int
main (int argc, const char *argv[])
{
hid_t fid_src=-1;
hid_t fid_dst=-1;
char *fname_src=NULL;
char *fname_dst=NULL;
char *oname_src=NULL;
char *oname_dst=NULL;
unsigned flag=0;
unsigned verbose=0;
unsigned parents=0;
hid_t ocpl_id = (-1); /* Object copy property list */
hid_t lcpl_id = (-1); /* Link creation property list */
char str_flag[20];
int opt;
int li_ret;
h5tool_link_info_t linkinfo;
int i, len;
char *str_ptr=NULL;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* initialize h5tools lib */
h5tools_init();
/* init linkinfo struct */
HDmemset(&linkinfo, 0, sizeof(h5tool_link_info_t));
/* Check for no command line parameters */
if(argc == 1)
{
usage();
leave(EXIT_FAILURE);
} /* end if */
/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
{
switch ((char)opt)
{
case 'd':
oname_dst = HDstrdup(opt_arg);
break;
case 'f':
/* validate flag */
if (parse_flag(opt_arg,&flag)<0)
{
usage();
leave(EXIT_FAILURE);
}
HDstrcpy(str_flag,opt_arg);
break;
case 'h':
usage();
leave(EXIT_SUCCESS);
break;
case 'i':
fname_src = HDstrdup(opt_arg);
break;
case 'o':
fname_dst = HDstrdup(opt_arg);
break;
case 'p':
parents = 1;
break;
case 's':
oname_src = HDstrdup(opt_arg);
break;
case 'V':
print_version(h5tools_getprogname());
leave(EXIT_SUCCESS);
break;
case 'v':
verbose = 1;
break;
default:
usage();
leave(EXIT_FAILURE);
}
} /* end of while */
/*-------------------------------------------------------------------------
* check for missing file/object names
*-------------------------------------------------------------------------*/
if (fname_src==NULL)
{
error_msg("Input file name missing\n");
usage();
leave(EXIT_FAILURE);
}
if (fname_dst==NULL)
{
error_msg("Output file name missing\n");
usage();
leave(EXIT_FAILURE);
}
if (oname_src==NULL)
{
error_msg("Source object name missing\n");
usage();
leave(EXIT_FAILURE);
}
if (oname_dst==NULL)
{
error_msg("Destination object name missing\n");
usage();
leave(EXIT_FAILURE);
}
/*-------------------------------------------------------------------------
* open output file
*-------------------------------------------------------------------------*/
/* Attempt to open an existing HDF5 file first. Need to open the dst file
before the src file just in case that the dst and src are the same file
*/
fid_dst = h5tools_fopen(fname_dst, H5F_ACC_RDWR, H5P_DEFAULT, NULL, NULL, 0);
/*-------------------------------------------------------------------------
* open input file
*-------------------------------------------------------------------------*/
fid_src = h5tools_fopen(fname_src, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0);
/*-------------------------------------------------------------------------
* test for error in opening input file
*-------------------------------------------------------------------------*/
if (fid_src==-1)
{
error_msg("Could not open input file <%s>...Exiting\n", fname_src);
if (fname_src)
HDfree(fname_src);
leave(EXIT_FAILURE);
}
/*-------------------------------------------------------------------------
* create an output file when failed to open it
*-------------------------------------------------------------------------*/
/* If we couldn't open an existing file, try creating file */
/* (use "EXCL" instead of "TRUNC", so we don't blow away existing non-HDF5 file) */
if(fid_dst < 0)
fid_dst = H5Fcreate(fname_dst, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
/*-------------------------------------------------------------------------
* test for error in opening output file
*-------------------------------------------------------------------------*/
if (fid_dst==-1)
{
error_msg("Could not open output file <%s>...Exiting\n", fname_dst);
if (fname_src)
HDfree(fname_src);
if (fname_dst)
HDfree(fname_dst);
leave(EXIT_FAILURE);
}
/*-------------------------------------------------------------------------
* print some info
*-------------------------------------------------------------------------*/
if (verbose)
{
printf("Copying file <%s> and object <%s> to file <%s> and object <%s>\n",
fname_src, oname_src, fname_dst, oname_dst);
if (flag)
printf("Using %s flag\n", str_flag);
}
/*-------------------------------------------------------------------------
* create property lists for copy
*-------------------------------------------------------------------------*/
/* create property to pass copy options */
if ( (ocpl_id = H5Pcreate(H5P_OBJECT_COPY)) < 0)
goto error;
/* set options for object copy */
if (flag)
{
if ( H5Pset_copy_object(ocpl_id, flag) < 0)
goto error;
}
/* Create link creation property list */
if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) {
error_msg("Could not create link creation property list\n");
goto error;
} /* end if */
/* Check for creating intermediate groups */
if(parents) {
/* Set the intermediate group creation property */
if(H5Pset_create_intermediate_group(lcpl_id, 1) < 0) {
error_msg("Could not set property for creating parent groups\n");
goto error;
} /* end if */
/* Display some output if requested */
if(verbose)
printf("%s: Creating parent groups\n", h5tools_getprogname());
} /* end if */
else /* error, if parent groups doesn't already exist in destination file */
{
len = HDstrlen(oname_dst);
/* check if all the parents groups exist. skip root group */
for (i = 1; i < len; i++)
{
if ('/'==oname_dst[i])
{
str_ptr = (char*)HDcalloc((size_t)i+1, sizeof(char));
HDstrncpy (str_ptr, oname_dst, (size_t)i);
str_ptr[i]='\0';
if (H5Lexists(fid_dst, str_ptr, H5P_DEFAULT) <= 0)
{
error_msg("group <%s> doesn't exist. Use -p to create parent groups.\n", str_ptr);
HDfree(str_ptr);
goto error;
}
HDfree(str_ptr);
}
}
}
/*-------------------------------------------------------------------------
* do the copy
*-------------------------------------------------------------------------*/
if(verbose)
linkinfo.opt.msg_mode = 1;
li_ret = H5tools_get_symlink_info(fid_src, oname_src, &linkinfo, 1);
if (li_ret == 0) /* dangling link */
{
if(H5Lcopy(fid_src, oname_src,
fid_dst, oname_dst,
H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
}
else /* valid link */
{
if (H5Ocopy(fid_src, /* Source file or group identifier */
oname_src, /* Name of the source object to be copied */
fid_dst, /* Destination file or group identifier */
oname_dst, /* Name of the destination object */
ocpl_id, /* Object copy property list */
lcpl_id)<0) /* Link creation property list */
goto error;
}
/* free link info path */
if (linkinfo.trg_path)
HDfree(linkinfo.trg_path);
/* close propertis */
if(H5Pclose(ocpl_id)<0)
goto error;
if(H5Pclose(lcpl_id)<0)
goto error;
/* close files */
if (H5Fclose(fid_src)<0)
goto error;
if (H5Fclose(fid_dst)<0)
goto error;
if (fname_src)
HDfree(fname_src);
if (fname_dst)
HDfree(fname_dst);
if (oname_dst)
HDfree(oname_dst);
if (oname_src)
HDfree(oname_src);
h5tools_close();
return EXIT_SUCCESS;
error:
printf("Error in copy...Exiting\n");
/* free link info path */
if (linkinfo.trg_path)
HDfree(linkinfo.trg_path);
H5E_BEGIN_TRY {
H5Pclose(ocpl_id);
H5Pclose(lcpl_id);
H5Fclose(fid_src);
H5Fclose(fid_dst);
} H5E_END_TRY;
if (fname_src)
HDfree(fname_src);
if (fname_dst)
HDfree(fname_dst);
if (oname_dst)
HDfree(oname_dst);
if (oname_src)
HDfree(oname_src);
h5tools_close();
return EXIT_FAILURE;
}
int
main(void)
{
hid_t src_sid = -1; /* source dataset's dataspace ID */
hid_t src_dcplid = -1; /* source dataset property list ID */
hid_t vds_sid = -1; /* VDS dataspace ID */
hid_t vds_dcplid = -1; /* VDS dataset property list ID */
hid_t fid = -1; /* HDF5 file ID */
hid_t did = -1; /* dataset ID */
hid_t msid = -1; /* memory dataspace ID */
hid_t fsid = -1; /* file dataspace ID */
hsize_t extent[RANK]; /* source dataset extents */
hsize_t start[RANK]; /* starting point for hyperslab */
hsize_t stride[RANK]; /* hypserslab stride */
hsize_t count[RANK]; /* hypserslab count */
int map_start = -1; /* starting point in the VDS map */
int *buffer = NULL; /* data buffer */
int value = -1; /* value written to datasets */
hsize_t n = 0; /* number of elements in a plane */
int i; /* iterator */
int j; /* iterator */
int k; /* iterator */
/* Start by creating the virtual dataset (VDS) dataspace and creation
* property list. The individual source datasets are then created
* and the VDS map (stored in the VDS property list) is updated.
