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hdf5/test/use_common.c
Vailin Choi 4f62c084f1 Fixed fprintf to HDfprintf in the following routines: 
1) read_uc_file() in use_common.c
2) main() of use_append_chunk.c and use_append_mchunks.c
2018-11-01 12:03:34 -05:00

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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* 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 COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5test.h"
/* This test uses many POSIX things that are not available on
* Windows. We're using a check for fork(2) here as a proxy for
* all POSIX/Unix/Linux things until this test can be made
* more platform-independent.
*/
#ifdef H5_HAVE_FORK
#include "use.h"
#define H5D_FRIEND /*suppress error about including H5Dpkg */
#define H5D_TESTING
#include "H5Dpkg.h"
void
usage(const char *prog)
{
HDfprintf(stderr, "usage: %s [OPTIONS]\n", prog);
HDfprintf(stderr, " OPTIONS\n");
HDfprintf(stderr, " -h, --help Print a usage message and exit\n");
HDfprintf(stderr, " -f FN Test file name [default: %s.h5]\n", prog);
HDfprintf(stderr, " -i N, --iteration=N Number of iterations to repeat the whole thing. [default: 1]\n");
HDfprintf(stderr, " -l w|r launch writer or reader only. [default: launch both]\n");
HDfprintf(stderr, " -n N, --nplanes=N Number of planes to write/read. [default: 1000]\n");
HDfprintf(stderr, " -s N, --swmr=N Use SWMR mode (0: no, non-0: yes) default is yes\n");
HDfprintf(stderr, " -z N, --chunksize=N Chunk size [default: %d]\n", Chunksize_DFT);
HDfprintf(stderr, " -y N, --chunkplanes=N Number of planes per chunk [default: 1]\n");
HDfprintf(stderr, "\n");
} /* end usage() */
/* Setup Use Case parameters by parsing command line options.
* Setup default values if not set by options. */
int
parse_option(int argc, char * const argv[])
{
int ret_value=0;
int c;
int use_swmr; /* Need an int to detect errors */
/* command line options: See function usage for a description */
const char *nagg_options = "f:hi:l:n:s:y:z:";
/* suppress getopt from printing error */
opterr = 0;
while (1){
c = getopt (argc, argv, nagg_options);
if (-1 == c)
break;
switch (c) {
case 'h':
usage(progname_g);
exit(0);
break;
case 'f': /* usecase data file name */
UC_opts.filename = optarg;
break;
case 'i': /* iterations */
if ((UC_opts.iterations = HDatoi(optarg)) <= 0) {
fprintf(stderr, "bad iterations number %s, must be a positive integer\n", optarg);
usage(progname_g);
Hgoto_error(-1);
};
break;
case 'l': /* launch reader or writer only */
switch (*optarg) {
case 'r': /* reader only */
UC_opts.launch = UC_READER;
break;
case 'w': /* writer only */
UC_opts.launch = UC_WRITER;
break;
default:
fprintf(stderr, "launch value(%c) should be w or r only.\n", *optarg);
usage(progname_g);
Hgoto_error(-1);
break;
}
break;
case 'n': /* number of planes to write/read */
if ((UC_opts.nplanes = HDstrtoul(optarg, NULL, 0)) <= 0) {
fprintf(stderr, "bad number of planes %s, must be a positive integer\n", optarg);
usage(progname_g);
Hgoto_error(-1);
};
break;
case 's': /* use swmr file open mode */
use_swmr = HDatoi(optarg);
if (use_swmr != 0 && use_swmr != 1) {
HDfprintf(stderr, "swmr value should be 0(no) or 1(yes)\n");
usage(progname_g);
Hgoto_error(-1);
}
UC_opts.use_swmr = (hbool_t)use_swmr;
break;
case 'y': /* Number of planes per chunk */
if ((UC_opts.chunkplanes = HDstrtoul(optarg, NULL, 0)) <= 0) {
fprintf(stderr, "bad number of planes per chunk %s, must be a positive integer\n", optarg);
usage(progname_g);
Hgoto_error(-1);
};
break;
case 'z': /* size of chunk=(z,z) */
if ((UC_opts.chunksize = HDstrtoull(optarg, NULL, 0)) <= 0) {
fprintf(stderr, "bad chunksize %s, must be a positive integer\n", optarg);
usage(progname_g);
Hgoto_error(-1);
};
break;
case '?':
