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hdf5/testpar/t_mdset.c
John Mainzer f950d7bdb9 [svn-r19722] Bug fix for failure in the round robin metadata write ojbect header 
metadata confusion test that appeared after Albert modified the test.

Cursory commit test.  No test on Abe as that system is down, the
fix is very minor, and it seems to work in the 1.8.6 branch
2010-11-03 16:17:12 -05:00

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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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "testphdf5.h"
#define DIM 2
#define SIZE 32
#define NDATASET 4
#define GROUP_DEPTH 128
enum obj_type { is_group, is_dset };
static int get_size(void);
static void write_dataset(hid_t, hid_t, hid_t);
static int read_dataset(hid_t, hid_t, hid_t);
static void create_group_recursive(hid_t, hid_t, hid_t, int);
static void recursive_read_group(hid_t, hid_t, hid_t, int);
static void group_dataset_read(hid_t fid, int mpi_rank, int m);
static void write_attribute(hid_t, int, int);
static int read_attribute(hid_t, int, int);
static int check_value(DATATYPE *, DATATYPE *, int);
static void get_slab(hsize_t[], hsize_t[], hsize_t[], hsize_t[], int);
/*
* The size value computed by this function is used extensively in
* configuring tests for the current number of processes.
*
* This function was created as part of an effort to allow the
* test functions in this file to run on an arbitrary number of
* processors.
* JRM - 8/11/04
*/
static int
get_size(void)
{
int mpi_rank;
int mpi_size;
int size = SIZE;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank); /* needed for VRFY */
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
if(mpi_size > size ) {
if((mpi_size % 2) == 0 ) {
size = mpi_size;
} else {
size = mpi_size + 1;
}
}
VRFY((mpi_size <= size), "mpi_size <= size");
VRFY(((size % 2) == 0), "size isn't even");
return(size);
} /* get_size() */
/*
* Example of using PHDF5 to create ndatasets datasets. Each process write
* a slab of array to the file.
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* JRM - 8/11/04
*/
void multiple_dset_write(void)
{
int i, j, n, mpi_size, mpi_rank, size;
hid_t iof, plist, dataset, memspace, filespace;
hid_t dcpl; /* Dataset creation property list */
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
hsize_t chunk_origin [DIM];
hsize_t chunk_dims [DIM], file_dims [DIM];
hsize_t count[DIM]={1,1};
double * outme = NULL;
double fill=1.0; /* Fill value */
char dname [100];
herr_t ret;
const H5Ptest_param_t *pt;
char *filename;
int ndatasets;
pt = GetTestParameters();
filename = pt->name;
ndatasets = pt->count;
size = get_size();
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
outme = HDmalloc((size_t)(size * size * sizeof(double)));
VRFY((outme != NULL), "HDmalloc succeeded for outme");
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
VRFY((plist>=0), "create_faccess_plist succeeded");
iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
VRFY((iof>=0), "H5Fcreate succeeded");
ret = H5Pclose(plist);
VRFY((ret>=0), "H5Pclose succeeded");
/* decide the hyperslab according to process number. */
get_slab(chunk_origin, chunk_dims, count, file_dims, size);
memspace = H5Screate_simple(DIM, chunk_dims, NULL);
filespace = H5Screate_simple(DIM, file_dims, NULL);
ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims);
VRFY((ret>=0), "mdata hyperslab selection");
/* Create a dataset creation property list */
dcpl = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl>=0), "dataset creation property list succeeded");
ret = H5Pset_fill_value(dcpl, H5T_NATIVE_DOUBLE, &fill);
VRFY((ret>=0), "set fill-value succeeded");
for(n = 0; n < ndatasets; n++) {
sprintf(dname, "dataset %d", n);
dataset = H5Dcreate2(iof, dname, H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
VRFY((dataset > 0), dname);
/* calculate data to write */
for(i = 0; i < size; i++)
for(j = 0; j < size; j++)
outme [(i * size) + j] = n*1000 + mpi_rank;
H5Dwrite(dataset, H5T_NATIVE_DOUBLE, memspace, filespace, H5P_DEFAULT, outme);
H5Dclose(dataset);
#ifdef BARRIER_CHECKS
if(!((n+1) % 10)) {
printf("created %d datasets\n", n+1);
MPI_Barrier(MPI_COMM_WORLD);
}
#endif /* BARRIER_CHECKS */
}
H5Sclose(filespace);
H5Sclose(memspace);
H5Pclose(dcpl);
H5Fclose(iof);
HDfree(outme);
}
/* Example of using PHDF5 to create, write, and read compact dataset.
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* JRM - 8/11/04
*/
void compact_dataset(void)
{
int i, j, mpi_size, mpi_rank, size, err_num=0;
hbool_t use_gpfs = FALSE;
hid_t iof, plist, dcpl, dxpl, dataset, filespace;
hsize_t file_dims [DIM];
double * outme;
double * inme;
char dname[]="dataset";
herr_t ret;
const char *filename;
size = get_size();
for(i = 0; i < DIM; i++ )
file_dims[i] = size;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
outme = HDmalloc((size_t)(size * size * sizeof(double)));
VRFY((outme != NULL), "HDmalloc succeeded for outme");
inme = HDmalloc((size_t)(size * size * sizeof(double)));
VRFY((outme != NULL), "HDmalloc succeeded for inme");
filename = GetTestParameters();
VRFY((mpi_size <= size), "mpi_size <= size");
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
/* Define data space */
filespace = H5Screate_simple(DIM, file_dims, NULL);
/* Create a compact dataset */
dcpl = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl>=0), "dataset creation property list succeeded");
ret = H5Pset_layout(dcpl, H5D_COMPACT);
VRFY((dcpl >= 0), "set property list for compact dataset");
ret = H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_EARLY);
VRFY((ret >= 0), "set space allocation time for compact dataset");
dataset = H5Dcreate2(iof, dname, H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dcreate2 succeeded");
/* set up the collective transfer properties list */
dxpl = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl >= 0), "");
ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO);
VRFY((ret>= 0),"set independent IO collectively succeeded");
}
/* Recalculate data to write. Each process writes the same data. */
for(i = 0; i < size; i++)
for(j = 0; j < size; j++)
outme[(i * size) + j] =(i + j) * 1000;
ret = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, dxpl, outme);
VRFY((ret >= 0), "H5Dwrite succeeded");
H5Pclose(dcpl);
H5Pclose(plist);
H5Dclose(dataset);
H5Sclose(filespace);
H5Fclose(iof);
/* Open the file and dataset, read and compare the data. */
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
iof = H5Fopen(filename, H5F_ACC_RDONLY, plist);
VRFY((iof >= 0), "H5Fopen succeeded");
/* set up the collective transfer properties list */
dxpl = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl >= 0), "");
ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
ret = H5Pset_dxpl_mpio_collective_opt(dxpl,H5FD_MPIO_INDIVIDUAL_IO);
VRFY((ret>= 0),"set independent IO collectively succeeded");
}
dataset = H5Dopen2(iof, dname, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dopen2 succeeded");
ret = H5Dread(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, dxpl, inme);
VRFY((ret >= 0), "H5Dread succeeded");
/* Verify data value */
for(i = 0; i < size; i++)
for(j = 0; j < size; j++)
if(inme[(i * size) + j] != outme[(i * size) + j])
if(err_num++ < MAX_ERR_REPORT || VERBOSE_MED)
printf("Dataset Verify failed at [%d][%d]: expect %f, got %f\n", i, j, outme[(i * size) + j], inme[(i * size) + j]);
H5Pclose(plist);
H5Pclose(dxpl);
H5Dclose(dataset);
H5Fclose(iof);
HDfree(inme);
HDfree(outme);
}
/*
* Example of using PHDF5 to create, write, and read dataset and attribute
* of Null dataspace.
*
* Changes: Removed the assert that mpi_size <= the SIZE #define.
* As best I can tell, this assert isn't needed here,
* and in any case, the SIZE #define is being removed
* in an update of the functions in this file to run
* with an arbitrary number of processes.
