Calculate offset of write within a dataset/file */ + switch (parms->io_type) { + case POSIXIO: + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Contiguous pattern */ + if (parms->interleaved==0) { + /* Compute file offset */ + file_offset = posix_file_offset + (off_t)nbytes_xfer; + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc==0), "POSIXSEEK"); + + /* check if all bytes are written */ + rc = ((ssize_t)buf_size == + POSIXWRITE(fd->posixfd, buffer, buf_size)); + VRFY((rc != 0), "POSIXWRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Set the base of user's buffer */ + buf_p=(unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size; + + /* Loop over the buffers to write */ + while(nbytes_toxfer>0) { + /* Skip offset over blocks of other processes */ + file_offset = posix_file_offset + + (off_t)(nbytes_xfer*pio_mpi_nprocs_g); + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc==0), "POSIXSEEK"); + + /* check if all bytes are written */ + rc = ((ssize_t)blk_size == + POSIXWRITE(fd->posixfd, buf_p, blk_size)); + VRFY((rc != 0), "POSIXWRITE"); + + /* Advance location in buffer */ + buf_p+=blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=blk_size; + } /* end while */ + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* Contiguous pattern */ + if (parms->interleaved==0){ + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size*blk_size; + + /* Compute file offset */ + file_offset=posix_file_offset+(off_t)(((nbytes_xfer/blk_size)/(snbytes))* + (blk_size*snbytes)+((nbytes_xfer/blk_size)%(snbytes))); + + /* Loop over portions of the buffer to write */ + while(nbytes_toxfer>0){ + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc==0), "POSIXSEEK"); + + /* check if all bytes are written */ + rc = ((ssize_t)buf_size == + POSIXWRITE(fd->posixfd, buffer, buf_size)); + VRFY((rc != 0), "POSIXWRITE"); + + /* Advance location in buffer */ + buf_p+=buf_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=buf_size; + + /* Partially advance file offset */ + file_offset+=(off_t)(snbytes); + } /* end while */ + } /* end if */ + /* Interleaved access pattern */ + else{ + /* Set the base of user's buffer */ + buf_p=(unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer=buf_size*blk_size; + + /* Compute file offset */ + file_offset=posix_file_offset+(off_t)(((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)/(snbytes)* + (buf_size*snbytes)+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)%(snbytes)); + + /* Loop over portions of the buffer to write */ + while(nbytes_toxfer>0){ + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc==0), "POSIXSEEK"); + + /* check if all bytes are written */ + rc = ((ssize_t)blk_size == + POSIXWRITE(fd->posixfd, buffer, blk_size)); + VRFY((rc != 0), "POSIXWRITE"); + + /* Advance location in buffer */ + buf_p+=blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=blk_size; + + /* Partially advance file offset */ + file_offset+=(off_t)(snbytes); + } /* end while */ + }/* end else */ + } /* end else */ + break; + + case MPIO: + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Independent file access */ + if(parms->collective==0) { + /* Contiguous pattern */ + if (parms->interleaved==0){ + /* Compute offset in file */ + mpi_offset = mpi_file_offset + + nbytes_xfer; + + /* Perform independent write */ + mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buffer, + (int)(buf_size/blk_size), mpi_blk_type, + &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Set the base of user's buffer */ + buf_p=(unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size; + + /* Loop over the buffers to write */ + while(nbytes_toxfer>0) { + /* Skip offset over blocks of other processes */ + mpi_offset = mpi_file_offset + + (nbytes_xfer*pio_mpi_nprocs_g); + + /* Perform independent write */ + mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buf_p, + (int)1, mpi_blk_type, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance location in buffer */ + buf_p+=blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=blk_size; + } /* end while */ + } /* end else */ + } /* end if */ + /* Collective file access */ + else { + /* Contiguous access pattern */ + if (parms->interleaved==0){ + /* Compute offset in file */ + mpi_offset = mpi_file_offset + + nbytes_xfer; + + /* Perform independent write */ + mrc = MPI_File_write_at_all(fd->mpifd, mpi_offset, buffer, + (int)(buf_size/blk_size), mpi_blk_type, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + + (nbytes_xfer*pio_mpi_nprocs_g); + + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, mpi_blk_type, + mpi_file_type, (char*)"native", h5_io_info_g); + VRFY((mrc==MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform write */ + mrc = MPI_File_write_at_all(fd->mpifd, 0, buffer, + (int)(buf_size/blk_size), mpi_blk_type, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + } /* end else */ + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* Independent file access */ + if (parms->collective==0) + /* Contiguous pattern */ + if (parms->interleaved==0){ + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size*blk_size; + + /* Compute offset in file */ + mpi_offset=mpi_file_offset+((nbytes_xfer/blk_size)/(snbytes))* + (blk_size*snbytes)+((nbytes_xfer/blk_size)%(snbytes)); + + /* Loop over portions of the buffer to write */ + while(nbytes_toxfer>0){ + + /* Perform independent write */ + mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buf_p, (int)buf_size, MPI_BYTE, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance location in buffer */ + buf_p+=buf_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=buf_size; + + /* Partially advance global offset in dataset */ + mpi_offset+=snbytes; + } /* end while */ + } /* end if */ + /* Interleaved access pattern */ + else{ + /* Set the base of user's buffer */ + buf_p=(unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer=buf_size*blk_size; + + /* Compute offset in file */ + mpi_offset=mpi_file_offset+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)/(snbytes)* + (buf_size*snbytes)+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)%(snbytes); + + /* Loop over portions of the buffer to write */ + while(nbytes_toxfer>0){ + /* Perform independent write */ + mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buf_p, (int)blk_size, MPI_BYTE, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); + + /* Advance location in buffer */ + buf_p+=blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=blk_size; + + /* Partially advance global offset in dataset */ + mpi_offset+=snbytes; + } /* end while */ + } /* end else */ + /* end if */ + /* Collective file access */ + else + /* Contiguous access pattern */ + if (parms->interleaved==0){ + /* Compute offset in file */ + mpi_offset=mpi_file_offset+((nbytes_xfer/blk_size)/(snbytes))* + (blk_size*snbytes)+((nbytes_xfer/blk_size)%(snbytes)); + + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, MPI_BYTE, mpi_cont_type, (char *)"native", h5_io_info_g); + VRFY((mrc==MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform write */ + MPI_File_write_at_all(fd->mpifd, 0, buffer,(int)(buf_size*blk_size),MPI_BYTE, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); + + nbytes_xfer+=buf_size*blk_size; + } /* end if */ + /* Interleaved access pattern */ + else{ + /* Compute offset in file */ + mpi_offset=mpi_file_offset+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)/(snbytes)* + (buf_size*snbytes)+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)%(snbytes); + + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, MPI_BYTE, mpi_inter_type, (char *)"native", h5_io_info_g); + VRFY((mrc==MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform write */ + MPI_File_write_at_all(fd->mpifd, 0, buffer, (int)(buf_size*blk_size), MPI_BYTE, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE"); + + nbytes_xfer+=buf_size*blk_size; + } /* end else */ + /* end else */ + } /* end else */ + break; + + case PHDF5: + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Set up the file dset space id to move the selection to process */ + if (parms->interleaved==0){ + /* Contiguous pattern */ + h5offset[0] = nbytes_xfer; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5offset[0] = (nbytes_xfer*pio_mpi_nprocs_g); + } /* end else */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Write the buffer out */ + hrc = H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, + h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dwrite"); + + /* Increment number of bytes transferred */ + nbytes_xfer += buf_size; + } /* end if */ + /* 2D dataspace */ + else { + /* Set up the file dset space id to move the selection to process */ + if (parms->interleaved==0){ + /* Contiguous pattern */ + h5offset[0] = (nbytes_xfer/(snbytes*blk_size))*blk_size; + h5offset[1] = (nbytes_xfer%(snbytes*blk_size))/blk_size; + + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5offset[0] = ((nbytes_xfer*pio_mpi_nprocs_g)/(snbytes*buf_size))*buf_size; + h5offset[1] = ((nbytes_xfer*pio_mpi_nprocs_g)%(snbytes*buf_size))/buf_size; + + } /* end else */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Write the buffer out */ + hrc = H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, + h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dwrite"); + + /* Increment number of bytes transferred */ + nbytes_xfer += buf_size*blk_size; + + } /* end else */ + + break; + } /* switch (parms->io_type) */ + } /* end while */ + + /* Stop "raw data" write timer */ + set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, STOP); + + /* Calculate write time */ + + /* Close dataset. Only HDF5 needs to do an explicit close. */ + if (parms->io_type == PHDF5) { + hrc = H5Dclose(h5ds_id); + + if (hrc < 0) { + fprintf(stderr, "HDF5 Dataset Close failed\n"); + GOTOERROR(FAIL); + } + + h5ds_id = -1; + } /* end if */ } /* end for */ done: /* release MPI-I/O objects */ if (parms->io_type == MPIO) { - /* Free file type */ - mrc = MPI_Type_free( &mpi_file_type ); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); - - /* Free buffer type */ - mrc = MPI_Type_free( &mpi_blk_type ); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Free file type */ + mrc = MPI_Type_free( &mpi_file_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free buffer type */ + mrc = MPI_Type_free( &mpi_blk_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + } /* end if */ + /* 2D dataspace */ + else { + /* Free file type */ + mrc = MPI_Type_free( &mpi_cont_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free partial buffer type */ + mrc = MPI_Type_free( &contig_cont ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free file type */ + mrc = MPI_Type_free( &mpi_inter_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free partial buffer type */ + mrc = MPI_Type_free( &contig_inter ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + } /* end else */ } /* end if */ /* release HDF5 objects */ if (h5dset_space_id != -1) { - hrc = H5Sclose(h5dset_space_id); - if (hrc < 0){ - fprintf(stderr, "HDF5 Dataset Space Close failed\n"); - ret_code = FAIL; - } else { - h5dset_space_id = -1; - } + hrc = H5Sclose(h5dset_space_id); + if (hrc < 0){ + fprintf(stderr, "HDF5 Dataset Space Close failed\n"); + ret_code = FAIL; + } else { + h5dset_space_id = -1; + } } if (h5mem_space_id != -1) { - hrc = H5Sclose(h5mem_space_id); - if (hrc < 0) { - fprintf(stderr, "HDF5 Memory Space Close failed\n"); - ret_code = FAIL; - } else { - h5mem_space_id = -1; - } + hrc = H5Sclose(h5mem_space_id); + if (hrc < 0) { + fprintf(stderr, "HDF5 Memory Space Close failed\n"); + ret_code = FAIL; + } else { + h5mem_space_id = -1; + } } if (h5dxpl != -1) { - hrc = H5Pclose(h5dxpl); - if (hrc < 0) { - fprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n"); - ret_code = FAIL; - } else { - h5dxpl = -1; - } + hrc = H5Pclose(h5dxpl); + if (hrc < 0) { + fprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n"); + ret_code = FAIL; + } else { + h5dxpl = -1; + } } return ret_code; } /* - * Function: do_read - * Purpose: read the required amount of data from the file. - * Return: SUCCESS or FAIL - * Programmer: Albert Cheng 2001/12/13 + * Function: do_read + * Purpose: read the required amount of data from the file. + * Return: SUCCESS or FAIL + * Programmer: Albert Cheng 2001/12/13 * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) */ -static herr_t + static herr_t do_read(results *res, file_descr *fd, parameters *parms, long ndsets, - off_t nbytes, size_t buf_size, void *buffer /*out*/) + off_t nbytes, size_t buf_size, void *buffer /*out*/) { int ret_code = SUCCESS; int rc; /*routine return code */ long ndset; size_t blk_size; /* The block size to subdivide the xfer buffer into */ + size_t bsize; off_t nbytes_xfer; /* Total number of bytes transferred so far */ size_t nbytes_toxfer; /* Number of bytes to transfer a particular time */ char dname[64]; off_t dset_offset=0; /*dataset offset in a file */ - off_t bytes_begin; /*first elmt this process transfer */ + off_t bytes_begin[2]; /*first elmt this process transfer */ off_t bytes_count; /*number of elmts this process transfer */ + off_t snbytes=0; /*size of a side of the dataset square */ unsigned char *buf_p; /* Current buffer pointer */ /* POSIX variables */ @@ -987,22 +1397,26 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets, /* MPI variables */ MPI_Offset mpi_file_offset;/* Base file offset of the next transfer*/ MPI_Offset mpi_offset; /* Offset in MPI file */ - MPI_Datatype mpi_file_type; /* MPI derived type for file */ - MPI_Datatype mpi_blk_type; /* MPI derived type for buffer */ + MPI_Datatype mpi_file_type; /* MPI derived type for 1D file */ + MPI_Datatype mpi_blk_type; /* MPI derived type for 1D buffer */ + MPI_Datatype mpi_cont_type; /* MPI derived type for 2D contiguous file */ + MPI_Datatype contig_cont; /* MPI derived type for 2D contiguous buffer */ + MPI_Datatype mpi_inter_type;/* MPI derived type for 2D interleaved file */ + MPI_Datatype contig_inter; /* MPI derived type for 2D interleaved buffer*/ MPI_Status mpi_status; int mrc; /* MPI return code */ /* HDF5 variables */ herr_t hrc; /*HDF5 return code */ - hsize_t h5dims[1]; /*dataset dim sizes */ + hsize_t h5dims[2]; /*dataset dim sizes */ hid_t h5dset_space_id = -1; /*dataset space ID */ hid_t h5mem_space_id = -1; /*memory dataspace ID */ hid_t h5ds_id = -1; /*dataset handle */ - hsize_t h5block[1]; /*dataspace selection */ - hsize_t h5stride[1]; - hsize_t h5count[1]; - hsize_t h5start[1]; - hssize_t h5offset[1]; /* Selection offset within dataspace */ + hsize_t h5block[2]; /*dataspace selection */ + hsize_t h5stride[2]; + hsize_t h5count[2]; + hsize_t h5start[2]; + hssize_t h5offset[2]; /* Selection offset within dataspace */ hid_t h5dxpl = -1; /* Dataset transfer property list */ /* Get the parameters from the parameter block */ @@ -1017,14 +1431,40 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets, * 012...n012...n... * These are all in the scope of one dataset. */ - if (parms->interleaved==0) { - /* Contiguous Pattern: */ - bytes_begin = (off_t)(((double)nbytes*pio_mpi_rank_g)/pio_mpi_nprocs_g); - } /* end if */ + + /* 1D dataspace */ + if (parms->dim2d==0){ + bsize = buf_size; + if (parms->interleaved==0) { + /* Contiguous Pattern: */ + bytes_begin[0] = (off_t)(((double)nbytes*pio_mpi_rank_g)/pio_mpi_nprocs_g); + } /* end if */ + else { + /* Interleaved Pattern: */ + bytes_begin[0] = (off_t)(blk_size*pio_mpi_rank_g); + } /* end else */ + }/* end if */ + /* 2D dataspace */ else { - /* Interleaved Pattern: */ - bytes_begin = (off_t)(blk_size*pio_mpi_rank_g); - } /* end else */ + snbytes = (off_t)sqrt(nbytes); + bsize = buf_size * blk_size; + /* nbytes is always the number of bytes per dataset (1D or 2D). If the + dataspace is 2D, snbytes is the size of a side of the 'dataset square'. + */ + if (parms->interleaved==0) { + /* Contiguous Pattern: */ + bytes_begin[0] = (off_t)((double)snbytes*pio_mpi_rank_g / pio_mpi_nprocs_g); + bytes_begin[1] = 0; + } /* end if */ + else { + /* Interleaved Pattern: */ + bytes_begin[0] = 0; + bytes_begin[1] = (off_t)(blk_size*pio_mpi_rank_g); + } /* end else */ + } + + /* end else */ + /* Calculate the total number of bytes (bytes_count) to be * transferred by this process. It may be different for different @@ -1037,125 +1477,217 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets, * (This is tricky, don't mess with the formula, rounding errors * can easily get introduced) */ bytes_count = (off_t)(((double)nbytes*(pio_mpi_rank_g+1)) / pio_mpi_nprocs_g) - - (off_t)(((double)nbytes*pio_mpi_rank_g) / pio_mpi_nprocs_g); + - (off_t)(((double)nbytes*pio_mpi_rank_g) / pio_mpi_nprocs_g); /* debug */ if (pio_debug_level >= 4) { - HDprint_rank(output); - HDfprintf(output, "Debug(do_read): " - "buf_size=%Hd, bytes_begin=%Hd, bytes_count=%Hd\n", - (long_long)buf_size, (long_long)bytes_begin, - (long_long)bytes_count); + HDprint_rank(output); + HDfprintf(output, "Debug(do_read): " + "buf_size=%Hd, bytes_begin=%Hd, bytes_count=%Hd\n", + (long_long)buf_size, (long_long)bytes_begin, + (long_long)bytes_count); } /* I/O Access specific setup */ switch (parms->io_type) { - case POSIXIO: - /* No extra setup */ - break; - - case MPIO: /* MPI-I/O setup */ - /* Build block's derived type */ - mrc = MPI_Type_contiguous((int)blk_size, - MPI_BYTE, &mpi_blk_type); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); - - /* Build file's derived type */ - mrc = MPI_Type_vector((int)(buf_size/blk_size), (int)1, - (int)pio_mpi_nprocs_g, mpi_blk_type, &mpi_file_type); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); - - /* Commit file type */ - mrc = MPI_Type_commit( &mpi_file_type ); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); - - /* Commit buffer type */ - mrc = MPI_Type_commit( &mpi_blk_type ); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); - break; - - case PHDF5: /* HDF5 setup */ - if(nbytes>0) { - /* define a contiquous dataset of nbytes native bytes */ - h5dims[0] = nbytes; - h5dset_space_id = H5Screate_simple(1, h5dims, NULL); - VRFY((h5dset_space_id >= 0), "H5Screate_simple"); - - /* Set up the file dset space id to select the pattern to access */ - if (parms->interleaved==0){ - /* Contiguous pattern */ - h5start[0] = bytes_begin; - h5stride[0] = h5block[0] = blk_size; - h5count[0] = buf_size/blk_size; - } /* end if */ - else { - /* Interleaved access pattern */ - /* Skip offset over blocks of other processes */ - h5start[0] = bytes_begin; - h5stride[0] = blk_size*pio_mpi_nprocs_g; - h5block[0] = blk_size; - h5count[0] = buf_size/blk_size; - } /* end else */ - hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, - h5start, h5stride, h5count, h5block); - VRFY((hrc >= 0), "H5Sselect_hyperslab"); - } /* end if */ - else { - h5dset_space_id = H5Screate(H5S_SCALAR); - VRFY((h5dset_space_id >= 0), "H5Screate"); - } /* end else */ - - /* Create the memory dataspace that corresponds to the xfer buffer */ - if(buf_size>0) { - h5dims[0] = buf_size; - h5mem_space_id = H5Screate_simple(1, h5dims, NULL); - VRFY((h5mem_space_id >= 0), "H5Screate_simple"); - } /* end if */ - else { - h5mem_space_id = H5Screate(H5S_SCALAR); - VRFY((h5mem_space_id >= 0), "H5Screate"); - } /* end else */ - - /* Create the dataset transfer property list */ - h5dxpl = H5Pcreate(H5P_DATASET_XFER); - if (h5dxpl < 0) { - fprintf(stderr, "HDF5 Property List Create failed\n"); - GOTOERROR(FAIL); - } - - /* Change to collective I/O, if asked */ - if(parms->collective) { - hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE); - if (hrc < 0) { - fprintf(stderr, "HDF5 Property List Set failed\n"); - GOTOERROR(FAIL); - } /* end if */ - } /* end if */ - break; + case POSIXIO: + /* No extra setup */ + break; + + case MPIO: /* MPI-I/O setup */ + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Build block's derived type */ + mrc = MPI_Type_contiguous((int)blk_size, + MPI_BYTE, &mpi_blk_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Build file's derived type */ + mrc = MPI_Type_vector((int)(buf_size/blk_size), (int)1, + (int)pio_mpi_nprocs_g, mpi_blk_type, &mpi_file_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit file type */ + mrc = MPI_Type_commit( &mpi_file_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Commit buffer type */ + mrc = MPI_Type_commit( &mpi_blk_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + } /* end if */ + /* 2D dataspace */ + else { + /* Build partial buffer derived type for contiguous access */ + mrc = MPI_Type_contiguous((int)buf_size, MPI_BYTE, + &contig_cont); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Build contiguous file's derived type */ + mrc = MPI_Type_vector((int)blk_size, (int)1, (int)(snbytes/buf_size), + contig_cont, &mpi_cont_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit contiguous file type */ + mrc = MPI_Type_commit(&mpi_cont_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + + /* Build partial buffer derived type for interleaved access */ + mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, + &contig_inter); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Build interleaved file's derived type */ + mrc = MPI_Type_vector((int)buf_size, (int)1, (int)(snbytes/blk_size), + contig_inter, &mpi_inter_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_CREATE"); + + /* Commit interleaved buffer type */ + mrc = MPI_Type_commit(&mpi_inter_type); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_COMMIT"); + } /* end else */ + break; + + case PHDF5: /* HDF5 setup */ + /* 1D dataspace */ + if (parms->dim2d==0){ + if(nbytes>0) { + /* define a contiguous dataset of nbytes native bytes */ + h5dims[0] = nbytes; + h5dset_space_id = H5Screate_simple(1, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + /* Set up the file dset space id to select the pattern to access */ + if (parms->interleaved==0){ + /* Contiguous pattern */ + h5start[0] = bytes_begin[0]; + h5stride[0] = h5block[0] = blk_size; + h5count[0] = buf_size/blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5start[0] = bytes_begin[0]; + h5stride[0] = blk_size*pio_mpi_nprocs_g; + h5block[0] = blk_size; + h5count[0] = buf_size/blk_size; + } /* end else */ + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, + h5start, h5stride, h5count, h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + } /* end if */ + else { + h5dset_space_id = H5Screate(H5S_SCALAR); + VRFY((h5dset_space_id >= 0), "H5Screate"); + } /* end else */ + + /* Create the memory dataspace that corresponds to the xfer buffer */ + if(buf_size>0) { + h5dims[0] = buf_size; + h5mem_space_id = H5Screate_simple(1, h5dims, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + } /* end if */ + else { + h5mem_space_id = H5Screate(H5S_SCALAR); + VRFY((h5mem_space_id >= 0), "H5Screate"); + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + if(nbytes>0) { + /* define a contiguous dataset of nbytes native bytes */ + h5dims[0] = snbytes; + h5dims[1] = snbytes; + h5dset_space_id = H5Screate_simple(2, h5dims, NULL); + VRFY((h5dset_space_id >= 0), "H5Screate_simple"); + + /* Set up the file dset space id to select the pattern to access */ + if (parms->interleaved==0){ + /* Contiguous pattern */ + h5start[0] = bytes_begin[0]; + h5start[1] = bytes_begin[1]; + h5stride[0] = 1; + h5stride[1] = h5block[0] = h5block[1] = blk_size; + h5count[0] = 1; + h5count[1] = buf_size/blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5start[0] = bytes_begin[0]; + h5start[1] = bytes_begin[1]; + h5stride[0] = blk_size; + h5stride[1] = blk_size*pio_mpi_nprocs_g; + h5block[0] = h5block[1] = blk_size; + h5count[0] = buf_size/blk_size; + h5count[1] = 1; + } /* end else */ + hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, + h5start, h5stride, h5count, h5block); + VRFY((hrc >= 0), "H5Sselect_hyperslab"); + } /* end if */ + else { + h5dset_space_id = H5Screate(H5S_SCALAR); + VRFY((h5dset_space_id >= 0), "H5Screate"); + } /* end else */ + + /* Create the memory dataspace that corresponds to the xfer buffer */ + if(buf_size>0) { + if (parms->interleaved==0){ + h5dims[0] = blk_size; + h5dims[1] = buf_size; + }else{ + h5dims[0] = buf_size; + h5dims[1] = blk_size; + } + h5mem_space_id = H5Screate_simple(2, h5dims, NULL); + VRFY((h5mem_space_id >= 0), "H5Screate_simple"); + } /* end if */ + else { + h5mem_space_id = H5Screate(H5S_SCALAR); + VRFY((h5mem_space_id >= 0), "H5Screate"); + } /* end else */ + } /* end else */ + + /* Create the dataset transfer property list */ + h5dxpl = H5Pcreate(H5P_DATASET_XFER); + if (h5dxpl < 0) { + fprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + /* Change to collective I/O, if asked */ + if(parms->collective) { + hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE); + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } /* end if */ + } /* end if */ + break; } /* end switch */ for (ndset = 1; ndset <= ndsets; ++ndset) { - /* Calculate dataset offset within a file */ + /* Calculate dataset offset within a file */ - /* create dataset */ - switch (parms->io_type) { - case POSIXIO: - case MPIO: - /* both posix and mpi io just need dataset offset in file*/ - dset_offset = (ndset - 1) * nbytes; - break; + /* create dataset */ + switch (parms->io_type) { + case POSIXIO: + case MPIO: + /* both posix and mpi io just need dataset offset in file*/ + dset_offset = (ndset - 1) * nbytes; + break; - case PHDF5: - sprintf(dname, "Dataset_%ld", ndset); - h5ds_id = H5Dopen(fd->h5fd, dname); - if (h5ds_id < 0) { - fprintf(stderr, "HDF5 Dataset open failed\n"); - GOTOERROR(FAIL); - } + case PHDF5: + sprintf(dname, "Dataset_%ld", ndset); + h5ds_id = H5Dopen(fd->h5fd, dname); + if (h5ds_id < 0) { + fprintf(stderr, "HDF5 Dataset open failed\n"); + GOTOERROR(FAIL); + } - break; - } + break; + } /* The task is to transfer bytes_count bytes, starting at * bytes_begin position, using transfer buffer of buf_size bytes. @@ -1163,201 +1695,427 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets, * fashion, according to number of process. Otherwise, select * all bytes_count in contiguous. */ - nbytes_xfer = 0 ; - - /* Set base file offset for all I/O patterns and POSIX access */ - posix_file_offset = dset_offset + bytes_begin; - - /* Set base file offset for all I/O patterns and MPI access */ - mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin); - - /* Start "raw data" read timer */ - set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, START); - - while (nbytes_xfer < bytes_count){ - /* Read */ - /* Calculate offset of read within a dataset/file */ - switch (parms->io_type) { - case POSIXIO: - /* Contiguous pattern */ - if (parms->interleaved==0) { - /* Compute file offset */ - file_offset = posix_file_offset + (off_t)nbytes_xfer; - - /* only care if seek returns error */ - rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; - VRFY((rc==0), "POSIXSEEK"); - - /* check if all bytes are written */ - rc = ((ssize_t)buf_size == - POSIXREAD(fd->posixfd, buffer, buf_size)); - VRFY((rc != 0), "POSIXREAD"); - - /* Advance global offset in dataset */ - nbytes_xfer+=buf_size; - } /* end if */ - /* Interleaved access pattern */ - else { - /* Set the base of user's buffer */ - buf_p=(unsigned char *)buffer; - - /* Set the number of bytes to transfer this time */ - nbytes_toxfer = buf_size; - - /* Loop over the buffers to read */ - while(nbytes_toxfer>0) { - /* Skip offset over blocks of other processes */ - file_offset = posix_file_offset + - (off_t)(nbytes_xfer*pio_mpi_nprocs_g); - - /* only care if seek returns error */ - rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; - VRFY((rc==0), "POSIXSEEK"); - - /* check if all bytes are written */ - rc = ((ssize_t)blk_size == - POSIXREAD(fd->posixfd, buf_p, blk_size)); - VRFY((rc != 0), "POSIXREAD"); - - /* Advance location in buffer */ - buf_p+=blk_size; - - /* Advance global offset in dataset */ - nbytes_xfer+=blk_size; - - /* Decrement number of bytes left this time */ - nbytes_toxfer-=blk_size; - } /* end while */ - } /* end else */ - break; - - case MPIO: - /* Independent file access */ - if(parms->collective==0) { - /* Contiguous pattern */ - if (parms->interleaved==0){ - /* Compute offset in file */ - mpi_offset = mpi_file_offset + - nbytes_xfer; - - /* Perform independent read */ - mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buffer, - (int)(buf_size/blk_size), mpi_blk_type, - &mpi_status); - VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); - - /* Advance global offset in dataset */ - nbytes_xfer+=buf_size; - } /* end if */ - /* Interleaved access pattern */ - else { - /* Set the base of user's buffer */ - buf_p=(unsigned char *)buffer; - - /* Set the number of bytes to transfer this time */ - nbytes_toxfer = buf_size; - - /* Loop over the buffers to read */ - while(nbytes_toxfer>0) { - /* Skip offset over blocks of other processes */ - mpi_offset = mpi_file_offset + - (nbytes_xfer*pio_mpi_nprocs_g); - - /* Perform independent read */ - mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buf_p, - (int)1, mpi_blk_type, &mpi_status); - VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); - - /* Advance location in buffer */ - buf_p+=blk_size; - - /* Advance global offset in dataset */ - nbytes_xfer+=blk_size; - - /* Decrement number of bytes left this time */ - nbytes_toxfer-=blk_size; - } /* end while */ - } /* end else */ - } /* end if */ - /* Collective file access */ - else { - /* Contiguous access pattern */ - if (parms->interleaved==0){ - /* Compute offset in file */ - mpi_offset = mpi_file_offset + - nbytes_xfer; - - /* Perform collective read */ - mrc = MPI_File_read_at_all(fd->mpifd, mpi_offset, buffer, - (int)(buf_size/blk_size), mpi_blk_type, &mpi_status); - VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); - - /* Advance global offset in dataset */ - nbytes_xfer+=buf_size; - } /* end if */ - /* Interleaved access pattern */ - else { - /* Compute offset in file */ - mpi_offset = mpi_file_offset + - (nbytes_xfer*pio_mpi_nprocs_g); - - /* Set the file view */ - mrc = MPI_File_set_view(fd->mpifd, mpi_offset, mpi_blk_type, - mpi_file_type, (char*)"native", h5_io_info_g); - VRFY((mrc==MPI_SUCCESS), "MPIO_VIEW"); - - /* Perform collective read */ - mrc = MPI_File_read_at_all(fd->mpifd, 0, buffer, - (int)(buf_size/blk_size), mpi_blk_type, &mpi_status); - VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); - - /* Advance global offset in dataset */ - nbytes_xfer+=buf_size; - } /* end else */ - } /* end else */ - break; - - case PHDF5: - /* Set up the file dset space id to move the selection to process */ - if (parms->interleaved==0){ - /* Contiguous pattern */ - h5offset[0] = nbytes_xfer; - } /* end if */ - else { - /* Interleaved access pattern */ - /* Skip offset over blocks of other processes */ - h5offset[0] = (nbytes_xfer*pio_mpi_nprocs_g); - } /* end else */ - hrc = H5Soffset_simple(h5dset_space_id, h5offset); - VRFY((hrc >= 0), "H5Soffset_simple"); - - /* Read the buffer in */ - hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, - h5dset_space_id, h5dxpl, buffer); - VRFY((hrc >= 0), "H5Dread"); - - /* Increment number of bytes transferred */ - nbytes_xfer += buf_size; - - break; - } /* switch (parms->io_type) */ - - /* Verify raw data, if asked */ + nbytes_xfer = 0 ; + + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Set base file offset for all I/O patterns and POSIX access */ + posix_file_offset = dset_offset + bytes_begin[0]; + + /* Set base file offset for all I/O patterns and MPI access */ + mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0]); + } /* end if */ + else { + /* Set base file offset for all I/O patterns and POSIX access */ + posix_file_offset=dset_offset + bytes_begin[0]*snbytes+ + bytes_begin[1]; + + /* Set base file offset for all I/O patterns and MPI access */ + mpi_file_offset=(MPI_Offset)(dset_offset + bytes_begin[0]*snbytes+ + bytes_begin[1]); + } /* end else */ + + /* Start "raw data" read timer */ + set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, START); + + while (nbytes_xfer < bytes_count){ + /* Read */ + /* Calculate offset of read within a dataset/file */ + switch (parms->io_type) { + case POSIXIO: + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Contiguous pattern */ + if (parms->interleaved==0) { + /* Compute file offset */ + file_offset = posix_file_offset + (off_t)nbytes_xfer; + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc==0), "POSIXSEEK"); + + /* check if all bytes are read */ + rc = ((ssize_t)buf_size == + POSIXREAD(fd->posixfd, buffer, buf_size)); + VRFY((rc != 0), "POSIXREAD"); + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Set the base of user's buffer */ + buf_p=(unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size; + + /* Loop over the buffers to read */ + while(nbytes_toxfer>0) { + /* Skip offset over blocks of other processes */ + file_offset = posix_file_offset + + (off_t)(nbytes_xfer*pio_mpi_nprocs_g); + + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc==0), "POSIXSEEK"); + + /* check if all bytes are read */ + rc = ((ssize_t)blk_size == + POSIXREAD(fd->posixfd, buf_p, blk_size)); + VRFY((rc != 0), "POSIXREAD"); + + /* Advance location in buffer */ + buf_p+=blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=blk_size; + } /* end while */ + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* Contiguous pattern */ + if (parms->interleaved==0){ + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size*blk_size; + + /* Compute file offset */ + file_offset=posix_file_offset+(off_t)(((nbytes_xfer/blk_size)/(snbytes))* + (blk_size*snbytes)+((nbytes_xfer/blk_size)%(snbytes))); + + /* Loop over portions of the buffer to read */ + while(nbytes_toxfer>0){ + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc==0), "POSIXSEEK"); + + /* check if all bytes are read */ + rc = ((ssize_t)buf_size == + POSIXREAD(fd->posixfd, buffer, buf_size)); + VRFY((rc != 0), "POSIXREAD"); + + /* Advance location in buffer */ + buf_p+=buf_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=buf_size; + + /* Partially advance file offset */ + file_offset+=(off_t)(snbytes); + } /* end while */ + } /* end if */ + /* Interleaved access pattern */ + else{ + /* Set the base of user's buffer */ + buf_p=(unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer=buf_size*blk_size; + + /* Compute file offset */ + file_offset=posix_file_offset+(off_t)(((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)/(snbytes)* + (buf_size*snbytes)+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)%(snbytes)); + + /* Loop over portions of the buffer to read */ + while(nbytes_toxfer>0){ + /* only care if seek returns error */ + rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0; + VRFY((rc==0), "POSIXSEEK"); + + /* check if all bytes are read */ + rc = ((ssize_t)blk_size == + POSIXREAD(fd->posixfd, buffer, blk_size)); + VRFY((rc != 0), "POSIXREAD"); + + /* Advance location in buffer */ + buf_p+=blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=blk_size; + + /* Partially advance file offset */ + file_offset+=(off_t)(snbytes); + } /* end while */ + }/* end else */ + } /* end else */ + break; + + case MPIO: + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Independent file access */ + if(parms->collective==0) { + /* Contiguous pattern */ + if (parms->interleaved==0){ + /* Compute offset in file */ + mpi_offset = mpi_file_offset + + nbytes_xfer; + + /* Perform independent read */ + mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buffer, + (int)(buf_size/blk_size), mpi_blk_type, + &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Set the base of user's buffer */ + buf_p=(unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size; + + /* Loop over the buffers to read */ + while(nbytes_toxfer>0) { + /* Skip offset over blocks of other processes */ + mpi_offset = mpi_file_offset + + (nbytes_xfer*pio_mpi_nprocs_g); + + /* Perform independent read */ + mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buf_p, + (int)1, mpi_blk_type, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); + + /* Advance location in buffer */ + buf_p+=blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=blk_size; + } /* end while */ + } /* end else */ + } /* end if */ + /* Collective file access */ + else { + /* Contiguous access pattern */ + if (parms->interleaved==0){ + /* Compute offset in file */ + mpi_offset = mpi_file_offset + + nbytes_xfer; + + /* Perform collective read */ + mrc = MPI_File_read_at_all(fd->mpifd, mpi_offset, buffer, + (int)(buf_size/blk_size), mpi_blk_type, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + } /* end if */ + /* Interleaved access pattern */ + else { + /* Compute offset in file */ + mpi_offset = mpi_file_offset + + (nbytes_xfer*pio_mpi_nprocs_g); + + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, mpi_blk_type, + mpi_file_type, (char*)"native", h5_io_info_g); + VRFY((mrc==MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform collective read */ + mrc = MPI_File_read_at_all(fd->mpifd, 0, buffer, + (int)(buf_size/blk_size), mpi_blk_type, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + } /* end else */ + } /* end else */ + } /* end if */ + /* 2D dataspace */ + else { + /* Independent file access */ + if (parms->collective==0) + /* Contiguous pattern */ + if (parms->interleaved==0){ + /* Set the base of user's buffer */ + buf_p = (unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer = buf_size*blk_size; + + /* Compute offset in file */ + mpi_offset=mpi_file_offset+((nbytes_xfer/blk_size)/(snbytes))* + (blk_size*snbytes)+((nbytes_xfer/blk_size)%(snbytes)); + + /* Loop over portions of the buffer to read */ + while(nbytes_toxfer>0){ + + /* Perform independent write */ + mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buf_p, (int)buf_size, MPI_BYTE, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); + + /* Advance location in buffer */ + buf_p+=buf_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=buf_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=buf_size; + + /* Partially advance global offset in dataset */ + mpi_offset+=snbytes; + } /* end while */ + } /* end if */ + /* Interleaved access pattern */ + else{ + /* Set the base of user's buffer */ + buf_p=(unsigned char *)buffer; + + /* Set the number of bytes to transfer this time */ + nbytes_toxfer=buf_size*blk_size; + + /* Compute offset in file */ + mpi_offset=mpi_file_offset+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)/(snbytes)* + (buf_size*snbytes)+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)%(snbytes); + + /* Loop over portions of the buffer to read */ + while(nbytes_toxfer>0){ + /* Perform independent write */ + mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buf_p, (int)blk_size, MPI_BYTE, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); + + /* Advance location in buffer */ + buf_p+=blk_size; + + /* Advance global offset in dataset */ + nbytes_xfer+=blk_size; + + /* Decrement number of bytes left this time */ + nbytes_toxfer-=blk_size; + + /* Partially advance global offset in dataset */ + mpi_offset+=snbytes; + } /* end while */ + } /* end else */ + /* end if */ + /* Collective file access */ + else + /* Contiguous access pattern */ + if (parms->interleaved==0){ + /* Compute offset in file */ + mpi_offset=mpi_file_offset+((nbytes_xfer/blk_size)/(snbytes))* + (blk_size*snbytes)+((nbytes_xfer/blk_size)%(snbytes)); + + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, MPI_BYTE, mpi_cont_type, (char *)"native", h5_io_info_g); + VRFY((mrc==MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform read */ + mrc = MPI_File_read_at_all(fd->mpifd, 0, buffer,(int)(buf_size*blk_size),MPI_BYTE, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); + + nbytes_xfer+=buf_size*blk_size; + } /* end if */ + /* Interleaved access pattern */ + else{ + /* Compute offset in file */ + mpi_offset=mpi_file_offset+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)/(snbytes)* + (buf_size*snbytes)+((nbytes_xfer/buf_size)*pio_mpi_nprocs_g)%(snbytes); + + /* Set the file view */ + mrc = MPI_File_set_view(fd->mpifd, mpi_offset, MPI_BYTE, mpi_inter_type, (char *)"native", h5_io_info_g); + VRFY((mrc==MPI_SUCCESS), "MPIO_VIEW"); + + /* Perform read */ + mrc = MPI_File_read_at_all(fd->mpifd, 0, buffer, (int)(buf_size*blk_size), MPI_BYTE, &mpi_status); + VRFY((mrc==MPI_SUCCESS), "MPIO_READ"); + + nbytes_xfer+=buf_size*blk_size; + } /* end else */ + /* end else */ + } /* end else */ + break; + + case PHDF5: + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Set up the file dset space id to move the selection to process */ + if (parms->interleaved==0){ + /* Contiguous pattern */ + h5offset[0] = nbytes_xfer; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5offset[0] = (nbytes_xfer*pio_mpi_nprocs_g); + } /* end else */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Read the buffer in */ + hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, + h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dread"); + + /* Increment number of bytes transferred */ + nbytes_xfer += buf_size; + } /* end if */ + /* 2D dataspace */ + else { + /* Set up the file dset space id to move the selection to process */ + if (parms->interleaved==0){ + /* Contiguous pattern */ + h5offset[0] = (nbytes_xfer/(snbytes*blk_size))*blk_size; + h5offset[1] = (nbytes_xfer%(snbytes*blk_size))/blk_size; + } /* end if */ + else { + /* Interleaved access pattern */ + /* Skip offset over blocks of other processes */ + h5offset[0] = ((nbytes_xfer*pio_mpi_nprocs_g)/(snbytes*buf_size))*buf_size; + h5offset[1] = ((nbytes_xfer*pio_mpi_nprocs_g)%(snbytes*buf_size))/buf_size; + + } /* end else */ + hrc = H5Soffset_simple(h5dset_space_id, h5offset); + VRFY((hrc >= 0), "H5Soffset_simple"); + + /* Write the buffer out */ + hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, + h5dset_space_id, h5dxpl, buffer); + VRFY((hrc >= 0), "H5Dread"); + + /* Increment number of bytes transferred */ + nbytes_xfer += buf_size*blk_size; + + } /* end else */ + break; + } /* switch (parms->io_type) */ + + /* Verify raw data, if asked */ if (parms->verify) { /* Verify data read */ - unsigned char *ucharptr = (unsigned char *)buffer; - size_t i; + unsigned char *ucharptr = (unsigned char *)buffer; + size_t i; int nerror=0; - for (i = 0; i < buf_size; ++i){ - if (*ucharptr++ != pio_mpi_rank_g) { + for (i = 0; i < bsize; ++i){ + if (*ucharptr++ != pio_mpi_rank_g+1) { if (++nerror < 20){ /* report at most 20 errors */ HDprint_rank(output); HDfprintf(output, "read data error, expected (%Hd), " - "got (%Hd)\n", - (long_long)pio_mpi_rank_g, - (long_long)*(ucharptr-1)); + "got (%Hd)\n", + (long_long)pio_mpi_rank_g+1, + (long_long)*(ucharptr-1)); } /* end if */ } /* end if */ } /* end for */ @@ -1367,69 +2125,90 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets, HDfprintf(output, "total read data errors=%d\n", nerror); } /* end if */ - } /* if (parms->verify) */ + } /* if (parms->verify) */ - } /* end while */ + } /* end while */ - /* Stop "raw data" read timer */ - set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, STOP); + /* Stop "raw data" read timer */ + set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, STOP); - /* Calculate read time */ + /* Calculate read time */ - /* Close dataset. Only HDF5 needs to do an explicit close. */ - if (parms->io_type == PHDF5) { - hrc = H5Dclose(h5ds_id); + /* Close dataset. Only HDF5 needs to do an explicit close. */ + if (parms->io_type == PHDF5) { + hrc = H5Dclose(h5ds_id); - if (hrc < 0) { - fprintf(stderr, "HDF5 Dataset Close failed\n"); - GOTOERROR(FAIL); - } + if (hrc < 0) { + fprintf(stderr, "HDF5 Dataset Close failed\n"); + GOTOERROR(FAIL); + } - h5ds_id = -1; - } /* end if */ + h5ds_id = -1; + } /* end if */ } /* end for */ done: /* release MPI-I/O objects */ if (parms->io_type == MPIO) { - /* Free file type */ - mrc = MPI_Type_free( &mpi_file_type ); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); - - /* Free buffer type */ - mrc = MPI_Type_free( &mpi_blk_type ); - VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + /* 1D dataspace */ + if (parms->dim2d==0){ + /* Free file type */ + mrc = MPI_Type_free( &mpi_file_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free buffer type */ + mrc = MPI_Type_free( &mpi_blk_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + } /* end if */ + /* 2D dataspace */ + else { + /* Free file type */ + mrc = MPI_Type_free( &mpi_cont_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free partial buffer type */ + mrc = MPI_Type_free( &contig_cont ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free file type */ + mrc = MPI_Type_free( &mpi_inter_type ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + + /* Free partial buffer type */ + mrc = MPI_Type_free( &contig_inter ); + VRFY((mrc==MPI_SUCCESS), "MPIO_TYPE_FREE"); + } /* end else */ } /* end if */ /* release HDF5 objects */ if (h5dset_space_id != -1) { - hrc = H5Sclose(h5dset_space_id); - if (hrc < 0){ - fprintf(stderr, "HDF5 Dataset Space Close failed\n"); - ret_code = FAIL; - } else { - h5dset_space_id = -1; - } + hrc = H5Sclose(h5dset_space_id); + if (hrc < 0){ + fprintf(stderr, "HDF5 Dataset Space Close failed\n"); + ret_code = FAIL; + } else { + h5dset_space_id = -1; + } } if (h5mem_space_id != -1) { - hrc = H5Sclose(h5mem_space_id); - if (hrc < 0) { - fprintf(stderr, "HDF5 Memory Space Close failed\n"); - ret_code = FAIL; - } else { - h5mem_space_id = -1; - } + hrc = H5Sclose(h5mem_space_id); + if (hrc < 0) { + fprintf(stderr, "HDF5 Memory Space Close failed\n"); + ret_code = FAIL; + } else { + h5mem_space_id = -1; + } } if (h5dxpl != -1) { - hrc = H5Pclose(h5dxpl); - if (hrc < 0) { - fprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n"); - ret_code = FAIL; - } else { - h5dxpl = -1; - } + hrc = H5Pclose(h5dxpl); + if (hrc < 0) { + fprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n"); + ret_code = FAIL; + } else { + h5dxpl = -1; + } } return ret_code; @@ -1442,7 +2221,7 @@ done: * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 * Modifications: */ -static herr_t + static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags) { int ret_code = SUCCESS, mrc; @@ -1451,115 +2230,115 @@ do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags) hbool_t use_gpfs = FALSE; /* use GPFS hints */ switch (param->io_type) { - case POSIXIO: - if (flags & (PIO_CREATE | PIO_WRITE)) - fd->posixfd = POSIXCREATE(fname); - else - fd->posixfd = POSIXOPEN(fname, O_RDONLY); - - if (fd->posixfd < 0 ) { - fprintf(stderr, "POSIX File Open failed(%s)\n", fname); - GOTOERROR(FAIL); - } - - - /* The perils of POSIX I/O in a parallel environment. The problem is: - * - * - Process n opens a file with truncation and then starts - * writing to the file. - * - Process m