fprintf(stderr, "getopt returned '%c'.\n", c);
Hgoto_error(-1);
default:
fprintf(stderr, "getopt returned unexpected value.\n");
fprintf(stderr, "Unexpected value is %d\n", c);
Hgoto_error(-1);
}
}
/* set test file name if not given */
if (!UC_opts.filename){
/* default data file name is <progname>.h5 */
if ((UC_opts.filename=(char*)HDmalloc(HDstrlen(progname_g)+4))==NULL) {
fprintf(stderr, "malloc: failed\n");
Hgoto_error(-1);
};
HDstrcpy(UC_opts.filename, progname_g);
HDstrcat(UC_opts.filename, ".h5");
}
done:
/* All done. */
return(ret_value);
}
/* Show parameters used for this use case */
void show_parameters(void){
printf("===Parameters used:===\n");
printf("chunk dims=(%llu, %llu, %llu)\n", (unsigned long long)UC_opts.chunkdims[0],
(unsigned long long)UC_opts.chunkdims[1], (unsigned long long)UC_opts.chunkdims[2]);
printf("dataset max dims=(%llu, %llu, %llu)\n", (unsigned long long)UC_opts.max_dims[0],
(unsigned long long)UC_opts.max_dims[1], (unsigned long long)UC_opts.max_dims[2]);
printf("number of planes to write=%llu\n", (unsigned long long)UC_opts.nplanes);
printf("using SWMR mode=%s\n", UC_opts.use_swmr ? "yes(1)" : "no(0)");
printf("data filename=%s\n", UC_opts.filename);
printf("launch part=");
switch (UC_opts.launch){
case UC_READWRITE:
printf("Reader/Writer\n");
break;
case UC_WRITER:
printf("Writer\n");
break;
case UC_READER:
printf("Reader\n");
break;
default:
/* should not happen */
printf("Illegal part(%d)\n", UC_opts.launch);
};
printf("number of iterations=%d (not used yet)\n", UC_opts.iterations);
printf("===Parameters shown===\n");
}
/* Create the skeleton use case file for testing.
* It has one 3d dataset using chunked storage.
* The dataset is (unlimited, chunksize, chunksize).
* Dataset type is 2 bytes integer.
* It starts out "empty", i.e., first dimension is 0.
*
* Return: 0 succeed; -1 fail.
*/
int create_uc_file(void)
{
hsize_t dims[3]; /* Dataset starting dimensions */
hid_t fid; /* File ID for new HDF5 file */
hid_t dcpl; /* Dataset creation property list */
hid_t sid; /* Dataspace ID */
hid_t dsid; /* Dataset ID */
hid_t fapl; /* File access property list */
H5D_chunk_index_t idx_type; /* Chunk index type */
/* Create the file */
if((fapl = h5_fileaccess()) < 0)
return -1;
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
return -1;
if((fid = H5Fcreate(UC_opts.filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
return -1;
/* Set up dimension sizes */
dims[0] = 0;
dims[1] = dims[2] = UC_opts.max_dims[1];
/* Create dataspace for creating datasets */
if((sid = H5Screate_simple(3, dims, UC_opts.max_dims)) < 0)
return -1;
/* Create dataset creation property list */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
return -1;
if(H5Pset_chunk(dcpl, 3, UC_opts.chunkdims) < 0)
return -1;
/* create dataset of progname */
if((dsid = H5Dcreate2(fid, progname_g, UC_DATATYPE, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
return -1;
/* Check that the chunk index type is not version 1 B-tree.
* Version 1 B-trees are not supported under SWMR.
*/
if(H5D__layout_idx_type_test(dsid, &idx_type) < 0)
return -1;
if(idx_type == H5D_CHUNK_IDX_BTREE) {
fprintf(stderr, "ERROR: Chunk index is version 1 B-tree: aborting.\n");
return -1;
}
/* Close everything */
if(H5Dclose(dsid) < 0)
return -1;
if(H5Pclose(fapl) < 0)
return -1;
if(H5Pclose(dcpl) < 0)
return -1;
if(H5Sclose(sid) < 0)
return -1;
if(H5Fclose(fid) < 0)
return -1;
return 0;
}
/* Append planes, each of (1,2*chunksize,2*chunksize) to the dataset.
* In other words, 4 chunks are appended to the dataset at a time.
* Fill each plan with the plane number and then write it at the nth plane.
* Increase the plane number and repeat till the end of dataset, when it
* reaches chunksize long. End product is a (2*chunksize)^3 cube.
*
* Return: 0 succeed; -1 fail.