*
* JRM - 8/24/04
*/
void null_dataset(void)
{
int mpi_size, mpi_rank;
hbool_t use_gpfs = FALSE;
hid_t iof, plist, dxpl, dataset, attr, sid;
unsigned uval=2; /* Buffer for writing to dataset */
int val=1; /* Buffer for writing to attribute */
int nelem;
char dname[]="dataset";
char attr_name[]="attribute";
herr_t ret;
const char *filename;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
filename = GetTestParameters();
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL,
facc_type, use_gpfs);
iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
/* Define data space */
sid = H5Screate(H5S_NULL);
/* Check that the null dataspace actually has 0 elements */
nelem = H5Sget_simple_extent_npoints(sid);
VRFY((nelem == 0), "H5Sget_simple_extent_npoints");
/* Create a compact dataset */
dataset = H5Dcreate2(iof, dname, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dcreate2 succeeded");
/* set up the collective transfer properties list */
dxpl = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl >= 0), "");
ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO);
VRFY((ret>= 0),"set independent IO collectively succeeded");
}
/* Write "nothing" to the dataset(with type conversion) */
ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, dxpl, &uval);
VRFY((ret >= 0), "H5Dwrite succeeded");
/* Create an attribute for the group */
attr = H5Acreate2(dataset, attr_name, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT);
VRFY((attr >= 0), "H5Acreate2");
/* Write "nothing" to the attribute(with type conversion) */
ret = H5Awrite(attr, H5T_NATIVE_INT, &val);
VRFY((ret >= 0), "H5Awrite");
H5Aclose(attr);
H5Dclose(dataset);
H5Pclose(plist);
H5Sclose(sid);
H5Fclose(iof);
/* Open the file and dataset, read and compare the data. */
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
iof = H5Fopen(filename, H5F_ACC_RDONLY, plist);
VRFY((iof >= 0), "H5Fopen succeeded");
/* set up the collective transfer properties list */
dxpl = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl >= 0), "");
ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pcreate xfer succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
ret = H5Pset_dxpl_mpio_collective_opt(dxpl,H5FD_MPIO_INDIVIDUAL_IO);
VRFY((ret>= 0),"set independent IO collectively succeeded");
}
dataset = H5Dopen2(iof, dname, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dopen2 succeeded");
/* Try reading from the dataset(make certain our buffer is unmodified) */
ret = H5Dread(dataset, H5T_NATIVE_UINT, H5S_ALL, H5S_ALL, dxpl, &uval);
VRFY((ret>=0), "H5Dread");
VRFY((uval==2), "H5Dread");
/* Open the attribute for the dataset */
attr = H5Aopen(dataset, attr_name, H5P_DEFAULT);
VRFY((attr >= 0), "H5Aopen");
/* Try reading from the attribute(make certain our buffer is unmodified) */ ret = H5Aread(attr, H5T_NATIVE_INT, &val);
VRFY((ret>=0), "H5Aread");
VRFY((val==1), "H5Aread");
H5Pclose(plist);
H5Pclose(dxpl);
H5Aclose(attr);
H5Dclose(dataset);
H5Fclose(iof);
}
/* Example of using PHDF5 to create "large" datasets. (>2GB, >4GB, >8GB)
* Actual data is _not_ written to these datasets. Dataspaces are exact
* sizes(2GB, 4GB, etc.), but the metadata for the file pushes the file over
* the boundary of interest.
*
* Changes: Removed the assert that mpi_size <= the SIZE #define.
* As best I can tell, this assert isn't needed here,
* and in any case, the SIZE #define is being removed
* in an update of the functions in this file to run
* with an arbitrary number of processes.
*
* JRM - 8/11/04
*/
void big_dataset(void)
{
int mpi_size, mpi_rank; /* MPI info */
hbool_t use_gpfs = FALSE; /* Don't use GPFS stuff for this test */
hid_t iof, /* File ID */
fapl, /* File access property list ID */
dataset, /* Dataset ID */
filespace; /* Dataset's dataspace ID */
hsize_t file_dims [4]; /* Dimensions of dataspace */
char dname[]="dataset"; /* Name of dataset */
MPI_Offset file_size; /* Size of file on disk */
herr_t ret; /* Generic return value */
const char *filename;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
/* Verify MPI_Offset can handle larger than 2GB sizes */
VRFY((sizeof(MPI_Offset) > 4), "sizeof(MPI_Offset)>4");
filename = GetTestParameters();
fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
VRFY((fapl >= 0), "create_faccess_plist succeeded");
/*
* Create >2GB HDF5 file
*/
iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
VRFY((iof >= 0), "H5Fcreate succeeded");
/* Define dataspace for 2GB dataspace */
file_dims[0]= 2;
file_dims[1]= 1024;
file_dims[2]= 1024;
file_dims[3]= 1024;
filespace = H5Screate_simple(4, file_dims, NULL);
VRFY((filespace >= 0), "H5Screate_simple succeeded");
dataset = H5Dcreate2(iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dcreate2 succeeded");
/* Close all file objects */
ret = H5Dclose(dataset);
VRFY((ret >= 0), "H5Dclose succeeded");
ret = H5Sclose(filespace);
VRFY((ret >= 0), "H5Sclose succeeded");
ret = H5Fclose(iof);
VRFY((ret >= 0), "H5Fclose succeeded");
/* Check that file of the correct size was created */
file_size = h5_get_file_size(filename, fapl);
VRFY((file_size == 2147485792ULL), "File is correct size(~2GB)");
/*
* Create >4GB HDF5 file
*/
iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
VRFY((iof >= 0), "H5Fcreate succeeded");
/* Define dataspace for 4GB dataspace */
file_dims[0]= 4;
file_dims[1]= 1024;
file_dims[2]= 1024;
file_dims[3]= 1024;
filespace = H5Screate_simple(4, file_dims, NULL);
VRFY((filespace >= 0), "H5Screate_simple succeeded");
dataset = H5Dcreate2(iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dcreate2 succeeded");
/* Close all file objects */
ret = H5Dclose(dataset);
VRFY((ret >= 0), "H5Dclose succeeded");
ret = H5Sclose(filespace);
VRFY((ret >= 0), "H5Sclose succeeded");
ret = H5Fclose(iof);
VRFY((ret >= 0), "H5Fclose succeeded");
/* Check that file of the correct size was created */
file_size = h5_get_file_size(filename, fapl);
VRFY((file_size == 4294969440ULL), "File is correct size(~4GB)");
/*
* Create >8GB HDF5 file
*/
iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
VRFY((iof >= 0), "H5Fcreate succeeded");
/* Define dataspace for 8GB dataspace */
file_dims[0]= 8;
file_dims[1]= 1024;
file_dims[2]= 1024;
file_dims[3]= 1024;
filespace = H5Screate_simple(4, file_dims, NULL);
VRFY((filespace >= 0), "H5Screate_simple succeeded");
dataset = H5Dcreate2(iof, dname, H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dcreate2 succeeded");
/* Close all file objects */
ret = H5Dclose(dataset);
VRFY((ret >= 0), "H5Dclose succeeded");
ret = H5Sclose(filespace);
VRFY((ret >= 0), "H5Sclose succeeded");
ret = H5Fclose(iof);
VRFY((ret >= 0), "H5Fclose succeeded");
/* Check that file of the correct size was created */
file_size = h5_get_file_size(filename, fapl);
VRFY((file_size == 8589936736ULL), "File is correct size(~8GB)");
/* Close fapl */
ret = H5Pclose(fapl);
VRFY((ret >= 0), "H5Pclose succeeded");
}
/* Example of using PHDF5 to read a partial written dataset. The dataset does
* not have actual data written to the entire raw data area and relies on the
* default fill value of zeros to work correctly.
*
* Changes: Removed the assert that mpi_size <= the SIZE #define.
* As best I can tell, this assert isn't needed here,
* and in any case, the SIZE #define is being removed
* in an update of the functions in this file to run
* with an arbitrary number of processes.
*
* Also added code to free dynamically allocated buffers.
*
* JRM - 8/11/04
*/
void dataset_fillvalue(void)
{
int mpi_size, mpi_rank; /* MPI info */
hbool_t use_gpfs = FALSE; /* Don't use GPFS stuff for this test */
int err_num; /* Number of errors */
hid_t iof, /* File ID */
fapl, /* File access property list ID */
dxpl, /* Data transfer property list ID */
dataset, /* Dataset ID */
memspace, /* Memory dataspace ID */
filespace; /* Dataset's dataspace ID */
char dname[]="dataset"; /* Name of dataset */
hsize_t dset_dims[4] = {0, 6, 7, 8};
hsize_t req_start[4] = {0, 0, 0, 0};
hsize_t req_count[4] = {1, 6, 7, 8};
hsize_t dset_size; /* Dataset size */
int *rdata, *wdata; /* Buffers for data to read and write */
int *twdata, *trdata; /* Temporary pointer into buffer */
int acc, i, j, k, l; /* Local index variables */
herr_t ret; /* Generic return value */
const char *filename;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
filename = GetTestParameters();
/* Set the dataset dimension to be one row more than number of processes */
/* and calculate the actual dataset size. */
dset_dims[0]=mpi_size+1;
dset_size=dset_dims[0]*dset_dims[1]*dset_dims[2]*dset_dims[3];
/* Allocate space for the buffers */
rdata=HDmalloc((size_t)(dset_size*sizeof(int)));
VRFY((rdata != NULL), "HDcalloc succeeded for read buffer");
wdata=HDmalloc((size_t)(dset_size*sizeof(int)));
VRFY((wdata != NULL), "HDmalloc succeeded for write buffer");
fapl = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
VRFY((fapl >= 0), "create_faccess_plist succeeded");
/*
* Create HDF5 file
*/
iof = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
VRFY((iof >= 0), "H5Fcreate succeeded");
filespace = H5Screate_simple(4, dset_dims, NULL);
VRFY((filespace >= 0), "File H5Screate_simple succeeded");
dataset = H5Dcreate2(iof, dname, H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dataset >= 0), "H5Dcreate2 succeeded");
memspace = H5Screate_simple(4, dset_dims, NULL);
VRFY((memspace >= 0), "Memory H5Screate_simple succeeded");
/*
* Read dataset before any data is written.
*/
/* set entire read buffer with the constant 2 */
HDmemset(rdata,2,(size_t)(dset_size*sizeof(int)));
/* Independently read the entire dataset back */
ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
VRFY((ret >= 0), "H5Dread succeeded");
/* Verify all data read are the fill value 0 */
trdata = rdata;
err_num = 0;
for(i = 0; i < (int)dset_dims[0]; i++)
for(j = 0; j < (int)dset_dims[1]; j++)
for(k = 0; k < (int)dset_dims[2]; k++)
for(l = 0; l < (int)dset_dims[3]; l++, twdata++, trdata++)
if(*trdata != 0)
if(err_num++ < MAX_ERR_REPORT || VERBOSE_MED)
printf("Dataset Verify failed at [%d][%d][%d][%d]: expect 0, got %d\n", i, j, k, l, *trdata);
if(err_num > MAX_ERR_REPORT && !VERBOSE_MED)
printf("[more errors ...]\n");
if(err_num){
printf("%d errors found in check_value\n", err_num);
nerrors++;
}
/* Barrier to ensure all processes have completed the above test. */
MPI_Barrier(MPI_COMM_WORLD);
/*
* Each process writes 1 row of data. Thus last row is not written.
