From 8aa520584463a5151699dc5768bcdef39f5564a6 Mon Sep 17 00:00:00 2001 From: "M. Scot Breitenfeld" Date: Mon, 18 Dec 2017 13:42:09 -0600 Subject: Optimized version of avoid truncate patch. --- src/H5FDmpio.c | 198 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ src/H5FDprivate.h | 3 + src/H5Fint.c | 11 +++ 3 files changed, 212 insertions(+) diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index f594d8e..3fe6ed9 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -56,6 +56,7 @@ static char H5FD_mpi_native_g[] = "native"; * library to determine whether the file is empty, truncated, or okay. The MPIO * driver doesn't bother to keep it updated since it's an expensive operation. */ +#if 0 /* original version */ /* JRM */ typedef struct H5FD_mpio_t { H5FD_t pub; /*public stuff, must be first */ MPI_File f; /*MPIO file handle */ @@ -68,6 +69,26 @@ typedef struct H5FD_mpio_t { haddr_t last_eoa; /* Last known end-of-address marker */ haddr_t local_eof; /* Local end-of-file address for each process */ } H5FD_mpio_t; +#else /* modified version */ /* JRM */ +typedef struct H5FD_mpio_t { + H5FD_t pub; /*public stuff, must be first */ + MPI_File f; /*MPIO file handle */ + MPI_Comm comm; /*communicator */ + MPI_Info info; /*file information */ + int mpi_rank; /* This process's rank */ + int mpi_size; /* Total number of processes */ + haddr_t eof; /*end-of-file marker */ + haddr_t eoa; /*end-of-address marker */ + haddr_t last_eoa; /* Last known end-of-address marker */ + haddr_t local_eof; /* Local end-of-file address for each process */ + herr_t do_pre_trunc_barrier; /* hack to allow us to skip */ + /* unnecessary barriers in */ + /* H5FD_mpio_trucate() without a VFD */ + /* API change. This should be removed */ + /* as soon as be make the necessary */ + /* VFD API change. */ +} H5FD_mpio_t; +#endif /* modified version */ /* JRM */ /* Private Prototypes */ @@ -1039,6 +1060,11 @@ H5FD_mpio_open(const char *name, unsigned flags, hid_t fapl_id, file->eof = H5FD_mpi_MPIOff_to_haddr(size); file->local_eof = file->eof; +#if 1 /* JRM */ + /* Mark initial barriers in H5FD_mpio_truncate() as necessary */ + file->do_pre_trunc_barrier = TRUE; +#endif /* JRM */ + /* Set return value */ ret_value=(H5FD_t*)file; @@ -1930,6 +1956,7 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5FD_mpio_flush() */ +#if 0 /* original version */ /*------------------------------------------------------------------------- * Function: H5FD_mpio_truncate @@ -1996,6 +2023,177 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5FD_mpio_truncate() */ +#else /* modified versin */ + + +/*------------------------------------------------------------------------- + * Function: H5FD_mark_pre_trunc_barrier_unecessary + * + * Purpose: Hack to allow us to avoid most unnecessary barriers + * prior in H5FD_mpio_truncate(). + * + * This function should be deleted when next we modify the + * VFD interface. This change should allow us to tell the + * truncate function to omit the initial barrier if no + * file I/O has occurred since the last barrier. + * + * Return: void + * + * + * Programmer: John Mainzer + * 12/14/17 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +void +H5FD_mpio_mark_pre_trunc_barrier_unecessary(H5FD_t *_file) +{ + H5FD_mpio_t *file = (H5FD_mpio_t*)_file; + + FUNC_ENTER_NOAPI_NOINIT_NOERR + + HDassert(file); + HDassert(H5FD_MPIO == file->pub.driver_id); + + file->do_pre_trunc_barrier = FALSE; + + FUNC_LEAVE_NOAPI_VOID + +} /* end H5FD_mpio_mark_pre_trunc_barrier_unecessary() */ + + +/*------------------------------------------------------------------------- + * Function: H5FD_mpio_truncate + * + * Purpose: Make certain the file's size matches it's allocated size + * + * This is a little sticky in the mpio case, as it is not + * easy for us to track the current EOF by extracting it from + * write calls. + * + * Instead, we first check to see if the eoa has changed since + * the last call to this function. If it has, we call + * MPI_File_get_size() to determine the current EOF, and + * only call MPI_File_set_size() if this value disagrees + * with the current eoa. + * + * Return: Success: Non-negative + * Failure: Negative + * + * Programmer: Quincey Koziol + * January 31, 2008 + * + * Changes: Heavily