*/
int write_uc_file(hbool_t tosend, hid_t fid)
{
hid_t dsid; /* dataset ID */
hid_t dcpl; /* Dataset creation property list */
UC_CTYPE *buffer, *bufptr; /* data buffer */
hsize_t cz=UC_opts.chunksize; /* Chunk size */
hid_t f_sid; /* dataset file space id */
hid_t m_sid; /* memory space id */
int rank; /* rank */
hsize_t chunk_dims[3]; /* Chunk dimensions */
hsize_t dims[3]; /* Dataspace dimensions */
hsize_t memdims[3]; /* Memory space dimensions */
hsize_t start[3] = {0,0,0}, count[3]; /* Hyperslab selection values */
hsize_t i, j, k;
if(tosend)
/* Send a message that H5Fopen is complete--releasing the file lock */
h5_send_message(WRITER_MESSAGE, NULL, NULL);
/* Open the dataset of the program name */
if((dsid = H5Dopen2(fid, progname_g, H5P_DEFAULT)) < 0){
fprintf(stderr, "H5Dopen2 failed\n");
return -1;
}
/* Find chunksize used */
if ((dcpl = H5Dget_create_plist(dsid)) < 0){
fprintf(stderr, "H5Dget_create_plist failed\n");
return -1;
}
if (H5D_CHUNKED != H5Pget_layout(dcpl)){
fprintf(stderr, "storage layout is not chunked\n");
return -1;
}
if ((rank = H5Pget_chunk(dcpl, 3, chunk_dims)) != 3){
fprintf(stderr, "storage rank is not 3\n");
return -1;
}
/* verify chunk_dims against set paramenters */
if (chunk_dims[0]!=UC_opts.chunkdims[0] || chunk_dims[1] != cz || chunk_dims[2] != cz){
fprintf(stderr, "chunk size is not as expected. Got dims=(%llu,%llu,%llu)\n",
(unsigned long long)chunk_dims[0], (unsigned long long)chunk_dims[1],
(unsigned long long)chunk_dims[2]);
return -1;
}
/* allocate space for data buffer 1 X dims[1] X dims[2] of UC_CTYPE */
memdims[0]=1;
memdims[1] = UC_opts.dims[1];
memdims[2] = UC_opts.dims[2];
if ((buffer=(UC_CTYPE*)HDmalloc((size_t)memdims[1]*(size_t)memdims[2]*sizeof(UC_CTYPE)))==NULL) {
fprintf(stderr, "malloc: failed\n");
return -1;
};
/*
* Get dataset rank and dimension.
*/
f_sid = H5Dget_space(dsid); /* Get filespace handle first. */
rank = H5Sget_simple_extent_ndims(f_sid);
if (rank != UC_RANK){
fprintf(stderr, "rank(%d) of dataset does not match\n", rank);
return -1;
}
if (H5Sget_simple_extent_dims(f_sid, dims, NULL) < 0){
fprintf(stderr, "H5Sget_simple_extent_dims got error\n");
return -1;
}
printf("dataset rank %d, dimensions %llu x %llu x %llu\n",
rank, (unsigned long long)(dims[0]), (unsigned long long)(dims[1]),
(unsigned long long)(dims[2]));
/* verify that file space dims are as expected and are consistent with memory space dims */
if (dims[0] != 0 || dims[1] != memdims[1] || dims[2] != memdims[2]){
fprintf(stderr, "dataset is not empty. Got dims=(%llu,%llu,%llu)\n",
(unsigned long long)dims[0], (unsigned long long)dims[1],
(unsigned long long)dims[2]);
return -1;
}
/* setup mem-space for buffer */
if ((m_sid=H5Screate_simple(rank, memdims, NULL))<0){
fprintf(stderr, "H5Screate_simple for memory failed\n");
return -1;
};
/* write planes */
count[0]=1;
count[1]=dims[1];
count[2]=dims[2];
for (i=0; i<UC_opts.nplanes; i++){
/* fill buffer with value i+1 */
bufptr = buffer;
for (j=0; j<dims[1]; j++)
for (k=0; k<dims[2]; k++)
*bufptr++ = (UC_CTYPE)i;
/* Cork the dataset's metadata in the cache, if SWMR is enabled */
if(UC_opts.use_swmr)
if(H5Odisable_mdc_flushes(dsid) < 0) {
fprintf(stderr, "H5Odisable_mdc_flushes failed\n");
return -1;
}
/* extend the dataset by one for new plane */
dims[0]=i+1;
if(H5Dset_extent(dsid, dims) < 0){
fprintf(stderr, "H5Dset_extent failed\n");
return -1;
}
/* Get the dataset's dataspace */
if((f_sid = H5Dget_space(dsid)) < 0){
fprintf(stderr, "H5Dset_extent failed\n");
return -1;
}
start[0]=i;
/* Choose the next plane to write */
if(H5Sselect_hyperslab(f_sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0){
fprintf(stderr, "Failed H5Sselect_hyperslab\n");
return -1;
}
/* Write plane to the dataset */
if(H5Dwrite(dsid, UC_DATATYPE, m_sid, f_sid, H5P_DEFAULT, buffer) < 0){
fprintf(stderr, "Failed H5Dwrite\n");
return -1;
}
/* Uncork the dataset's metadata from the cache, if SWMR is enabled */
if(UC_opts.use_swmr)
if(H5Oenable_mdc_flushes(dsid) < 0) {
fprintf(stderr, "H5Oenable_mdc_flushes failed\n");
return -1;
}
/* flush file to make the just written plane available. */
if(H5Dflush(dsid) < 0)
{
fprintf(stderr, "Failed to H5Fflush file\n");
return -1;
}
}
/* Done writing. Free/Close all resources including data file */
HDfree(buffer);
if (H5Dclose(dsid) < 0){
fprintf(stderr, "Failed to close datasete\n");
return -1;
}
if (H5Sclose(m_sid) < 0){
fprintf(stderr, "Failed to close memory space\n");
return -1;
}
if (H5Sclose(f_sid) < 0){
fprintf(stderr, "Failed to close file space\n");
return -1;
}
return 0;
}
/* Read planes from the dataset.