*/
/* Create hyperslabs in memory and file dataspaces */
req_start[0]=mpi_rank;
ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, req_start, NULL, req_count, NULL);
VRFY((ret >= 0), "H5Sselect_hyperslab succeeded on memory dataspace");
ret = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, req_start, NULL, req_count, NULL);
VRFY((ret >= 0), "H5Sselect_hyperslab succeeded on memory dataspace");
/* Create DXPL for collective I/O */
dxpl = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
ret = H5Pset_dxpl_mpio_collective_opt(dxpl,H5FD_MPIO_INDIVIDUAL_IO);
VRFY((ret>= 0),"set independent IO collectively succeeded");
}
/* Fill write buffer with some values */
twdata=wdata;
for(i=0, acc=0; i<(int)dset_dims[0]; i++)
for(j=0; j<(int)dset_dims[1]; j++)
for(k=0; k<(int)dset_dims[2]; k++)
for(l=0; l<(int)dset_dims[3]; l++)
*twdata++ = acc++;
/* Collectively write a hyperslab of data to the dataset */
ret = H5Dwrite(dataset, H5T_NATIVE_INT, memspace, filespace, dxpl, wdata);
VRFY((ret >= 0), "H5Dwrite succeeded");
/* Barrier here, to allow MPI-posix I/O to sync */
MPI_Barrier(MPI_COMM_WORLD);
/*
* Read dataset after partial write.
*/
/* set entire read buffer with the constant 2 */
HDmemset(rdata,2,(size_t)(dset_size*sizeof(int)));
/* Independently read the entire dataset back */
ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata);
VRFY((ret >= 0), "H5Dread succeeded");
/* Verify correct data read */
twdata=wdata;
trdata=rdata;
err_num=0;
for(i=0; i<(int)dset_dims[0]; i++)
for(j=0; j<(int)dset_dims[1]; j++)
for(k=0; k<(int)dset_dims[2]; k++)
for(l=0; l<(int)dset_dims[3]; l++, twdata++, trdata++)
if(i<mpi_size) {
if(*twdata != *trdata )
if(err_num++ < MAX_ERR_REPORT || VERBOSE_MED)
printf("Dataset Verify failed at [%d][%d][%d][%d]: expect %d, got %d\n", i,j,k,l, *twdata, *trdata);
} /* end if */
else {
if(*trdata != 0)
if(err_num++ < MAX_ERR_REPORT || VERBOSE_MED)
printf("Dataset Verify failed at [%d][%d][%d][%d]: expect 0, got %d\n", i,j,k,l, *trdata);
} /* end else */
if(err_num > MAX_ERR_REPORT && !VERBOSE_MED)
printf("[more errors ...]\n");
if(err_num){
printf("%d errors found in check_value\n", err_num);
nerrors++;
}
/* Close all file objects */
ret = H5Dclose(dataset);
VRFY((ret >= 0), "H5Dclose succeeded");
ret = H5Sclose(filespace);
VRFY((ret >= 0), "H5Sclose succeeded");
ret = H5Fclose(iof);
VRFY((ret >= 0), "H5Fclose succeeded");
/* Close memory dataspace */
ret = H5Sclose(memspace);
VRFY((ret >= 0), "H5Sclose succeeded");
/* Close dxpl */
ret = H5Pclose(dxpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/* Close fapl */
ret = H5Pclose(fapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/* free the buffers */
HDfree(rdata);
HDfree(wdata);
}
/* Write multiple groups with a chunked dataset in each group collectively.
* These groups and datasets are for testing independent read later.
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* JRM - 8/16/04
*/
void collective_group_write(void)
{
int mpi_rank, mpi_size, size;
int i, j, m;
hbool_t use_gpfs = FALSE;
char gname[64], dname[32];
hid_t fid, gid, did, plist, dcpl, memspace, filespace;
DATATYPE * outme = NULL;
hsize_t chunk_origin[DIM];
hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM];
hsize_t chunk_size[2]; /* Chunk dimensions - computed shortly */
herr_t ret1, ret2;
const H5Ptest_param_t *pt;
char *filename;
int ngroups;
pt = GetTestParameters();
filename = pt->name;
ngroups = pt->count;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
size = get_size();
chunk_size[0] =(hsize_t)(size / 2);
chunk_size[1] =(hsize_t)(size / 2);
outme = HDmalloc((size_t)(size * size * sizeof(DATATYPE)));
VRFY((outme != NULL), "HDmalloc succeeded for outme");
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
H5Pclose(plist);
/* decide the hyperslab according to process number. */
get_slab(chunk_origin, chunk_dims, count, file_dims, size);
/* select hyperslab in memory and file spaces. These two operations are
* identical since the datasets are the same. */
memspace = H5Screate_simple(DIM, file_dims, NULL);
ret1 = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin,
chunk_dims, count, chunk_dims);
filespace = H5Screate_simple(DIM, file_dims, NULL);
ret2 = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin,
chunk_dims, count, chunk_dims);
VRFY((memspace>=0), "memspace");
VRFY((filespace>=0), "filespace");
VRFY((ret1>=0), "mgroup memspace selection");
VRFY((ret2>=0), "mgroup filespace selection");
dcpl = H5Pcreate(H5P_DATASET_CREATE);
ret1 = H5Pset_chunk(dcpl, 2, chunk_size);
VRFY((dcpl>=0), "dataset creation property");
VRFY((ret1>=0), "set chunk for dataset creation property");
/* creates ngroups groups under the root group, writes chunked
* datasets in parallel. */
for(m = 0; m < ngroups; m++) {
sprintf(gname, "group%d", m);
gid = H5Gcreate2(fid, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((gid > 0), gname);
sprintf(dname, "dataset%d", m);
did = H5Dcreate2(gid, dname, H5T_NATIVE_INT, filespace, H5P_DEFAULT, dcpl, H5P_DEFAULT);
VRFY((did > 0), dname);
for(i = 0; i < size; i++)
for(j = 0; j < size; j++)
outme[(i * size) + j] =(i + j) * 1000 + mpi_rank;
H5Dwrite(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT,
outme);
H5Dclose(did);
H5Gclose(gid);
#ifdef BARRIER_CHECKS
if(!((m+1) % 10)) {
printf("created %d groups\n", m+1);
MPI_Barrier(MPI_COMM_WORLD);
}
#endif /* BARRIER_CHECKS */
}
H5Pclose(dcpl);
H5Sclose(filespace);
H5Sclose(memspace);
H5Fclose(fid);
HDfree(outme);
}
/* Let two sets of processes open and read different groups and chunked
* datasets independently.
*/
void independent_group_read(void)
{
int mpi_rank, m;
hid_t plist, fid;
hbool_t use_gpfs = FALSE;
const H5Ptest_param_t *pt;
char *filename;
int ngroups;
pt = GetTestParameters();
filename = pt->name;
ngroups = pt->count;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
fid = H5Fopen(filename, H5F_ACC_RDONLY, plist);
H5Pclose(plist);
/* open groups and read datasets. Odd number processes read even number
* groups from the end; even number processes read odd number groups
* from the beginning. */
if(mpi_rank%2==0) {
for(m=ngroups-1; m==0; m-=2)
group_dataset_read(fid, mpi_rank, m);
} else {
for(m=0; m<ngroups; m+=2)
group_dataset_read(fid, mpi_rank, m);
}
H5Fclose(fid);
}
/* Open and read datasets and compare data
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* Also added code to verify the results of dynamic memory
* allocations, and to free dynamically allocated memeory
* when we are done with it.
*
* JRM - 8/16/04
*/
static void
group_dataset_read(hid_t fid, int mpi_rank, int m)
{
int ret, i, j, size;
char gname[64], dname[32];
hid_t gid, did;
DATATYPE *outdata = NULL;
DATATYPE *indata = NULL;
size = get_size();
indata =(DATATYPE*)HDmalloc((size_t)(size * size * sizeof(DATATYPE)));
VRFY((indata != NULL), "HDmalloc succeeded for indata");
outdata =(DATATYPE*)HDmalloc((size_t)(size * size * sizeof(DATATYPE)));
VRFY((outdata != NULL), "HDmalloc succeeded for outdata");
/* open every group under root group. */
sprintf(gname, "group%d", m);
gid = H5Gopen2(fid, gname, H5P_DEFAULT);
VRFY((gid > 0), gname);
/* check the data. */
sprintf(dname, "dataset%d", m);
did = H5Dopen2(gid, dname, H5P_DEFAULT);
VRFY((did>0), dname);
H5Dread(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, indata);
/* this is the original value */
for(i=0; i<size; i++)
for(j=0; j<size; j++) {
outdata[(i * size) + j] =(i+j)*1000 + mpi_rank;
}
/* compare the original value(outdata) to the value in file(indata).*/
ret = check_value(indata, outdata, size);
VRFY((ret==0), "check the data");
H5Dclose(did);
H5Gclose(gid);
HDfree(indata);
HDfree(outdata);
}
/*
* Example of using PHDF5 to create multiple groups. Under the root group,
* it creates ngroups groups. Under the first group just created, it creates
* recursive subgroups of depth GROUP_DEPTH. In each created group, it
* generates NDATASETS datasets. Each process write a hyperslab of an array
* into the file. The structure is like
*
* root group
* |
* ---------------------------- ... ... ------------------------
* | | | ... ... | |
* group0*+' group1*+' group2*+' ... ... group ngroups*+'
* |
* 1st_child_group*'
* |
* 2nd_child_group*'
* |
* :
* :
* |
* GROUP_DEPTHth_child_group*'
*
* * means the group has dataset(s).