reworked to avoid unnecessary MPI_File_set_size() + * calls. The hope is that these calls are superfluous in the + * typical case, allowing us to avoid truncates most of the + * time. + * + * The basic idea is to query the file system to get the + * current eof, and only truncate if the file systems + * conception of the eof disagrees with our eoa. + * + * JRM -- 10/27/17 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_mpio_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_UNUSED closing) +{ + H5FD_mpio_t *file = (H5FD_mpio_t*)_file; + herr_t ret_value = SUCCEED; + + FUNC_ENTER_NOAPI_NOINIT + +#ifdef H5FDmpio_DEBUG + if(H5FD_mpio_Debug[(int)'t']) + HDfprintf(stdout, "Entering %s\n", FUNC); +#endif + HDassert(file); + HDassert(H5FD_MPIO == file->pub.driver_id); + + if ( !H5F_addr_eq(file->eoa, file->last_eoa) ) { + + int mpi_code; /* mpi return code */ + MPI_Offset size; + MPI_Offset needed_eof; + + /* In principle, it is possible for the size returned by the + * call to MPI_File_get_size() to depend on whether writes from + * all proceeses have completed at the time process 0 makes the + * call. + * + * In practice, most (all?) truncate calls will come after a barrier + * and with no interviening writes to the file (with the possible + * exception of sueprblock / superblock extension message updates). + * + * Unfortunately, the current VFD API doesn't let us pass in a + * flag indicating whether this particular call is unnecessary. + * To work around this, I have added the new function + * H5FD_mpio_mark_pre_trunc_barrier_unecessary() allow us to + * set a flag in H5FD_mpio_t indicating that we can skip the + * barrier. + * + * This is a pretty ugly hack, but until we revise the VFD API, + * it is about the best we can do. + */ + if (file->do_pre_trunc_barrier) { + if (MPI_SUCCESS!= (mpi_code=MPI_Barrier(file->comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed(1)", mpi_code) + } + + /* Only processor p0 will get the filesize and broadcast it. */ + if (file->mpi_rank == 0) { + if (MPI_SUCCESS != (mpi_code=MPI_File_get_size(file->f, &size))) + HMPI_GOTO_ERROR(FAIL, "MPI_File_get_size failed", mpi_code) + } /* end if */ + + /* Broadcast file size */ + if(MPI_SUCCESS != (mpi_code = MPI_Bcast(&size, (int)sizeof(MPI_Offset), + MPI_BYTE, 0, file->comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code) + + if(H5FD_mpi_haddr_to_MPIOff(file->eoa, &needed_eof) < 0) + HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, \ + "cannot convert from haddr_t to MPI_Offset") + + if (size != needed_eof) /* eoa != eof. Set eof to eoa */ { + + /* Extend the file's size */ + if(MPI_SUCCESS != (mpi_code=MPI_File_set_size(file->f, needed_eof))) + HMPI_GOTO_ERROR(FAIL, "MPI_File_set_size failed", mpi_code) + + /* In general, we must wait until all processes have finished + * the truncate before any process can continue, since it is + * possible that a process would write at the end of the + * file, and this write would be discarded by the truncate. + * + * While this is an issue for a user initiated flush, it may + * not be an issue at file close. If so, we may be able to + * optimize out the following barrier in that case. + */ + if(MPI_SUCCESS != (mpi_code = MPI_Barrier(file->comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) + } + + /* Update the 'last' eoa value */ + file->last_eoa = file->eoa; + } /* end if */ + +done: + file->do_pre_trunc_barrier = TRUE; + +#ifdef H5FDmpio_DEBUG + if(H5FD_mpio_Debug[(int)'t']) + HDfprintf(stdout, "Leaving %s\n", FUNC); +#endif + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5FD_mpio_truncate() */ + +#endif /* modified version */ + /*------------------------------------------------------------------------- * Function: H5FD_mpio_mpi_rank diff --git a/src/H5FDprivate.h b/src/H5FDprivate.h index e758951..f7be327 100644 --- a/src/H5FDprivate.h +++ b/src/H5FDprivate.h @@ -203,6 +203,9 @@ H5_DLL int H5FD_mpi_get_rank(const H5FD_t *file); H5_DLL int H5FD_mpi_get_size(const H5FD_t *file); H5_DLL MPI_Comm H5FD_mpi_get_comm(const H5FD_t *_file); H5_DLL herr_t H5FD_get_mpi_info(H5FD_t *file, void** file_info); +#if 1 /* JRM */ +H5_DLL void H5FD_mpio_mark_pre_trunc_barrier_unecessary(H5FD_t *_file); +#endif /* JRM */ #endif /* H5_HAVE_PARALLEL */ #endif /* !