*/
/* Create VDS dcpl */
if((vds_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
UC_ERROR
if(H5Pset_fill_value(vds_dcplid, UC_5_VDS_DATATYPE,
&UC_5_VDS_FILL_VALUE) < 0)
UC_ERROR
/* Create VDS dataspace */
if((vds_sid = H5Screate_simple(RANK, UC_5_VDS_DIMS,
UC_5_VDS_MAX_DIMS)) < 0)
UC_ERROR
/*********************************
* Map source files and datasets *
*********************************/
/* Hyperslab array setup */
start[0] = 0;
start[1] = 0;
start[2] = 0;
map_start = 0;
stride[0] = UC_5_N_SOURCES;
stride[1] = 1;
stride[2] = 1;
count[0] = H5S_UNLIMITED;
count[1] = 1;
count[2] = 1;
extent[0] = UC_5_SRC_PLANES;
extent[1] = UC_5_HEIGHT;
extent[2] = UC_5_WIDTH;
for(i = 0; i < UC_5_N_SOURCES; i++) {
/* source dataset dcpl */
if((src_dcplid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
UC_ERROR
if(H5Pset_chunk(src_dcplid, RANK, UC_5_PLANE) < 0)
UC_ERROR
if(H5Pset_fill_value(src_dcplid, UC_5_SOURCE_DATATYPE,
&UC_5_FILL_VALUES[i]) < 0)
UC_ERROR
if(H5Pset_deflate(src_dcplid, COMPRESSION_LEVEL) < 0)
UC_ERROR
/* Create source file, dataspace, and dataset */
if((fid = H5Fcreate(UC_5_FILE_NAMES[i], H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
UC_ERROR
if((src_sid = H5Screate_simple(RANK, UC_5_SOURCE_DIMS,
UC_5_SOURCE_MAX_DIMS)) < 0)
UC_ERROR
if((did = H5Dcreate2(fid, UC_5_SOURCE_DSET_NAME,
UC_5_SOURCE_DATATYPE, src_sid,
H5P_DEFAULT, src_dcplid, H5P_DEFAULT)) < 0)
UC_ERROR
/* Set the dataset's extent */
if(H5Dset_extent(did, extent) < 0)
UC_ERROR
/* Create a data buffer that represents a plane */
n = UC_5_PLANE[1] * UC_5_PLANE[2];
if(NULL == (buffer = (int *)malloc(n * sizeof(int))))
UC_ERROR
/* Create the memory dataspace */
if((msid = H5Screate_simple(RANK, UC_5_PLANE, NULL)) < 0)
UC_ERROR
/* Get the file dataspace */
if((fsid = H5Dget_space(did)) < 0)
UC_ERROR
/* Write planes to the dataset */
for(j = 0; j < UC_5_SRC_PLANES; j++) {
value = ((i + 1) * 10) + j;
for(k = 0; k < n; k++)
buffer[k] = value;
start[0] = j;
start[1] = 0;
start[2] = 0;
if(H5Sselect_hyperslab(fsid, H5S_SELECT_SET, start, NULL, UC_5_PLANE, NULL) < 0)
UC_ERROR
if(H5Dwrite(did, H5T_NATIVE_INT, msid, fsid, H5P_DEFAULT, buffer) < 0)
UC_ERROR
} /* end for */
/* set up hyperslabs for source and destination datasets */
start[0] = 0;
start[1] = 0;
start[2] = 0;
if(H5Sselect_hyperslab(src_sid, H5S_SELECT_SET, start, NULL,
UC_5_SOURCE_MAX_DIMS, NULL) < 0)
UC_ERROR
start[0] = map_start;
if(H5Sselect_hyperslab(vds_sid, H5S_SELECT_SET, start, stride,
count, UC_5_PLANE) < 0)
UC_ERROR
map_start += 1;
/* Add VDS mapping */
if(H5Pset_virtual(vds_dcplid, vds_sid, UC_5_FILE_NAMES[i],
UC_5_SOURCE_DSET_PATH, src_sid) < 0)
UC_ERROR
/* close */
if(H5Sclose(msid) < 0)
UC_ERROR
if(H5Sclose(fsid) < 0)
UC_ERROR
if(H5Sclose(src_sid) < 0)
UC_ERROR
if(H5Pclose(src_dcplid) < 0)
UC_ERROR
if(H5Dclose(did) < 0)
UC_ERROR
if(H5Fclose(fid) < 0)
UC_ERROR
free(buffer);
} /* end for */
/*******************
* Create VDS file *
*******************/
/* file */
if((fid = H5Fcreate(UC_5_VDS_FILE_NAME, H5F_ACC_TRUNC,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
UC_ERROR
/* dataset */
if((did = H5Dcreate2(fid, UC_5_VDS_DSET_NAME, UC_5_VDS_DATATYPE, vds_sid,
H5P_DEFAULT, vds_dcplid, H5P_DEFAULT)) < 0)
UC_ERROR
/* close */
if(H5Pclose(vds_dcplid) < 0)
UC_ERROR
if(H5Sclose(vds_sid) < 0)
UC_ERROR
if(H5Dclose(did) < 0)
UC_ERROR
if(H5Fclose(fid) < 0)
UC_ERROR
return EXIT_SUCCESS;
error:
H5E_BEGIN_TRY {
if(src_sid >= 0)
(void)H5Sclose(src_sid);
if(src_dcplid >= 0)
(void)H5Pclose(src_dcplid);
if(vds_sid >= 0)
(void)H5Sclose(vds_sid);
if(vds_dcplid >= 0)
(void)H5Pclose(vds_dcplid);
if(fid >= 0)
(void)H5Fclose(fid);
if(did >= 0)
(void)H5Dclose(did);
if(msid >= 0)
(void)H5Sclose(msid);
if(fsid >= 0)
(void)H5Sclose(fsid);
if(buffer != NULL)
free(buffer);
} H5E_END_TRY
return EXIT_FAILURE;
} /* end main() */
int main(void)
{
hid_t file=(-1), fapl, space=(-1), dset=(-1);
char dname[]="dataset";
int i, j;
int buf[FAMILY_NUMBER][FAMILY_SIZE];
hsize_t dims[2]={FAMILY_NUMBER, FAMILY_SIZE};
/* Set property list and file name for FAMILY driver */
if ((fapl=H5Pcreate(H5P_FILE_ACCESS)) < 0) {
perror ("H5Pcreate");
exit (1);
}
if(H5Pset_fapl_family(fapl, (hsize_t)FAMILY_SIZE, H5P_DEFAULT) < 0) {
perror ("H5Pset_fapl_family");
exit (1);
}
if((file = H5Fcreate(FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) {
perror("H5Fcreate");
exit(1);
}
/* Create and write dataset */
if((space = H5Screate_simple(2, dims, NULL)) < 0) {
perror("H5Screate_simple");
exit(1);
}
if((dset = H5Dcreate2(file, dname, H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
perror("H5Dcreate2");
exit(1);
}
for(i = 0; i<FAMILY_NUMBER; i++)
for(j = 0; j<FAMILY_SIZE; j++)
buf[i][j] = i * 10000 + j;
if(H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0) {
perror("H5Dwrite");
exit(1);
}
if(H5Sclose(space) < 0) {
perror ("H5Sclose");
exit (1);
}
if(H5Dclose(dset) < 0) {
perror ("H5Dclose");
exit (1);
}
if(H5Pclose(fapl) < 0) {
perror ("H5Pclose");
exit (1);
}
if(H5Fclose(file) < 0) {
perror ("H5Fclose");
exit (1);
}
puts(" PASSED"); fflush(stdout);
return 0;
}
/*
* Verify that object headers are held in the cache until they are linked
* to a location in the graph, or assigned an ID. This is done by
* creating an object header, then forcing it out of the cache by creating
* local heaps until the object header is evicted from the cache, then
* modifying the object header. The refcount on the object header is
* checked as verifying that the object header has remained in the cache.
*/
static herr_t
test_ohdr_cache(char *filename, hid_t fapl)
{
hid_t file = -1; /* File ID */
hid_t my_fapl; /* FAPL ID */
hid_t my_dxpl; /* DXPL ID */
H5AC_cache_config_t mdc_config; /* Metadata cache configuration info */
H5F_t *f = NULL; /* File handle */
H5HL_t *lheap, *lheap2, *lheap3; /* Pointer to local heaps */
haddr_t lheap_addr, lheap_addr2, lheap_addr3; /* Local heap addresses */
H5O_loc_t oh_loc; /* Object header location */
time_t time_new; /* Time value for modification time message */
unsigned rc; /* Refcount for object */
TESTING("object header creation in cache");
/* Make a copy of the FAPL */
if((my_fapl = H5Pcopy(fapl)) < 0)
FAIL_STACK_ERROR
/* Tweak down the size of the metadata cache to only 64K */
mdc_config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
if(H5Pget_mdc_config(my_fapl, &mdc_config) < 0)
FAIL_STACK_ERROR
mdc_config.set_initial_size = TRUE;
mdc_config.initial_size = 32 * 1024;
mdc_config.max_size = 64 * 1024;
mdc_config.min_size = 8 * 1024;
if(H5Pset_mdc_config(my_fapl, &mdc_config) < 0)
FAIL_STACK_ERROR
/* Make a copy of the default DXPL */
if((my_dxpl = H5Pcopy(H5P_DATASET_XFER_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Create the file to operate on */
if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, my_fapl)) < 0)
FAIL_STACK_ERROR
if(H5Pclose(my_fapl) < 0)
FAIL_STACK_ERROR
if(NULL == (f = (H5F_t *)H5I_object(file)))
FAIL_STACK_ERROR
/* Create object (local heap) that occupies most of cache */
if(H5HL_create(f, my_dxpl, (31 * 1024), &lheap_addr) < 0)
FAIL_STACK_ERROR
/* Protect local heap (which actually pins it in the cache) */
if(NULL == (lheap = H5HL_protect(f, my_dxpl, lheap_addr, H5AC_READ)))
FAIL_STACK_ERROR
/* Create an object header */
HDmemset(&oh_loc, 0, sizeof(oh_loc));
if(H5O_create(f, my_dxpl, (size_t)2048, (size_t)1, H5P_GROUP_CREATE_DEFAULT, &oh_loc/*out*/) < 0)
FAIL_STACK_ERROR
/* Query object header information */
rc = 0;
if(H5O_get_rc(&oh_loc, my_dxpl, &rc) < 0)
FAIL_STACK_ERROR
if(0 != rc)
TEST_ERROR
/* Create object (local heap) that occupies most of cache */
if(H5HL_create(f, my_dxpl, (31 * 1024), &lheap_addr2) < 0)
FAIL_STACK_ERROR
/* Protect local heap (which actually pins it in the cache) */
if(NULL == (lheap2 = H5HL_protect(f, my_dxpl, lheap_addr2, H5AC_READ)))
FAIL_STACK_ERROR
/* Unprotect local heap (which actually unpins it from the cache) */
if(H5HL_unprotect(lheap2) < 0)
FAIL_STACK_ERROR
/* Create object header message in new object header */
time_new = 11111111;
if(H5O_msg_create(&oh_loc, H5O_MTIME_NEW_ID, 0, 0, &time_new, my_dxpl) < 0)
FAIL_STACK_ERROR
/* Create object (local heap) that occupies most of cache */
if(H5HL_create(f, my_dxpl, (31 * 1024), &lheap_addr3) < 0)
FAIL_STACK_ERROR
/* Protect local heap (which actually pins it in the cache) */
if(NULL == (lheap3 = H5HL_protect(f, my_dxpl, lheap_addr3, H5AC_READ)))
FAIL_STACK_ERROR
/* Unprotect local heap (which actually unpins it from the cache) */
if(H5HL_unprotect(lheap3) < 0)
FAIL_STACK_ERROR
/* Query object header information */