* + means the group has attribute(s).
* ' means the datasets in the groups have attribute(s).
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* JRM - 8/16/04
*/
void multiple_group_write(void)
{
int mpi_rank, mpi_size, size;
int m;
hbool_t use_gpfs = FALSE;
char gname[64];
hid_t fid, gid, plist, memspace, filespace;
hsize_t chunk_origin[DIM];
hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM];
herr_t ret;
const H5Ptest_param_t *pt;
char *filename;
int ngroups;
pt = GetTestParameters();
filename = pt->name;
ngroups = pt->count;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
size = get_size();
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
H5Pclose(plist);
/* decide the hyperslab according to process number. */
get_slab(chunk_origin, chunk_dims, count, file_dims, size);
/* select hyperslab in memory and file spaces. These two operations are
* identical since the datasets are the same. */
memspace = H5Screate_simple(DIM, file_dims, NULL);
VRFY((memspace>=0), "memspace");
ret = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin,
chunk_dims, count, chunk_dims);
VRFY((ret>=0), "mgroup memspace selection");
filespace = H5Screate_simple(DIM, file_dims, NULL);
VRFY((filespace>=0), "filespace");
ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin,
chunk_dims, count, chunk_dims);
VRFY((ret>=0), "mgroup filespace selection");
/* creates ngroups groups under the root group, writes datasets in
* parallel. */
for(m = 0; m < ngroups; m++) {
sprintf(gname, "group%d", m);
gid = H5Gcreate2(fid, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((gid > 0), gname);
/* create attribute for these groups. */
write_attribute(gid, is_group, m);
if(m != 0)
write_dataset(memspace, filespace, gid);
H5Gclose(gid);
#ifdef BARRIER_CHECKS
if(!((m+1) % 10)) {
printf("created %d groups\n", m+1);
MPI_Barrier(MPI_COMM_WORLD);
}
#endif /* BARRIER_CHECKS */
}
/* recursively creates subgroups under the first group. */
gid = H5Gopen2(fid, "group0", H5P_DEFAULT);
create_group_recursive(memspace, filespace, gid, 0);
ret = H5Gclose(gid);
VRFY((ret>=0), "H5Gclose");
ret = H5Sclose(filespace);
VRFY((ret>=0), "H5Sclose");
ret = H5Sclose(memspace);
VRFY((ret>=0), "H5Sclose");
ret = H5Fclose(fid);
VRFY((ret>=0), "H5Fclose");
}
/*
* In a group, creates NDATASETS datasets. Each process writes a hyperslab
* of a data array to the file.
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* JRM - 8/16/04
*/
static void
write_dataset(hid_t memspace, hid_t filespace, hid_t gid)
{
int i, j, n, size;
int mpi_rank, mpi_size;
char dname[32];
DATATYPE * outme = NULL;
hid_t did;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
size = get_size();
outme = HDmalloc((size_t)(size * size * sizeof(double)));
VRFY((outme != NULL), "HDmalloc succeeded for outme");
for(n = 0; n < NDATASET; n++) {
sprintf(dname, "dataset%d", n);
did = H5Dcreate2(gid, dname, H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((did > 0), dname);
for(i = 0; i < size; i++)
for(j = 0; j < size; j++)
outme[(i * size) + j] = n * 1000 + mpi_rank;
H5Dwrite(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, outme);
/* create attribute for these datasets.*/
write_attribute(did, is_dset, n);
H5Dclose(did);
}
HDfree(outme);
}
/*
* Creates subgroups of depth GROUP_DEPTH recursively. Also writes datasets
* in parallel in each group.
*/
static void
create_group_recursive(hid_t memspace, hid_t filespace, hid_t gid, int counter)
{
hid_t child_gid;
int mpi_rank;
char gname[64];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
#ifdef BARRIER_CHECKS
if(!((counter+1) % 10)) {
printf("created %dth child groups\n", counter+1);
MPI_Barrier(MPI_COMM_WORLD);
}
#endif /* BARRIER_CHECKS */
sprintf(gname, "%dth_child_group", counter+1);
child_gid = H5Gcreate2(gid, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((child_gid > 0), gname);
/* write datasets in parallel. */
write_dataset(memspace, filespace, gid);
if(counter < GROUP_DEPTH )
create_group_recursive(memspace, filespace, child_gid, counter+1);
H5Gclose(child_gid);
}
/*
* This function is to verify the data from multiple group testing. It opens
* every dataset in every group and check their correctness.
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* JRM - 8/11/04
*/
void multiple_group_read(void)
{
int mpi_rank, mpi_size, error_num, size;
int m;
hbool_t use_gpfs = FALSE;
char gname[64];
hid_t plist, fid, gid, memspace, filespace;
hsize_t chunk_origin[DIM];
hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM];
const H5Ptest_param_t *pt;
char *filename;
int ngroups;
pt = GetTestParameters();
filename = pt->name;
ngroups = pt->count;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
size = get_size();
plist = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type, use_gpfs);
fid = H5Fopen(filename, H5F_ACC_RDONLY, plist);
H5Pclose(plist);
/* decide hyperslab for each process */
get_slab(chunk_origin, chunk_dims, count, file_dims, size);
/* select hyperslab for memory and file space */
memspace = H5Screate_simple(DIM, file_dims, NULL);
H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin, chunk_dims,
count, chunk_dims);
filespace = H5Screate_simple(DIM, file_dims, NULL);
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims,
count, chunk_dims);
/* open every group under root group. */
for(m=0; m<ngroups; m++) {
sprintf(gname, "group%d", m);
gid = H5Gopen2(fid, gname, H5P_DEFAULT);
VRFY((gid > 0), gname);
/* check the data. */
if(m != 0)
if((error_num = read_dataset(memspace, filespace, gid))>0)
nerrors += error_num;
/* check attribute.*/
error_num = 0;
if((error_num = read_attribute(gid, is_group, m))>0 )
nerrors += error_num;
H5Gclose(gid);
#ifdef BARRIER_CHECKS
if(!((m+1)%10))
MPI_Barrier(MPI_COMM_WORLD);
#endif /* BARRIER_CHECKS */
}
/* open all the groups in vertical direction. */
gid = H5Gopen2(fid, "group0", H5P_DEFAULT);
VRFY((gid>0), "group0");
recursive_read_group(memspace, filespace, gid, 0);
H5Gclose(gid);
H5Sclose(filespace);
H5Sclose(memspace);
H5Fclose(fid);
}
/*
* This function opens all the datasets in a certain, checks the data using
* dataset_vrfy function.
*
* Changes: Updated function to use a dynamically calculated size,
* instead of the old SIZE #define. This should allow it
* to function with an arbitrary number of processors.
*
* JRM - 8/11/04
*/
static int
read_dataset(hid_t memspace, hid_t filespace, hid_t gid)
{
int i, j, n, mpi_rank, mpi_size, size, attr_errors=0, vrfy_errors=0;
char dname[32];
DATATYPE *outdata = NULL, *indata = NULL;
hid_t did;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
size = get_size();
indata =(DATATYPE*)HDmalloc((size_t)(size * size * sizeof(DATATYPE)));
VRFY((indata != NULL), "HDmalloc succeeded for indata");
outdata =(DATATYPE*)HDmalloc((size_t)(size * size * sizeof(DATATYPE)));
VRFY((outdata != NULL), "HDmalloc succeeded for outdata");
for(n=0; n<NDATASET; n++) {
sprintf(dname, "dataset%d", n);
did = H5Dopen2(gid, dname, H5P_DEFAULT);
VRFY((did>0), dname);
H5Dread(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT,
indata);
/* this is the original value */
for(i=0; i<size; i++)
for(j=0; j<size; j++) {
*outdata = n*1000 + mpi_rank;
outdata++;
}
outdata -= size * size;
/* compare the original value(outdata) to the value in file(indata).*/
vrfy_errors = check_value(indata, outdata, size);
/* check attribute.*/
if((attr_errors = read_attribute(did, is_dset, n))>0 )
vrfy_errors += attr_errors;
H5Dclose(did);
}
HDfree(indata);
HDfree(outdata);
return vrfy_errors;
}
/*
* This recursive function opens all the groups in vertical direction and
* checks the data.
*/
static void
recursive_read_group(hid_t memspace, hid_t filespace, hid_t gid, int counter)
{
hid_t child_gid;
int mpi_rank, err_num=0;
char gname[64];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
#ifdef BARRIER_CHECKS
if((counter+1) % 10)
MPI_Barrier(MPI_COMM_WORLD);
#endif /* BARRIER_CHECKS */
if((err_num = read_dataset(memspace, filespace, gid)) )
nerrors += err_num;
if(counter < GROUP_DEPTH ) {
sprintf(gname, "%dth_child_group", counter+1);
child_gid = H5Gopen2(gid, gname, H5P_DEFAULT);
VRFY((child_gid>0), gname);
recursive_read_group(memspace, filespace, child_gid, counter+1);
H5Gclose(child_gid);
}
}
/* Create and write attribute for a group or a dataset. For groups, attribute
* is a scalar datum; for dataset, it is a one-dimensional array.
