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hdf5/testpar/t_chunk_alloc.c

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* 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 DSET_NAME "ExtendibleArray"
#define CHUNK_SIZE 1000 /* #elements per chunk */
#define CHUNK_FACTOR 200 /* default dataset size in terms of chunks */
#define CLOSE 1
#define NO_CLOSE 0
static MPI_Offset
get_filesize(const char *filename)
{
int mpierr;
MPI_File fd;
MPI_Offset filesize;
#ifndef H5_HAVE_MPI_GET_SIZE
struct stat stat_buf;
#endif
#ifdef H5_HAVE_MPI_GET_SIZE
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), "");
#else
/* Some systems (only SGI Altix Propack 4 so far) doesn't return correct
* file size for MPI_File_get_size. Use stat instead.
*/
if((mpierr=stat(filename, &stat_buf))<0)
VRFY((mpierr == MPI_SUCCESS), "");
/* Hopefully this casting is safe */
filesize = (MPI_Offset)(stat_buf.st_size);
#endif
return(filesize);
}
typedef enum write_pattern {
none,
sec_last,
all
} write_type;
typedef enum access_ {
write_all,
open_only,
extend_only
} access_type;
/*
* 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 chunk_factor, write_type write_pattern)
{
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] ={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[CHUNK_SIZE];
long nchunks;
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){
nchunks=chunk_factor*mpi_size;
dims[0]=nchunks*CHUNK_SIZE;
/* 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(h5_rmprefix(filename), H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
VRFY((file_id >= 0), "H5Fcreate");
/* 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 = 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, CHUNK_SIZE);
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");
} /* end if */
/* 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 * CHUNK_SIZE * 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*CHUNK_SIZE, and it only
* opens the dataset. At the end, it verifies the size of the dataset to be
* consistent with argument 'chunk_factor'.
*/
static void
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 */
hid_t access_plist; /* HDF5 ID for file access property list */
herr_t hrc; /* HDF5 return code */
hsize_t size[1];
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[CHUNK_SIZE];
int i;
long nchunks;
/* MPI Gubbins */
MPI_Offset filesize, /* actual file size */
est_filesize; /* estimated file size */
/* Initialize MPI */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
nchunks=chunk_factor*mpi_size;
/* 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 = H5Dopen2(*file_id, DSET_NAME, H5P_DEFAULT);
VRFY((*dataset >= 0), "");
}
memspace = H5Screate_simple(1, chunk_dims, NULL);
VRFY((memspace >= 0), "");
dataspace = H5Dget_space(*dataset);
VRFY((dataspace >= 0), "");
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, CHUNK_SIZE);
count[0] = 1;
stride[0] = 1;
block[0] = chunk_dims[0];
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);
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:
/* 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 */
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*CHUNK_SIZE*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_pattern'.
* 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.
*/
static void
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] ={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[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);
nchunks=chunk_factor*mpi_size;
/* 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 = H5Dopen2(*file_id, DSET_NAME, H5P_DEFAULT);
VRFY((*dataset >= 0), "");
}
memspace = H5Screate_simple(1, chunk_dims, NULL);
VRFY((memspace >= 0), "");
dataspace = H5Dget_space(*dataset);
VRFY((dataspace >= 0), "");
/* all processes check all chunks. */
count[0] = 1;
stride[0] = 1;
block[0] = chunk_dims[0];
for (i=0; i<nchunks; i++){
/* reset buffer values */
memset(buffer, -1, CHUNK_SIZE);
offset[0] = i*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");
/* set expected value according the write pattern */
switch (write_pattern) {
case all:
value = i%mpi_size + 1;
break;
case none:
value = 0;
break;
case sec_last:
if (i==nchunks-2)
value = 100;
else
value = 0;
}
/* verify content of the chunk */
for (index = 0; index < CHUNK_SIZE; 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;
/* Initialize MPI */
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
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, CHUNK_FACTOR, none);
/* reopen dataset in parallel and check for file size */
parallel_access_dataset(filename, CHUNK_FACTOR, open_only, &file_id, &dataset);
/* reopen dataset in parallel, read and verify the data */
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, CHUNK_FACTOR, extend_only, &file_id, &dataset);
/* reopen dataset in parallel, read and verify the data */
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, CHUNK_FACTOR, sec_last);
/* Reopen dataset in parallel, read and verify the data. The file and dataset are not closed*/
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, CHUNK_FACTOR, write_all, &file_id, &dataset);
/* reopen dataset in parallel, read and verify the data */
verify_data(filename, CHUNK_FACTOR, all, CLOSE, &file_id, &dataset);
}
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