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| -rw-r--r-- | testpar/t_chunk_alloc.c | 550 |
1 files changed, 550 insertions, 0 deletions
diff --git a/testpar/t_chunk_alloc.c b/testpar/t_chunk_alloc.c new file mode 100644 index 0000000..88ab3ff --- /dev/null +++ b/testpar/t_chunk_alloc.c @@ -0,0 +1,550 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * This verifies if the storage space allocation methods are compatible between + * serial and parallel modes. + * + * Created by: Christian Chilan and Albert Cheng + * Date: 2006/05/25 + */ + +#include "testphdf5.h" +static int mpi_size, mpi_rank; + +#define DATASETNAME "ExtendibleArray" +#define CHUNKSIZE 1000 /* #elements per chunk */ +#define DSETCHUNKS 20000 +#define CLOSE 1 +#define NO_CLOSE 0 + +static MPI_Offset +get_filesize(const char *filename) +{ + int mpierr; + MPI_File fd; + MPI_Offset filesize; + + mpierr = MPI_File_open(MPI_COMM_SELF, (char*)filename, MPI_MODE_RDONLY, + MPI_INFO_NULL, &fd); + VRFY((mpierr == MPI_SUCCESS), ""); + + mpierr = MPI_File_get_size(fd, &filesize); + VRFY((mpierr == MPI_SUCCESS), ""); + + mpierr = MPI_File_close(&fd); + VRFY((mpierr == MPI_SUCCESS), ""); + + return(filesize); +} + +typedef enum write_ { + none, + sec_last, + all +} write_type; + +typedef enum access_ { + write_all, + open_only, + extend_only +} access_type; + + +/* + * This creates a dataset serially with 'nchunks' chunks, each of CHUNKSIZE + * elements. The allocation time is set to H5D_ALLOC_TIME_EARLY. Another + * routine will open this in parallel for extension test. + */ +void +create_chunked_dataset(const char *filename, int nchunks, write_type write) +{ + hid_t file_id, dataset; /* handles */ + hid_t dataspace,memspace; + hid_t cparms; + hsize_t dims[1]; + hsize_t maxdims[1] = {H5S_UNLIMITED}; + + hsize_t chunk_dims[1] ={CHUNKSIZE}; + 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]; + int i; + + herr_t hrc; + + MPI_Offset filesize, /* actual file size */ + est_filesize; /* estimated file size */ + + /* set up MPI parameters */ + MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + + /* Only MAINPROCESS should create the file. Others just wait. */ + if (MAINPROCESS){ + + dims[0]=nchunks*CHUNKSIZE; + /* Create the data space with unlimited dimensions. */ + dataspace = H5Screate_simple (1, dims, maxdims); + VRFY((dataspace >= 0), ""); + + memspace = H5Screate_simple(1, chunk_dims, NULL); + VRFY((memspace >= 0), ""); + + /* Create a new file. If file exists its contents will be overwritten. */ + file_id = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + VRFY((file_id >= 0), ""); + + /* Modify dataset creation properties, i.e. enable chunking */ + cparms = H5Pcreate (H5P_DATASET_CREATE); + VRFY((cparms >= 0), ""); + + hrc = H5Pset_alloc_time(cparms, H5D_ALLOC_TIME_EARLY); + VRFY((hrc >= 0), ""); + + hrc = H5Pset_chunk ( cparms, 1, chunk_dims); + VRFY((hrc >= 0), ""); + + /* Create a new dataset within the file using cparms creation properties. */ + dataset = H5Dcreate (file_id, DATASETNAME, H5T_NATIVE_UCHAR, dataspace, cparms); + VRFY((dataset >= 0), ""); + + switch (write) { + + /* writes only the second to last chunk */ + case sec_last: + + memset(buffer, 100, CHUNKSIZE); + + count[0] = 1; + stride[0] = 1; + block[0] = chunk_dims[0]; + offset[0] = (nchunks-2)*chunk_dims[0]; + + hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block); + VRFY((hrc >= 0), ""); + + /* Write sec_last chunk */ + hrc = H5Dwrite(dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer); + VRFY((hrc >= 0), "H5Dwrite"); + + break; + + + /* doesn't write anything */ + case none: + + break; + } + + /* Close resources */ + hrc = H5Dclose (dataset); + VRFY((hrc >= 0), ""); + dataset = -1; + + hrc = H5Sclose (dataspace); + VRFY((hrc >= 0), ""); + + hrc = H5Sclose (memspace); + VRFY((hrc >= 0), ""); + + hrc = H5Pclose (cparms); + VRFY((hrc >= 0), ""); + + hrc = H5Fclose (file_id); + VRFY((hrc >= 0), ""); + file_id = -1; + + /* verify file size */ + filesize = get_filesize(filename); + est_filesize = nchunks*CHUNKSIZE*sizeof(unsigned char); + VRFY((filesize >= est_filesize), "file size check"); + + } + + /* Make sure all processes are done before exiting this routine. Otherwise, + * other tests may start and change the test data file before some processes + * of this test are still accessing the file. + */ + + MPI_Barrier(MPI_COMM_WORLD); +} + + +/* + * 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 + * opens the dataset. At the end, it verifies the size of the dataset to be + * consistent with