*/
static void
write_attribute(hid_t obj_id, int this_type, int num)
{
hid_t sid, aid;
hsize_t dspace_dims[1]={8};
int i, mpi_rank, attr_data[8], dspace_rank=1;
char attr_name[32];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
if(this_type == is_group) {
sprintf(attr_name, "Group Attribute %d", num);
sid = H5Screate(H5S_SCALAR);
aid = H5Acreate2(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(aid, H5T_NATIVE_INT, &num);
H5Aclose(aid);
H5Sclose(sid);
} /* end if */
else if(this_type == is_dset) {
sprintf(attr_name, "Dataset Attribute %d", num);
for(i=0; i<8; i++)
attr_data[i] = i;
sid = H5Screate_simple(dspace_rank, dspace_dims, NULL);
aid = H5Acreate2(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(aid, H5T_NATIVE_INT, attr_data);
H5Aclose(aid);
H5Sclose(sid);
} /* end else-if */
}
/* Read and verify attribute for group or dataset. */
static int
read_attribute(hid_t obj_id, int this_type, int num)
{
hid_t aid;
hsize_t group_block[2]={1,1}, dset_block[2]={1, 8};
int i, mpi_rank, in_num, in_data[8], out_data[8], vrfy_errors = 0;
char attr_name[32];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
if(this_type == is_group) {
sprintf(attr_name, "Group Attribute %d", num);
aid = H5Aopen(obj_id, attr_name, H5P_DEFAULT);
if(MAINPROCESS) {
H5Aread(aid, H5T_NATIVE_INT, &in_num);
vrfy_errors = dataset_vrfy(NULL, NULL, NULL, group_block, &in_num, &num);
}
H5Aclose(aid);
}
else if(this_type == is_dset) {
sprintf(attr_name, "Dataset Attribute %d", num);
for(i=0; i<8; i++)
out_data[i] = i;
aid = H5Aopen(obj_id, attr_name, H5P_DEFAULT);
if(MAINPROCESS) {
H5Aread(aid, H5T_NATIVE_INT, in_data);
vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data, out_data);
}
H5Aclose(aid);
}
return vrfy_errors;
}
/* This functions compares the original data with the read-in data for its
* hyperslab part only by process ID.
*
* Changes: Modified function to use a passed in size parameter
* instead of the old SIZE #define. This should let us
* run with an arbitrary number of processes.
*
* JRM - 8/16/04
*/
static int
check_value(DATATYPE *indata, DATATYPE *outdata, int size)
{
int mpi_rank, mpi_size, err_num=0;
hsize_t i, j;
hsize_t chunk_origin[DIM];
hsize_t chunk_dims[DIM], count[DIM];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
get_slab(chunk_origin, chunk_dims, count, NULL, size);
indata += chunk_origin[0]*size;
outdata += chunk_origin[0]*size;
for(i=chunk_origin[0]; i<(chunk_origin[0]+chunk_dims[0]); i++)
for(j=chunk_origin[1]; j<(chunk_origin[1]+chunk_dims[1]); j++) {
if(*indata != *outdata )
if(err_num++ < MAX_ERR_REPORT || VERBOSE_MED)
printf("Dataset Verify failed at [%lu][%lu](row %lu, col%lu): expect %d, got %d\n",(unsigned long)i,(unsigned long)j,(unsigned long)i,(unsigned long)j, *outdata, *indata);
}
if(err_num > MAX_ERR_REPORT && !VERBOSE_MED)
printf("[more errors ...]\n");
if(err_num)
printf("%d errors found in check_value\n", err_num);
return err_num;
}
/* Decide the portion of data chunk in dataset by process ID.
*
* Changes: Modified function to use a passed in size parameter
* instead of the old SIZE #define. This should let us
* run with an arbitrary number of processes.
*
* JRM - 8/11/04
*/
static void
get_slab(hsize_t chunk_origin[], hsize_t chunk_dims[], hsize_t count[],
hsize_t file_dims[], int size)
{
int mpi_rank, mpi_size;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
if(chunk_origin != NULL) {
chunk_origin[0] = mpi_rank *(size/mpi_size);
chunk_origin[1] = 0;
}
if(chunk_dims != NULL) {
chunk_dims[0] = size/mpi_size;
chunk_dims[1] = size;
}
if(file_dims != NULL)
file_dims[0] = file_dims[1] = size;
if(count != NULL)
count[0] = count[1] = 1;
}
/*
* This function is based on bug demonstration code provided by Thomas
* Guignon(thomas.guignon@ifp.fr), and is intended to verify the
* correctness of my fix for that bug.
*
* In essence, the bug appeared when at least one process attempted to
* write a point selection -- for which collective I/O is not supported,
* and at least one other attempted to write some other type of selection
* for which collective I/O is supported.
*
* Since the processes did not compare notes before performing the I/O,
* some would attempt collective I/O while others performed independent
* I/O. A hang resulted.
*
* This function reproduces this situation. At present the test hangs
* on failure.
* JRM - 9/13/04
*
* Changes: None.
*/
#define N 4
void io_mode_confusion(void)
{
/*
* HDF5 APIs definitions
*/
const int rank = 1;
const char *dataset_name = "IntArray";
hid_t file_id, dset_id; /* file and dataset identifiers */
hid_t filespace, memspace; /* file and memory dataspace */
/* identifiers */
hsize_t dimsf[1]; /* dataset dimensions */
int data[N] = {1}; /* pointer to data buffer to write */
hsize_t coord[N] = {0L,1L,2L,3L};
hid_t plist_id; /* property list identifier */
herr_t status;
/*
* MPI variables
*/
int mpi_size, mpi_rank;
/*
* test bed related variables
*/
const char * fcn_name = "io_mode_confusion";
const hbool_t verbose = FALSE;
const H5Ptest_param_t * pt;
char * filename;
pt = GetTestParameters();
filename = pt->name;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
/*
* Set up file access property list with parallel I/O access
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Setting up property list.\n",
mpi_rank, fcn_name);
plist_id = H5Pcreate(H5P_FILE_ACCESS);
VRFY((plist_id != -1), "H5Pcreate() failed");
status = H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);
VRFY((status >= 0 ), "H5Pset_fapl_mpio() failed");
/*
* Create a new file collectively and release property list identifier.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Creating new file.\n", mpi_rank, fcn_name);
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
VRFY((file_id >= 0 ), "H5Fcreate() failed");
status = H5Pclose(plist_id);
VRFY((status >= 0 ), "H5Pclose() failed");
/*
* Create the dataspace for the dataset.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Creating the dataspace for the dataset.\n",
mpi_rank, fcn_name);
dimsf[0] = N;
filespace = H5Screate_simple(rank, dimsf, NULL);
VRFY((filespace >= 0 ), "H5Screate_simple() failed.");
/*
* Create the dataset with default properties and close filespace.
*/
if(verbose )
HDfprintf(stdout,
"%0d:%s: Creating the dataset, and closing filespace.\n",
mpi_rank, fcn_name);
dset_id = H5Dcreate2(file_id, dataset_name, H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dset_id >= 0 ), "H5Dcreate2() failed");
status = H5Sclose(filespace);
VRFY((status >= 0 ), "H5Sclose() failed");
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling H5Screate_simple().\n",
mpi_rank, fcn_name);
memspace = H5Screate_simple(rank, dimsf, NULL);
VRFY((memspace >= 0 ), "H5Screate_simple() failed.");
if(mpi_rank == 0 ) {
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling H5Sselect_all(memspace).\n",
mpi_rank, fcn_name);
status = H5Sselect_all(memspace);
VRFY((status >= 0 ), "H5Sselect_all() failed");
} else {
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling H5Sselect_none(memspace).\n",
mpi_rank, fcn_name);
status = H5Sselect_none(memspace);
VRFY((status >= 0 ), "H5Sselect_none() failed");
}
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling MPI_Barrier().\n",
mpi_rank, fcn_name);
MPI_Barrier(MPI_COMM_WORLD);
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling H5Dget_space().\n",
mpi_rank, fcn_name);
filespace = H5Dget_space(dset_id);
VRFY((filespace >= 0 ), "H5Dget_space() failed");
/* select all */
if(mpi_rank == 0 ) {
if(verbose )
HDfprintf(stdout,
"%0d:%s: Calling H5Sselect_elements() -- set up hang?\n",
mpi_rank, fcn_name);
status = H5Sselect_elements(filespace, H5S_SELECT_SET, N, (const hsize_t *)&coord);
VRFY((status >= 0 ), "H5Sselect_elements() failed");
} else { /* select nothing */
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling H5Sselect_none().\n",
mpi_rank, fcn_name);
status = H5Sselect_none(filespace);
VRFY((status >= 0 ), "H5Sselect_none() failed");
}
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling MPI_Barrier().\n",
mpi_rank, fcn_name);
MPI_Barrier(MPI_COMM_WORLD);
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling H5Pcreate().\n", mpi_rank, fcn_name);
plist_id = H5Pcreate(H5P_DATASET_XFER);
VRFY((plist_id != -1 ), "H5Pcreate() failed");
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling H5Pset_dxpl_mpio().\n",
mpi_rank, fcn_name);
status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
VRFY((status >= 0 ), "H5Pset_dxpl_mpio() failed");
if(dxfer_coll_type == DXFER_INDEPENDENT_IO) {
status = H5Pset_dxpl_mpio_collective_opt(plist_id, H5FD_MPIO_INDIVIDUAL_IO);
VRFY((status>= 0),"set independent IO collectively succeeded");
}
if(verbose )
HDfprintf(stdout, "%0d:%s: Calling H5Dwrite() -- hang here?.\n",
mpi_rank, fcn_name);
status = H5Dwrite(dset_id, H5T_NATIVE_INT, memspace, filespace,
plist_id, data);
if(verbose )
HDfprintf(stdout, "%0d:%s: Returned from H5Dwrite(), status=%d.\n",
mpi_rank, fcn_name, status);
VRFY((status >= 0 ), "H5Dwrite() failed");
/*
* Close/release resources.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Cleaning up from test.\n",
mpi_rank, fcn_name);
status = H5Dclose(dset_id);
VRFY((status >= 0 ), "H5Dclose() failed");
status = H5Sclose(filespace);
VRFY((status >= 0 ), "H5Dclose() failed");
status = H5Sclose(memspace);
VRFY((status >= 0 ), "H5Sclose() failed");
status = H5Pclose(plist_id);
VRFY((status >= 0 ), "H5Pclose() failed");
status = H5Fclose(file_id);
VRFY((status >= 0 ), "H5Fclose() failed");
if(verbose )
HDfprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name);
return;
} /* io_mode_confusion() */
#undef N
/*
* At present, the object header code maintains an image of its on disk
* representation, which is updates as necessary instead of generating on
* request.
