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hdf5/testpar/t_mdset.c
Quincey Koziol 0313cbb91d Final merge of page buffering branch to develop
2017-03-13 21:30:37 -07:00

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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 a zero sized dataset.
*
*/
void zero_dim_dset(void)
{
int mpi_size, mpi_rank;
const char *filename;
hid_t fid, plist, dcpl, dsid, sid;
hsize_t dim, chunk_dim;
herr_t ret;
int data[1];
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);
VRFY((plist>=0), "create_faccess_plist succeeded");
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
VRFY((fid>=0), "H5Fcreate succeeded");
ret = H5Pclose(plist);
VRFY((ret>=0), "H5Pclose succeeded");
dcpl = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl>=0), "failed H5Pcreate");
/* Set 1 chunk size */
chunk_dim = 1;
ret = H5Pset_chunk(dcpl, 1, &chunk_dim);
VRFY((ret>=0), "failed H5Pset_chunk");
/* Create 1D dataspace with 0 dim size */
dim = 0;
sid = H5Screate_simple(1, &dim, NULL);
VRFY((sid>=0), "failed H5Screate_simple");
/* Create chunked dataset */
dsid = H5Dcreate2(fid, "dset", H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT);
VRFY((dsid>=0), "failed H5Dcreate2");
/* write 0 elements from dataset */
ret = H5Dwrite(dsid, H5T_NATIVE_INT, sid, sid, H5P_DEFAULT, data);
VRFY((ret>=0), "failed H5Dwrite");
/* Read 0 elements from dataset */
ret = H5Dread(dsid, H5T_NATIVE_INT, sid, sid, H5P_DEFAULT, data);
VRFY((ret>=0), "failed H5Dread");
H5Pclose(dcpl);
H5Dclose(dsid);
H5Sclose(sid);
H5Fclose(fid);
}
/*
* 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 */
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);
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;
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);
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);
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;
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);
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);
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 */
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);
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 == 2147485696ULL), "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 == 4294969344ULL), "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 == 8589936640ULL), "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 */
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);
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 processes 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;
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);
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;
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);
H5Pset_all_coll_metadata_ops(plist, FALSE);
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;
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);
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;
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);
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);
HDassert(mpi_size > 2);
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
/*
* Test creating a chunked dataset in parallel in a file with an alignment set
* and an alignment threshold large enough to avoid aligning the chunks but
* small enough that the raw data aggregator will be aligned if it is treated as
* an object that must be aligned by the library
*/
#define CHUNK_SIZE 72
#define NCHUNKS 32
#define AGGR_SIZE 2048
#define EXTRA_ALIGN 100
void chunk_align_bug_1(void)
{
int mpi_rank;
hid_t file_id, dset_id, fapl_id, dcpl_id, space_id;
hsize_t dims = CHUNK_SIZE * NCHUNKS, cdims = CHUNK_SIZE;
h5_stat_size_t file_size;
hsize_t align;
herr_t ret;
const char *filename;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
filename = (const char *)GetTestParameters();
/* Create file without alignment */
fapl_id = create_faccess_plist(MPI_COMM_WORLD, MPI_INFO_NULL, facc_type);
VRFY((fapl_id >= 0), "create_faccess_plist succeeded");
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
VRFY((file_id >= 0), "H5Fcreate succeeded");
/* Close file */
ret = H5Fclose(file_id);
VRFY((ret >= 0), "H5Fclose succeeded");
/* Get file size */
file_size = h5_get_file_size(filename, fapl_id);
VRFY((file_size >= 0), "h5_get_file_size succeeded");
/* Calculate alignment value, set to allow a chunk to squeak in between the
* original EOF and the aligned location of the aggregator. Add some space
* for the dataset metadata */
align = (hsize_t)file_size + CHUNK_SIZE + EXTRA_ALIGN;
/* Set aggregator size and alignment, disable metadata aggregator */
HDassert(AGGR_SIZE > CHUNK_SIZE);
ret = H5Pset_small_data_block_size(fapl_id, AGGR_SIZE);
VRFY((ret >= 0), "H5Pset_small_data_block_size succeeded");
ret = H5Pset_meta_block_size(fapl_id, 0);
VRFY((ret >= 0), "H5Pset_meta_block_size succeeded");
ret = H5Pset_alignment(fapl_id, CHUNK_SIZE + 1, align);
VRFY((ret >= 0), "H5Pset_small_data_block_size succeeded");
/* Reopen file with new settings */
file_id = H5Fopen(filename, H5F_ACC_RDWR, fapl_id);
VRFY((file_id >= 0), "H5Fopen succeeded");
/* Create dataset */
space_id = H5Screate_simple(1, &dims, NULL);
VRFY((space_id >= 0), "H5Screate_simple succeeded");
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl_id >= 0), "H5Pcreate succeeded");
ret = H5Pset_chunk(dcpl_id, 1, &cdims);
VRFY((ret >= 0), "H5Pset_chunk succeeded");
dset_id = H5Dcreate2(file_id, "dset", H5T_NATIVE_CHAR, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
VRFY((dset_id >= 0), "H5Dcreate2 succeeded");
/* Close ids */
ret = H5Dclose(dset_id);
VRFY((dset_id >= 0), "H5Dclose succeeded");
ret = H5Sclose(space_id);
VRFY((space_id >= 0), "H5Sclose succeeded");
ret = H5Pclose(dcpl_id);
VRFY((dcpl_id >= 0), "H5Pclose succeeded");
ret = H5Pclose(fapl_id);
VRFY((fapl_id >= 0), "H5Pclose succeeded");
/* Close file */
ret = H5Fclose(file_id);
VRFY((ret >= 0), "H5Fclose succeeded");
return;
} /* end chunk_align_bug_1() */
/*=============================================================================
* End of t_mdset.c
*===========================================================================*/
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