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authorQuincey Koziol <koziol@hdfgroup.org>2003-06-05 20:05:52 (GMT)
committerQuincey Koziol <koziol@hdfgroup.org>2003-06-05 20:05:52 (GMT)
commitc134146b3ee754526e9b976de799226b6469de47 (patch)
tree0a4ac12de7093ab917ccc9836098dea80b848150 /testpar
parent51b427848d17421d3922741e46cf0c0a6f2ce40b (diff)
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[svn-r6975] Purpose:
Bug fix Description: Don't attempt to perform collective I/O on chunked datasets. Platforms tested: FreeBSD 4.8 (sleipnir) w/parallel h5committested
Diffstat (limited to 'testpar')
-rw-r--r--testpar/t_dset.c432
-rw-r--r--testpar/testphdf5.c6
-rw-r--r--testpar/testphdf5.h2
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);