*
* Prior to the fix that this test in designed to verify, the image of the
* on disk representation was only updated on flush -- not when the object
* header was marked clean.
*
* This worked perfectly well as long as all writes of a given object
* header were written from a single process. However, with the implementation
* of round robin metadata data writes in parallel HDF5, this is no longer
* the case -- it is possible for a given object header to be flushed from
* several different processes, with the object header simply being marked
* clean in all other processes on each flush. This resulted in NULL or
* out of data object header information being written to disk.
*
* To repair this, I modified the object header code to update its
* on disk image both on flush on when marked clean.
*
* This test is directed at verifying that the fix performs as expected.
*
* The test functions by creating a HDF5 file with several small datasets,
* and then flushing the file. This should result of at least one of
* the associated object headers being flushed by a process other than
* process 0.
*
* Then for each data set, add an attribute and flush the file again.
*
* Close the file and re-open it.
*
* Open the each of the data sets in turn. If all opens are successful,
* the test passes. Otherwise the test fails.
*
* Note that this test will probably become irrelevent shortly, when we
* land the journaling modifications on the trunk -- at which point all
* cache clients will have to construct on disk images on demand.
*
* JRM -- 10/13/10
*
* Changes:
* Break it into two parts, a writer to write the file and a reader
* the correctness of the writer. AKC -- 2010/10/27
*/
#define NUM_DATA_SETS 4
#define LOCAL_DATA_SIZE 4
#define LARGE_ATTR_SIZE 256
/* Since all even and odd processes are split into writer and reader comm
* respectively, process 0 and 1 in COMM_WORLD become the root process of
* the writer and reader comm respectively.
*/
#define Writer_Root 0
#define Reader_Root 1
#define Reader_wait(mpi_err, xsteps) \
mpi_err = MPI_Bcast(&xsteps, 1, MPI_INT, Writer_Root, MPI_COMM_WORLD)
#define Reader_result(mpi_err, xsteps_done) \
mpi_err = MPI_Bcast(&xsteps_done, 1, MPI_INT, Reader_Root, MPI_COMM_WORLD)
#define Reader_check(mpi_err, xsteps, xsteps_done) \
{ Reader_wait(mpi_err, xsteps); \
Reader_result(mpi_err, xsteps_done);}
/* object names used by both rr_obj_hdr_flush_confusion and
* rr_obj_hdr_flush_confusion_reader.
*/
const char * dataset_name[NUM_DATA_SETS] =
{
"dataset_0",
"dataset_1",
"dataset_2",
"dataset_3"
};
const char * att_name[NUM_DATA_SETS] =
{
"attribute_0",
"attribute_1",
"attribute_2",
"attribute_3"
};
const char * lg_att_name[NUM_DATA_SETS] =
{
"large_attribute_0",
"large_attribute_1",
"large_attribute_2",
"large_attribute_3"
};
void rr_obj_hdr_flush_confusion(void)
{
/* MPI variables */
/* private communicator size and rank */
int mpi_size;
int mpi_rank;
int mrc; /* mpi error code */
int is_reader; /* 1 for reader process; 0 for writer process. */
MPI_Comm comm;
/* test bed related variables */
const char * fcn_name = "rr_obj_hdr_flush_confusion";
const hbool_t verbose = FALSE;
/* Create two new private communicators from MPI_COMM_WORLD.
* Even and odd ranked processes go to comm_writers and comm_readers
* respectively.
*/
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
if (mpi_size < 3){
HDfprintf(stdout, "%s needs at least 3 processes to run. Terminated.\n",
fcn_name);
nerrors++;
return;
}
is_reader = mpi_rank % 2;
mrc = MPI_Comm_split(MPI_COMM_WORLD, is_reader, mpi_rank, &comm);
VRFY((mrc==MPI_SUCCESS), "MPI_Comm_split");
/* The reader proocesses branches off to do reading
* while the writer processes continues to do writing
* Whenever writers finish one writing step, including a H5Fflush,
* they inform the readers, via MPI_COMM_WORLD, to verify.
* They will wait for the result from the readers before doing the next
* step. When all steps are done, they inform readers to end.
*/
if (is_reader)
rr_obj_hdr_flush_confusion_reader(comm);
else
rr_obj_hdr_flush_confusion_writer(comm);
MPI_Comm_free(&comm);
if(verbose )
HDfprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name);
return;
} /* rr_obj_hdr_flush_confusion() */
void rr_obj_hdr_flush_confusion_writer(MPI_Comm comm)
{
int i;
int j;
hid_t file_id = -1;
hid_t fapl_id = -1;
hid_t dxpl_id = -1;
hid_t att_id[NUM_DATA_SETS];
hid_t att_space[NUM_DATA_SETS];
hid_t lg_att_id[NUM_DATA_SETS];
hid_t lg_att_space[NUM_DATA_SETS];
hid_t disk_space[NUM_DATA_SETS];
hid_t mem_space[NUM_DATA_SETS];
hid_t dataset[NUM_DATA_SETS];
hsize_t att_size[1];
hsize_t lg_att_size[1];
hsize_t disk_count[1];
hsize_t disk_size[1];
hsize_t disk_start[1];
hsize_t mem_count[1];
hsize_t mem_size[1];
hsize_t mem_start[1];
herr_t err;
double data[LOCAL_DATA_SIZE];
double att[LOCAL_DATA_SIZE];
double lg_att[LARGE_ATTR_SIZE];
/* MPI variables */
/* world communication size and rank */
int mpi_world_size;
int mpi_world_rank;
/* private communicator size and rank */
int mpi_size;
int mpi_rank;
int mrc; /* mpi error code */
/* steps to verify and have been verified */
int steps = 0;
int steps_done = 0;
/* test bed related variables */
const char * fcn_name = "rr_obj_hdr_flush_confusion_writer";
const hbool_t verbose = FALSE;
const H5Ptest_param_t * pt;
char * filename;
/*
* setup test bed related variables:
*/
pt = (const H5Ptest_param_t *)GetTestParameters();
filename = pt->name;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_world_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_world_size);
MPI_Comm_rank(comm, &mpi_rank);
MPI_Comm_size(comm, &mpi_size);
/*
* Set up file access property list with parallel I/O access
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Setting up property list.\n",
mpi_rank, fcn_name);
fapl_id = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl_id != -1), "H5Pcreate(H5P_FILE_ACCESS) failed");
err = H5Pset_fapl_mpio(fapl_id, comm, MPI_INFO_NULL);
VRFY((err >= 0 ), "H5Pset_fapl_mpio() failed");
/*
* Create a new file collectively and release property list identifier.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Creating new file \"%s\".\n",
mpi_rank, fcn_name, filename);
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((file_id >= 0 ), "H5Fcreate() failed");
err = H5Pclose(fapl_id);
VRFY((err >= 0 ), "H5Pclose(fapl_id) failed");
/*
* Step 1: create the data sets and write data.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Creating the datasets.\n",
mpi_rank, fcn_name);
disk_size[0] = (hsize_t)(LOCAL_DATA_SIZE * mpi_size);
mem_size[0] = (hsize_t)(LOCAL_DATA_SIZE);
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
disk_space[i] = H5Screate_simple(1, disk_size, NULL);
VRFY((disk_space[i] >= 0), "H5Screate_simple(1) failed.\n");
dataset[i] = H5Dcreate2(file_id, dataset_name[i], H5T_NATIVE_DOUBLE,
disk_space[i], H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dataset[i] >= 0), "H5Dcreate(1) failed.\n");
}
/*
* setup data transfer property list
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Setting up dxpl.\n", mpi_rank, fcn_name);
dxpl_id = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl_id != -1), "H5Pcreate(H5P_DATASET_XFER) failed.\n");
err = H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE);
VRFY((err >= 0),
"H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) failed.\n");
/*
* write data to the data sets
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Writing datasets.\n", mpi_rank, fcn_name);
disk_count[0] = (hsize_t)(LOCAL_DATA_SIZE);
disk_start[0] = (hsize_t)(LOCAL_DATA_SIZE * mpi_rank);
mem_count[0] = (hsize_t)(LOCAL_DATA_SIZE);
mem_start[0] = (hsize_t)(0);
for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
data[j] = (double)(mpi_rank + 1);
}
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
err = H5Sselect_hyperslab(disk_space[i], H5S_SELECT_SET, disk_start,
NULL, disk_count, NULL);
VRFY((err >= 0), "H5Sselect_hyperslab(1) failed.\n");
mem_space[i] = H5Screate_simple(1, mem_size, NULL);
VRFY((mem_space[i] >= 0), "H5Screate_simple(2) failed.\n");
err = H5Sselect_hyperslab(mem_space[i], H5S_SELECT_SET,
mem_start, NULL, mem_count, NULL);
VRFY((err >= 0), "H5Sselect_hyperslab(2) failed.\n");
err = H5Dwrite(dataset[i], H5T_NATIVE_DOUBLE, mem_space[i],
disk_space[i], dxpl_id, data);
VRFY((err >= 0), "H5Dwrite(1) failed.\n");
for ( j = 0; j < LOCAL_DATA_SIZE; j++ )
data[j] *= 10.0;
}
/*
* close the data spaces
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing dataspaces.\n", mpi_rank, fcn_name);