/* (Note that this is somewhat of a weak test, since it doesn't actually
* verify that the object header was evicted from the cache, but it's
* very difficult to verify when an entry is evicted from the cache in
* a non-invasive way -QAK)
*/
rc = 0;
if(H5O_get_rc(&oh_loc, my_dxpl, &rc) < 0)
FAIL_STACK_ERROR
if(0 != rc)
TEST_ERROR
/* Decrement reference count o object header */
if(H5O_dec_rc_by_loc(&oh_loc, my_dxpl) < 0)
FAIL_STACK_ERROR
/* Close object header created */
if(H5O_close(&oh_loc) < 0)
FAIL_STACK_ERROR
/* Unprotect local heap (which actually unpins it from the cache) */
if(H5HL_unprotect(lheap) < 0)
FAIL_STACK_ERROR
if(H5Pclose(my_dxpl) < 0)
FAIL_STACK_ERROR
if(H5Fclose(file) < 0)
FAIL_STACK_ERROR
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Fclose(file);
} H5E_END_TRY;
return -1;
} /* test_ohdr_cache() */
int FileIO::create(Setup *setup) {
hid_t file_plist = H5Pcreate(H5P_FILE_ACCESS);
#ifdef GKC_PARALLEL_MPI
// pass some information onto the underlying MPI_File_open call
MPI_Info file_info;
check(MPI_Info_create(&file_info), DMESG("File info"));
/*
H5Pset_sieve_buf_size(file_plist, 262144);
H5Pset_alignment(file_plist, 524288, 262144);
MPI_Info_set(file_info, (char *) "access_style" , (char *) "write_once");
MPI_Info_set(file_info, (char *) "collective_buffering", (char *) "true");
MPI_Info_set(file_info, (char *) "cb_block_size" , (char *) "1048576");
MPI_Info_set(file_info, (char *) "cb_buffer_size" , (char *) "4194304");
* */
check( H5Pset_fapl_mpio(file_plist, parallel->Comm[DIR_ALL], file_info), DMESG("Set MPI Property"));
#endif
file = check(H5Fcreate(outputFileName.c_str(), (overwriteFile ? H5F_ACC_TRUNC : H5F_ACC_EXCL),
H5P_DEFAULT, file_plist ), DMESG("H5FCreate : HDF5 File (File already exists ? use -f to overwrite) : " + outputFileName));
check( H5Pclose(file_plist), DMESG("H5Pclose"));
#ifdef GKC_PARALLEL_MPI
MPI_Info_free(&file_info);
#endif
//////////////////////////////////////////////////////////////// Info Group ////////////////////////////////////////////////////////
hid_t infoGroup = check(H5Gcreate(file, "/Info",H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT), DMESG("Error creating group file for Phasespace : H5Gcreate"));
check(H5LTset_attribute_string(infoGroup, ".", "Output", outputFileName.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Input", inputFileName.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Version", PACKAGE_VERSION), DMESG("H5LTset_attribute"));
// Some Simulation specific stuff
//check(H5LTset_attribute_string(infoGroup, ".", "Solver", ((setup->Solver & VL_LIN) ? "Linear" : "Non-Linear")), DMESG("H5LTset_attribute"));
//heck(H5LTset_attribute_string(infoGroup, ".", "Type", ((setup->VlasovType & VLASOV_LOCAL ) ? "Local" : "Global" )), DMESG("H5LTset_attribute"));
//heck(H5LTset_attribute_string(infoGroup, ".", "FFTSolverS", ((setup->VlasovType & VLASOV_LOCAL ) ? "Local" : "Global" )), DMESG("H5LTset_attribute"));
//check(H5LTset_attribute_string(infoGroup, ".", "Initial Condition", setup->PerturbationMethod.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Info", info.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Config", setup->configFileString.c_str()), DMESG("H5LTset_attribute"));
H5Gclose(infoGroup);
/// Wrote setup constants, ugly here ////
hid_t constantsGroup = check(H5Gcreate(file, "/Constants",H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT), DMESG("Error creating group file for Phasespace : H5Gcreate"));
//
if (!setup->parser_constants.empty()) {
std::vector<std::string> const_vec = Setup::split(setup->parser_constants, ",");
for(int s = 0; s < const_vec.size(); s++) {
std::vector<std::string> key_value = Setup::split(const_vec[s],"=");
double value = Setup::string_to_double(key_value[1]);
int dim[] = { 1 };
// check(H5LTmake_dataset_double(constantsGroup, Setup::trimLower(key_value[0], false).c_str(), 1, dim, &value ), DMESG("Write Constants Attributes"));
check(H5LTset_attribute_double(constantsGroup, ".", Setup::trimLower(key_value[0], false).c_str(), &value, 1), DMESG("H5LTset_attribute"));
//check(H5LTset_attribute_double(constantsGroup, ".", Setup::trimLower(key_value[0], false).c_str(), &(Setup::string_to_double(key_value[1])), 1), DMESG("H5LTset_attribute"));
};
}
H5Gclose(constantsGroup);
// ********************* setup Table for CFL *****************88
cfl_table = new CFLTable();
cfl_offset[0] = HOFFSET( CFLTable, timeStep );
cfl_offset[1] = HOFFSET( CFLTable, time );
cfl_offset[2] = HOFFSET( CFLTable, Fx );
cfl_offset[3] = HOFFSET( CFLTable, Fy );
cfl_offset[4] = HOFFSET( CFLTable, Fz );
cfl_offset[5] = HOFFSET( CFLTable, Fv );
cfl_offset[6] = HOFFSET( CFLTable, total );
for(int i = 1; i < 7; i++) cfl_sizes[i] = sizeof(double); cfl_sizes[0] = sizeof(int);
hid_t cfl_type[7]; for(int i = 1; i < 7; i++) cfl_type [i] = H5T_NATIVE_DOUBLE; cfl_type[0] = H5T_NATIVE_INT;
const char *cfl_names[7];
cfl_names[0] = "timeStep";
cfl_names[1] = "time";
cfl_names[2] = "Fx"; cfl_names[3] = "Fy"; cfl_names[4] = "Fz"; cfl_names[5] = "Fv"; cfl_names[6] = "Total";
check(H5TBmake_table("cflTable", file, "cfl", (hsize_t) 7, (hsize_t) 0, sizeof(CFLTable), (const char**) cfl_names,
cfl_offset, cfl_type, 32, NULL, 0, cfl_table ), DMESG("H5Tmake_table : cfl"));
return HELIOS_SUCCESS;
}
/*-------------------------------------------------------------------------
* Function: check_file
*
* Purpose: Part 2 of a two-part H5Fflush() test.
*
* Return: Success: 0
*
* Failure: 1
*
* Programmer: Leon Arber
* Sept. 26, 2006.
*
*-------------------------------------------------------------------------
*/
static int
check_file(char* name, hid_t fapl)
{
hid_t file, space, dset, groups, grp, plist;
hsize_t ds_size[2];
double error;
hsize_t i, j;
plist = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE);
if((file = H5Fopen(name, H5F_ACC_RDONLY, fapl)) < 0) goto error;
/* Open the dataset */
if((dset = H5Dopen2(file, "dset", H5P_DEFAULT)) < 0) goto error;
if((space = H5Dget_space(dset)) < 0) goto error;
if(H5Sget_simple_extent_dims(space, ds_size, NULL) < 0) goto error;
assert(100==ds_size[0] && 100==ds_size[1]);
/* Read some data */
if (H5Dread(dset, H5T_NATIVE_DOUBLE, space, space, plist,
the_data) < 0) goto error;
for (i=0; i<ds_size[0]; i++) {
for (j=0; j<ds_size[1]; j++) {
/*
* The extra cast in the following statement is a bug workaround
* for the Win32 version 5.0 compiler.
* 1998-11-06 ptl
*/
error = fabs(the_data[i][j]-(double)(hssize_t)i/((hssize_t)j+1));
if (error>0.0001) {
H5_FAILED();
printf(" dset[%lu][%lu] = %g\n",
(unsigned long)i, (unsigned long)j, the_data[i][j]);
printf(" should be %g\n",
(double)(hssize_t)i/(hssize_t)(j+1));
goto error;
}
}
}
/* Open some groups */
if((groups = H5Gopen2(file, "some_groups", H5P_DEFAULT)) < 0) goto error;
for(i = 0; i < 100; i++) {
sprintf(name, "grp%02u", (unsigned)i);
if((grp = H5Gopen2(groups, name, H5P_DEFAULT)) < 0) goto error;
if(H5Gclose(grp) < 0) goto error;
}
if(H5Gclose(groups) < 0) goto error;
if(H5Dclose(dset) < 0) goto error;
if(H5Fclose(file) < 0) goto error;
if(H5Pclose(plist) < 0) goto error;
if(H5Sclose(space) < 0) goto error;
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(plist);
H5Gclose(groups);
H5Dclose(dset);
H5Fclose(file);
H5Sclose(space);
} H5E_END_TRY;
return 1;
}
void writehdf5file(rundata_t rundata, double **dens, double ***vel) {
/* identifiers */
hid_t file_id, arr_group_id, dens_dataset_id, vel_dataset_id;
hid_t dens_dataspace_id, vel_dataspace_id;
hid_t loc_dens_dataspace_id, loc_vel_dataspace_id;
hid_t globaldensspace,globalvelspace;
hid_t dist_id;
hid_t fap_id;
/* sizes */
hsize_t densdims[2], veldims[3];
hsize_t locdensdims[2], locveldims[3];
/* status */
herr_t status;
/* MPI-IO hints for performance */
MPI_Info info;
/* parameters of the hyperslab */
hsize_t counts[3];
hsize_t strides[3];
hsize_t offsets[3];
hsize_t blocks[3];
/* set the MPI-IO hints for better performance on GPFS */
MPI_Info_create(&info);
MPI_Info_set(info,"IBM_largeblock_io","true");
/* Set up the parallel environment for file access*/
fap_id = H5Pcreate(H5P_FILE_ACCESS);
/* Include the file access property with IBM hint */
H5Pset_fapl_mpio(fap_id, MPI_COMM_WORLD, info);
/* Set up the parallel environment */
dist_id = H5Pcreate(H5P_DATASET_XFER);
/* we'll be writing collectively */
H5Pset_dxpl_mpio(dist_id, H5FD_MPIO_COLLECTIVE);
/* Create a new file - truncate anything existing, use default properties */
file_id = H5Fcreate(rundata.filename, H5F_ACC_TRUNC, H5P_DEFAULT, fap_id);
/* HDF5 routines generally return a negative number on failure.