_H5FDprivate_H */ diff --git a/src/H5Fint.c b/src/H5Fint.c index 8212eb5..25df964 100644 --- a/src/H5Fint.c +++ b/src/H5Fint.c @@ -1532,6 +1532,17 @@ H5F__flush_phase2(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t closi HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush metadata cache") /* Truncate the file to the current allocated size */ +#if 1 /* JRM */ +#ifdef H5_HAVE_PARALLEL + if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) { + /* Since we just returned from a call to H5AC_flush(), we just + * passed through a barrier. Hence we can skip the barrier on + * entry to the mpio file driver call below. + */ + H5FD_mpio_mark_pre_trunc_barrier_unecessary(f->shared->lf); + } +#endif /* H5_HAVE_PARALLEL */ +#endif /* JRM */ if(H5FD_truncate(f->shared->lf, meta_dxpl_id, closing) < 0) /* Push error, but keep going*/ HDONE_ERROR(H5E_FILE, H5E_WRITEERROR, FAIL, "low level truncate failed") -- cgit v0.12 From 4823abf3ee0d9df1c3f23ae7e36ce4d1d146afd6 Mon Sep 17 00:00:00 2001 From: mainzer Date: Sun, 11 Mar 2018 22:32:09 -0500 Subject: Removed commented out code from H5FDmpio.c, H5FDprivate.h and H5Fint.c Tested parallel (debug and production) and serial (production) --- src/H5FDmpio.c | 88 ------------------------------------------------------- src/H5FDprivate.h | 2 -- src/H5Fint.c | 2 -- 3 files changed, 92 deletions(-) diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index 3fe6ed9..08b1a3f 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -56,20 +56,6 @@ static char H5FD_mpi_native_g[] = "native"; * library to determine whether the file is empty, truncated, or okay. The MPIO * driver doesn't bother to keep it updated since it's an expensive operation. */ -#if 0 /* original version */ /* JRM */ -typedef struct H5FD_mpio_t { - H5FD_t pub; /*public stuff, must be first */ - MPI_File f; /*MPIO file handle */ - MPI_Comm comm; /*communicator */ - MPI_Info info; /*file information */ - int mpi_rank; /* This process's rank */ - int mpi_size; /* Total number of processes */ - haddr_t eof; /*end-of-file marker */ - haddr_t eoa; /*end-of-address marker */ - haddr_t last_eoa; /* Last known end-of-address marker */ - haddr_t local_eof; /* Local end-of-file address for each process */ -} H5FD_mpio_t; -#else /* modified version */ /* JRM */ typedef struct H5FD_mpio_t { H5FD_t pub; /*public stuff, must be first */ MPI_File f; /*MPIO file handle */ @@ -88,7 +74,6 @@ typedef struct H5FD_mpio_t { /* as soon as be make the necessary */ /* VFD API change. */ } H5FD_mpio_t; -#endif /* modified version */ /* JRM */ /* Private Prototypes */ @@ -1060,10 +1045,8 @@ H5FD_mpio_open(const char *name, unsigned flags, hid_t fapl_id, file->eof = H5FD_mpi_MPIOff_to_haddr(size); file->local_eof = file->eof; -#if 1 /* JRM */ /* Mark initial barriers in H5FD_mpio_truncate() as necessary */ file->do_pre_trunc_barrier = TRUE; -#endif /* JRM */ /* Set return value */ ret_value=(H5FD_t*)file; @@ -1956,75 +1939,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5FD_mpio_flush() */ -#if 0 /* original version */ - -/*------------------------------------------------------------------------- - * Function: H5FD_mpio_truncate - * - * Purpose: Make certain the file's size matches it's allocated size - * - * Return: Success: Non-negative - * Failure: Negative - * - * Programmer: Quincey Koziol - * January 31, 2008 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpio_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t H5_ATTR_UNUSED closing) -{ - H5FD_mpio_t *file = (H5FD_mpio_t*)_file; - herr_t ret_value = SUCCEED; - - FUNC_ENTER_NOAPI_NOINIT - -#ifdef H5FDmpio_DEBUG - if(H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "Entering %s\n", FUNC); -#endif - HDassert(file); - HDassert(H5FD_MPIO == file->pub.driver_id); - - /* Extend the file to make sure it's large enough, then sync. - * Unfortunately, keeping track of EOF is an expensive operation, so - * we can't just check whether EOFeoa > file->last_eoa) { - int mpi_code; /* mpi return code */ - MPI_Offset mpi_off; - - if(H5FD_mpi_haddr_to_MPIOff(file->eoa, &mpi_off) < 0) - HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "cannot convert from haddr_t to MPI_Offset") - - /* Extend the file's size */ - if(MPI_SUCCESS != (mpi_code = MPI_File_set_size(file->f, mpi_off))) - HMPI_GOTO_ERROR(FAIL, "MPI_File_set_size failed", mpi_code) - - /* Don't let any proc return until all have extended the file. - * (Prevents race condition where some processes go ahead and write - * more data to the file before all the processes have finished making - * it the shorter length, potentially truncating the file and dropping - * the new data written) - */ - if(MPI_SUCCESS != (mpi_code = MPI_Barrier(file->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) - - /* Update the 'last' eoa value */ - file->last_eoa = file->eoa; - } /* end if */ - -done: -#ifdef H5FDmpio_DEBUG - if(H5FD_mpio_Debug[(int)'t']) - HDfprintf(stdout, "Leaving %s\n", FUNC); -#endif - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpio_truncate() */ - -#else /* modified versin */ - /*------------------------------------------------------------------------- * Function: H5FD_mark_pre_trunc_barrier_unecessary @@ -2192,8 +2106,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5FD_mpio_truncate() */ -#endif /* modified version */ - /*------------------------------------------------------------------------- * Function: H5FD_mpio_mpi_rank diff --git a/src/H5FDprivate.h b/src/H5FDprivate.h index f7be327..f7cd931 100644 --- a/src/H5FDprivate.h +++ b/src/H5FDprivate.h @@ -203,9 +203,7 @@ H5_DLL int H5FD_mpi_get_rank(const H5FD_t *file); H5_DLL int H5FD_mpi_get_size(const H5FD_t *file); H5_DLL MPI_Comm H5FD_mpi_get_comm(const H5FD_t *_file); H5_DLL herr_t H5FD_get_mpi_info(H5FD_t *file, void** file_info); -#if 1 /* JRM */ H5_DLL void H5FD_mpio_mark_pre_trunc_barrier_unecessary(H5FD_t *_file); -#endif /* JRM */ #endif /* H5_HAVE_PARALLEL */ #endif /* !_H5FDprivate_H */ diff --git a/src/H5Fint.c b/src/H5Fint.c index 135d878..cc5931a 100644 --- a/src/H5Fint.c +++ b/src/H5Fint.c @@ -1788,7 +1788,6 @@ H5F__flush_phase2(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t closi HDONE_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush metadata cache") /* Truncate the file to the current allocated size */ -#if 1 /* JRM */ #ifdef H5_HAVE_PARALLEL if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) { /* Since we just returned from a call to H5AC_flush(), we just @@ -1798,7 +1797,6 @@ H5F__flush_phase2(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t closi H5FD_mpio_mark_pre_trunc_barrier_unecessary(f->shared->lf); } #endif /* H5_HAVE_PARALLEL */ -#endif /* JRM */ if(H5FD_truncate(f->shared->lf, meta_dxpl_id, closing) < 0) /* Push error, but keep going*/ HDONE_ERROR(H5E_FILE, H5E_WRITEERROR, FAIL, "low level truncate failed") -- cgit v0.12 From 6a53c14240872fcc82504fffaa010d754a8c73e0 Mon Sep 17 00:00:00 2001 From: lrknox Date: Mon, 12 Mar 2018 13:47:27 -0500 Subject: Add HDfree of vector, matrix_out and matrix_out1 previously HDmalloced in coll_write_test(). --- testpar/t_span_tree.c | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/testpar/t_span_tree.c b/testpar/t_span_tree.c index 20bc4ac..f4de133 100644 --- a/testpar/t_span_tree.c +++ b/testpar/t_span_tree.c @@ -255,7 +255,7 @@ void coll_write_test(int chunk_factor) #endif - int *matrix_out, *matrix_out1, *vector; + int *matrix_out = NULL, *matrix_out1 = NULL, *vector = NULL; int mpi_size,mpi_rank; @@ -662,6 +662,13 @@ void coll_write_test(int chunk_factor) ret = H5Fclose(file); VRFY((ret >= 0),""); + if (vector != NULL) + HDfree(vector); + if (matrix_out != NULL) + HDfree(matrix_out); + if (matrix_out1 != NULL) + HDfree(matrix_out1); + return ; } -- cgit v0.12 From 5d7c18fcfc14a53f4d6321460463357fbda61f4b Mon Sep 17 00:00:00 2001 From: lrknox Date: Mon, 12 Mar 2018 14:10:59 -0500 Subject: Remove comparison to NULL for variables to be freed. --- testpar/t_span_tree.c | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/testpar/t_span_tree.c b/testpar/t_span_tree.c index f4de133..3c836ad 100644 --- a/testpar/t_span_tree.c +++ b/testpar/t_span_tree.c @@ -662,11 +662,11 @@ void coll_write_test(int chunk_factor) ret = H5Fclose(file); VRFY((ret >= 0),""); - if (vector != NULL) + if (vector) HDfree(vector); - if (matrix_out != NULL) + if (matrix_out) HDfree(matrix_out); - if (matrix_out1 != NULL) + if (matrix_out1) HDfree(matrix_out1); return ; -- cgit v0.12 From 1a3beaadce81ad257d186c9dca8906577cce58b0 