diff options
Diffstat (limited to 'testpar')
| -rw-r--r-- | testpar/t_dset.c | 432 | ||||
| -rw-r--r-- | testpar/testphdf5.c | 6 | ||||
| -rw-r--r-- | testpar/testphdf5.h | 2 |
3 files changed, 440 insertions, 0 deletions
diff --git a/testpar/t_dset.c b/testpar/t_dset.c index a425793..97f193a 100644 --- a/testpar/t_dset.c +++ b/testpar/t_dset.c @@ -1454,3 +1454,435 @@ extend_readInd(char *filename) if (data_array2) free(data_array2); if (data_origin1) free(data_origin1); } + +/* + * Part 3--Collective read/write for extendible datasets. + */ + +/* + * Example of using the parallel HDF5 library to create two extendible + * datasets in one HDF5 file with collective parallel MPIO access support. + * The Datasets are of sizes (number-of-mpi-processes x dim0) x dim1. + * Each process controls only a slab of size dim0 x dim1 within each + * dataset. + */ + +void +extend_writeAll(char *filename) +{ + hid_t fid; /* HDF5 file ID */ + hid_t acc_tpl; /* File access templates */ + hid_t xfer_plist; /* Dataset transfer properties list */ + hid_t sid; /* Dataspace ID */ + hid_t file_dataspace; /* File dataspace ID */ + hid_t mem_dataspace; /* memory dataspace ID */ + hid_t dataset1, dataset2; /* Dataset ID */ + hbool_t use_gpfs = FALSE; /* Use GPFS hints */ + hsize_t dims[RANK]; /* dataset dim sizes */ + hsize_t max_dims[RANK] = + {H5S_UNLIMITED, H5S_UNLIMITED}; /* dataset maximum dim sizes */ + DATATYPE *data_array1 = NULL; /* data buffer */ + hsize_t chunk_dims[RANK]; /* chunk sizes */ + hid_t dataset_pl; /* dataset create prop. list */ + + hssize_t start[RANK]; /* for hyperslab setting */ + hsize_t count[RANK]; /* for hyperslab setting */ + hsize_t stride[RANK]; /* for hyperslab setting */ + hsize_t block[RANK]; /* for hyperslab setting */ + + herr_t ret; /* Generic return value */ + int mpi_size, mpi_rank; + + MPI_Comm comm = MPI_COMM_WORLD; + MPI_Info info = MPI_INFO_NULL; + + if (verbose) + printf("Extend independent write test on file %s\n", filename); + + /* set up MPI parameters */ + MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + + /* setup chunk-size. Make sure sizes are > 0 */ + chunk_dims[0] = chunkdim0; + chunk_dims[1] = chunkdim1; + + /* allocate memory for data buffer */ + data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); + + /* ------------------- + * START AN HDF5 FILE + * -------------------*/ + /* setup file access template */ + acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); + VRFY((acc_tpl >= 0), ""); + +/* Reduce the number of metadata cache slots, so that there are cache + * collisions during the raw data I/O on the chunked dataset. This stresses + * the metadata cache and tests for cache bugs. -QAK + */ +{ + int mdc_nelmts; + size_t rdcc_nelmts; + size_t rdcc_nbytes; + double rdcc_w0; + + ret=H5Pget_cache(acc_tpl,&mdc_nelmts,&rdcc_nelmts,&rdcc_nbytes,&rdcc_w0); + VRFY((ret >= 0), "H5Pget_cache succeeded"); + mdc_nelmts=4; + ret=H5Pset_cache(acc_tpl,mdc_nelmts,rdcc_nelmts,rdcc_nbytes,rdcc_w0); + VRFY((ret >= 0), "H5Pset_cache succeeded"); +} + + /* create the file collectively */ + fid=H5Fcreate(filename,H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl); + VRFY((fid >= 0), "H5Fcreate succeeded"); + + /* Release file-access template */ + ret=H5Pclose(acc_tpl); + VRFY((ret >= 0), ""); + + + /* -------------------------------------------------------------- + * Define the dimensions of the overall datasets and create them. + * ------------------------------------------------------------- */ + + /* set up dataset storage chunk sizes and creation property list */ + if (verbose) + printf("chunks[]=%lu,%lu\n", (unsigned long)chunk_dims[0], (unsigned long)chunk_dims[1]); + dataset_pl = H5Pcreate(H5P_DATASET_CREATE); + VRFY((dataset_pl >= 0), "H5Pcreate succeeded"); + ret = H5Pset_chunk(dataset_pl, RANK, chunk_dims); + VRFY((ret >= 0), "H5Pset_chunk succeeded"); + + /* setup dimensionality object */ + /* start out with no rows, extend it later. */ + dims[0] = dims[1] = 0; + sid = H5Screate_simple (RANK, dims, max_dims); + VRFY((sid >= 0), "H5Screate_simple succeeded"); + + /* create an extendible dataset collectively */ + dataset1 = H5Dcreate(fid, DATASETNAME1, H5T_NATIVE_INT, sid, dataset_pl); + VRFY((dataset1 >= 0), "H5Dcreate succeeded"); + + /* create another extendible dataset collectively */ + dataset2 = H5Dcreate(fid, DATASETNAME2, H5T_NATIVE_INT, sid, dataset_pl); + VRFY((dataset2 >= 0), "H5Dcreate succeeded"); + + /* release resource */ + H5Sclose(sid); + H5Pclose(dataset_pl); + + + + /* ------------------------- + * Test writing to dataset1 + * -------------------------*/ + /* set up dimensions of the slab this process accesses */ + slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); + + /* put some trivial data in the data_array */ + dataset_fill(start, block, data_array1); + MESG("data_array initialized"); + if (verbose){ + MESG("data_array