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
err = H5Sclose(disk_space[i]);
VRFY((err >= 0), "H5Sclose(disk_space[i]) failed.\n");
err = H5Sclose(mem_space[i]);
VRFY((err >= 0), "H5Sclose(mem_space[i]) failed.\n");
}
/* End of Step 1: create the data sets and write data. */
/*
* flush the metadata cache
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: flushing metadata cache.\n",
mpi_rank, fcn_name);
err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
VRFY((err >= 0), "H5Fflush(1) failed.\n");
/* Tell the reader to check the file up to steps. */
steps++;
Reader_check(mrc, steps, steps_done);
/*
* Step 2: write attributes to each dataset
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: writing attributes.\n", mpi_rank, fcn_name);
att_size[0] = (hsize_t)(LOCAL_DATA_SIZE);
for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
att[j] = (double)(j + 1);
}
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
att_space[i] = H5Screate_simple(1, att_size, NULL);
VRFY((att_space[i] >= 0), "H5Screate_simple(3) failed.\n");
att_id[i] = H5Acreate2(dataset[i], att_name[i], H5T_NATIVE_DOUBLE,
att_space[i], H5P_DEFAULT, H5P_DEFAULT);
VRFY((att_id[i] >= 0), "H5Acreate(1) failed.\n");
err = H5Awrite(att_id[i], H5T_NATIVE_DOUBLE, att);
VRFY((err >= 0), "H5Awrite(1) failed.\n");
for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
att[j] /= 10.0;
}
}
/*
* close attribute IDs and spaces
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing attr ids and spaces .\n",
mpi_rank, fcn_name);
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
err = H5Sclose(att_space[i]);
VRFY((err >= 0), "H5Sclose(att_space[i]) failed.\n");
err = H5Aclose(att_id[i]);
VRFY((err >= 0), "H5Aclose(att_id[i]) failed.\n");
}
/* End of Step 2: write attributes to each dataset */
/*
* flush the metadata cache again
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: flushing metadata cache.\n",
mpi_rank, fcn_name);
err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
VRFY((err >= 0), "H5Fflush(2) failed.\n");
/* Tell the reader to check the file up to steps. */
steps++;
Reader_check(mrc, steps, steps_done);
/*
* Step 3: write large attributes to each dataset
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: writing large attributes.\n",
mpi_rank, fcn_name);
lg_att_size[0] = (hsize_t)(LARGE_ATTR_SIZE);
for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
lg_att[j] = (double)(j + 1);
}
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
lg_att_space[i] = H5Screate_simple(1, lg_att_size, NULL);
VRFY((lg_att_space[i] >= 0), "H5Screate_simple(4) failed.\n");
lg_att_id[i] = H5Acreate2(dataset[i], lg_att_name[i], H5T_NATIVE_DOUBLE,
lg_att_space[i], H5P_DEFAULT, H5P_DEFAULT);
VRFY((lg_att_id[i] >= 0), "H5Acreate(2) failed.\n");
err = H5Awrite(lg_att_id[i], H5T_NATIVE_DOUBLE, lg_att);
VRFY((err >= 0), "H5Awrite(2) failed.\n");
for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
lg_att[j] /= 10.0;
}
}
/* Step 3: write large attributes to each dataset */
/*
* flush the metadata cache yet again to clean the object headers.
*
* This is an attempt to crate a situation where we have dirty
* object header continuation chunks, but clean opject headers
* to verify a speculative bug fix -- it doesn't seem to work,
* but I will leave the code in anyway, as the object header
* code is going to change a lot in the near future.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: flushing metadata cache.\n",
mpi_rank, fcn_name);
err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
VRFY((err >= 0), "H5Fflush(3) failed.\n");
/* Tell the reader to check the file up to steps. */
steps++;
Reader_check(mrc, steps, steps_done);
/*
* Step 4: write different large attributes to each dataset
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: writing different large attributes.\n",
mpi_rank, fcn_name);
for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
lg_att[j] = (double)(j + 2);
}
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
err = H5Awrite(lg_att_id[i], H5T_NATIVE_DOUBLE, lg_att);
VRFY((err >= 0), "H5Awrite(2) failed.\n");
for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
lg_att[j] /= 10.0;
}
}
/* End of Step 4: write different large attributes to each dataset */
/*
* flush the metadata cache again
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: flushing metadata cache.\n",
mpi_rank, fcn_name);
err = H5Fflush(file_id, H5F_SCOPE_GLOBAL);
VRFY((err >= 0), "H5Fflush(3) failed.\n");
/* Tell the reader to check the file up to steps. */
steps++;
Reader_check(mrc, steps, steps_done);
/* Step 5: Close all objects and the file */
/*
* close large attribute IDs and spaces
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing large attr ids and spaces .\n",
mpi_rank, fcn_name);
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
err = H5Sclose(lg_att_space[i]);
VRFY((err >= 0), "H5Sclose(lg_att_space[i]) failed.\n");
err = H5Aclose(lg_att_id[i]);
VRFY((err >= 0), "H5Aclose(lg_att_id[i]) failed.\n");
}
/*
* close the data sets
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing datasets .\n", mpi_rank, fcn_name);
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
err = H5Dclose(dataset[i]);
VRFY((err >= 0), "H5Dclose(dataset[i])1 failed.\n");
}
/*
* close the data transfer property list.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing dxpl .\n", mpi_rank, fcn_name);
err = H5Pclose(dxpl_id);
VRFY((err >= 0), "H5Pclose(dxpl_id) failed.\n");
/*
* Close file.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing file.\n", mpi_rank, fcn_name);
err = H5Fclose(file_id);
VRFY((err >= 0 ), "H5Fclose(1) failed");
/* End of Step 5: Close all objects and the file */
/* Tell the reader to check the file up to steps. */
steps++;
Reader_check(mrc, steps, steps_done);
/* All done. Inform reader to end. */
steps=0;
Reader_check(mrc, steps, steps_done);
if(verbose )
HDfprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name);
return;
} /* rr_obj_hdr_flush_confusion_writer() */
void rr_obj_hdr_flush_confusion_reader(MPI_Comm comm)
{
int i;
int j;
hid_t file_id = -1;
hid_t fapl_id = -1;
hid_t dxpl_id = -1;
hid_t lg_att_id[NUM_DATA_SETS];
hid_t lg_att_type[NUM_DATA_SETS];
hid_t disk_space[NUM_DATA_SETS];
hid_t mem_space[NUM_DATA_SETS];
hid_t dataset[NUM_DATA_SETS];
hsize_t disk_count[1];
hsize_t disk_start[1];
hsize_t mem_count[1];
hsize_t mem_size[1];
hsize_t mem_start[1];
herr_t err;
htri_t tri_err;
double data[LOCAL_DATA_SIZE];
double data_read[LOCAL_DATA_SIZE];
double att[LOCAL_DATA_SIZE];
double att_read[LOCAL_DATA_SIZE];
double lg_att[LARGE_ATTR_SIZE];
double lg_att_read[LARGE_ATTR_SIZE];
/* MPI variables */
/* world communication size and rank */
int mpi_world_size;
int mpi_world_rank;
/* private communicator size and rank */
int mpi_size;
int mpi_rank;
int mrc; /* mpi error code */
int steps = -1; /* How far (steps) to verify the file */
int steps_done = -1; /* How far (steps) have been verified */
/* test bed related variables */
const char * fcn_name = "rr_obj_hdr_flush_confusion_reader";
const hbool_t verbose = FALSE;
const H5Ptest_param_t * pt;
char * filename;
/*
* setup test bed related variables:
*/
pt = (const H5Ptest_param_t *)GetTestParameters();
filename = pt->name;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_world_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_world_size);
MPI_Comm_rank(comm, &mpi_rank);
MPI_Comm_size(comm, &mpi_size);
/* Repeatedly re-open the file and verify its contents until it is */
/* told to end (when steps=0). */
while (steps_done != 0){
Reader_wait(mrc, steps);
VRFY((mrc >= 0), "Reader_wait failed");
steps_done = 0;
if (steps > 0 ){
/*
* Set up file access property list with parallel I/O access
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Setting up property list.\n",
mpi_rank, fcn_name);
fapl_id = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl_id != -1), "H5Pcreate(H5P_FILE_ACCESS) failed");
err = H5Pset_fapl_mpio(fapl_id, comm, MPI_INFO_NULL);
VRFY((err >= 0 ), "H5Pset_fapl_mpio() failed");
/*
* Create a new file collectively and release property list identifier.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Re-open file \"%s\".\n",
mpi_rank, fcn_name, filename);
file_id = H5Fopen(filename, H5F_ACC_RDONLY, fapl_id);
VRFY((file_id >= 0 ), "H5Fopen() failed");
err = H5Pclose(fapl_id);
VRFY((err >= 0 ), "H5Pclose(fapl_id) failed");
#if 1
if (steps >= 1){
/*=====================================================*
* Step 1: open the data sets and read data.