* Should check return values! */
if (file_id < 0) {
fprintf(stderr,"Could not open file %s\n", rundata.filename);
return;
}
/* Create a new group within the new file */
arr_group_id = H5Gcreate(file_id,"/ArrayData", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* Give this group an attribute listing the time of calculation */
{
hid_t attr_id,attr_sp_id;
struct tm *t;
time_t now;
int yyyymm;
now = time(NULL);
t = localtime(&now);
yyyymm = (1900+t->tm_year)*100+t->tm_mon;
attr_sp_id = H5Screate(H5S_SCALAR);
attr_id = H5Acreate(arr_group_id, "Calculated on (YYYYMM)", H5T_STD_U32LE, attr_sp_id, H5P_DEFAULT, H5P_DEFAULT);
printf("yymm = %d\n",yyyymm);
H5Awrite(attr_id, H5T_NATIVE_INT, &yyyymm);
H5Aclose(attr_id);
H5Sclose(attr_sp_id);
}
/* Create the data space for the two global datasets. */
densdims[0] = rundata.globalnx; densdims[1] = rundata.globalny;
veldims[0] = 2; veldims[1] = rundata.globalnx; veldims[2] = rundata.globalny;
dens_dataspace_id = H5Screate_simple(2, densdims, NULL);
vel_dataspace_id = H5Screate_simple(3, veldims, NULL);
/* Create the datasets within the file.
* H5T_IEEE_F64LE is a standard (IEEE) double precision (64 bit) floating (F) data type
* and will work on any machine. H5T_NATIVE_DOUBLE would work too, but would give
* different results on GPC and TCS */
dens_dataset_id = H5Dcreate(file_id, "/ArrayData/dens", H5T_IEEE_F64LE,
dens_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
vel_dataset_id = H5Dcreate(file_id, "/ArrayData/vel", H5T_IEEE_F64LE,
vel_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* Now create the data space for our sub-regions. These are the data spaces
* of our actual local data in memory. */
locdensdims[0] = rundata.localnx; locdensdims[1] = rundata.localny;
locveldims[0] = 2; locveldims[1] = rundata.localnx; locveldims[2] = rundata.localny;
loc_dens_dataspace_id = H5Screate_simple(2, locdensdims, NULL);
loc_vel_dataspace_id = H5Screate_simple(3, locveldims, NULL);
/*
*
* Now we have to figure out the `hyperslab' within the global
* data that corresponds to our local data.
*
* Hyperslabs are described by an array of counts, strides, offsets,
* and block sizes.
*
* |-offx--|
* +-------|----|-------+ -+-
* | | |
* | | offy
* | | |
* - +----+ - -+-
* | | | | |
* | | | | localny
* | | | | |
* - +----+ - -+-
* | |
* | |
* +-------|----|-------+
* localnx
*
* In this case the blocksizes are (localnx,localny) and the offsets are
* (offx,offy) = ((myx)/nxp*globalnx, (myy/nyp)*globalny)
*/
offsets[0] = (rundata.globalnx/rundata.npx)*rundata.myx;
offsets[1] = (rundata.globalny/rundata.npy)*rundata.myy;
blocks[0] = rundata.localnx;
blocks[1] = rundata.localny;
strides[0] = strides[1] = 1;
counts[0] = counts[1] = 1;
/* select this subset of the density variable's space in the file */
globaldensspace = H5Dget_space(dens_dataset_id);
H5Sselect_hyperslab(globaldensspace,H5S_SELECT_SET, offsets, strides, counts, blocks);
/* For the velocities, it's the same thing but there's a count of two,
* (one for each velocity component) */
offsets[1] = (rundata.globalnx/rundata.npx)*rundata.myx;
offsets[2] = (rundata.globalny/rundata.npy)*rundata.myy;
blocks[1] = rundata.localnx;
blocks[2] = rundata.localny;
strides[0] = strides[1] = strides[2] = 1;
counts[0] = 2; counts[1] = counts[2] = 1;
offsets[0] = 0;
blocks[0] = 1;
globalvelspace = H5Dget_space(vel_dataset_id);
H5Sselect_hyperslab(globalvelspace,H5S_SELECT_SET, offsets, strides, counts, blocks);
/* Write the data. We're writing it from memory, where it is saved
* in NATIVE_DOUBLE format */
status = H5Dwrite(dens_dataset_id, H5T_NATIVE_DOUBLE, loc_dens_dataspace_id, globaldensspace, dist_id, &(dens[0][0]));
status = H5Dwrite(vel_dataset_id, H5T_NATIVE_DOUBLE, loc_vel_dataspace_id, globalvelspace, dist_id, &(vel[0][0][0]));
/* We'll create another group for related info and put some things in there */
{
hid_t other_group_id;
hid_t timestep_id, timestep_space;
hid_t comptime_id, comptime_space;
hid_t author_id, author_space, author_type;
char *authorname="Jonathan Dursi";
int timestep=13;
float comptime=81.773;
/* create group */
other_group_id = H5Gcreate(file_id,"/OtherStuff", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* scalar space, data for integer timestep */
timestep_space = H5Screate(H5S_SCALAR);
timestep_id = H5Dcreate(other_group_id, "Timestep", H5T_STD_U32LE,
timestep_space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite(timestep_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, ×tep);
H5Dclose(timestep_id);
H5Sclose(timestep_space);
/* scalar space, data for floating compute time */
comptime_space = H5Screate(H5S_SCALAR);
comptime_id = H5Dcreate(other_group_id, "Compute Time", H5T_IEEE_F32LE,
comptime_space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite(comptime_id, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &comptime);
H5Dclose(comptime_id);
H5Sclose(comptime_space);
/* scalar space, data for author name */
author_space = H5Screate(H5S_SCALAR);
author_type = H5Tcopy(H5T_C_S1); /* copy the character type.. */
status = H5Tset_size (author_type, strlen(authorname)); /* and make it longer */
author_id = H5Dcreate(other_group_id, "Simulator Name", author_type, author_space,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite(author_id, author_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, authorname);
H5Dclose(author_id);
H5Sclose(author_space);
H5Tclose(author_type);
H5Gclose(other_group_id);
}
/* End access to groups & data sets and release resources used by them */
status = H5Sclose(dens_dataspace_id);
status = H5Dclose(dens_dataset_id);
status = H5Sclose(vel_dataspace_id);
status = H5Dclose(vel_dataset_id);
status = H5Gclose(arr_group_id);
status = H5Pclose(fap_id);
status = H5Pclose(dist_id);
/* Close the file */
status = H5Fclose(file_id);
return;
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: HDF5 user block unjammer
*
* Return: Success: 0
* Failure: 1
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main (int argc, const char *argv[])
{
char *ifname;
void *edata;
H5E_auto2_t func;
hid_t ifile;
hsize_t usize;
htri_t testval;
herr_t status;
hid_t plist;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Initialize h5tools lib */
h5tools_init();
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
parse_command_line (argc, argv);
if (argc <= (opt_ind))
{
error_msg("missing file name\n");
usage (h5tools_getprogname());
return (EXIT_FAILURE);
}
ifname = HDstrdup (argv[opt_ind]);
testval = H5Fis_hdf5 (ifname);
if (testval <= 0)
{
error_msg("Input HDF5 file is not HDF \"%s\"\n", ifname);
return (EXIT_FAILURE);
}
ifile = H5Fopen (ifname, H5F_ACC_RDONLY, H5P_DEFAULT);
if (ifile < 0)
{
error_msg("Can't open input HDF5 file \"%s\"\n", ifname);
return (EXIT_FAILURE);
}
plist = H5Fget_create_plist (ifile);
if (plist < 0)
{
error_msg("Can't get file creation plist for file \"%s\"\n",
ifname);
return (EXIT_FAILURE);
}
status = H5Pget_userblock (plist, &usize);
if (status < 0)
{
error_msg("Can't get user block for file \"%s\"\n", ifname);
return (EXIT_FAILURE);
}
printf ("%ld\n", (long) usize);
H5Pclose (plist);
H5Fclose (ifile);
return (EXIT_SUCCESS);
}
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
int mpirank;
MPI_Comm_rank(MPI_COMM_WORLD, &mpirank);
int nbprocess;
MPI_Comm_size(MPI_COMM_WORLD, &nbprocess);
if(nbprocess != 3)
{
print(mpirank, "Please relaunch with three process.\n");
return EXIT_FAILURE;
}
// Open properties of the file
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
MPI_Info info = MPI_INFO_NULL;
// Create the pro
herr_t status = H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, info);
// Create the file
hid_t hdf = H5Fcreate("ut_paral2.h5", H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
// close the properties
H5Pclose(plist_id);
char *message;
message = test_assym_low(hdf, mpirank);
if(message!=NULL)
{
printf("%d** %s\n", mpirank, message);
return EXIT_FAILURE;
}
message = test_assym(hdf, mpirank);
if(message!=NULL)
{
printf("%d** %s\n", mpirank, message);
return EXIT_FAILURE;
}
H5Fclose(hdf);
MPI_Finalize();
print(mpirank, "SUCCESS\n");
return EXIT_SUCCESS;
}
void HDFWalkerIOEngine::readAll(hid_t grp, const char* name, Communicate* comm)
{
int mynode=comm->rank();
int nprocs=comm->size();
vector<int> woffset(nprocs+1,0);
const int RANK = 3;
hsize_t offset[]={1,1,1};
hsize_t gcount[RANK],count[RANK];
hsize_t stride[]={1,1,1};
hid_t dataset = H5Dopen(grp,name);
hid_t dataspace = H5Dget_space(dataset);
int rank_n = H5Sget_simple_extent_ndims(dataspace);
int status_n = H5Sget_simple_extent_dims(dataspace, gcount, NULL);