also opens the file with truncation, but after - * process n has already started to write to the file. Thus, - * all of the stuff process n wrote is now lost. - */ - MPI_Barrier(pio_comm_g); - - break; - - case MPIO: - if (flags & (PIO_CREATE | PIO_WRITE)) { - MPI_File_delete(fname, h5_io_info_g); - mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_CREATE | MPI_MODE_RDWR, - h5_io_info_g, &fd->mpifd); - - if (mrc != MPI_SUCCESS) { - fprintf(stderr, "MPI File Open failed(%s)\n", fname); - GOTOERROR(FAIL); - } - - /*since MPI_File_open with MPI_MODE_CREATE does not truncate */ - /*filesize , set size to 0 explicitedly. */ - mrc = MPI_File_set_size(fd->mpifd, (MPI_Offset)0); - - if (mrc != MPI_SUCCESS) { - fprintf(stderr, "MPI_File_set_size failed\n"); - GOTOERROR(FAIL); - } - } else { - mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_RDONLY, - h5_io_info_g, &fd->mpifd); - - if (mrc != MPI_SUCCESS) { - fprintf(stderr, "MPI File Open failed(%s)\n", fname); - GOTOERROR(FAIL); - } - } - - break; - - case PHDF5: - acc_tpl = H5Pcreate(H5P_FILE_ACCESS); - if (acc_tpl < 0) { - fprintf(stderr, "HDF5 Property List Create failed\n"); - GOTOERROR(FAIL); - } - - /* Use the appropriate VFL driver */ - if(param->h5_use_mpi_posix) { - /* Set the file driver to the MPI-posix driver */ - hrc = H5Pset_fapl_mpiposix(acc_tpl, pio_comm_g, use_gpfs); - if (hrc < 0) { - fprintf(stderr, "HDF5 Property List Set failed\n"); - GOTOERROR(FAIL); - } - } /* end if */ - else { - /* Set the file driver to the MPI-I/O driver */ - hrc = H5Pset_fapl_mpio(acc_tpl, pio_comm_g, h5_io_info_g); - if (hrc < 0) { - fprintf(stderr, "HDF5 Property List Set failed\n"); - GOTOERROR(FAIL); - } - } /* end else */ - - /* Set the alignment of objects in HDF5 file */ - hrc = H5Pset_alignment(acc_tpl, param->h5_thresh, param->h5_align); - if (hrc < 0) { - fprintf(stderr, "HDF5 Property List Set failed\n"); - GOTOERROR(FAIL); - } - - /* create the parallel file */ - if (flags & (PIO_CREATE | PIO_WRITE)) { - fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); - } else { - fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, acc_tpl); - } - - hrc = H5Pclose(acc_tpl); - - if (fd->h5fd < 0) { - fprintf(stderr, "HDF5 File Create failed(%s)\n", fname); - GOTOERROR(FAIL); - } - - /* verifying the close of the acc_tpl */ - if (hrc < 0) { - fprintf(stderr, "HDF5 Property List Close failed\n"); - GOTOERROR(FAIL); - } - - break; - } + case POSIXIO: + if (flags & (PIO_CREATE | PIO_WRITE)) + fd->posixfd = POSIXCREATE(fname); + else + fd->posixfd = POSIXOPEN(fname, O_RDONLY); + + if (fd->posixfd < 0 ) { + fprintf(stderr, "POSIX File Open failed(%s)\n", fname); + GOTOERROR(FAIL); + } + + + /* The perils of POSIX I/O in a parallel environment. The problem is: + * + * - Process n opens a file with truncation and then starts + * writing to the file. + * - Process m also opens the file with truncation, but after + * process n has already started to write to the file. Thus, + * all of the stuff process n wrote is now lost. + */ + MPI_Barrier(pio_comm_g); + + break; + + case MPIO: + if (flags & (PIO_CREATE | PIO_WRITE)) { + MPI_File_delete(fname, h5_io_info_g); + mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_CREATE | MPI_MODE_RDWR, + h5_io_info_g, &fd->mpifd); + + if (mrc != MPI_SUCCESS) { + fprintf(stderr, "MPI File Open failed(%s)\n", fname); + GOTOERROR(FAIL); + } + + /*since MPI_File_open with MPI_MODE_CREATE does not truncate */ + /*filesize , set size to 0 explicitedly. */ + mrc = MPI_File_set_size(fd->mpifd, (MPI_Offset)0); + + if (mrc != MPI_SUCCESS) { + fprintf(stderr, "MPI_File_set_size failed\n"); + GOTOERROR(FAIL); + } + } else { + mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_RDONLY, + h5_io_info_g, &fd->mpifd); + + if (mrc != MPI_SUCCESS) { + fprintf(stderr, "MPI File Open failed(%s)\n", fname); + GOTOERROR(FAIL); + } + } + + break; + + case PHDF5: + acc_tpl = H5Pcreate(H5P_FILE_ACCESS); + if (acc_tpl < 0) { + fprintf(stderr, "HDF5 Property List Create failed\n"); + GOTOERROR(FAIL); + } + + /* Use the appropriate VFL driver */ + if(param->h5_use_mpi_posix) { + /* Set the file driver to the MPI-posix driver */ + hrc = H5Pset_fapl_mpiposix(acc_tpl, pio_comm_g, use_gpfs); + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } + } /* end if */ + else { + /* Set the file driver to the MPI-I/O driver */ + hrc = H5Pset_fapl_mpio(acc_tpl, pio_comm_g, h5_io_info_g); + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } + } /* end else */ + + /* Set the alignment of objects in HDF5 file */ + hrc = H5Pset_alignment(acc_tpl, param->h5_thresh, param->h5_align); + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Set failed\n"); + GOTOERROR(FAIL); + } + + /* create the parallel file */ + if (flags & (PIO_CREATE | PIO_WRITE)) { + fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); + } else { + fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, acc_tpl); + } + + hrc = H5Pclose(acc_tpl); + + if (fd->h5fd < 0) { + fprintf(stderr, "HDF5 File Create failed(%s)\n", fname); + GOTOERROR(FAIL); + } + + /* verifying the close of the acc_tpl */ + if (hrc < 0) { + fprintf(stderr, "HDF5 Property List Close failed\n"); + GOTOERROR(FAIL); + } + + break; + } done: return ret_code; @@ -1572,45 +2351,45 @@ done: * Programmer: Albert Cheng, Bill Wendling, 2001/12/13 * Modifications: */ -static herr_t + static herr_t do_fclose(iotype iot, file_descr *fd /*out*/) { herr_t ret_code = SUCCESS, hrc; int mrc = 0, rc = 0; switch (iot) { - case POSIXIO: - rc = POSIXCLOSE(fd->posixfd); + case POSIXIO: + rc = POSIXCLOSE(fd->posixfd); - if (rc != 0){ - fprintf(stderr, "POSIX File Close failed\n"); - GOTOERROR(FAIL); - } + if (rc != 0){ + fprintf(stderr, "POSIX File Close failed\n"); + GOTOERROR(FAIL); + } - fd->posixfd = -1; - break; + fd->posixfd = -1; + break; - case MPIO: - mrc = MPI_File_close(&fd->mpifd); + case MPIO: + mrc = MPI_File_close(&fd->mpifd); - if (mrc != MPI_SUCCESS){ - fprintf(stderr, "MPI File close failed\n"); - GOTOERROR(FAIL); - } + if (mrc != MPI_SUCCESS){ + fprintf(stderr, "MPI File close failed\n"); + GOTOERROR(FAIL); + } - fd->mpifd = MPI_FILE_NULL; - break; + fd->mpifd = MPI_FILE_NULL; + break; - case PHDF5: - hrc = H5Fclose(fd->h5fd); + case PHDF5: + hrc = H5Fclose(fd->h5fd); - if (hrc < 0) { - fprintf(stderr, "HDF5 File Close failed\n"); - GOTOERROR(FAIL); - } + if (hrc < 0) { + fprintf(stderr, "HDF5 File Close failed\n"); + GOTOERROR(FAIL); + } - fd->h5fd = -1; - break; + fd->h5fd = -1; + break; } done: @@ -1627,31 +2406,31 @@ done: * Programmer: Albert Cheng 2001/12/12 * Modifications: */ -static void + static void do_cleanupfile(iotype iot, char *fname) { if (pio_mpi_rank_g != 0) - return; + return; if (clean_file_g == -1) - clean_file_g = (getenv("HDF5_NOCLEANUP")==NULL) ? 1 : 0; + clean_file_g = (getenv("HDF5_NOCLEANUP")==NULL) ? 1 : 0; if (clean_file_g){ - switch (iot){ - case POSIXIO: - remove(fname); - break; - case MPIO: - case PHDF5: - MPI_File_delete(fname, h5_io_info_g); - break; - } + switch (iot){ + case POSIXIO: + remove(fname); + break; + case MPIO: + case PHDF5: + MPI_File_delete(fname, h5_io_info_g); + break; + } } } #ifdef H5_HAVE_GPFS - /* Descriptions here come from the IBM GPFS Manual */ +/* Descriptions here come from the IBM GPFS Manual */ /* * Function: gpfs_access_range @@ -1682,12 +2461,12 @@ do_cleanupfile(iotype iot, char *fname) * Programmer: Bill Wendling, 03. June 2002 * Modifications: */ -static void + static void gpfs_access_range(int handle, off_t start, off_t length, int is_write) { struct { - gpfsFcntlHeader_t hdr; - gpfsAccessRange_t access; + gpfsFcntlHeader_t hdr; + gpfsAccessRange_t access; } access_range; access_range.hdr.totalLength = sizeof(access_range); @@ -1700,10 +2479,10 @@ gpfs_access_range(int handle, off_t start, off_t length, int is_write) access_range.access.isWrite = is_write; if (gpfs_fcntl(handle, &access_range) != 0) { - fprintf(stderr, - "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n", - errno, access_range.hdr.errorOffset); - exit(EXIT_FAILURE); + fprintf(stderr, + "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n", + errno, access_range.hdr.errorOffset); + exit(EXIT_FAILURE); } } @@ -1731,12 +2510,12 @@ gpfs_access_range(int handle, off_t start, off_t length, int is_write) * Programmer: Bill Wendling, 03. June 2002 * Modifications: */ -static void + static void gpfs_free_range(int handle, off_t start, off_t length) { struct { - gpfsFcntlHeader_t hdr; - gpfsFreeRange_t range; + gpfsFcntlHeader_t hdr; + gpfsFreeRange_t range; } free_range; /* Issue the invalidate hint */ @@ -1749,10 +2528,10 @@ gpfs_free_range(int handle, off_t start, off_t length) free_range.range.length = length; if (gpfs_fcntl(handle, &free_range) != 0) { - fprintf(stderr, - "gpfs_fcntl free range failed for range %d:%d. errno=%d errorOffset=%d\n", - start, length, errno, free_range.hdr.errorOffset); - exit(EXIT_FAILURE); + fprintf(stderr, + "gpfs_fcntl free range failed for range %d:%d. errno=%d errorOffset=%d\n", + start, length, errno, free_range.hdr.errorOffset); + exit(EXIT_FAILURE); } } @@ -1775,12 +2554,12 @@ gpfs_free_range(int handle, off_t start, off_t length) * Programmer: Bill Wendling, 03. June 2002 * Modifications: */ -static void + static void gpfs_clear_file_cache(int handle) { struct { - gpfsFcntlHeader_t hdr; - gpfsClearFileCache_t