* It expects the dataset is being changed (growing).
* It checks the unlimited dimension (1st one). When it increases,
* it will read in the new planes, one by one, and verify the data correctness.
* (The nth plan should contain all "n".)
* When the unlimited dimension grows to the chunksize (it becomes a cube),
* that is the expected end of data, the reader exits.
*
* Return: 0 succeed; -1 fail.
*/
int read_uc_file(hbool_t towait)
{
hid_t fapl; /* file access property list ID */
hid_t fid; /* File ID for new HDF5 file */
hid_t dsid; /* dataset ID */
char *name;
UC_CTYPE *buffer, *bufptr; /* read data buffer */
hid_t f_sid; /* dataset file space id */
hid_t m_sid; /* memory space id */
int rank; /* rank */
hsize_t dims[3]; /* Dataspace dimensions */
hsize_t memdims[3]; /* Memory space dimensions */
hsize_t nplane=0, nplane_old=0; /* nth plane, last nth plane */
hsize_t start[3] = {0,0,0}, count[3]; /* Hyperslab selection values */
hsize_t j, k;
int nreadererr=0;
int nerrs;
int nonewplane;
/* Before reading, wait for the message that H5Fopen is complete--file lock is released */
if(towait && h5_wait_message(WRITER_MESSAGE) < 0) {
HDfprintf(stderr, "Cannot find writer message file...failed\n");
return -1;
}
name = UC_opts.filename;
/* Open the file */
if((fapl = h5_fileaccess()) < 0)
return -1;
if((fid = H5Fopen(name, H5F_ACC_RDONLY | (UC_opts.use_swmr ? H5F_ACC_SWMR_READ : 0), fapl)) < 0){
HDfprintf(stderr, "H5Fopen failed\n");
return -1;
}
if (H5Pclose(fapl) < 0){
HDfprintf(stderr, "Failed to property list\n");
return -1;
}
/* Open the dataset of the program name */
if((dsid = H5Dopen2(fid, progname_g, H5P_DEFAULT)) < 0){
HDfprintf(stderr, "H5Dopen2 failed\n");
return -1;
}
/* allocate space for data buffer 1 X dims[1] X dims[2] of UC_CTYPE */
memdims[0]=1;
memdims[1] = UC_opts.dims[1];
memdims[2] = UC_opts.dims[2];
if ((buffer=(UC_CTYPE*)HDmalloc((size_t)memdims[1]*(size_t)memdims[2]*sizeof(UC_CTYPE)))==NULL) {
HDfprintf(stderr, "malloc: failed\n");
return -1;
};
/*
* Get dataset rank and dimension.
* Verify dimension is as expected (unlimited,2*chunksize,2*chunksize).