//assign offsets and size
FairDivideLow(gcount[0],nprocs,woffset);
offset[0]=woffset[mynode]; offset[1] = 0; offset[2] = 0;
count[0]=woffset[mynode+1]-woffset[mynode];
count[1]=gcount[1];
count[2]=gcount[2];
app_log() << " Initial walker distribution: ";
std::copy(woffset.begin(),woffset.end(),ostream_iterator<int>(app_log()," "));
app_log() << endl;
vector<MCWalkerConfiguration::PosType> posIn(count[0]*count[1]);
hid_t memspace = H5Screate_simple(RANK, count, NULL);
herr_t status = H5Sselect_hyperslab(dataspace,H5S_SELECT_SET, offset,NULL,count,NULL);
#if defined(H5_HAVE_PARALLEL)
xfer_plist = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(xfer_plist,H5FD_MPIO_COLLECTIVE);
#else
xfer_plist = H5P_DEFAULT;
#endif
hid_t type_id=get_h5_datatype(posIn[0][0]);
status = H5Dread(dataset, type_id, memspace, dataspace, xfer_plist, &(posIn[0][0]));
H5Sclose(dataspace);
H5Sclose(memspace);
H5Dclose(dataset);
#if defined(H5_HAVE_PARALLEL)
H5Pclose(xfer_plist);
#endif
int curWalker = W.getActiveWalkers();
if(curWalker) {
W.createWalkers(count[0]);
} else {
W.resize(count[0],count[1]);
}
MCWalkerConfiguration::iterator it = W.begin()+curWalker;
int ii=0;
for(int iw=0; iw<count[0]; iw++) {
//std::copy(Post_temp[iw],Post_temp[iw+1], (*it)->R.begin());
for(int iat=0; iat < count[1]; iat++,ii++){
(*it)->R(iat) = posIn[ii];
}
++it;
}
}
void Simulation3D::dumpFields(std::string filename) {
unsigned int p_x = xLine.rank(), p_y = yLine.rank(), p_z = zLine.rank();
hsize_t start[4];
start[0] = xLine.rank()*blockSize; start[1] = yLine.rank()*blockSize;
start[2] = zLine.rank()*blockSize; start[3] = 0;
hsize_t rhsx_start[3];
rhsx_start[0] = p_y*blockSize; rhsx_start[1] = p_z*blockSize; rhsx_start[2] = p_x*blockSize;
hsize_t rhsy_start[3];
rhsy_start[0] = p_x*blockSize; rhsy_start[1] = p_z*blockSize; rhsy_start[2] = p_y*blockSize;
hsize_t rhsz_start[3];
rhsz_start[0] = p_x*blockSize; rhsz_start[1] = p_y*blockSize; rhsz_start[2] = p_z*blockSize;
hsize_t rhs_count[3];
rhs_count[0] = blockSize; rhs_count[1] = blockSize; rhs_count[2] = blockSize;
hsize_t count[4];
count[0] = blockSize; count[1] = blockSize; count[2] = blockSize; count[3] = 3;
hsize_t dims[4];
dims[0] = blockSize*procsX; dims[1] = blockSize*procsY; dims[2] = blockSize*procsZ; dims[3] = 3;
hsize_t mem_dims[4];
mem_dims[0] = blockSize; mem_dims[1] = blockSize; mem_dims[2] = blockSize; mem_dims[3] = 3;
hid_t fa_p_list = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(fa_p_list, world, MPI_INFO_NULL);
hid_t file_id=H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, fa_p_list);
H5Pclose(fa_p_list);
hsize_t rhs_dims[3];
rhs_dims[0] = blockSize*procsX; rhs_dims[1] = blockSize*procsY; rhs_dims[2] = blockSize*procsZ;
hsize_t rhs_mem_dims[3];
rhs_mem_dims[0] = blockSize; rhs_mem_dims[1] = blockSize; rhs_mem_dims[2] = blockSize;
hid_t E_filespace = H5Screate_simple(4, dims, NULL);
hid_t E_memspace = H5Screate_simple(4, mem_dims, NULL);
hid_t B_filespace = H5Screate_simple(4, dims, NULL);
hid_t B_memspace = H5Screate_simple(4, mem_dims, NULL);
hid_t rhsx_filespace = H5Screate_simple(3, rhs_dims, NULL);
hid_t rhsx_memspace = H5Screate_simple(3, rhs_mem_dims, NULL);
hid_t rhsy_filespace = H5Screate_simple(3, rhs_dims, NULL);
hid_t rhsy_memspace = H5Screate_simple(3, rhs_mem_dims, NULL);
hid_t rhsz_filespace = H5Screate_simple(3, rhs_dims, NULL);
hid_t rhsz_memspace = H5Screate_simple(3, rhs_mem_dims, NULL);
hid_t E_dset_id = H5Dcreate(file_id, "E", H5T_NATIVE_DOUBLE, E_filespace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t E_wr_p_list = H5Pcreate(H5P_DATASET_XFER);
// H5Pset_dxpl_mpio(E_wr_p_list, H5FD_MPIO_COLLECTIVE);
H5Sselect_hyperslab(E_filespace, H5S_SELECT_SET, start, NULL, count, NULL);
herr_t status = H5Dwrite(E_dset_id, H5T_NATIVE_DOUBLE, E_memspace, E_filespace,
E_wr_p_list, E);
H5Dclose(E_dset_id);
H5Sclose(E_filespace);
H5Sclose(E_memspace);
H5Pclose(E_wr_p_list);
hid_t B_dset_id = H5Dcreate(file_id, "B", H5T_NATIVE_DOUBLE, B_filespace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t B_wr_p_list = H5Pcreate(H5P_DATASET_XFER);
// H5Pset_dxpl_mpio(B_wr_p_list, H5FD_MPIO_COLLECTIVE);
H5Sselect_hyperslab(B_filespace, H5S_SELECT_SET, start, NULL, count, NULL);
status = H5Dwrite(B_dset_id, H5T_NATIVE_DOUBLE, B_memspace, B_filespace,
B_wr_p_list, B);
H5Dclose(B_dset_id);
H5Sclose(B_filespace);
H5Sclose(B_memspace);
H5Pclose(B_wr_p_list);
hid_t rhsx_dset_id = H5Dcreate(file_id, "rhsx", H5T_NATIVE_DOUBLE, rhsx_filespace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t rhsx_wr_p_list = H5Pcreate(H5P_DATASET_XFER);
// H5Pset_dxpl_mpio(rhsx_wr_p_list, H5FD_MPIO_COLLECTIVE);
H5Sselect_hyperslab(rhsx_filespace, H5S_SELECT_SET, rhsx_start, NULL, rhs_count, NULL);
status = H5Dwrite(rhsx_dset_id, H5T_NATIVE_DOUBLE, rhsx_memspace, rhsx_filespace,
rhsx_wr_p_list, rhsx);
H5Dclose(rhsx_dset_id);
H5Sclose(rhsx_filespace);
H5Sclose(rhsx_memspace);
H5Pclose(rhsx_wr_p_list);
hid_t rhsy_dset_id = H5Dcreate(file_id, "rhsy", H5T_NATIVE_DOUBLE, rhsy_filespace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t rhsy_wr_p_list = H5Pcreate(H5P_DATASET_XFER);
// H5Pset_dxpl_mpio(rhsy_wr_p_list, H5FD_MPIO_COLLECTIVE);
H5Sselect_hyperslab(rhsy_filespace, H5S_SELECT_SET, rhsy_start, NULL, rhs_count, NULL);
status = H5Dwrite(rhsy_dset_id, H5T_NATIVE_DOUBLE, rhsy_memspace, rhsy_filespace,
rhsy_wr_p_list, rhsy);
H5Dclose(rhsy_dset_id);
H5Sclose(rhsy_filespace);
H5Sclose(rhsy_memspace);
H5Pclose(rhsy_wr_p_list);
hid_t rhsz_dset_id = H5Dcreate(file_id, "rhsz", H5T_NATIVE_DOUBLE, rhsz_filespace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
hid_t rhsz_wr_p_list = H5Pcreate(H5P_DATASET_XFER);
// H5Pset_dxpl_mpio(rhsx_wr_p_list, H5FD_MPIO_COLLECTIVE);
H5Sselect_hyperslab(rhsz_filespace, H5S_SELECT_SET, rhsz_start, NULL, rhs_count, NULL);
status = H5Dwrite(rhsz_dset_id, H5T_NATIVE_DOUBLE, rhsz_memspace, rhsz_filespace,
rhsz_wr_p_list, rhsz);
H5Dclose(rhsz_dset_id);
H5Sclose(rhsz_filespace);
H5Sclose(rhsz_memspace);
H5Pclose(rhsz_wr_p_list);
H5Fclose(file_id);
}
int
main(void)
{
hid_t dcpl1; /* dataset create prop. list */
hid_t dapl1; /* dataset access prop. list */
hid_t dxpl1; /* dataset xfer prop. list */
hid_t gcpl1; /* group create prop. list */
hid_t ocpypl1; /* object copy prop. list */
hid_t ocpl1; /* object create prop. list */
hid_t lcpl1; /* link create prop. list */
hid_t lapl1; /* link access prop. list */
hid_t fapl1; /* file access prop. list */
hid_t fcpl1; /* file create prop. list */
hid_t strcpl1; /* string create prop. list */
hid_t acpl1; /* attribute create prop. list */
herr_t ret = 0;
hsize_t chunk_size = 16384; /* chunk size */
int fill = 2; /* Fill value */
hsize_t max_size[1]; /* data space maximum size */
size_t nslots = 521 * 2;
size_t nbytes = 1048576 * 10;
double w0 = 0.5f;
unsigned max_compact;
unsigned min_dense;
const char* c_to_f = "x+32";
int little_endian;
int word_length;
H5AC_cache_config_t my_cache_config = {
H5AC__CURR_CACHE_CONFIG_VERSION,
1 /*TRUE*/,
0 /*FALSE*/,
0 /*FALSE*/,
"temp",
1 /*TRUE*/,
0 /*FALSE*/,
( 2 * 2048 * 1024),
0.3f,
(64 * 1024 * 1024),
(4 * 1024 * 1024),
60000,
H5C_incr__threshold,
0.8f,
3.0f,
1 /*TRUE*/,
(8 * 1024 * 1024),
H5C_flash_incr__add_space,
2.0f,
0.25f,
H5C_decr__age_out_with_threshold,
0.997f,
0.8f,
1 /*TRUE*/,
(3 * 1024 * 1024),
3,
0 /*FALSE*/,
0.2f,
(256 * 2048),
H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY};
H5AC_cache_image_config_t my_cache_image_config = {
H5AC__CURR_CACHE_IMAGE_CONFIG_VERSION,
TRUE,
FALSE,
-1};
/* check endianess */
{
short int word = 0x0001;
char *byte = (char *) &word;
if(byte[0] == 1)
/* little endian */
little_endian = 1;
else
/* big endian */
little_endian = 0;
}
/* check word length */
{
word_length = 8 * sizeof(void *);
}
/* Explicitly initialize the library, since we are including the private header file */
H5open();
/******* ENCODE/DECODE DCPLS *****/
if((dcpl1 = H5Pcreate(H5P_DATASET_CREATE)) < 0)
assert(dcpl1 > 0);
if((ret = encode_plist(dcpl1, little_endian, word_length, "testfiles/plist_files/def_dcpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_chunk(dcpl1, 1, &chunk_size)) < 0)
assert(ret > 0);
if((ret = H5Pset_alloc_time(dcpl1, H5D_ALLOC_TIME_LATE)) < 0)
assert(ret > 0);
ret = H5Tconvert(H5T_NATIVE_INT, H5T_STD_I32BE, (size_t)1, &fill, NULL, H5P_DEFAULT);
assert(ret >= 0);
if((ret = H5Pset_fill_value(dcpl1, H5T_STD_I32BE, &fill)) < 0)
assert(ret > 0);
max_size[0] = 100;
if((ret = H5Pset_external(dcpl1, "ext1.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4))) < 0)
assert(ret > 0);