clear; + gpfsFcntlHeader_t hdr; + gpfsClearFileCache_t clear; } clear_cache; clear_cache.hdr.totalLength = sizeof(clear_cache); @@ -1790,10 +2569,10 @@ gpfs_clear_file_cache(int handle) clear_cache.clear.structType = GPFS_CLEAR_FILE_CACHE; if (gpfs_fcntl(handle, &clear_cache) != 0) { - fprintf(stderr, - "gpfs_fcntl clear file cache directive failed. errno=%d errorOffset=%d\n", - errno, clear_cache.hdr.errorOffset); - exit(EXIT_FAILURE); + fprintf(stderr, + "gpfs_fcntl clear file cache directive failed. errno=%d errorOffset=%d\n", + errno, clear_cache.hdr.errorOffset); + exit(EXIT_FAILURE); } } @@ -1821,12 +2600,12 @@ gpfs_clear_file_cache(int handle) * Programmer: Bill Wendling, 03. June 2002 * Modifications: */ -static void + static void gpfs_cancel_hints(int handle) { struct { - gpfsFcntlHeader_t hdr; - gpfsCancelHints_t cancel; + gpfsFcntlHeader_t hdr; + gpfsCancelHints_t cancel; } cancel_hints; cancel_hints.hdr.totalLength = sizeof(cancel_hints); @@ -1836,10 +2615,10 @@ gpfs_cancel_hints(int handle) cancel_hints.cancel.structType = GPFS_CANCEL_HINTS; if (gpfs_fcntl(handle, &cancel_hints) != 0) { - fprintf(stderr, - "gpfs_fcntl cancel hints directive failed. errno=%d errorOffset=%d\n", - errno, cancel_hints.hdr.errorOffset); - exit(EXIT_FAILURE); + fprintf(stderr, + "gpfs_fcntl cancel hints directive failed. errno=%d errorOffset=%d\n", + errno, cancel_hints.hdr.errorOffset); + exit(EXIT_FAILURE); } } @@ -1867,12 +2646,12 @@ gpfs_cancel_hints(int handle) * Programmer: Bill Wendling, 28. May 2002 * Modifications: */ -static void + static void gpfs_start_data_shipping(int handle, int num_insts) { struct { - gpfsFcntlHeader_t hdr; - gpfsDataShipStart_t start; + gpfsFcntlHeader_t hdr; + gpfsDataShipStart_t start; } ds_start; ds_start.hdr.totalLength = sizeof(ds_start); @@ -1884,10 +2663,10 @@ gpfs_start_data_shipping(int handle, int num_insts) ds_start.start.reserved = 0; if (gpfs_fcntl(handle, &ds_start) != 0) { - fprintf(stderr, - "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n", - errno, ds_start.hdr.errorOffset); - exit(EXIT_FAILURE); + fprintf(stderr, + "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n", + errno, ds_start.hdr.errorOffset); + exit(EXIT_FAILURE); } } @@ -1910,14 +2689,14 @@ gpfs_start_data_shipping(int handle, int num_insts) * Programmer: Bill Wendling, 10. Jul 2002 * Modifications: */ -static void + static void gpfs_start_data_ship_map(int handle, int partition_size, int agent_count, - int *agent_node_num) + int *agent_node_num) { int i; struct { - gpfsFcntlHeader_t hdr; - gpfsDataShipMap_t map; + gpfsFcntlHeader_t hdr; + gpfsDataShipMap_t map; } ds_map; ds_map.hdr.totalLength = sizeof(ds_map); @@ -1929,13 +2708,13 @@ gpfs_start_data_ship_map(int handle, int partition_size, int agent_count, ds_map.map.agentCount = agent_count; for (i = 0; i < agent_count; ++i) - ds_map.map.agentNodeNumber[i] = agent_node_num[i]; + ds_map.map.agentNodeNumber[i] = agent_node_num[i]; if (gpfs_fcntl(handle, &ds_map) != 0) { - fprintf(stderr, - "gpfs_fcntl DS map directive failed. errno=%d errorOffset=%d\n", - errno, ds_map.hdr.errorOffset); - exit(EXIT_FAILURE); + fprintf(stderr, + "gpfs_fcntl DS map directive failed. errno=%d errorOffset=%d\n", + errno, ds_map.hdr.errorOffset); + exit(EXIT_FAILURE); } } @@ -1963,12 +2742,12 @@ gpfs_start_data_ship_map(int handle, int partition_size, int agent_count, * Programmer: Bill Wendling, 28. May 2002 * Modifications: */ -static void + static void gpfs_stop_data_shipping(int handle) { struct { - gpfsFcntlHeader_t hdr; - gpfsDataShipStop_t stop; + gpfsFcntlHeader_t hdr; + gpfsDataShipStop_t stop; } ds_stop; ds_stop.hdr.totalLength = sizeof(ds_stop); @@ -1978,9 +2757,9 @@ gpfs_stop_data_shipping(int handle) ds_stop.stop.structType = GPFS_DATA_SHIP_STOP; if (gpfs_fcntl(handle, &ds_stop) != 0) - fprintf(stderr, - "gpfs_fcntl DS stop directive failed. errno=%d errorOffset=%d\n", - errno, ds_stop.hdr.errorOffset); + fprintf(stderr, + "gpfs_fcntl DS stop directive failed. errno=%d errorOffset=%d\n", + errno, ds_stop.hdr.errorOffset); } /* @@ -1991,20 +2770,20 @@ gpfs_stop_data_shipping(int handle) * Programmer: Bill Wendling, 03. June 2002 * Modifications: */ -static void + static void gpfs_invalidate_file_cache(const char *filename) { int handle; struct { - gpfsFcntlHeader_t hdr; - gpfsClearFileCache_t inv; + gpfsFcntlHeader_t hdr; + gpfsClearFileCache_t inv; } inv_cache_hint; /* Open the file. If the open fails, the file cannot be cached. */ handle = open(filename, O_RDONLY, 0); if (handle == -1) - return; + return; /* Issue the invalidate hint */ inv_cache_hint.hdr.totalLength = sizeof(inv_cache_hint); @@ -2014,21 +2793,21 @@ gpfs_invalidate_file_cache(const char *filename) inv_cache_hint.inv.structType = GPFS_CLEAR_FILE_CACHE; if (gpfs_fcntl(handle, &inv_cache_hint) != 0) { - fprintf(stderr, - "gpfs_fcntl clear cache hint failed for file '%s'.", - filename); - fprintf(stderr, " errno=%d errorOffset=%d\n", - errno, inv_cache_hint.hdr.errorOffset); - exit(1); + fprintf(stderr, + "gpfs_fcntl clear cache hint failed for file '%s'.", + filename); + fprintf(stderr, " errno=%d errorOffset=%d\n", + errno, inv_cache_hint.hdr.errorOffset); + exit(1); } /* Close the file */ if (close(handle) == -1) { - fprintf(stderr, - "could not close file '%s' after flushing file cache, ", - filename); - fprintf(stderr, "errno=%d\n", errno); - exit(1); + fprintf(stderr, + "could not close file '%s' after flushing file cache, ", + filename); + fprintf(stderr, "errno=%d\n", errno); + exit(1); } } @@ -2038,51 +2817,51 @@ gpfs_invalidate_file_cache(const char *filename) #if 0 /* H5_HAVE_GPFS isn't defined...stub functions */ -static void + static void gpfs_access_range(int UNUSED handle, off_t UNUSED start, off_t UNUSED length, - int UNUSED is_write) + int UNUSED is_write) { return; } -static void + static void gpfs_free_range(int UNUSED handle, off_t UNUSED start, off_t UNUSED length) { return; } -static void + static void gpfs_clear_file_cache(int UNUSED handle) { return; } -static void + static void gpfs_cancel_hints(int UNUSED handle) { return; } -static void + static void gpfs_start_data_shipping(int UNUSED handle, int UNUSED num_insts) { return; } -static void + static void gpfs_stop_data_shipping(int UNUSED handle) { return; } -static void + static void gpfs_start_data_ship_map(int UNUSED handle, int UNUSED partition_size, - int UNUSED agent_count, int UNUSED *agent_node_num) + int UNUSED agent_count, int UNUSED *agent_node_num) { return; } -static void + static void gpfs_invalidate_file_cache(const char UNUSED *filename) { return; @@ -2097,7 +2876,7 @@ gpfs_invalidate_file_cache(const char UNUSED *filename) * pure time spent in MPI_File code. */ int MPI_File_read_at(MPI_File fh, MPI_Offset offset, void *buf, - int count, MPI_Datatype datatype, MPI_Status *status) + int count, MPI_Datatype datatype, MPI_Status *status) { int err; set_time(timer_g, HDF5_MPI_READ, START); @@ -2118,7 +2897,7 @@ int MPI_File_read_at_all(MPI_File fh, MPI_Offset offset, void *buf, } int MPI_File_write_at(MPI_File fh, MPI_Offset offset, void *buf, - int count, MPI_Datatype datatype, MPI_Status *status) + int count, MPI_Datatype datatype, MPI_Status *status) { int err; set_time(timer_g, HDF5_MPI_WRITE, START); @@ -2128,7 +2907,7 @@ int MPI_File_write_at(MPI_File fh, MPI_Offset offset, void *buf, } int MPI_File_write_at_all(MPI_File fh, MPI_Offset offset, void *buf, - int count, MPI_Datatype datatype, MPI_Status *status) + int count, MPI_Datatype datatype, MPI_Status *status) { int err; set_time(timer_g, HDF5_MPI_WRITE, START); diff --git a/perform/pio_perf.c b/perform/pio_perf.c index cde0545..d436e5c 100644 --- a/perform/pio_perf.c +++ b/perform/pio_perf.c @@ -116,9 +116,9 @@ static const char *progname = "h5perf"; * adding more, make sure that they don't clash with each other. */ #if 1 -static const char *s_opts = "a:A:B:cCd:D:e:F:hi:Imno:p:P:stT:wx:X:"; +static const char *s_opts = "a:A:B:cCd:D:e:F:ghi:Imno:p:P:stT:wx:X:"; #else -static const char *s_opts = "a:A:bB:cCd:D:e:F:hi:Imno:p:P:stT:wx:X:"; +static const char *s_opts = "a:A:bB:cCd:D:e:F:ghi:Imno:p:P:stT:wx:X:"; #endif /* 1 */ static struct long_options l_opts[] = { { "align", require_arg, 'a' }, @@ -161,6 +161,13 @@ static struct long_options l_opts[] = { { "debu", require_arg, 'D' }, { "deb", require_arg, 'D' }, { "de", require_arg, 'D' }, + { "geometry", no_arg, 'g' }, + { "geometr", no_arg, 'g' }, + { "geomet", no_arg, 'g' }, + { "geome", no_arg, 'g' }, + { "geom", no_arg, 'g' }, + { "geo", no_arg, 'g' }, + { "ge", no_arg, 'g' }, { "help", no_arg, 'h' }, { "hel", no_arg, 'h' }, { "he", no_arg, 'h' }, @@ -270,7 +277,7 @@ struct options { const char *output_file; /* file to print report to */ long num_dsets; /* number of datasets */ long num_files; /* number of files */ - size_t num_bpp; /* number of bytes per proc per dset */ + off_t num_bpp; /* number of bytes per proc per dset */ int num_iters; /* number of iterations */ int max_num_procs; /* maximum number of processes to use */ int min_num_procs; /* minimum number of processes to use */ @@ -279,6 +286,7 @@ struct options { size_t blk_size; /* Block size */ unsigned interleaved; /* Interleaved vs. contiguous blocks */ unsigned collective; /* Collective vs. independent I/O */ + unsigned dim2d; /* 1D vs. 2D */ int print_times; /* print times as well as throughputs */ int print_raw; /* print raw data throughput info */ off_t h5_alignment; /* alignment in HDF5 file */ @@ -408,6 +416,7 @@ finish: * Return: Nothing * Programmer: Bill Wendling, 30. October 2001 * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) */ static void run_test_loop(struct options *opts) @@ -415,6 +424,7 @@ run_test_loop(struct options *opts) parameters parms; int num_procs; int doing_pio; /* if this process is doing PIO */ + off_t snbytes; parms.num_files = opts->num_files; parms.num_dsets = opts->num_dsets; @@ -422,6 +432,7 @@ run_test_loop(struct options *opts) parms.blk_size = opts->blk_size; parms.interleaved = opts->interleaved; parms.collective = opts->collective; + parms.dim2d = opts->dim2d; parms.h5_align = opts->h5_alignment; parms.h5_thresh = opts->h5_threshold; parms.h5_use_chunks = opts->h5_use_chunks; @@ -449,16 +460,34 @@ run_test_loop(struct options *opts) for (buf_size = opts->min_xfer_size; buf_size <= opts->max_xfer_size; buf_size <<= 1) { parms.buf_size = buf_size; - parms.num_bytes = (off_t)opts->num_bpp*parms.num_procs; - print_indent(1); - output_report("Transfer Buffer Size: %ld bytes, File size: %.2f MBs\n", - buf_size, - ((double)parms.num_dsets * (double)parms.num_bytes) - / ONE_MB); - print_indent(1); - output_report(" # of files: %ld, # of datasets: %ld, dataset size: %.2f MBs\n", - parms.num_files, parms.num_dsets, (double)parms.num_bytes/ONE_MB); + if (parms.dim2d){ + parms.num_bytes = (off_t)pow((double)(opts->num_bpp*parms.num_procs),2); + if (parms.interleaved) + output_report("Transfer Buffer Size: %ldx%ld bytes, File size: %.2f MBs\n", + buf_size, opts->blk_size, + ((double)parms.num_dsets * (double)parms.num_bytes) + / ONE_MB); + else + output_report("Transfer Buffer Size: %ldx%ld bytes, File size: %.2f MBs\n", + opts->blk_size, buf_size, + ((double)parms.num_dsets * (double)parms.num_bytes) + / ONE_MB); + + print_indent(1); + output_report(" # of files: %ld, # of datasets: %ld, dataset size: %.2fx%.2f KBs\n", + parms.num_files, parms.num_dsets, (double)(opts->num_bpp*parms.num_procs)/ONE_KB, + (double)(opts->num_bpp*parms.num_procs)/ONE_KB); + } + else{ + parms.num_bytes = (off_t)opts->num_bpp*parms.num_procs; + output_report("Transfer Buffer Size: %ld bytes, File size: %.2f MBs\n", + buf_size,((double)parms.num_dsets * (double)parms.num_bytes) / ONE_MB); + + print_indent(1); + output_report(" # of files: %ld, # of datasets: %ld, dataset size: %.2f MBs\n", + parms.num_files, parms.num_dsets, (double)(opts->num_bpp*parms.num_procs)/ONE_MB); + } if (opts->io_types & PIO_POSIX) run_test(POSIXIO, parms, opts); @@ -1008,9 +1037,6 @@ report_parameters(struct options *opts) HDfprintf(output, "rank %d: IO API=", rank); print_io_api(opts->io_types); - HDfprintf(output, "rank %d: Number of bytes per process per dataset=", rank); - recover_size_and_print((long_long)opts->num_bpp, "\n"); - HDfprintf(output, "rank %d: Number of files=%Hd\n", rank, (long_long)opts->num_files); HDfprintf(output, "rank %d: Number of datasets=%Hd\n", rank, @@ -1020,21 +1046,60 @@ report_parameters(struct options *opts) HDfprintf(output, "rank %d: Number of processes=%d:%d\n", rank, opts->min_num_procs, opts->max_num_procs); - HDfprintf(output, "rank %d: Size of dataset(s)=", rank); - recover_size_and_print((long_long)(opts->num_bpp * opts->min_num_procs), ":"); - recover_size_and_print((long_long)(opts->num_bpp * opts->max_num_procs), "\n"); - - HDfprintf(output, "rank %d: File size=", rank); - recover_size_and_print((long_long)(opts->num_bpp * opts->min_num_procs - * opts->num_dsets), ":"); - recover_size_and_print((long_long)(opts->num_bpp * opts->max_num_procs - * opts->num_dsets), "\n"); - - HDfprintf(output, "rank %d: Transfer buffer size=", rank); - recover_size_and_print((long_long)opts->min_xfer_size, ":"); - recover_size_and_print((long_long)opts->max_xfer_size, "\n"); - HDfprintf(output, "rank %d: Block size=", rank); - recover_size_and_print((long_long)opts->blk_size, "\n"); + if (opts->dim2d){ + HDfprintf(output, "rank %d: Number of bytes per process per dataset=", rank); + recover_size_and_print((long_long)(opts->num_bpp * opts->num_bpp * opts->min_num_procs), ":"); + recover_size_and_print((long_long)(opts->num_bpp * opts->num_bpp * opts->max_num_procs), "\n"); + + HDfprintf(output, "rank %d: Size of dataset(s)=", rank); + recover_size_and_print((long_long)(opts->num_bpp * opts->min_num_procs), "x"); + recover_size_and_print((long_long)(opts->num_bpp * opts->min_num_procs), ":"); + recover_size_and_print((long_long)(opts->num_bpp * opts->max_num_procs), "x"); + recover_size_and_print((long_long)(opts->num_bpp * opts->max_num_procs), "\n"); + + HDfprintf(output, "rank %d: File size=", rank); + recover_size_and_print((long_long)(pow(opts->num_bpp * opts->min_num_procs,2) + * opts->num_dsets), ":"); + recover_size_and_print((long_long)(pow(opts->num_bpp * opts->max_num_procs,2) + * opts->num_dsets), "\n"); + + HDfprintf(output, "rank %d: Transfer buffer size=", rank); + if(opts->interleaved){ + recover_size_and_print((long_long)opts->min_xfer_size, "x"); + recover_size_and_print((long_long)opts->blk_size, ":"); + recover_size_and_print((long_long)opts->max_xfer_size, "x"); + recover_size_and_print((long_long)opts->blk_size, "\n"); + } + else{ + recover_size_and_print((long_long)opts->blk_size, "x"); + recover_size_and_print((long_long)opts->min_xfer_size, ":"); + recover_size_and_print((long_long)opts->blk_size, "x"); + recover_size_and_print((long_long)opts->max_xfer_size, "\n"); + } + HDfprintf(output, "rank %d: Block size=", rank); + recover_size_and_print((long_long)opts->blk_size, "x"); + recover_size_and_print((long_long)opts->blk_size, "\n"); + } + else{ + HDfprintf(output, "rank %d: Number of bytes per process per dataset=", rank); + recover_size_and_print((long_long)opts->num_bpp, "\n"); + + HDfprintf(output, "rank %d: Size of dataset(s)=", rank); + recover_size_and_print((long_long)(opts->num_bpp * opts->min_num_procs), ":"); + recover_size_and_print((long_long)(opts->num_bpp * opts->max_num_procs), "\n"); + + HDfprintf(output, "rank %d: File size=", rank); + recover_size_and_print((long_long)(opts->num_bpp * opts->min_num_procs + * opts->num_dsets), ":"); + recover_size_and_print((long_long)(opts->num_bpp * opts->max_num_procs + * opts->num_dsets), "\n"); + + HDfprintf(output, "rank %d: Transfer buffer size=", rank); + recover_size_and_print((long_long)opts->min_xfer_size, ":"); + recover_size_and_print((long_long)opts->max_xfer_size, "\n"); + HDfprintf(output, "rank %d: Block size=", rank); + recover_size_and_print((long_long)opts->blk_size, "\n"); + } HDfprintf(output, "rank %d: Block Pattern in Dataset=", rank); if(opts->interleaved) @@ -1048,6 +1113,12 @@ report_parameters(struct options *opts) else HDfprintf(output, "Independent\n"); + HDfprintf(output, "rank %d: Geometry=", rank); + if(opts->dim2d) + HDfprintf(output, "2D\n"); + else + HDfprintf(output, "1D\n"); + HDfprintf(output, "rank %d: VFL used for HDF5 I/O=", rank); if(opts->h5_use_mpi_posix) HDfprintf(output, "MPI-posix driver\n"); @@ -1081,6 +1152,7 @@ report_parameters(struct options *opts) * Return: Pointer to an OPTIONS structure * Programmer: Bill Wendling, 31. October 2001 * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) */ static struct options * parse_command_line(int argc, char *argv[]) @@ -1103,6 +1175,7 @@ parse_command_line(int argc, char *argv[]) cl_opts->blk_size = 128 * ONE_KB; /* Default to writing 128K per block */ cl_opts->interleaved = 0; /* Default to contiguous blocks in dataset */ cl_opts->collective = 0; /* Default to independent I/O access */ + cl_opts->dim2d = 0; /* Default to 1D */ cl_opts->print_times = FALSE; /* Printing times is off by default */ cl_opts->print_raw = FALSE; /* Printing raw data throughput is off by default */ cl_opts->h5_alignment = 1; /* No alignment for HDF5 objects by default */ @@ -1233,6 +1306,9 @@ parse_command_line(int argc, char *argv[]) case 'F': cl_opts->num_files = atoi(opt_arg); break; + case 'g': + cl_opts->dim2d = 1; + break; case 'i': cl_opts->num_iters = atoi(opt_arg); break; @@ -1354,6 +1430,7 @@ parse_size_directive(const char *size) * Return: Nothing * Programmer: Bill Wendling, 31. October 2001 * Modifications: + * Added 2D testing (Christian Chilan, 10. August 2005) */ static void usage(const char *prog) @@ -1384,6 +1461,7 @@ usage(const char *prog) printf(" -e S, --num-bytes=S Number of bytes per process per dataset\n"); printf(" [default: 256K]\n"); printf(" -F N, --num-files=N Number of files [default: 1]\n"); + printf(" -g, --geometry Use 2D geometry [default: 1D]\n"); printf(" -i N, --num-iterations=N Number of iterations to perform [default: 1]\n"); printf(" -I, --interleaved Interleaved block I/O (see below for example)\n"); printf(" [default: Contiguous block I/O]\n"); diff --git a/perform/pio_perf.h b/perform/pio_perf.h index cc0fce8..a8fa0da 100644 --- a/perform/pio_perf.h +++ b/perform/pio_perf.h @@ -47,6 +47,7 @@ typedef struct parameters_ { size_t blk_size; /* Block size */ unsigned interleaved; /* Interleaved vs. contiguous blocks */ unsigned collective; /* Collective vs. independent I/O */ + unsigned dim2d; /* 1D vs. 2D */ hsize_t h5_align; /* HDF5 object alignment */ hsize_t h5_thresh; /* HDF5 object alignment threshold */ int h5_use_chunks; /* Make HDF5 dataset chunked */ |