created"); + dataset_print(start, block, data_array1); + } + + /* create a memory dataspace independently */ + mem_dataspace = H5Screate_simple (RANK, block, NULL); + VRFY((mem_dataspace >= 0), ""); + + /* Extend its current dim sizes before writing */ + dims[0] = dim0; + dims[1] = dim1; + ret = H5Dextend (dataset1, dims); + VRFY((ret >= 0), "H5Dextend succeeded"); + + /* create a file dataspace independently */ + file_dataspace = H5Dget_space (dataset1); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); + ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); + + /* write data collectively */ + ret = H5Dwrite(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dwrite succeeded"); + + /* release resource */ + H5Sclose(file_dataspace); + H5Sclose(mem_dataspace); + H5Pclose(xfer_plist); + + + /* ------------------------- + * Test writing to dataset2 + * -------------------------*/ + /* set up dimensions of the slab this process accesses */ + slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); + + /* put some trivial data in the data_array */ + dataset_fill(start, block, data_array1); + MESG("data_array initialized"); + if (verbose){ + MESG("data_array created"); + dataset_print(start, block, data_array1); + } + + /* create a memory dataspace independently */ + mem_dataspace = H5Screate_simple (RANK, block, NULL); + VRFY((mem_dataspace >= 0), ""); + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); + ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); + + /* Try write to dataset2 beyond its current dim sizes. Should fail. */ + /* Temporary turn off auto error reporting */ + H5Eget_auto(&old_func, &old_client_data); + H5Eset_auto(NULL, NULL); + + /* create a file dataspace independently */ + file_dataspace = H5Dget_space (dataset2); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); + + /* write data independently. Should fail. */ + ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret < 0), "H5Dwrite failed as expected"); + + /* restore auto error reporting */ + H5Eset_auto(old_func, old_client_data); + H5Sclose(file_dataspace); + + /* Extend dataset2 and try again. Should succeed. */ + dims[0] = dim0; + dims[1] = dim1; + ret = H5Dextend (dataset2, dims); + VRFY((ret >= 0), "H5Dextend succeeded"); + + /* create a file dataspace independently */ + file_dataspace = H5Dget_space (dataset2); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); + + /* write data independently */ + ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dwrite succeeded"); + + /* release resource */ + ret=H5Sclose(file_dataspace); + VRFY((ret >= 0), "H5Sclose succeeded"); + ret=H5Sclose(mem_dataspace); + VRFY((ret >= 0), "H5Sclose succeeded"); + ret=H5Pclose(xfer_plist); + VRFY((ret >= 0), "H5Pclose succeeded"); + + + /* close dataset collectively */ + ret=H5Dclose(dataset1); + VRFY((ret >= 0), "H5Dclose1 succeeded"); + ret=H5Dclose(dataset2); + VRFY((ret >= 0), "H5Dclose2 succeeded"); + + /* close the file collectively */ + H5Fclose(fid); + + /* release data buffers */ + if (data_array1) free(data_array1); +} + +/* Example of using the parallel HDF5 library to read an extendible dataset */ +void +extend_readAll(char *filename) +{ + hid_t fid; /* HDF5 file ID */ + hid_t acc_tpl; /* File access templates */ + hid_t xfer_plist; /* Dataset transfer properties list */ + hid_t file_dataspace; /* File dataspace ID */ + hid_t mem_dataspace; /* memory dataspace ID */ + hid_t dataset1, dataset2; /* Dataset ID */ + hbool_t use_gpfs = FALSE; /* Use GPFS hints */ + hsize_t dims[RANK]; /* dataset dim sizes */ + DATATYPE *data_array1 = NULL; /* data buffer */ + DATATYPE *data_array2 = NULL; /* data buffer */ + DATATYPE *data_origin1 = NULL; /* expected data buffer */ + + hssize_t start[RANK]; /* for hyperslab setting */ + hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ + hsize_t block[RANK]; /* for hyperslab setting */ + + herr_t ret; /* Generic return value */ + int mpi_size, mpi_rank; + + MPI_Comm comm = MPI_COMM_WORLD; + MPI_Info info = MPI_INFO_NULL; + + if (verbose) + printf("Extend independent read test on file %s\n", filename); + + /* set up MPI parameters */ + MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + + /* allocate memory for data buffer */ + data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); + data_array2 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_array2 != NULL), "data_array2 malloc succeeded"); + data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded"); + + /* ------------------- + * OPEN AN HDF5 FILE + * -------------------*/ + /* setup file access template */ + acc_tpl = create_faccess_plist(comm, info, facc_type, use_gpfs); + VRFY((acc_tpl >= 0), ""); + + /* open the file collectively */ + fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl); + VRFY((fid >= 0), ""); + + /* Release file-access template */ + ret=H5Pclose(acc_tpl); + VRFY((ret >= 0), ""); + + /* open the