From 326486ef7c01fa5daf3d737337dae5c0f1072eba Mon Sep 17 00:00:00 2001 From: jhendersonHDF Date: Thu, 24 Aug 2023 10:54:13 -0500 Subject: [PATCH] Skip atomicity tests for OpenMPI major versions < 5 (#3421) --- release_docs/RELEASE.txt | 9 ++ testpar/t_2Gio.c | 338 --------------------------------------- testpar/testphdf5.c | 9 ++ 3 files changed, 18 insertions(+), 338 deletions(-) diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index d817117810a..70e8d6e8fc0 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -769,6 +769,15 @@ Bug Fixes since HDF5-1.14.0 release Testing ------- + - Disabled running of MPI Atomicity tests for OpenMPI major versions < 5 + + Support for MPI atomicity operations is not implemented for major + versions of OpenMPI less than version 5. This would cause the MPI + atomicity tests for parallel HDF5 to sporadically fail when run + with OpenMPI. Testphdf5 now checks if OpenMPI is being used and will + skip running the atomicity tests if the major version of OpenMPI is + < 5. + - Fixed a testing failure in testphdf5 on Cray machines On some Cray machines, what appears to be a bug in Cray MPICH was causing diff --git a/testpar/t_2Gio.c b/testpar/t_2Gio.c index e651b1b2693..1edec566aa4 100644 --- a/testpar/t_2Gio.c +++ b/testpar/t_2Gio.c @@ -4200,344 +4200,6 @@ no_collective_cause_tests(void) return; } -/* - * Test consistency semantics of atomic mode - */ - -/* - * Example of using the parallel HDF5 library to create a dataset, - * where process 0 writes and the other processes read at the same - * time. If atomic mode is set correctly, the other processes should - * read the old values in the dataset or the new ones. - */ - -void -dataset_atomicity(void) -{ - hid_t fid; /* HDF5 file ID */ - hid_t acc_tpl; /* File access templates */ - hid_t sid; /* Dataspace ID */ - hid_t dataset1; /* Dataset IDs */ - hsize_t dims[MAX_RANK]; /* dataset dim sizes */ - int *write_buf = NULL; /* data buffer */ - int *read_buf = NULL; /* data buffer */ - int buf_size; - hid_t dataset2; - hid_t file_dataspace; /* File dataspace ID */ - hid_t mem_dataspace; /* Memory dataspace ID */ - hsize_t start[MAX_RANK]; - hsize_t stride[MAX_RANK]; - hsize_t count[MAX_RANK]; - hsize_t block[MAX_RANK]; - const char *filename; - herr_t ret; /* Generic return value */ - int mpi_size, mpi_rank; - int i, j, k; - hbool_t atomicity = FALSE; - MPI_Comm comm = test_comm; - MPI_Info info = MPI_INFO_NULL; - - dim0 = 64; - dim1 = 32; - filename = GetTestParameters(); - if (facc_type != FACC_MPIO) { - printf("Atomicity tests will not work without the MPIO VFD\n"); - return; - } - if (VERBOSE_MED) - printf("atomic writes to file %s\n", filename); - - /* set up MPI parameters */ - MPI_Comm_size(test_comm, &mpi_size); - MPI_Comm_rank(test_comm, &mpi_rank); - - buf_size = dim0 * dim1; - /* allocate memory for data buffer */ - write_buf = (int *)calloc((size_t)buf_size, sizeof(int)); - VRFY((write_buf != NULL), "write_buf calloc succeeded"); - /* allocate memory for data buffer */ - read_buf = (int *)calloc((size_t)buf_size, sizeof(int)); - VRFY((read_buf != NULL), "read_buf calloc succeeded"); - - /* setup file access template */ - acc_tpl = create_faccess_plist(comm, info, facc_type); - VRFY((acc_tpl >= 0), ""); - - /* 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), "H5Pclose succeeded"); - - /* setup dimensionality object */ - dims[0] = (hsize_t)dim0; - dims[1] = (hsize_t)dim1; - sid = H5Screate_simple(MAX_RANK, dims, NULL); - VRFY((sid >= 0), "H5Screate_simple succeeded"); - - /* create datasets */ - dataset1 = H5Dcreate2(fid, DATASETNAME5, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - VRFY((dataset1 >= 0), "H5Dcreate2 succeeded"); - - dataset2 = H5Dcreate2(fid, DATASETNAME6, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - VRFY((dataset2 >= 0), "H5Dcreate2 succeeded"); - - /* initialize datasets to 0s */ - if (0 == mpi_rank) { - ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf); - VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); - - ret = H5Dwrite(dataset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf); - VRFY((ret >= 0), "H5Dwrite dataset2 succeeded"); - } - - ret = H5Dclose(dataset1); - VRFY((ret >= 0), "H5Dclose succeeded"); - ret = H5Dclose(dataset2); - VRFY((ret >= 0), "H5Dclose succeeded"); - ret = H5Sclose(sid); - VRFY((ret >= 0), "H5Sclose succeeded"); - ret = H5Fclose(fid); - VRFY((ret >= 0), "H5Fclose succeeded"); - - MPI_Barrier(comm); - - /* make sure setting atomicity fails on a serial file ID */ - /* file locking allows only one file open (serial) for writing */ - if (MAINPROCESS) { - fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT); - VRFY((fid >= 0), "H5Fopen succeeded"); - } - - /* should fail */ - ret = H5Fset_mpi_atomicity(fid, TRUE); - VRFY((ret == FAIL), "H5Fset_mpi_atomicity failed"); - - if (MAINPROCESS) { - ret = H5Fclose(fid); - VRFY((ret >= 0), "H5Fclose succeeded"); - } - - MPI_Barrier(comm); - - /* setup file access template */ - acc_tpl = create_faccess_plist(comm, info, facc_type); - VRFY((acc_tpl >= 0), ""); - - /* open the file collectively */ - fid = H5Fopen(filename, H5F_ACC_RDWR, acc_tpl); - VRFY((fid >= 0), "H5Fopen succeeded"); - - /* Release file-access template */ - ret = H5Pclose(acc_tpl); - VRFY((ret >= 0), "H5Pclose succeeded"); - - ret = H5Fset_mpi_atomicity(fid, TRUE); - VRFY((ret >= 0), "H5Fset_mpi_atomicity succeeded"); - - /* open dataset1 (contiguous case) */ - dataset1 = H5Dopen2(fid, DATASETNAME5, H5P_DEFAULT); - VRFY((dataset1 >= 0), "H5Dopen2 succeeded"); - - if (0 == mpi_rank) { - for (i = 0; i < buf_size; i++) { - write_buf[i] = 5; - } - } - else { - for (i = 0; i < buf_size; i++) { - read_buf[i] = 8; - } - } - - /* check that the atomicity flag is set */ - ret = H5Fget_mpi_atomicity(fid, &atomicity); - VRFY((ret >= 0), "atomcity get failed"); - VRFY((atomicity == TRUE), "atomcity set failed"); - - MPI_Barrier(comm); - - /* Process 0 writes contiguously to the entire dataset */ - if (0 == mpi_rank) { - ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf); - VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); - } - /* The other processes read the entire dataset */ - else { - ret = H5Dread(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, read_buf); - VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded"); - } - - if (VERBOSE_MED) { - i = 0; - j = 0; - k = 0; - for (i = 0; i < dim0; i++) { - printf("\n"); - for (j = 0; j < dim1; j++) - printf("%d ", read_buf[k++]); - } - } - - /* The processes that read the dataset must either read all values - as 0 (read happened before process 0 wrote to dataset 1), or 5 - (read happened after process 0 wrote to dataset 1) */ - if (0 != mpi_rank) { - int compare = read_buf[0]; - - VRFY((compare == 0 || compare == 5), - "Atomicity Test Failed Process %d: Value read should be 0 or 5\n"); - for (i = 1; i < buf_size; i++) { - if (read_buf[i] != compare) { - printf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank, i, - read_buf[i], compare); - nerrors++; - } - } - } - - ret = H5Dclose(dataset1); - VRFY((ret >= 0), "H5D close succeeded"); - - /* release data buffers */ - if (write_buf) - free(write_buf); - if (read_buf) - free(read_buf); - - /* open dataset2 (non-contiguous case) */ - dataset2 = H5Dopen2(fid, DATASETNAME6, H5P_DEFAULT); - VRFY((dataset2 >= 0), "H5Dopen2 succeeded"); - - /* allocate memory for data buffer */ - write_buf = (int *)calloc((size_t)buf_size, sizeof(int)); - VRFY((write_buf != NULL), "write_buf calloc succeeded"); - /* allocate memory for data buffer */ - read_buf = (int *)calloc((size_t)buf_size, sizeof(int)); - VRFY((read_buf != NULL), "read_buf calloc succeeded"); - - for (i = 0; i < buf_size; i++) { - write_buf[i] = 5; - } - for (i = 0; i < buf_size; i++) { - read_buf[i] = 8; - } - - atomicity = FALSE; - /* check that the atomicity flag is set */ - ret = H5Fget_mpi_atomicity(fid, &atomicity); - VRFY((ret >= 0), "atomcity get failed"); - VRFY((atomicity == TRUE), "atomcity set failed"); - - block[0] = (hsize_t)(dim0 / mpi_size) - 1; - block[1] = (hsize_t)(dim1 / mpi_size) - 1; - stride[0] = block[0] + 1; - stride[1] = block[1] + 1; - count[0] = (hsize_t)mpi_size; - count[1] = (hsize_t)mpi_size; - start[0] = 0; - start[1] = 0; - - /* create a file dataspace */ - 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"); - - /* create a memory dataspace */ - mem_dataspace = H5Screate_simple(MAX_RANK, dims, NULL); - VRFY((mem_dataspace >= 0), ""); - - ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); - VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); - - MPI_Barrier(comm); - - /* Process 0 writes to the dataset */ - if (0 == mpi_rank) { - ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, write_buf); - VRFY((ret >= 0), "H5Dwrite dataset2 succeeded"); - } - /* All processes wait for the write to finish. This works because - atomicity is set to true */ - MPI_Barrier(comm); - /* The other processes read the entire dataset */ - if (0 != mpi_rank) { - ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, read_buf); - VRFY((ret >= 0), "H5Dread dataset2 succeeded"); - } - - if (VERBOSE_MED) { - if (mpi_rank == 1) { - i = 0; - j = 0; - k = 0; - for (i = 0; i < dim0; i++) { - printf("\n"); - for (j = 0; j < dim1; j++) - printf("%d ", read_buf[k++]); - } - printf("\n"); - } - } - - /* The processes that read the dataset must either read all values - as 5 (read happened after process 0 wrote to dataset 1) */ - if (0 != mpi_rank) { - int compare; - i = 0; - j = 0; - k = 0; - - compare = 5; - - for (i = 0; i < dim0; i++) { - if ((hsize_t)i >= (hsize_t)mpi_rank * (block[0] + 1)) { - break; - } - if (((hsize_t)i + 1) % (block[0] + 1) == 0) { - k += dim1; - continue; - } - for (j = 0; j < dim1; j++) { - if ((hsize_t)j >= (hsize_t)mpi_rank * (block[1] + 1)) { - H5_CHECKED_ASSIGN(k, int, (hsize_t)dim1 - (hsize_t)mpi_rank * (block[1] + 1) + (hsize_t)k, - hsize_t); - break; - } - if (((hsize_t)j + 1) % (block[1] + 1) == 0) { - k++; - continue; - } - else if (compare != read_buf[k]) { - printf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank, - k, read_buf[k], compare); - nerrors++; - } - k++; - } - } - } - - ret = H5Dclose(dataset2); - VRFY((ret >= 0), "H5Dclose succeeded"); - ret = H5Sclose(file_dataspace); - VRFY((ret >= 0), "H5Sclose succeeded"); - ret = H5Sclose(mem_dataspace); - VRFY((ret >= 0), "H5Sclose succeeded"); - - /* release data buffers */ - if (write_buf) - free(write_buf); - if (read_buf) - free(read_buf); - - ret = H5Fclose(fid); - VRFY((ret >= 0), "H5Fclose succeeded"); -} - /* Function: dense_attr_test * * Purpose: Test cases for writing dense attributes in parallel diff --git a/testpar/testphdf5.c b/testpar/testphdf5.c index 430b8a69884..ed0510cd55a 100644 --- a/testpar/testphdf5.c +++ b/testpar/testphdf5.c @@ -487,6 +487,14 @@ main(int argc, char **argv) AddTest((mpi_size < 2) ? "-fiodc" : "fiodc", file_image_daisy_chain_test, NULL, "file image ops daisy chain", NULL); + /* Atomicity operations are not supported for OpenMPI versions < major + * version 5 and will sporadically fail. + */ +#if defined(OPEN_MPI) && defined(OMPI_MAJOR_VERSION) && (OMPI_MAJOR_VERSION < 5) + if (MAINPROCESS) + printf("OpenMPI major version is < 5. Atomicity tests will be skipped due to support for atomicity " + "operations not being implemented.\n"); +#else if ((mpi_size < 2) && MAINPROCESS) { printf("Atomicity tests need at least 2 processes to participate\n"); printf("8 is more recommended.. Atomicity tests will be skipped \n"); @@ -497,6 +505,7 @@ main(int argc, char **argv) else if (mpi_size >= 2 && facc_type == FACC_MPIO) { AddTest("atomicity", dataset_atomicity, NULL, "dataset atomic updates", PARATESTFILE); } +#endif AddTest("denseattr", test_dense_attr, NULL, "Store Dense Attributes", PARATESTFILE);