argument 'nchunks'. + */ +void +parallel_access_dataset(const char *filename, int nchunks, access_type action, hid_t *file_id, hid_t *dataset) +{ + /* HDF5 gubbins */ + hid_t memspace, dataspace; /* HDF5 file identifier */ + hid_t access_plist; /* HDF5 ID for file access property list */ + herr_t hrc; /* HDF5 return code */ + hsize_t size[1]; + hsize_t dim_size; + + hsize_t chunk_dims[1] ={CHUNKSIZE}; + 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]; + int i; + + /* MPI Gubbins */ + MPI_Offset filesize, /* actual file size */ + est_filesize; /* estimated file size */ + int mpierr; + + /* Initialize MPI */ + MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + + /* Set up MPIO file access property lists */ + access_plist = H5Pcreate(H5P_FILE_ACCESS); + VRFY((access_plist >= 0), ""); + + hrc = H5Pset_fapl_mpio(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL); + VRFY((hrc >= 0), ""); + + /* Open the file */ + if (*file_id<0){ + *file_id = H5Fopen(filename, H5F_ACC_RDWR, access_plist); + VRFY((*file_id >= 0), ""); + } + + /* Open dataset*/ + if (*dataset<0){ + *dataset = H5Dopen(*file_id, DATASETNAME); + VRFY((*dataset >= 0), ""); + } + + memspace = H5Screate_simple(1, chunk_dims, NULL); + VRFY((memspace >= 0), ""); + + dataspace = H5Dget_space(*dataset); + VRFY((dataspace >= 0), ""); + + size[0] = nchunks*CHUNKSIZE; + + switch (action) { + + /* all chunks are written by all the processes in an interleaved way*/ + case write_all: + + for (i=0; i<nchunks/mpi_size; i++){ + + memset(buffer, mpi_rank+1, CHUNKSIZE); + + offset[0] = (i*mpi_size+mpi_rank)*chunk_dims[0]; + count[0] = 1; + stride[0] = 1; + block[0] = chunk_dims[0]; + + hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block); + VRFY((hrc >= 0), ""); + + /* Write the buffer out */ + hrc = H5Dwrite(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer); + VRFY((hrc >= 0), "H5Dwrite"); + + } + + /* remainder writing */ + if (mpi_rank < nchunks%mpi_size){ + + memset(buffer, mpi_rank+1, CHUNKSIZE); + + offset[0] = ((nchunks/mpi_size)*mpi_size+mpi_rank)*chunk_dims[0]; + count[0] = 1; + stride[0] = 1; + block[0] = chunk_dims[0]; + + hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block); + VRFY((hrc >= 0), ""); + + /* 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 = H5Dextend(*dataset, size); + VRFY((hrc >= 0), ""); + + break; + + /* only opens the dataset */ + case open_only: + + break; + } + + /* Close up */ + hrc = H5Dclose(*dataset); + VRFY((hrc >= 0), ""); + *dataset = -1; + + hrc = H5Sclose (dataspace); + VRFY((hrc >= 0), ""); + + hrc = H5Sclose (memspace); + VRFY((hrc >= 0), ""); + + hrc = H5Fclose(*file_id); + VRFY((hrc >= 0), ""); + *file_id = -1; + + /* verify file size */ + filesize = get_filesize(filename); + est_filesize = nchunks*CHUNKSIZE*sizeof(unsigned char); + VRFY((filesize >= est_filesize), "file size check"); + + /* Can close some plists */ + hrc = H5Pclose(access_plist); + VRFY((hrc >= 0), ""); + + /* Make sure all processes are done before exiting this routine. Otherwise, + * other tests may start and change the test data file before some processes + * of this test are still accessing the file. + */ + MPI_Barrier(MPI_COMM_WORLD); +} + +/* + * This routine verifies the data written in the dataset. It does one of the + * three cases according to the value of parameter `write'. + * 1. it returns correct fill values though the dataset has not been written; + * 2. it still returns correct fill values though only a small part is written; + * 3. it returns correct values when the whole dataset has been written in an + * interleaved pattern. + */ +void verify_data(const char *filename, int nchunks, write_type write, 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 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]; + int value, i; + int index, current; + + /* MPI Gubbins */ + MPI_Offset filesize, /* actual file size */ + est_filesize; /* estimated file size */ + int mpierr; + + /* Initialize MPI */ + MPI_Comm_size(MPI_COMM_WORLD,&mpi_size); + MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank); + + /* Set up MPIO file access property lists */ + access_plist = H5Pcreate(H5P_FILE_ACCESS); + VRFY((access_plist >= 0), ""); + + hrc = H5Pset_fapl_mpio(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL); + VRFY((hrc >= 0), ""); + + /* Open the file */ + if (*file_id<0){ + *file_id = H5Fopen(filename, H5F_ACC_RDWR, access_plist); + VRFY((*file_id >= 0), ""); + } + + /* Open dataset*/ + if (*dataset<0){ + *dataset = H5Dopen(*file_id, DATASETNAME); + VRFY((*dataset >= 0), ""); + } + + memspace = H5Screate_simple(1, chunk_dims, NULL); + VRFY((memspace >= 0), ""); + + dataspace = H5Dget_space(*dataset); + VRFY((dataspace >= 0), ""); + + /* expected value in the dataset */ + if (write == all) + value = mpi_rank + 1; + else + value =0; + + /* checks main portion of the dataset */ + for (i=0; i<nchunks/mpi_size; i++){ + + memset(buffer, -1, CHUNKSIZE); + + offset[0] = (i*mpi_size+mpi_rank)*chunk_dims[0]; + count[0] = 1; + stride[0] = 1; + block[0] = chunk_dims[0]; + + hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block); + VRFY((hrc >= 0), ""); + + /* Read the chunk */ + hrc = H5Dread(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer); + VRFY((hrc >= 0), "H5Dread"); + + /* adjust expected value for sec_last chunk */ + if (i == nchunks/mpi_size-1 && !(nchunks%mpi_size) && write==sec_last){ + if (mpi_rank == mpi_size-2) + value = 100; + else + value = 0; + } + + /* verify content of the chunk */ + for (index = 0; index < CHUNKSIZE; index++) + VRFY((buffer[index] == value), "data verification"); + + } + + /* remainder checking */ + if (mpi_rank < nchunks%mpi_size){ + + memset(buffer, -1, CHUNKSIZE); + + offset[0] = ((nchunks/mpi_size)*mpi_size+mpi_rank)*chunk_dims[0]; + count[0] = 1; + stride[0] = 1; + block[0] = chunk_dims[0]; + + hrc = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, stride, count, block); + VRFY((hrc >= 0), ""); + + /* read the buffer out */ + hrc = H5Dread(*dataset, H5T_NATIVE_UCHAR, memspace, dataspace, H5P_DEFAULT, buffer); + VRFY((hrc >= 0), "H5Dread"); + + /* adjust expected value for sec_last chunk */ + if (write == sec_last){ + if (mpi_rank == nchunks%mpi_size-2) + value = 100; + else + value = 0; + } + + /* verify content of the chunk */ + for (index = 0; index < CHUNKSIZE; index++) + VRFY((buffer[index] == value), "data verification"); + + } + + hrc = H5Sclose (dataspace); + VRFY((hrc >= 0), ""); + + hrc = H5Sclose (memspace); + VRFY((hrc >= 0), ""); + + /* Can close some plists */ + hrc = H5Pclose(access_plist); + VRFY((hrc >= 0), ""); + + /* Close up */ + if (close){ + hrc = H5Dclose(*dataset); + VRFY((hrc >= 0), ""); + *dataset = -1; + + hrc = H5Fclose(*file_id); + VRFY((hrc >= 0), ""); + *file_id = -1; + } + + /* Make sure all processes are done before exiting this routine. Otherwise, + * other tests may start and change the test data file before some processes + * of this test are still accessing the file. + */ + MPI_Barrier(MPI_COMM_WORLD); +} + + + +/* + * Test following possible scenarios, + * Case 1: + * Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY and large + * size, no write, close, reopen in parallel, read to verify all return + * the fill value. + * Case 2: + * Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY but small + * size, no write, close, reopen in parallel, extend to large size, then close, + * then reopen in parallel and read to verify all return the fill value. + * Case 3: + * Sequential create a file and dataset with H5D_ALLOC_TIME_EARLY and large + * size, write just a small part of the dataset (second to the last), close, + * then reopen in parallel, read to verify all return the fill value except + * those small portion that has been written. Without closing it, writes + * all parts of the dataset in a interleave pattern, close it, and reopen + * it, read to verify all data are as written. + */ +void +test_chunk_alloc(void) +{ + const char *filename; + hid_t file_id, dataset; + + file_id = dataset = -1; + + filename = GetTestParameters(); + if (VERBOSE_MED) + printf("Extend Chunked allocation test on file %s\n", filename); + + /* Case 1 */ + /* Create chunked dataset without writing anything.*/ + create_chunked_dataset(filename, DSETCHUNKS, none); + /* reopen dataset in parallel and check for file size */ + parallel_access_dataset(filename, DSETCHUNKS, open_only, &file_id, &dataset); + /* reopen dataset in parallel, read and verify the data */ + verify_data(filename, DSETCHUNKS, 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); + /* reopen dataset in parallel, read and verify the data */ + verify_data(filename, DSETCHUNKS, 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); + /* 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); + /* All processes write in all the chunks in a interleaved way */ + parallel_access_dataset(filename, DSETCHUNKS, write_all, &file_id, &dataset); + /* reopen dataset in parallel, read and verify the data */ + verify_data(filename, DSETCHUNKS, all, CLOSE, &file_id, &dataset); + +} |