if((ret = H5Pset_external(dcpl1, "ext2.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4))) < 0)
assert(ret > 0);
if((ret = H5Pset_external(dcpl1, "ext3.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4))) < 0)
assert(ret > 0);
if((ret = H5Pset_external(dcpl1, "ext4.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4))) < 0)
assert(ret > 0);
if((ret = encode_plist(dcpl1, little_endian, word_length, "testfiles/plist_files/dcpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(dcpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE DAPLS *****/
if((dapl1 = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
assert(dapl1 > 0);
if((ret = encode_plist(dapl1, little_endian, word_length, "testfiles/plist_files/def_dapl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_chunk_cache(dapl1, nslots, nbytes, w0)) < 0)
assert(ret > 0);
if((ret = encode_plist(dapl1, little_endian, word_length, "testfiles/plist_files/dapl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(dapl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE DXPLS *****/
if((dxpl1 = H5Pcreate(H5P_DATASET_XFER)) < 0)
assert(dxpl1 > 0);
if((ret = encode_plist(dxpl1, little_endian, word_length, "testfiles/plist_files/def_dxpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_btree_ratios(dxpl1, 0.2f, 0.6f, 0.2f)) < 0)
assert(ret > 0);
if((ret = H5Pset_hyper_vector_size(dxpl1, 5)) < 0)
assert(ret > 0);
#ifdef H5_HAVE_PARALLEL
if((ret = H5Pset_dxpl_mpio(dxpl1, H5FD_MPIO_COLLECTIVE)) < 0)
assert(ret > 0);
if((ret = H5Pset_dxpl_mpio_collective_opt(dxpl1, H5FD_MPIO_INDIVIDUAL_IO)) < 0)
assert(ret > 0);
if((ret = H5Pset_dxpl_mpio_chunk_opt(dxpl1, H5FD_MPIO_CHUNK_MULTI_IO)) < 0)
assert(ret > 0);
if((ret = H5Pset_dxpl_mpio_chunk_opt_ratio(dxpl1, 30)) < 0)
assert(ret > 0);
if((ret = H5Pset_dxpl_mpio_chunk_opt_num(dxpl1, 40)) < 0)
assert(ret > 0);
#endif/* H5_HAVE_PARALLEL */
if((ret = H5Pset_edc_check(dxpl1, H5Z_DISABLE_EDC)) < 0)
assert(ret > 0);
if((ret = H5Pset_data_transform(dxpl1, c_to_f)) < 0)
assert(ret > 0);
if((ret = encode_plist(dxpl1, little_endian, word_length, "testfiles/plist_files/dxpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(dxpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE GCPLS *****/
if((gcpl1 = H5Pcreate(H5P_GROUP_CREATE)) < 0)
assert(gcpl1 > 0);
if((ret = encode_plist(gcpl1, little_endian, word_length, "testfiles/plist_files/def_gcpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_local_heap_size_hint(gcpl1, 256)) < 0)
assert(ret > 0);
if((ret = H5Pset_link_phase_change(gcpl1, 2, 2)) < 0)
assert(ret > 0);
/* Query the group creation properties */
if((ret = H5Pget_link_phase_change(gcpl1, &max_compact, &min_dense)) < 0)
assert(ret > 0);
if((ret = H5Pset_est_link_info(gcpl1, 3, 9)) < 0)
assert(ret > 0);
if((ret = H5Pset_link_creation_order(gcpl1, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED))) < 0)
assert(ret > 0);
if((ret = encode_plist(gcpl1, little_endian, word_length, "testfiles/plist_files/gcpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(gcpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE LCPLS *****/
if((lcpl1 = H5Pcreate(H5P_LINK_CREATE)) < 0)
assert(lcpl1 > 0);
if((ret = encode_plist(lcpl1, little_endian, word_length, "testfiles/plist_files/def_lcpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_create_intermediate_group(lcpl1, 1 /*TRUE*/)) < 0)
assert(ret > 0);
if((ret = encode_plist(lcpl1, little_endian, word_length, "testfiles/plist_files/lcpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(lcpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE OCPYLS *****/
if((ocpypl1 = H5Pcreate(H5P_OBJECT_COPY)) < 0)
assert(ocpypl1 > 0);
if((ret = encode_plist(ocpypl1, little_endian, word_length, "testfiles/plist_files/def_ocpypl_")) < 0)
assert(ret > 0);
ret = H5Pset_copy_object(ocpypl1, H5O_COPY_EXPAND_EXT_LINK_FLAG);
assert(ret >= 0);
ret = H5Padd_merge_committed_dtype_path(ocpypl1, "foo");
assert(ret >= 0);
ret = H5Padd_merge_committed_dtype_path(ocpypl1, "bar");
assert(ret >= 0);
if((ret = encode_plist(ocpypl1, little_endian, word_length, "testfiles/plist_files/ocpypl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(ocpypl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE OCPLS *****/
if((ocpl1 = H5Pcreate(H5P_OBJECT_CREATE)) < 0)
assert(ocpl1 > 0);
if((ret = encode_plist(ocpl1, little_endian, word_length, "testfiles/plist_files/def_ocpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_attr_creation_order(ocpl1, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED))) < 0)
assert(ret > 0);
if((ret = H5Pset_attr_phase_change (ocpl1, 110, 105)) < 0)
assert(ret > 0);
if((ret = H5Pset_filter (ocpl1, H5Z_FILTER_FLETCHER32, 0, (size_t)0, NULL)) < 0)
assert(ret > 0);
if((ret = encode_plist(ocpl1, little_endian, word_length, "testfiles/plist_files/ocpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(ocpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE LAPLS *****/
if((lapl1 = H5Pcreate(H5P_LINK_ACCESS)) < 0)
assert(lapl1 > 0);
if((ret = encode_plist(lapl1, little_endian, word_length, "testfiles/plist_files/def_lapl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_nlinks(lapl1, (size_t)134)) < 0)
assert(ret > 0);
if((ret = H5Pset_elink_acc_flags(lapl1, H5F_ACC_RDONLY)) < 0)
assert(ret > 0);
if((ret = H5Pset_elink_prefix(lapl1, "/tmpasodiasod")) < 0)
assert(ret > 0);
/* Create FAPL for the elink FAPL */
if((fapl1 = H5Pcreate(H5P_FILE_ACCESS)) < 0)
assert(fapl1 > 0);
if((ret = H5Pset_alignment(fapl1, 2, 1024)) < 0)
assert(ret > 0);
if((ret = H5Pset_elink_fapl(lapl1, fapl1)) < 0)
assert(ret > 0);
/* Close the elink's FAPL */
if((ret = H5Pclose(fapl1)) < 0)
assert(ret > 0);
if((ret = encode_plist(lapl1, little_endian, word_length, "testfiles/plist_files/lapl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(lapl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE FAPLS *****/
if((fapl1 = H5Pcreate(H5P_FILE_ACCESS)) < 0)
assert(fapl1 > 0);
if((ret = encode_plist(fapl1, little_endian, word_length, "testfiles/plist_files/def_fapl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_family_offset(fapl1, 1024)) < 0)
assert(ret > 0);
if((ret = H5Pset_meta_block_size(fapl1, 2098452)) < 0)
assert(ret > 0);
if((ret = H5Pset_sieve_buf_size(fapl1, 1048576)) < 0)
assert(ret > 0);
if((ret = H5Pset_alignment(fapl1, 2, 1024)) < 0)
assert(ret > 0);
if((ret = H5Pset_cache(fapl1, 1024, 128, 10485760, 0.3f)) < 0)
assert(ret > 0);
if((ret = H5Pset_elink_file_cache_size(fapl1, 10485760)) < 0)
assert(ret > 0);
if((ret = H5Pset_gc_references(fapl1, 1)) < 0)
assert(ret > 0);
if((ret = H5Pset_small_data_block_size(fapl1, 2048)) < 0)
assert(ret > 0);
if((ret = H5Pset_libver_bounds(fapl1, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST)) < 0)
assert(ret > 0);
if((ret = H5Pset_fclose_degree(fapl1, H5F_CLOSE_WEAK)) < 0)
assert(ret > 0);
if((ret = H5Pset_multi_type(fapl1, H5FD_MEM_GHEAP)) < 0)
assert(ret > 0);
if((ret = H5Pset_mdc_config(fapl1, &my_cache_config)) < 0)
assert(ret > 0);
if((ret = H5Pset_mdc_image_config(fapl1, &my_cache_image_config)) < 0)
assert(ret > 0);
if((ret = H5Pset_core_write_tracking(fapl1, TRUE, (size_t)(1024 * 1024))) < 0)
assert(ret > 0);
if((ret = encode_plist(fapl1, little_endian, word_length, "testfiles/plist_files/fapl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(fapl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE FCPLS *****/
if((fcpl1 = H5Pcreate(H5P_FILE_CREATE)) < 0)
assert(fcpl1 > 0);
if((ret = encode_plist(fcpl1, little_endian, word_length, "testfiles/plist_files/def_fcpl_")) < 0)
assert(ret > 0);
if((ret = H5Pset_userblock(fcpl1, 1024) < 0))
assert(ret > 0);
if((ret = H5Pset_istore_k(fcpl1, 3) < 0))
assert(ret > 0);
if((ret = H5Pset_sym_k(fcpl1, 4, 5) < 0))
assert(ret > 0);
if((ret = H5Pset_shared_mesg_nindexes(fcpl1, 8) < 0))
assert(ret > 0);
if((ret = H5Pset_shared_mesg_index(fcpl1, 1, H5O_SHMESG_SDSPACE_FLAG, 32) < 0))
assert(ret > 0);
if((ret = H5Pset_shared_mesg_phase_change(fcpl1, 60, 20) < 0))
assert(ret > 0);
if((ret = H5Pset_sizes(fcpl1, 8, 4) < 0))
assert(ret > 0);
if((ret = H5Pset_file_space_strategy(fcpl1, H5F_FSPACE_STRATEGY_PAGE, TRUE, (hsize_t)1)) < 0)
assert(ret > 0);
if((ret = H5Pset_file_space_page_size(fcpl1, (hsize_t)4096)) < 0)
assert(ret > 0);
if((ret = encode_plist(fcpl1, little_endian, word_length, "testfiles/plist_files/fcpl_")) < 0)
assert(ret > 0);
/* release resource */
if((ret = H5Pclose(fcpl1)) < 0)
assert(ret > 0);
/******* ENCODE/DECODE STRCPLS *****/
strcpl1 = H5Pcreate(H5P_STRING_CREATE);
assert(strcpl1 > 0);
ret = encode_plist(strcpl1, little_endian, word_length, "testfiles/plist_files/def_strcpl_");