Mon Sep 17 00:00:00 2001 From: Richard Warren Date: Mon, 12 Mar 2018 16:17:10 -0400 Subject: Unify the test (t_bigio.c) between hdf5_1_10 and develop --- testpar/t_bigio.c | 395 +++++++++++------------------------------------------- 1 file changed, 79 insertions(+), 316 deletions(-) diff --git a/testpar/t_bigio.c b/testpar/t_bigio.c index 611ff1a..fdd3488 100644 --- a/testpar/t_bigio.c +++ b/testpar/t_bigio.c @@ -3,7 +3,10 @@ #include "testphdf5.h" #include "H5Dprivate.h" /* For Chunk tests */ -// int TestVerbosity = VERBO_LO; /* Default Verbosity is Low */ +/* FILENAME and filenames must have the same number of names */ +const char *FILENAME[2]={ "bigio_test.h5", + NULL + }; /* Constants definitions */ #define MAX_ERR_REPORT 10 /* Maximum number of errors reported */ @@ -38,7 +41,6 @@ typedef hsize_t B_DATATYPE; int facc_type = FACC_MPIO; /*Test file access type */ int dxfer_coll_type = DXFER_COLLECTIVE_IO; size_t bigcount = DXFER_BIGCOUNT; -char filename[20] = "bigio_test.h5"; int nerrors = 0; int mpi_size, mpi_rank; @@ -506,7 +508,7 @@ dataset_big_write(void) H5Pset_fapl_mpio(acc_tpl, MPI_COMM_WORLD, MPI_INFO_NULL); /* create the file collectively */ - fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); + fid = H5Fcreate(FILENAME[0], H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl); VRFY((fid >= 0), "H5Fcreate succeeded"); /* Release file-access template */ @@ -515,7 +517,8 @@ dataset_big_write(void) /* Each process takes a slabs of rows. */ - printf("\nTesting Dataset1 write by ROW\n"); + if (mpi_rank == 0) + HDprintf("\nTesting Dataset1 write by ROW\n"); /* Create a large dataset */ dims[0] = bigcount; dims[1] = mpi_size; @@ -563,21 +566,6 @@ dataset_big_write(void) VRFY((ret>= 0),"set independent IO collectively succeeded"); } - /* write data collectively */ - MESG("writeAll by Row"); - { - int j,k =0; - for (i=0; i < block[0]; i++){ - for (j=0; j < block[1]; j++){ - if(k < 10) { - printf("%lld ", wdata[k]); - k++; - } - } - } - printf("\n"); - } - ret = H5Dwrite(dataset, H5T_NATIVE_LLONG, mem_dataspace, file_dataspace, xfer_plist, wdata); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); @@ -591,9 +579,9 @@ dataset_big_write(void) VRFY((ret >= 0), "H5Dclose1 succeeded"); - /* Each process takes a slabs of cols. */ - printf("\nTesting Dataset2 write by COL\n"); + if (mpi_rank == 0) + HDprintf("\nTesting Dataset2 write by COL\n"); /* Create a large dataset */ dims[0] = bigcount; dims[1] = mpi_size; @@ -641,21 +629,6 @@ dataset_big_write(void) VRFY((ret>= 0),"set independent IO collectively succeeded"); } - /* write data collectively */ - MESG("writeAll by Col"); - { - int j,k =0; - for (i=0; i < block[0]; i++){ - for (j=0; j < block[1]; j++){ - if(k < 10) { - printf("%lld ", wdata[k]); - k++; - } - } - } - printf("\n"); - } - ret = H5Dwrite(dataset, H5T_NATIVE_LLONG, mem_dataspace, file_dataspace, xfer_plist, wdata); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); @@ -671,7 +644,8 @@ dataset_big_write(void) /* ALL selection */ - printf("\nTesting Dataset3 write select ALL proc 0, NONE others\n"); + if (mpi_rank == 0) + HDprintf("\nTesting Dataset3 write select ALL proc 0, NONE others\n"); /* Create a large dataset */ dims[0] = bigcount; dims[1] = 1; @@ -685,7 +659,7 @@ dataset_big_write(void) /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); - if(MAINPROCESS) { + if(mpi_rank == 0) { ret = H5Sselect_all(file_dataspace); VRFY((ret >= 0), "H5Sset_all succeeded"); } @@ -697,7 +671,7 @@ dataset_big_write(void) /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, dims, NULL); VRFY((mem_dataspace >= 0), ""); - if(!MAINPROCESS) { + if(!mpi_rank == 0) { ret = H5Sselect_none(mem_dataspace); VRFY((ret >= 0), "H5Sset_none succeeded"); } @@ -719,21 +693,6 @@ dataset_big_write(void) MESG("data_array created"); } - /* write data collectively */ - MESG("writeAll by process 0"); - { - int j,k =0; - for (i=0; i < block[0]; i++){ - for (j=0; j < block[1]; j++){ - if(k < 10) { - printf("%lld ", wdata[k]); - k++; - } - } - } - printf("\n"); - } - ret = H5Dwrite(dataset, H5T_NATIVE_LLONG, mem_dataspace, file_dataspace, xfer_plist, wdata); VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); @@ -747,7 +706,8 @@ dataset_big_write(void) VRFY((ret >= 0), "H5Dclose1 succeeded"); /* Point selection */ - printf("\nTesting Dataset4 write point selection\n"); + if (mpi_rank == 0) + HDprintf("\nTesting Dataset4 write point selection\n"); /* Create a large dataset */ dims[0] = bigcount; dims[1] = mpi_size * 4; @@ -818,101 +778,7 @@ dataset_big_write(void) ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose1 succeeded"); - /* Irregular selection */ - /* Need larger memory for data buffer */ - free(wdata); -#if 0 - wdata = (B_DATATYPE *)malloc(bigcount*4*sizeof(B_DATATYPE)); - VRFY((wdata != NULL), "wdata malloc succeeded"); - - printf("\nTesting Dataset5 write irregular selection\n"); - /* Create a large dataset */ - dims[0] = bigcount/6; - dims[1] = mpi_size * 4; - - sid = H5Screate_simple (RANK, dims, NULL); - VRFY((sid >= 0), "H5Screate_simple succeeded"); - dataset = H5Dcreate2(fid, DATASET5, H5T_NATIVE_LLONG, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); - VRFY((dataset >= 0), "H5Dcreate2 succeeded"); - H5Sclose(sid); - - /* first select 1 col in this procs splice */ - block[0] = dims[0]; - block[1] = 1; - stride[0] = block[0]; - stride[1] = block[1]; - count[0] = 1; - count[1] = 1; - start[0] = 0; - start[1] = mpi_rank * 4; - - /* create a file dataspace */ - file_dataspace = H5Dget_space (dataset); - VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); - - // dims[1] = 4; - /* create a memory dataspace */ - mem_dataspace = H5Screate_simple (RANK, dims, NULL); - VRFY((mem_dataspace >= 0), ""); - - ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); - VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); - - start[1] = 0; - ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); - VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); - - /* select every other row in the process splice and OR it with - the col selection to create an irregular selection */ - for(h=0 ; h= 0), "H5Sset_hyperslab succeeded"); - - start[1] = 0; - ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_OR, start, stride, count, block); - VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); - } - printf("Setting up for collective transfer\n"); - /* 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"); - if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { - ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); - VRFY((ret>= 0),"set independent IO collectively succeeded"); - } - - /* fill the local slab with some trivial data */ - fill_datasets(start, dims, wdata); - MESG("data_array initialized"); - if(VERBOSE_MED){ - MESG("data_array created"); - } - - ret = H5Dwrite(dataset, H5T_NATIVE_LLONG, mem_dataspace, file_dataspace, - xfer_plist, wdata); - VRFY((ret >= 0), "H5Dwrite dataset1 succeeded"); - - /* release all temporary handles. */ - H5Sclose(file_dataspace); - H5Sclose(mem_dataspace); - H5Pclose(xfer_plist); - - ret = H5Dclose(dataset); - VRFY((ret >= 0), "H5Dclose1 succeeded"); - free(wdata); -#endif H5Fclose(fid); } @@ -960,15 +826,16 @@ dataset_big_read(void) H5Pset_fapl_mpio(acc_tpl, MPI_COMM_WORLD, MPI_INFO_NULL); /* open the file collectively */ - fid=H5Fopen(filename,H5F_ACC_RDONLY,acc_tpl); + fid=H5Fopen(FILENAME[0],H5F_ACC_RDONLY,acc_tpl); VRFY((fid >= 0), "H5Fopen succeeded"); /* Release file-access template */ ret = H5Pclose(acc_tpl); VRFY((ret >= 0), ""); + if (mpi_rank == 0) + HDprintf("\nRead Testing Dataset1 by COL\n"); - printf("\nRead Testing Dataset1 by COL\n"); dataset = H5Dopen2(fid, DATASET1, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dopen2 succeeded"); @@ -1016,18 +883,6 @@ dataset_big_read(void) xfer_plist, rdata); VRFY((ret >= 0), "H5Dread dataset1 succeeded"); - { - for (i=0; i < block[0]; i++){ - for (j=0; j < block[1]; j++){ - if(k < 10) { - printf("%lld ", rdata[k]); - k++; - } - } - } - printf("\n"); - } - /* verify the read data with original expected data */ ret = verify_data(start, count, stride, block, rdata, wdata); if(ret) {fprintf(stderr, "verify failed\n"); exit(1);} @@ -1040,7 +895,8 @@ dataset_big_read(void) VRFY((ret >= 0), "H5Dclose1 succeeded"); - printf("\nRead Testing Dataset2 by ROW\n"); + if (mpi_rank == 0) + HDprintf("\nRead Testing Dataset2 by ROW\n"); memset(rdata, 0, bigcount*sizeof(B_DATATYPE)); dataset = H5Dopen2(fid, DATASET2, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dopen2 succeeded"); @@ -1089,18 +945,6 @@ dataset_big_read(void) xfer_plist, rdata); VRFY((ret >= 0), "H5Dread dataset2 succeeded"); - { - for (i=0; i < block[0]; i++){ - for (j=0; j < block[1]; j++){ - if(k < 10) { - printf("%lld ", rdata[k]); - k++; - } - } - } - printf("\n"); - } - /* verify the read data with original expected data */ ret = verify_data(start, count, stride, block, rdata, wdata); if(ret) {fprintf(stderr, "verify failed\n"); exit(1);} @@ -1112,8 +956,8 @@ dataset_big_read(void) ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose1 succeeded"); - - printf("\nRead Testing Dataset3 read select ALL proc 0, NONE others\n"); + if (mpi_rank == 0) + HDprintf("\nRead Testing Dataset3 read select ALL proc 0, NONE others\n"); memset(rdata, 0, bigcount*sizeof(B_DATATYPE)); dataset = H5Dopen2(fid, DATASET3, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dopen2 succeeded"); @@ -1124,7 +968,7 @@ dataset_big_read(void) /* create a file dataspace independently */ file_dataspace = H5Dget_space (dataset); VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); - if(MAINPROCESS) { + if(mpi_rank == 0) { ret = H5Sselect_all(file_dataspace); VRFY((ret >= 0), "H5Sset_all succeeded"); } @@ -1136,7 +980,7 @@ dataset_big_read(void) /* create a memory dataspace independently */ mem_dataspace = H5Screate_simple (RANK, dims, NULL); VRFY((mem_dataspace >= 0), ""); - if(!MAINPROCESS) { + if(!mpi_rank == 0) { ret = H5Sselect_none(mem_dataspace); VRFY((ret >= 0), "H5Sset_none succeeded"); } @@ -1163,19 +1007,7 @@ dataset_big_read(void) xfer_plist, rdata); VRFY((ret >= 0), "H5Dread dataset3 succeeded"); - { - for (i=0; i < block[0]; i++){ - for (j=0; j < block[1]; j++){ - if(k < 10) { - printf("%lld ", rdata[k]); - k++; - } - } - } - printf("\n"); - } - - if(MAINPROCESS) { + if(mpi_rank == 0) { /* verify the read data with original expected data */ ret = verify_data(start, count, stride, block, rdata, wdata); if(ret) {fprintf(stderr, "verify failed\n"); exit(1);} @@ -1188,7 +1020,8 @@ dataset_big_read(void) ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose1 succeeded"); - printf("\nRead Testing Dataset4 with Point selection\n"); + if (mpi_rank == 0) + HDprintf("\nRead Testing Dataset4 with Point selection\n"); dataset = H5Dopen2(fid, DATASET4, H5P_DEFAULT); VRFY((dataset >= 0), "H5Dopen2 succeeded"); @@ -1258,131 +1091,33 @@ dataset_big_read(void) ret = H5Dclose(dataset); VRFY((ret >= 0), "H5Dclose1 succeeded"); - printf("\nRead Testing Dataset5 with Irregular selection\n"); - /* Need larger memory for data buffer */ free(wdata); free(rdata); -#if 0 - wdata = (B_DATATYPE *)malloc(bigcount*4*sizeof(B_DATATYPE)); - VRFY((wdata != NULL), "wdata malloc succeeded"); - rdata = (B_DATATYPE *)malloc(bigcount*4*sizeof(B_DATATYPE)); - VRFY((rdata != NULL), "rdata malloc succeeded"); - - dataset = H5Dopen2(fid, DATASET5, H5P_DEFAULT); - VRFY((dataset >= 0), "H5Dopen2 succeeded"); - - dims[0] = bigcount; - dims[1] = mpi_size * 4; - - /* first select 1 col in this proc splice */ - block[0] = dims[0]; - block[1] = 1; - stride[0] = block[0]; - stride[1] = block[1]; - count[0] = 1; - count[1] = 1; - start[0] = 0; - start[1] = mpi_rank * 4; - - /* get file dataspace */ - file_dataspace = H5Dget_space (dataset); - VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); - - /* create a memory dataspace */ - mem_dataspace = H5Screate_simple (RANK, dims, NULL); - VRFY((mem_dataspace >= 0), ""); - - ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); - VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); - - start[1] = 0; - ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); - VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); - - /* select every other row in the process splice and OR it with - the col selection to create an irregular selection */ - for(h=0 ; h= 0), "H5Sset_hyperslab succeeded"); - - start[1] = 0; - ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_OR, start, stride, count, block); - VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); - - //fprintf(stderr, "%d: %d - %d\n", mpi_rank, (int)h, (int)H5Sget_select_npoints(mem_dataspace)); - } - - /* set up the collective transfer properties list */ - xfer_plist = H5Pcreate (H5P_DATASET_XFER); - VRFY((xfer_plist >= 0), ""); - ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); - VRFY((ret >= 0), "H5Pcreate xfer succeeded"); - if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { - ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); - VRFY((ret>= 0),"set independent IO collectively succeeded"); - } - - /* read data collectively */ - ret = H5Dread(dataset, H5T_NATIVE_LLONG, mem_dataspace, file_dataspace, - xfer_plist, rdata); - VRFY((ret >= 0), "H5Dread dataset1 succeeded"); - - /* fill dataset with test data */ - fill_datasets(start, dims, wdata); - MESG("data_array initialized"); - if(VERBOSE_MED){ - MESG("data_array created"); - } - - - /* verify the read data with original expected data */ - block[0] = dims[0]; - block[1] = 1; - stride[0] = block[0]; - stride[1] = block[1]; - count[0] = 1; - count[1] = 1; - start[0] = 0; - start[1] = 0; - ret = verify_data(start, count, stride, block, rdata, wdata); - if(ret) {fprintf(stderr, "verify failed\n"); exit(1);} - - for(h=0 ; h= 0), "H5Dclose1 succeeded"); - + if (file_dataspace != -1) H5Sclose(file_dataspace); + if (mem_dataspace != -1) H5Sclose(mem_dataspace); + if (xfer_plist != -1) H5Pclose(xfer_plist); + if (dataset != -1) { + ret = H5Dclose(dataset); + VRFY((ret >= 0), "H5Dclose1 succeeded"); + } H5Fclose(fid); /* release data buffers */ if(rdata) free(rdata); if(wdata) free(wdata); -#endif + } /* dataset_large_readAll */ @@ -1478,7 +1213,8 @@ create_faccess_plist(MPI_Comm comm, MPI_Info info, int l_facc_type) void coll_chunk1(void) { - if (MAINPROCESS) + const char *filename = FILENAME[0]; + if (mpi_rank == 0) printf("coll_chunk1\n"); coll_chunktest(filename, 1, BYROW_CONT, API_NONE, HYPER, HYPER, OUT_OF_ORDER); @@ -1531,7 +1267,8 @@ coll_chunk1(void) void coll_chunk2(void) { - if (MAINPROCESS) + const char *filename = FILENAME[0]; + if (mpi_rank == 0) printf("coll_chunk2\n"); coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, HYPER, HYPER, OUT_OF_ORDER); @@ -1585,8 +1322,9 @@ coll_chunk2(void) void coll_chunk3(void) { - if (MAINPROCESS) - printf("coll_chunk3\n"); + const char *filename = FILENAME[0]; + if (mpi_rank == 0) + printf("coll_chunk3\n"); coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, HYPER, HYPER, OUT_OF_ORDER); coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, HYPER, POINT, OUT_OF_ORDER); @@ -1956,7 +1694,7 @@ coll_chunktest(const char* filename, acc_plist = create_faccess_plist(comm, info, facc_type); VRFY((acc_plist >= 0),"MPIO creation property list succeeded"); - file = H5Fopen(filename,H5F_ACC_RDONLY,acc_plist); + file = H5Fopen(FILENAME[0],H5F_ACC_RDONLY,acc_plist); VRFY((file >= 0),"H5Fcreate succeeded"); status = H5Pclose(acc_plist); @@ -2134,16 +1872,34 @@ int main(int argc, char **argv) { int ExpressMode = 0; hsize_t newsize = 1048576; + /* Set the bigio processing limit to be 'newsize' bytes */ hsize_t oldsize = H5S_mpio_set_bigio_count(newsize); + /* Having set the bigio handling to a size that is managable, + * we'll set our 'bigcount' variable to be 2X that limit so + * that we try to ensure that our bigio handling is actually + * envoked and tested. + */ if (newsize != oldsize) { - bigcount = newsize * 2; + bigcount = newsize * 2; } MPI_Init(&argc, &argv); MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + /* Attempt to turn off atexit post processing so that in case errors + * happen during the test and the process is aborted, it will not get + * hang in the atexit post processing in which it may try to make MPI + * calls. By then, MPI calls may not work. + */ + if (H5dont_atexit() < 0){ + HDprintf("Failed to turn off atexit processing. Continue.\n"); + }; + + /* set alarm. */ + ALARM_ON; + ExpressMode = do_express_test(mpi_rank); dataset_big_write(); @@ -2153,7 +1909,8 @@ int main(int argc, char **argv) MPI_Barrier(MPI_COMM_WORLD); if (ExpressMode > 0) { - printf("***Express test mode on. Several tests are skipped\n"); + if (mpi_rank == 0) + HDprintf("***Express test mode on. Several tests are skipped\n"); } else { coll_chunk1(); @@ -2163,6 +1920,12 @@ int main(int argc, char **argv) coll_chunk3(); } + /* turn off alarm */ + ALARM_OFF; + + if (mpi_rank == 0) + HDremove(FILENAME[0]); + /* close HDF5 library */ H5close(); -- cgit v0.12