*/
f_sid = H5Dget_space(dsid); /* Get filespace handle first. */
rank = H5Sget_simple_extent_ndims(f_sid);
if (rank != UC_RANK){
HDfprintf(stderr, "rank(%d) of dataset does not match\n", rank);
return -1;
}
if (H5Sget_simple_extent_dims(f_sid, dims, NULL) < 0){
HDfprintf(stderr, "H5Sget_simple_extent_dims got error\n");
return -1;
}
HDprintf("dataset rank %d, dimensions %llu x %llu x %llu\n",
rank, (unsigned long long)(dims[0]), (unsigned long long)(dims[1]),
(unsigned long long)(dims[2]));
/* verify that file space dims are as expected and are consistent with memory space dims */
if (dims[1] != memdims[1] || dims[2] != memdims[2]){
HDfprintf(stderr, "dataset dimension is not as expected. Got dims=(%llu,%llu,%llu)\n",
(unsigned long long)dims[0], (unsigned long long)dims[1],
(unsigned long long)dims[2]);
HDfprintf(stderr, "But memdims=(%llu,%llu,%llu)\n",
(unsigned long long)memdims[0], (unsigned long long)memdims[1],
(unsigned long long)memdims[2]);
return -1;
}
/* setup mem-space for buffer */
if ((m_sid=H5Screate_simple(rank, memdims, NULL))<0){
HDfprintf(stderr, "H5Screate_simple for memory failed\n");
return -1;
};
/* Read 1 plane at a time whenever the dataset grows larger
* (along dim[0]) */
count[0]=1;
count[1]=dims[1];
count[2]=dims[2];
/* quit when all nplanes have been read */
nonewplane=0;
while (nplane_old < UC_opts.nplanes ){
/* print progress message according to if new planes are availalbe */
if (nplane_old < dims[0]) {
if (nonewplane){
/* end the previous message */
HDprintf("\n");
nonewplane=0;
}
HDprintf("reading planes %llu to %llu\n", (unsigned long long)nplane_old,
(unsigned long long)dims[0]);
}else{
if (nonewplane){
HDprintf(".");
if (nonewplane>=30){
HDfprintf(stderr, "waited too long for new plane, quit.\n");
return -1;
}
}else{
/* print mesg only the first time; dots still no new plane */
HDprintf("no new planes to read ");
}
nonewplane++;
/* pause for a second */
HDsleep(1);
}
for (nplane=nplane_old; nplane < dims[0]; nplane++){
/* read planes between last old nplanes and current extent */
/* Get the dataset's dataspace */
if((f_sid = H5Dget_space(dsid)) < 0){
HDfprintf(stderr, "H5Dget_space failed\n");
return -1;
}
start[0]=nplane;
/* Choose the next plane to read */
if(H5Sselect_hyperslab(f_sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0){
HDfprintf(stderr, "H5Sselect_hyperslab failed\n");
return -1;
}
/* Read the plane from the dataset */
if(H5Dread(dsid, UC_DATATYPE, m_sid, f_sid, H5P_DEFAULT, buffer) < 0){
HDfprintf(stderr, "H5Dread failed\n");
return -1;
}
/* compare read data with expected data value which is nplane */
bufptr = buffer;
nerrs=0;
for (j=0; j<dims[1]; j++){
for (k=0; k<dims[2]; k++){
if ((hsize_t)*bufptr++ != nplane){
if (++nerrs < ErrorReportMax){
HDfprintf(stderr,
"found error %llu plane(%llu,%llu), expected %llu, got %d\n",
(unsigned long long)nplane, (unsigned long long)j,
(unsigned long long)k, (unsigned long long)nplane, (int)*(bufptr-1));
}
}
}
}
if (nerrs){
nreadererr++;
HDfprintf(stderr, "found %d unexpected values in plane %llu\n", nerrs,
(unsigned long long)nplane);
}
}
/* Have read all current planes */
nplane_old=dims[0];
/* check if dataset has grown since last time */
#if 0
/* close dsid and file, then reopen them */
if (H5Dclose(dsid) < 0){
HDfprintf(stderr, "H5Dclose failed\n");
return -1;
}
if (H5Fclose(fid) < 0){
HDfprintf(stderr, "H5Fclose failed\n");
return -1;
}
if((fid = H5Fopen(name, H5F_ACC_RDONLY | (UC_opts.use_swmr ? H5F_ACC_SWMR_READ : 0), H5P_DEFAULT)) < 0){
HDfprintf(stderr, "H5Fopen failed\n");
return -1;
}
if((dsid = H5Dopen2(fid, progname_g, H5P_DEFAULT)) < 0){
HDfprintf(stderr, "H5Dopen2 failed\n");
return -1;
}
#else
H5Drefresh(dsid);
#endif
f_sid = H5Dget_space(dsid); /* Get filespace handle first. */
if (H5Sget_simple_extent_dims(f_sid, dims, NULL) < 0){
HDfprintf(stderr, "H5Sget_simple_extent_dims got error\n");
return -1;
}
}
/* Close the file */
if(H5Fclose(fid) < 0) {
HDfprintf(stderr, "H5Fclose failed\n");
return -1;
}
if (nreadererr)
return -1;
else
return 0;
} /* read_uc_file() */
#endif /* H5_HAVE_FORK */
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