assert(ret > 0);
ret = H5Pset_char_encoding(strcpl1, H5T_CSET_UTF8);
assert(ret >= 0);
ret = encode_plist(strcpl1, little_endian, word_length, "testfiles/plist_files/strcpl_");
assert(ret > 0);
/* release resource */
ret = H5Pclose(strcpl1);
assert(ret >= 0);
/******* ENCODE/DECODE ACPLS *****/
acpl1 = H5Pcreate(H5P_ATTRIBUTE_CREATE);
assert(acpl1 > 0);
ret = encode_plist(acpl1, little_endian, word_length, "testfiles/plist_files/def_acpl_");
assert(ret > 0);
ret = H5Pset_char_encoding(acpl1, H5T_CSET_UTF8);
assert(ret >= 0);
ret = encode_plist(acpl1, little_endian, word_length, "testfiles/plist_files/acpl_");
assert(ret > 0);
/* release resource */
ret = H5Pclose(acpl1);
assert(ret >= 0);
return 0;
}
bool BAGRasterBand::Initialize( hid_t hDatasetID, const char *pszName )
{
SetDescription( pszName );
this->hDatasetID = hDatasetID;
hid_t datatype = H5Dget_type( hDatasetID );
dataspace = H5Dget_space( hDatasetID );
int n_dims = H5Sget_simple_extent_ndims( dataspace );
native = H5Tget_native_type( datatype, H5T_DIR_ASCEND );
hsize_t dims[3], maxdims[3];
eDataType = GH5_GetDataType( native );
if( n_dims == 2 )
{
H5Sget_simple_extent_dims( dataspace, dims, maxdims );
nRasterXSize = (int) dims[1];
nRasterYSize = (int) dims[0];
}
else
{
CPLError( CE_Failure, CPLE_AppDefined,
"Dataset not of rank 2." );
return false;
}
nBlockXSize = nRasterXSize;
nBlockYSize = 1;
/* -------------------------------------------------------------------- */
/* Check for chunksize, and use it as blocksize for optimized */
/* reading. */
/* -------------------------------------------------------------------- */
hid_t listid = H5Dget_create_plist( hDatasetID );
if (listid>0)
{
if(H5Pget_layout(listid) == H5D_CHUNKED)
{
hsize_t panChunkDims[3];
int nDimSize = H5Pget_chunk(listid, 3, panChunkDims);
nBlockXSize = (int) panChunkDims[nDimSize-1];
nBlockYSize = (int) panChunkDims[nDimSize-2];
}
int nfilters = H5Pget_nfilters( listid );
H5Z_filter_t filter;
char name[120];
size_t cd_nelmts = 20;
unsigned int cd_values[20];
unsigned int flags;
for (int i = 0; i < nfilters; i++)
{
filter = H5Pget_filter(listid, i, &flags, (size_t *)&cd_nelmts, cd_values, 120, name);
if (filter == H5Z_FILTER_DEFLATE)
poDS->SetMetadataItem( "COMPRESSION", "DEFLATE", "IMAGE_STRUCTURE" );
else if (filter == H5Z_FILTER_NBIT)
poDS->SetMetadataItem( "COMPRESSION", "NBIT", "IMAGE_STRUCTURE" );
else if (filter == H5Z_FILTER_SCALEOFFSET)
poDS->SetMetadataItem( "COMPRESSION", "SCALEOFFSET", "IMAGE_STRUCTURE" );
else if (filter == H5Z_FILTER_SZIP)
poDS->SetMetadataItem( "COMPRESSION", "SZIP", "IMAGE_STRUCTURE" );
}
H5Pclose(listid);
}
/* -------------------------------------------------------------------- */
/* Load min/max information. */
/* -------------------------------------------------------------------- */
if( EQUAL(pszName,"elevation")
&& GH5_FetchAttribute( hDatasetID, "Maximum Elevation Value",
dfMaximum )
&& GH5_FetchAttribute( hDatasetID, "Minimum Elevation Value",
dfMinimum ) )
bMinMaxSet = true;
else if( EQUAL(pszName,"uncertainty")
&& GH5_FetchAttribute( hDatasetID, "Maximum Uncertainty Value",
dfMaximum )
&& GH5_FetchAttribute( hDatasetID, "Minimum Uncertainty Value",
dfMinimum ) )
bMinMaxSet = true;
else if( EQUAL(pszName,"nominal_elevation")
&& GH5_FetchAttribute( hDatasetID, "max_value",
dfMaximum )
&& GH5_FetchAttribute( hDatasetID, "min_value",
dfMinimum ) )
bMinMaxSet = true;
return true;
}
void
test_plist_ed(void)
{
hid_t dcpl; /* dataset create prop. list */
hid_t dapl; /* dataset access prop. list */
hid_t dxpl; /* dataset transfer prop. list */
hid_t gcpl; /* group create prop. list */
hid_t lcpl; /* link create prop. list */
hid_t lapl; /* link access prop. list */
hid_t ocpypl; /* object copy prop. list */
hid_t ocpl; /* object create prop. list */
hid_t fapl; /* file access prop. list */
hid_t fcpl; /* file create prop. list */
hid_t strcpl; /* string create prop. list */
hid_t acpl; /* attribute create prop. list */
int mpi_size, mpi_rank, recv_proc;
hsize_t chunk_size = 16384; /* chunk size */
double fill = 2.7f; /* Fill value */
size_t nslots = 521*2;
size_t nbytes = 1048576 * 10;
double w0 = 0.5f;
unsigned max_compact;
unsigned min_dense;
hsize_t max_size[1]; /*data space maximum size */
const char* c_to_f = "x+32";
H5AC_cache_config_t my_cache_config = {
H5AC__CURR_CACHE_CONFIG_VERSION,
TRUE,
FALSE,
FALSE,
"temp",
TRUE,
FALSE,
( 2 * 2048 * 1024),
0.3f,
(64 * 1024 * 1024),
(4 * 1024 * 1024),
60000,
H5C_incr__threshold,
0.8f,
3.0f,
TRUE,
(8 * 1024 * 1024),
H5C_flash_incr__add_space,
2.0f,
0.25f,
H5C_decr__age_out_with_threshold,
0.997f,
0.8f,
TRUE,
(3 * 1024 * 1024),
3,
FALSE,
0.2f,
(256 * 2048),
H5AC__DEFAULT_METADATA_WRITE_STRATEGY};
herr_t ret; /* Generic return value */
if(VERBOSE_MED)
printf("Encode/Decode DCPLs\n");
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
if(mpi_size == 1)
recv_proc = 0;
else
recv_proc = 1;
dcpl = H5Pcreate(H5P_DATASET_CREATE);
VRFY((dcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_chunk(dcpl, 1, &chunk_size);
VRFY((ret >= 0), "H5Pset_chunk succeeded");
ret = H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_LATE);
VRFY((ret >= 0), "H5Pset_alloc_time succeeded");
ret = H5Pset_fill_value(dcpl, H5T_NATIVE_DOUBLE, &fill);
VRFY((ret>=0), "set fill-value succeeded");
max_size[0] = 100;
ret = H5Pset_external(dcpl, "ext1.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4));
VRFY((ret>=0), "set external succeeded");
ret = H5Pset_external(dcpl, "ext2.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4));
VRFY((ret>=0), "set external succeeded");
ret = H5Pset_external(dcpl, "ext3.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4));
VRFY((ret>=0), "set external succeeded");
ret = H5Pset_external(dcpl, "ext4.data", (off_t)0,
(hsize_t)(max_size[0] * sizeof(int)/4));
VRFY((ret>=0), "set external succeeded");
ret = test_encode_decode(dcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(dcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE DAPLS *****/
dapl = H5Pcreate(H5P_DATASET_ACCESS);
VRFY((dapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_chunk_cache(dapl, nslots, nbytes, w0);
VRFY((ret >= 0), "H5Pset_chunk_cache succeeded");
ret = test_encode_decode(dapl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(dapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE OCPLS *****/
ocpl = H5Pcreate(H5P_OBJECT_CREATE);
VRFY((ocpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_attr_creation_order(ocpl, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED));
VRFY((ret >= 0), "H5Pset_attr_creation_order succeeded");
ret = H5Pset_attr_phase_change(ocpl, 110, 105);
VRFY((ret >= 0), "H5Pset_attr_phase_change succeeded");
ret = H5Pset_filter(ocpl, H5Z_FILTER_FLETCHER32, 0, (size_t)0, NULL);
VRFY((ret >= 0), "H5Pset_filter succeeded");
ret = test_encode_decode(ocpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(ocpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE DXPLS *****/
dxpl = H5Pcreate(H5P_DATASET_XFER);
VRFY((dxpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_btree_ratios(dxpl, 0.2f, 0.6f, 0.2f);
VRFY((ret >= 0), "H5Pset_btree_ratios succeeded");
ret = H5Pset_hyper_vector_size(dxpl, 5);
VRFY((ret >= 0), "H5Pset_hyper_vector_size succeeded");
ret = H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);
VRFY((ret >= 0), "H5Pset_dxpl_mpio succeeded");
ret = H5Pset_dxpl_mpio_collective_opt(dxpl, H5FD_MPIO_INDIVIDUAL_IO);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_collective_opt succeeded");
ret = H5Pset_dxpl_mpio_chunk_opt(dxpl, H5FD_MPIO_CHUNK_MULTI_IO);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt succeeded");
ret = H5Pset_dxpl_mpio_chunk_opt_ratio(dxpl, 30);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_ratio succeeded");
ret = H5Pset_dxpl_mpio_chunk_opt_num(dxpl, 40);
VRFY((ret >= 0), "H5Pset_dxpl_mpio_chunk_opt_num succeeded");
ret = H5Pset_edc_check(dxpl, H5Z_DISABLE_EDC);
VRFY((ret >= 0), "H5Pset_edc_check succeeded");
ret = H5Pset_data_transform(dxpl, c_to_f);
VRFY((ret >= 0), "H5Pset_data_transform succeeded");
ret = test_encode_decode(dxpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(dxpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE GCPLS *****/
gcpl = H5Pcreate(H5P_GROUP_CREATE);
VRFY((gcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_local_heap_size_hint(gcpl, 256);
VRFY((ret >= 0), "H5Pset_local_heap_size_hint succeeded");
ret = H5Pset_link_phase_change(gcpl, 2, 2);
VRFY((ret >= 0), "H5Pset_link_phase_change succeeded");
/* Query the group creation properties */
