diff options
Diffstat (limited to 'testpar/t_chunk_alloc.c')
| -rw-r--r-- | testpar/t_chunk_alloc.c | 122 |
1 files changed, 72 insertions, 50 deletions
diff --git a/testpar/t_chunk_alloc.c b/testpar/t_chunk_alloc.c index a0cf0e2..6a2756b 100644 --- a/testpar/t_chunk_alloc.c +++ b/testpar/t_chunk_alloc.c @@ -24,9 +24,10 @@ #include "testphdf5.h" static int mpi_size, mpi_rank; -#define DATASETNAME "ExtendibleArray" -#define CHUNKSIZE 1000 /* #elements per chunk */ -#define DSETCHUNKS 20000 +#define DSET_NAME "ExtendibleArray" +#define CHUNK_SIZE 1000 /* #elements per chunk */ +#define CHUNK_FACTOR 2000 /* default dataset size in terms of chunks */ +#define MIN_CHUNK_FACTOR 2 /* dataset size in terms of chunks if mpi_size reaches threshold */ #define CLOSE 1 #define NO_CLOSE 0 @@ -78,12 +79,12 @@ typedef enum access_ { /* - * This creates a dataset serially with 'nchunks' chunks, each of CHUNKSIZE + * This creates a dataset serially with chunks, each of CHUNK_SIZE * elements. The allocation time is set to H5D_ALLOC_TIME_EARLY. Another * routine will open this in parallel for extension test. */ static void -create_chunked_dataset(const char *filename, int nchunks, write_type write_pattern) +create_chunked_dataset(const char *filename, int chunk_factor, write_type write_pattern) { hid_t file_id, dataset; /* handles */ hid_t dataspace,memspace; @@ -91,14 +92,14 @@ create_chunked_dataset(const char *filename, int nchunks, write_type write_patte hsize_t dims[1]; hsize_t maxdims[1] = {H5S_UNLIMITED}; - hsize_t chunk_dims[1] ={CHUNKSIZE}; + hsize_t chunk_dims[1] ={CHUNK_SIZE}; hsize_t count[1]; hsize_t stride[1]; hsize_t block[1]; hsize_t offset[1]; /* Selection offset within dataspace */ /* Variables used in reading data back */ - char buffer[CHUNKSIZE]; - + char buffer[CHUNK_SIZE]; + long nchunks; herr_t hrc; MPI_Offset filesize, /* actual file size */ @@ -110,8 +111,11 @@ create_chunked_dataset(const char *filename, int nchunks, write_type write_patte /* Only MAINPROCESS should create the file. Others just wait. */ if (MAINPROCESS){ - - dims[0]=nchunks*CHUNKSIZE; + if (mpi_size<PROCS_THRESHOLD) + nchunks=chunk_factor*mpi_size; + else + nchunks=MIN_CHUNK_FACTOR*(mpi_size-PROCS_THRESHOLD)+chunk_factor*PROCS_THRESHOLD; + dims[0]=nchunks*CHUNK_SIZE; /* Create the data space with unlimited dimensions. */ dataspace = H5Screate_simple (1, dims, maxdims); VRFY((dataspace >= 0), ""); @@ -135,11 +139,11 @@ create_chunked_dataset(const char *filename, int nchunks, write_type write_patte VRFY((hrc >= 0), ""); /* Create a new dataset within the file using cparms creation properties. */ - dataset = H5Dcreate2(file_id, DATASETNAME, H5T_NATIVE_UCHAR, dataspace, H5P_DEFAULT, cparms, H5P_DEFAULT); + dataset = H5Dcreate2(file_id, DSET_NAME, H5T_NATIVE_UCHAR, dataspace, H5P_DEFAULT, cparms, H5P_DEFAULT); VRFY((dataset >= 0), ""); if(write_pattern == sec_last) { - HDmemset(buffer, 100, CHUNKSIZE); + HDmemset(buffer, 100, CHUNK_SIZE); count[0] = 1; stride[0] = 1; @@ -174,7 +178,7 @@ create_chunked_dataset(const char *filename, int nchunks, write_type write_patte /* verify file size */ filesize = get_filesize(filename); - est_filesize = nchunks * CHUNKSIZE * sizeof(unsigned char); + est_filesize = nchunks * CHUNK_SIZE * sizeof(unsigned char); VRFY((filesize >= est_filesize), "file size check"); } @@ -190,12 +194,12 @@ create_chunked_dataset(const char *filename, int nchunks, write_type write_patte /* * This program performs three different types of parallel access. It writes on - * the entire dataset, it extends the dataset to nchunks*CHUNKSIZE, and it only + * the entire dataset, it extends the dataset to nchunks*CHUNK_SIZE, and it only * opens the dataset. At the end, it verifies the size of the dataset to be * consistent with argument 'nchunks'. */ static void -parallel_access_dataset(const char *filename, int nchunks, access_type action, hid_t *file_id, hid_t *dataset) +parallel_access_dataset(const char *filename, int chunk_factor, access_type action, hid_t *file_id, hid_t *dataset) { /* HDF5 gubbins */ hid_t memspace, dataspace; /* HDF5 file identifier */ @@ -203,15 +207,18 @@ parallel_access_dataset(const char *filename, int nchunks, access_type action, h herr_t hrc; /* HDF5 return code */ hsize_t size[1]; - hsize_t chunk_dims[1] ={CHUNKSIZE}; + hsize_t chunk_dims[1] ={CHUNK_SIZE}; hsize_t count[1]; hsize_t stride[1]; hsize_t block[1]; hsize_t offset[1]; /* Selection offset within dataspace */ + hsize_t dims[1]; + hsize_t maxdims[1]; + /* Variables used in reading data back */ - char buffer[CHUNKSIZE]; + char buffer[CHUNK_SIZE]; int i; - + long nchunks; /* MPI Gubbins */ MPI_Offset filesize, /* actual file size */ est_filesize; /* estimated file size */ @@ -220,6 +227,11 @@ parallel_access_dataset(const char *filename, int nchunks, access_type action, h MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + if (mpi_size<PROCS_THRESHOLD) + nchunks=chunk_factor*mpi_size; + else + nchunks=MIN_CHUNK_FACTOR*(mpi_size-PROCS_THRESHOLD)+chunk_factor*PROCS_THRESHOLD; + /* Set up MPIO file access property lists */ access_plist = H5Pcreate(H5P_FILE_ACCESS); VRFY((access_plist >= 0), ""); @@ -235,7 +247,7 @@ parallel_access_dataset(const char *filename, int nchunks, access_type action, h /* Open dataset*/ if (*dataset<0){ - *dataset = H5Dopen2(*file_id, DATASETNAME, H5P_DEFAULT); + *dataset = H5Dopen2(*file_id, DSET_NAME, H5P_DEFAULT); VRFY((*dataset >= 0), ""); } @@ -245,19 +257,18 @@ parallel_access_dataset(const char *filename, int nchunks, access_type action, h dataspace = H5Dget_space(*dataset); VRFY((dataspace >= 0), ""); - size[0] = nchunks*CHUNKSIZE; + size[0] = nchunks*CHUNK_SIZE; switch (action) { /* all chunks are written by all the processes in an interleaved way*/ case write_all: - memset(buffer, mpi_rank+1, CHUNKSIZE); + memset(buffer, mpi_rank+1, CHUNK_SIZE); count[0] = 1; stride[0] = 1; block[0] = chunk_dims[0]; - for (i=0; i<(nchunks+mpi_size-1)/mpi_size; i++){ - if (i*mpi_size+mpi_rank < nchunks){ + for (i=0; i<nchunks/mpi_size; i++){ offset[0] = (i*mpi_size+mpi_rank)*chunk_dims[0]; hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block); @@ -266,21 +277,24 @@ parallel_access_dataset(const char *filename, int nchunks, access_type action, h /* Write the buffer out */ hrc = H5Dwrite(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer); VRFY((hrc >= 0), "H5Dwrite"); - } - } break; /* only extends the dataset */ case extend_only: - /* Extend dataset*/ - hrc = H5Dset_extent(*dataset, size); + /* check if new size is larger than old size */ + hrc = H5Sget_simple_extent_dims(dataspace, dims, maxdims); VRFY((hrc >= 0), ""); + /* Extend dataset*/ + if (size[0] > dims[0]) { + hrc = H5Dset_extent(*dataset, size); + VRFY((hrc >= 0), ""); + } break; - /* only opens the dataset */ + /* only opens the *dataset */ case open_only: break; @@ -292,10 +306,10 @@ parallel_access_dataset(const char *filename, int nchunks, access_type action, h *dataset = -1; hrc = H5Sclose (dataspace); - VRFY((hrc >= 0), ""); + VRFY((hrc >= 0), ""); - hrc = H5Sclose (memspace); - VRFY((hrc >= 0), ""); + hrc = H5Sclose (memspace); + VRFY((hrc >= 0), ""); hrc = H5Fclose(*file_id); VRFY((hrc >= 0), ""); @@ -303,7 +317,7 @@ parallel_access_dataset(const char *filename, int nchunks, access_type action, h /* verify file size */ filesize = get_filesize(filename); - est_filesize = nchunks*CHUNKSIZE*sizeof(unsigned char); + est_filesize = nchunks*CHUNK_SIZE*sizeof(unsigned char); VRFY((filesize >= est_filesize), "file size check"); /* Can close some plists */ @@ -326,27 +340,32 @@ parallel_access_dataset(const char *filename, int nchunks, access_type action, h * interleaved pattern. */ static void -verify_data(const char *filename, int nchunks, write_type write_pattern, int close, hid_t *file_id, hid_t *dataset) +verify_data(const char *filename, int chunk_factor, write_type write_pattern, int close, hid_t *file_id, hid_t *dataset) { /* HDF5 gubbins */ hid_t dataspace, memspace; /* HDF5 file identifier */ hid_t access_plist; /* HDF5 