*=====================================================*/
if(verbose )
HDfprintf(stdout, "%0d:%s: opening the datasets.\n",
mpi_rank, fcn_name);
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
dataset[i] = -1;
}
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
dataset[i] = H5Dopen2(file_id, dataset_name[i], H5P_DEFAULT);
VRFY((dataset[i] >= 0), "H5Dopen(1) failed.\n");
disk_space[i] = H5Dget_space(dataset[i]);
VRFY((disk_space[i] >= 0), "H5Dget_space failed.\n");
}
/*
* setup data transfer property list
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Setting up dxpl.\n", mpi_rank, fcn_name);
dxpl_id = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl_id != -1), "H5Pcreate(H5P_DATASET_XFER) failed.\n");
err = H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE);
VRFY((err >= 0),
"H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE) failed.\n");
/*
* read data from the data sets
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: Reading datasets.\n", mpi_rank, fcn_name);
disk_count[0] = (hsize_t)(LOCAL_DATA_SIZE);
disk_start[0] = (hsize_t)(LOCAL_DATA_SIZE * mpi_rank);
mem_size[0] = (hsize_t)(LOCAL_DATA_SIZE);
mem_count[0] = (hsize_t)(LOCAL_DATA_SIZE);
mem_start[0] = (hsize_t)(0);
/* set up expected data for verification */
for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
data[j] = (double)(mpi_rank + 1);
}
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
err = H5Sselect_hyperslab(disk_space[i], H5S_SELECT_SET, disk_start,
NULL, disk_count, NULL);
VRFY((err >= 0), "H5Sselect_hyperslab(1) failed.\n");
mem_space[i] = H5Screate_simple(1, mem_size, NULL);
VRFY((mem_space[i] >= 0), "H5Screate_simple(2) failed.\n");
err = H5Sselect_hyperslab(mem_space[i], H5S_SELECT_SET,
mem_start, NULL, mem_count, NULL);
VRFY((err >= 0), "H5Sselect_hyperslab(2) failed.\n");
err = H5Dread(dataset[i], H5T_NATIVE_DOUBLE, mem_space[i],
disk_space[i], dxpl_id, data_read);
VRFY((err >= 0), "H5Dread(1) failed.\n");
/* compare read data with expected data */
for ( j = 0; j < LOCAL_DATA_SIZE; j++ )
if (data_read[j] != data[j]){
HDfprintf(stdout,
"%0d:%s: Reading datasets value failed in "
"Dataset %d, at position %d: expect %f, got %f.\n",
mpi_rank, fcn_name, i, j, data[j], data_read[j]);
nerrors++;
}
for ( j = 0; j < LOCAL_DATA_SIZE; j++ )
data[j] *= 10.0;
}
/*
* close the data spaces
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing dataspaces.\n", mpi_rank, fcn_name);
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
err = H5Sclose(disk_space[i]);
VRFY((err >= 0), "H5Sclose(disk_space[i]) failed.\n");
err = H5Sclose(mem_space[i]);
VRFY((err >= 0), "H5Sclose(mem_space[i]) failed.\n");
}
steps_done++;
}
/* End of Step 1: open the data sets and read data. */
#endif
#if 1
/*=====================================================*
* Step 2: reading attributes from each dataset
*=====================================================*/
if (steps >= 2){
if(verbose )
HDfprintf(stdout, "%0d:%s: reading attributes.\n", mpi_rank, fcn_name);
for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
att[j] = (double)(j + 1);
}
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
hid_t att_id, att_type;
att_id = H5Aopen(dataset[i], att_name[i], H5P_DEFAULT);
VRFY((att_id >= 0), "H5Aopen failed.\n");
att_type = H5Aget_type(att_id);
VRFY((att_type >= 0), "H5Aget_type failed.\n");
tri_err = H5Tequal(att_type, H5T_NATIVE_DOUBLE);
VRFY((tri_err >= 0), "H5Tequal failed.\n");
if (tri_err==0){
HDfprintf(stdout,
"%0d:%s: Mismatched Attribute type of Dataset %d.\n",
mpi_rank, fcn_name, i);
nerrors++;
}else{
/* should verify attribute size before H5Aread */
err = H5Aread(att_id, H5T_NATIVE_DOUBLE, att_read);
VRFY((err >= 0), "H5Aread failed.\n");
/* compare read attribute data with expected data */
for ( j = 0; j < LOCAL_DATA_SIZE; j++ )
if (att_read[j] != att[j]){
HDfprintf(stdout,
"%0d:%s: Mismatched attribute data read in Dataset %d, at position %d: expect %f, got %f.\n",
mpi_rank, fcn_name, i, j, att[j], att_read[j]);
nerrors++;
}
for ( j = 0; j < LOCAL_DATA_SIZE; j++ ) {
att[j] /= 10.0;
}
}
err = H5Aclose(att_id);
VRFY((err >= 0), "H5Aclose failed.\n");
}
steps_done++;
}
/* End of Step 2: reading attributes from each dataset */
#endif
#if 1
/*=====================================================*
* Step 3 or 4: read large attributes from each dataset.
* Step 4 has different attribute value from step 3.
*=====================================================*/
if (steps >= 3){
if(verbose )
HDfprintf(stdout, "%0d:%s: reading large attributes.\n", mpi_rank, fcn_name);
for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
lg_att[j] = (steps==3) ? (double)(j + 1) : (double)(j+2);
}
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
lg_att_id[i] = H5Aopen(dataset[i], lg_att_name[i], H5P_DEFAULT);
VRFY((lg_att_id[i] >= 0), "H5Aopen(2) failed.\n");
lg_att_type[i] = H5Aget_type(lg_att_id[i]);
VRFY((err >= 0), "H5Aget_type failed.\n");
tri_err = H5Tequal(lg_att_type[i], H5T_NATIVE_DOUBLE);
VRFY((tri_err >= 0), "H5Tequal failed.\n");
if (tri_err==0){
HDfprintf(stdout,
"%0d:%s: Mismatched Large attribute type of Dataset %d.\n",
mpi_rank, fcn_name, i);
nerrors++;
}else{
/* should verify large attribute size before H5Aread */
err = H5Aread(lg_att_id[i], H5T_NATIVE_DOUBLE, lg_att_read);
VRFY((err >= 0), "H5Aread failed.\n");
/* compare read attribute data with expected data */
for ( j = 0; j < LARGE_ATTR_SIZE; j++ )
if (lg_att_read[j] != lg_att[j]){
HDfprintf(stdout,
"%0d:%s: Mismatched large attribute data read in Dataset %d, at position %d: expect %f, got %f.\n",
mpi_rank, fcn_name, i, j, lg_att[j], lg_att_read[j]);
nerrors++;
}
for ( j = 0; j < LARGE_ATTR_SIZE; j++ ) {
lg_att[j] /= 10.0;
}
}
err = H5Tclose(lg_att_type[i]);
VRFY((err >= 0), "H5Tclose failed.\n");
err = H5Aclose(lg_att_id[i]);
VRFY((err >= 0), "H5Aclose failed.\n");
}
/* Both step 3 and 4 use this same read checking code. */
steps_done = (steps==3) ? 3 : 4;
}
/* End of Step 3 or 4: read large attributes from each dataset */
#endif
/*=====================================================*
* Step 5: read all objects from the file
*=====================================================*/
if (steps>=5){
/* nothing extra to verify. The file is closed normally. */
/* Just increment steps_done */
steps_done++;
}
/*
* Close the data sets
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing datasets again.\n",
mpi_rank, fcn_name);
for ( i = 0; i < NUM_DATA_SETS; i++ ) {
if ( dataset[i] >= 0 ) {
err = H5Dclose(dataset[i]);
VRFY((err >= 0), "H5Dclose(dataset[i])1 failed.\n");
}
}
/*
* close the data transfer property list.
*/
if(verbose )
HDfprintf(stdout, "%0d:%s: closing dxpl .\n", mpi_rank, fcn_name);
err = H5Pclose(dxpl_id);
VRFY((err >= 0), "H5Pclose(dxpl_id) failed.\n");
/*
* Close the file
*/
if(verbose)
HDfprintf(stdout, "%0d:%s: closing file again.\n",
mpi_rank, fcn_name);
err = H5Fclose(file_id);
VRFY((err >= 0 ), "H5Fclose(1) failed");
} /* else if (steps_done==0) */
Reader_result(mrc, steps_done);
} /* end while(1) */
if(verbose )
HDfprintf(stdout, "%0d:%s: Done.\n", mpi_rank, fcn_name);
return;
} /* rr_obj_hdr_flush_confusion_reader() */
#undef NUM_DATA_SETS
#undef LOCAL_DATA_SIZE
#undef LARGE_ATTR_SIZE
#undef Reader_check
#undef Reader_wait
#undef Reader_result
#undef Writer_Root
#undef Reader_Root
/*=============================================================================
* End of t_mdset.c
*===========================================================================*/
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