dataset1 collectively */ + dataset1 = H5Dopen(fid, DATASETNAME1); + VRFY((dataset1 >= 0), ""); + + /* open another dataset collectively */ + dataset2 = H5Dopen(fid, DATASETNAME1); + VRFY((dataset2 >= 0), ""); + + /* Try extend dataset1 which is open RDONLY. Should fail. */ + /* first turn off auto error reporting */ + H5Eget_auto(&old_func, &old_client_data); + H5Eset_auto(NULL, NULL); + + file_dataspace = H5Dget_space (dataset1); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret=H5Sget_simple_extent_dims(file_dataspace, dims, NULL); + VRFY((ret > 0), "H5Sget_simple_extent_dims succeeded"); + dims[0]++; + ret=H5Dextend(dataset1, dims); + VRFY((ret < 0), "H5Dextend failed as expected"); + + /* restore auto error reporting */ + H5Eset_auto(old_func, old_client_data); + H5Sclose(file_dataspace); + + + /* Read dataset1 using BYROW pattern */ + /* set up dimensions of the slab this process accesses */ + slab_set(mpi_rank, mpi_size, start, count, stride, block, BYROW); + + /* create a file dataspace independently */ + file_dataspace = H5Dget_space (dataset1); + VRFY((file_dataspace >= 0), ""); + ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), ""); + + /* create a memory dataspace independently */ + mem_dataspace = H5Screate_simple (RANK, block, NULL); + VRFY((mem_dataspace >= 0), ""); + + /* fill dataset with test data */ + dataset_fill(start, block, data_origin1); + if (verbose){ + MESG("data_array created"); + dataset_print(start, block, data_array1); + } + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); + ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); + + /* read data collectively */ + ret = H5Dread(dataset1, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dread succeeded"); + + /* verify the read data with original expected data */ + ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); + VRFY((ret == 0), "dataset1 read verified correct"); + if (ret) nerrors++; + + H5Sclose(mem_dataspace); + H5Sclose(file_dataspace); + H5Pclose(xfer_plist); + + + /* Read dataset2 using BYCOL pattern */ + /* set up dimensions of the slab this process accesses */ + slab_set(mpi_rank, mpi_size, start, count, stride, block, BYCOL); + + /* create a file dataspace independently */ + file_dataspace = H5Dget_space (dataset2); + VRFY((file_dataspace >= 0), ""); + ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), ""); + + /* create a memory dataspace independently */ + mem_dataspace = H5Screate_simple (RANK, block, NULL); + VRFY((mem_dataspace >= 0), ""); + + /* fill dataset with test data */ + dataset_fill(start, block, data_origin1); + if (verbose){ + MESG("data_array created"); + dataset_print(start, block, data_array1); + } + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), "H5Pcreate xfer succeeded"); + ret=H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded"); + + /* read data collectively */ + ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dread succeeded"); + + /* verify the read data with original expected data */ + ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); + VRFY((ret == 0), "dataset2 read verified correct"); + if (ret) nerrors++; + + H5Sclose(mem_dataspace); + H5Sclose(file_dataspace); + H5Pclose(xfer_plist); + + /* close dataset collectively */ + ret=H5Dclose(dataset1); + VRFY((ret >= 0), ""); + ret=H5Dclose(dataset2); + VRFY((ret >= 0), ""); + + + /* close the file collectively */ + H5Fclose(fid); + + /* release data buffers */ + if (data_array1) free(data_array1); + if (data_array2) free(data_array2); + if (data_origin1) free(data_origin1); +} diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c index 473659a..6a4a0b2 100644 --- a/testpar/testphdf5.c +++ b/testpar/testphdf5.c @@ -400,6 +400,9 @@ int main(int argc, char **argv) MPI_BANNER("extendible dataset independent write..."); extend_writeInd(filenames[2]); + + MPI_BANNER("extendible dataset collective write..."); + extend_writeAll(filenames[2]); } else{ MPI_BANNER("write tests skipped"); @@ -414,6 +417,9 @@ int main(int argc, char **argv) MPI_BANNER("extendible dataset independent read..."); extend_readInd(filenames[2]); + + MPI_BANNER("extendible dataset collective read..."); + extend_readAll(filenames[2]); } else{ MPI_BANNER("read tests skipped"); diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h index 4f3066f..ccf0191 100644 --- a/testpar/testphdf5.h +++ b/testpar/testphdf5.h @@ -134,9 +134,11 @@ void test_split_comm_access(char *filename); void dataset_writeInd(char *filename); void dataset_writeAll(char *filename); void extend_writeInd(char *filename); +void extend_writeAll(char *filename); void dataset_readInd(char *filename); void dataset_readAll(char *filename); void extend_readInd(char *filename); +void extend_readAll(char *filename); void compact_dataset(char *filename); int dataset_vrfy(hssize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE *dataset, DATATYPE *original); |