ID for file access property list */ herr_t hrc; /* HDF5 return code */ - hsize_t chunk_dims[1] ={CHUNKSIZE}; + hsize_t chunk_dims[1] ={CHUNK_SIZE}; hsize_t count[1]; hsize_t stride[1]; hsize_t block[1]; hsize_t offset[1]; /* Selection offset within dataspace */ /* Variables used in reading data back */ - char buffer[CHUNKSIZE]; + char buffer[CHUNK_SIZE]; int value, i; int index; - + long nchunks; /* Initialize MPI */ MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + if (mpi_size<PROCS_THRESHOLD) + nchunks=chunk_factor*mpi_size; + else + nchunks=MIN_CHUNK_FACTOR*(mpi_size-PROCS_THRESHOLD)+chunk_factor*PROCS_THRESHOLD; + /* Set up MPIO file access property lists */ access_plist = H5Pcreate(H5P_FILE_ACCESS); VRFY((access_plist >= 0), ""); @@ -362,7 +381,7 @@ verify_data(const char *filename, int nchunks, write_type write_pattern, int clo /* Open dataset*/ if (*dataset<0){ - *dataset = H5Dopen2(*file_id, DATASETNAME, H5P_DEFAULT); + *dataset = H5Dopen2(*file_id, DSET_NAME, H5P_DEFAULT); VRFY((*dataset >= 0), ""); } @@ -378,7 +397,7 @@ verify_data(const char *filename, int nchunks, write_type write_pattern, int clo block[0] = chunk_dims[0]; for (i=0; i<nchunks; i++){ /* reset buffer values */ - memset(buffer, -1, CHUNKSIZE); + memset(buffer, -1, CHUNK_SIZE); offset[0] = i*chunk_dims[0]; @@ -398,16 +417,15 @@ verify_data(const char *filename, int nchunks, write_type write_pattern, int clo value = 0; break; case sec_last: - if (i==(nchunks-2)) + if (i==nchunks-2) value = 100; else value = 0; } /* verify content of the chunk */ - for (index = 0; index < CHUNKSIZE; index++) + for (index = 0; index < CHUNK_SIZE; index++) VRFY((buffer[index] == value), "data verification"); - } hrc = H5Sclose (dataspace); @@ -465,6 +483,10 @@ test_chunk_alloc(void) hid_t file_id, dataset; file_id = dataset = -1; + + /* Initialize MPI */ + MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); filename = GetTestParameters(); if (VERBOSE_MED) @@ -472,28 +494,28 @@ test_chunk_alloc(void) /* Case 1 */ /* Create chunked dataset without writing anything.*/ - create_chunked_dataset(filename, DSETCHUNKS, none); + create_chunked_dataset(filename, CHUNK_FACTOR, none); /* reopen dataset in parallel and check for file size */ - parallel_access_dataset(filename, DSETCHUNKS, open_only, &file_id, &dataset); + parallel_access_dataset(filename, CHUNK_FACTOR, open_only, &file_id, &dataset); /* reopen dataset in parallel, read and verify the data */ - verify_data(filename, DSETCHUNKS, none, CLOSE, &file_id, &dataset); + verify_data(filename, CHUNK_FACTOR, none, CLOSE, &file_id, &dataset); /* Case 2 */ /* Create chunked dataset without writing anything */ create_chunked_dataset(filename, 20, none); /* reopen dataset in parallel and only extend it */ - parallel_access_dataset(filename, DSETCHUNKS, extend_only, &file_id, &dataset); + parallel_access_dataset(filename, CHUNK_FACTOR, extend_only, &file_id, &dataset); /* reopen dataset in parallel, read and verify the data */ - verify_data(filename, DSETCHUNKS, none, CLOSE, &file_id, &dataset); + verify_data(filename, CHUNK_FACTOR, none, CLOSE, &file_id, &dataset); /* Case 3 */ /* Create chunked dataset and write in the second to last chunk */ - create_chunked_dataset(filename, DSETCHUNKS, sec_last); + create_chunked_dataset(filename, CHUNK_FACTOR, sec_last); /* Reopen dataset in parallel, read and verify the data. The file and dataset are not closed*/ - verify_data(filename, DSETCHUNKS, sec_last, NO_CLOSE, &file_id, &dataset); + verify_data(filename, CHUNK_FACTOR, sec_last, NO_CLOSE, &file_id, &dataset); /* All processes write in all the chunks in a interleaved way */ - parallel_access_dataset(filename, DSETCHUNKS, write_all, &file_id, &dataset); + parallel_access_dataset(filename, CHUNK_FACTOR, write_all, &file_id, &dataset); /* reopen dataset in parallel, read and verify the data */ - verify_data(filename, DSETCHUNKS, all, CLOSE, &file_id, &dataset); + verify_data(filename, CHUNK_FACTOR, all, CLOSE, &file_id, &dataset); } |