ret = H5Pget_link_phase_change(gcpl, &max_compact, &min_dense);
VRFY((ret >= 0), "H5Pget_est_link_info succeeded");
ret = H5Pset_est_link_info(gcpl, 3, 9);
VRFY((ret >= 0), "H5Pset_est_link_info succeeded");
ret = H5Pset_link_creation_order(gcpl, (H5P_CRT_ORDER_TRACKED | H5P_CRT_ORDER_INDEXED));
VRFY((ret >= 0), "H5Pset_link_creation_order succeeded");
ret = test_encode_decode(gcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(gcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE LCPLS *****/
lcpl = H5Pcreate(H5P_LINK_CREATE);
VRFY((lcpl >= 0), "H5Pcreate succeeded");
ret= H5Pset_create_intermediate_group(lcpl, TRUE);
VRFY((ret >= 0), "H5Pset_create_intermediate_group succeeded");
ret = test_encode_decode(lcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(lcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE LAPLS *****/
lapl = H5Pcreate(H5P_LINK_ACCESS);
VRFY((lapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_nlinks(lapl, (size_t)134);
VRFY((ret >= 0), "H5Pset_nlinks succeeded");
ret = H5Pset_elink_acc_flags(lapl, H5F_ACC_RDONLY);
VRFY((ret >= 0), "H5Pset_elink_acc_flags succeeded");
ret = H5Pset_elink_prefix(lapl, "/tmpasodiasod");
VRFY((ret >= 0), "H5Pset_nlinks succeeded");
/* Create FAPL for the elink FAPL */
fapl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_alignment(fapl, 2, 1024);
VRFY((ret >= 0), "H5Pset_alignment succeeded");
ret = H5Pset_elink_fapl(lapl, fapl);
VRFY((ret >= 0), "H5Pset_elink_fapl succeeded");
/* Close the elink's FAPL */
ret = H5Pclose(fapl);
VRFY((ret >= 0), "H5Pclose succeeded");
ret = test_encode_decode(lapl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(lapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE OCPYPLS *****/
ocpypl = H5Pcreate(H5P_OBJECT_COPY);
VRFY((ocpypl >= 0), "H5Pcreate succeeded");
ret = H5Pset_copy_object(ocpypl, H5O_COPY_EXPAND_EXT_LINK_FLAG);
VRFY((ret >= 0), "H5Pset_copy_object succeeded");
ret = H5Padd_merge_committed_dtype_path(ocpypl, "foo");
VRFY((ret >= 0), "H5Padd_merge_committed_dtype_path succeeded");
ret = H5Padd_merge_committed_dtype_path(ocpypl, "bar");
VRFY((ret >= 0), "H5Padd_merge_committed_dtype_path succeeded");
ret = test_encode_decode(ocpypl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(ocpypl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE FAPLS *****/
fapl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_family_offset(fapl, 1024);
VRFY((ret >= 0), "H5Pset_family_offset succeeded");
ret = H5Pset_meta_block_size(fapl, 2098452);
VRFY((ret >= 0), "H5Pset_meta_block_size succeeded");
ret = H5Pset_sieve_buf_size(fapl, 1048576);
VRFY((ret >= 0), "H5Pset_sieve_buf_size succeeded");
ret = H5Pset_alignment(fapl, 2, 1024);
VRFY((ret >= 0), "H5Pset_alignment succeeded");
ret = H5Pset_cache(fapl, 1024, 128, 10485760, 0.3f);
VRFY((ret >= 0), "H5Pset_cache succeeded");
ret = H5Pset_elink_file_cache_size(fapl, 10485760);
VRFY((ret >= 0), "H5Pset_elink_file_cache_size succeeded");
ret = H5Pset_gc_references(fapl, 1);
VRFY((ret >= 0), "H5Pset_gc_references succeeded");
ret = H5Pset_small_data_block_size(fapl, 2048);
VRFY((ret >= 0), "H5Pset_small_data_block_size succeeded");
ret = H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
VRFY((ret >= 0), "H5Pset_libver_bounds succeeded");
ret = H5Pset_fclose_degree(fapl, H5F_CLOSE_WEAK);
VRFY((ret >= 0), "H5Pset_fclose_degree succeeded");
ret = H5Pset_multi_type(fapl, H5FD_MEM_GHEAP);
VRFY((ret >= 0), "H5Pset_multi_type succeeded");
ret = H5Pset_mdc_config(fapl, &my_cache_config);
VRFY((ret >= 0), "H5Pset_mdc_config succeeded");
ret = test_encode_decode(fapl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(fapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE FCPLS *****/
fcpl = H5Pcreate(H5P_FILE_CREATE);
VRFY((fcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_userblock(fcpl, 1024);
VRFY((ret >= 0), "H5Pset_userblock succeeded");
ret = H5Pset_istore_k(fcpl, 3);
VRFY((ret >= 0), "H5Pset_istore_k succeeded");
ret = H5Pset_sym_k(fcpl, 4, 5);
VRFY((ret >= 0), "H5Pset_sym_k succeeded");
ret = H5Pset_shared_mesg_nindexes(fcpl, 8);
VRFY((ret >= 0), "H5Pset_shared_mesg_nindexes succeeded");
ret = H5Pset_shared_mesg_index(fcpl, 1, H5O_SHMESG_SDSPACE_FLAG, 32);
VRFY((ret >= 0), "H5Pset_shared_mesg_index succeeded");
ret = H5Pset_shared_mesg_phase_change(fcpl, 60, 20);
VRFY((ret >= 0), "H5Pset_shared_mesg_phase_change succeeded");
ret = H5Pset_sizes(fcpl, 8, 4);
VRFY((ret >= 0), "H5Pset_sizes succeeded");
ret = test_encode_decode(fcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(fcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE STRCPLS *****/
strcpl = H5Pcreate(H5P_STRING_CREATE);
VRFY((strcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_char_encoding(strcpl, H5T_CSET_UTF8);
VRFY((ret >= 0), "H5Pset_char_encoding succeeded");
ret = test_encode_decode(strcpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(strcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
/******* ENCODE/DECODE ACPLS *****/
acpl = H5Pcreate(H5P_ATTRIBUTE_CREATE);
VRFY((acpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_char_encoding(acpl, H5T_CSET_UTF8);
VRFY((ret >= 0), "H5Pset_char_encoding succeeded");
ret = test_encode_decode(acpl, mpi_rank, recv_proc);
VRFY((ret >= 0), "test_encode_decode succeeded");
ret = H5Pclose(acpl);
VRFY((ret >= 0), "H5Pclose succeeded");
}
/*-------------------------------------------------------------------------
* Function: test_family_compat
*
* Purpose: Tests the backward compatibility for FAMILY driver.
* See if we can open files created with v1.6 library.
* The source file was created by the test/file_handle.c
* of the v1.6 library. Then tools/misc/h5repart.c was
* used to concantenated. The command was "h5repart -m 5k
* family_file%05d.h5 family_v16_%05d.h5".
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* June 3, 2005
*
*-------------------------------------------------------------------------
*/
static herr_t
test_family_compat(void)
{
hid_t file = (-1), fapl;
hid_t dset;
char dname[]="dataset";
char filename[1024];
char pathname[1024], pathname_individual[1024];
char newname[1024], newname_individual[1024];
int counter = 0;
TESTING("FAMILY file driver backward compatibility");
/* Set property list and file name for FAMILY driver */
fapl = h5_fileaccess();
if(H5Pset_fapl_family(fapl, (hsize_t)FAMILY_SIZE2, H5P_DEFAULT) < 0)
TEST_ERROR;
h5_fixname(COMPAT_BASENAME, fapl, filename, sizeof filename);
h5_fixname(FILENAME[3], fapl, newname, sizeof newname);
pathname[0] = '\0';
HDstrcat(pathname, filename);
/* The following code makes the copies of the family files in the source directory.
* Since we're going to open the files with write mode, this protects the original
* files.
*/
sprintf(newname_individual, newname, counter);
sprintf(pathname_individual, pathname, counter);
while (h5_make_local_copy(pathname_individual, newname_individual) >= 0) {
counter++;
sprintf(newname_individual, newname, counter);
sprintf(pathname_individual, pathname, counter);
}
/* Make sure we can open the file. Use the read and write mode to flush the
* superblock. */
if((file = H5Fopen(newname, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
if((dset = H5Dopen2(file, dname, H5P_DEFAULT)) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Open the file again to make sure it isn't corrupted. */
if((file = H5Fopen(newname, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
if((dset = H5Dopen2(file, dname, H5P_DEFAULT)) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Fclose(file);
H5Pclose(fapl);
} H5E_END_TRY;
return -1;
} /* end test_family_compat() */
/***********************************************************
**
** test_multiple_end(): Test full hyperslab selection of
** multiple blocks.
**
*************************************************************/
static void test_multiple_ends(hid_t file, hbool_t is_chunked)
{
hid_t sid, plid, did, msid;
char dset_name[NAME_LEN]; /* Dataset name */
herr_t ret; /* Generic error return */
int i, j, k, l, m, n, p;
hsize_t da_dims[8] = { 4, 5, 3, 4, 2, 3, 6, 2 };
hsize_t da_chunksize[8] = { 1, 5, 3, 2, 2, 3, 3, 2 };
int data_buf[4][5][3][4][2][3][6][2];
/* For testing the full selections in the fastest-growing end and in the middle dimensions */
int mem1_buffer[1][1][1][4][2][1][6][2];
hsize_t mem1_dims[8] = { 1, 1, 1, 4, 2, 1, 6, 2 };
hsize_t mem1_start[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
hsize_t mem1_count[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem1_stride[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem1_block[8] = { 1, 1, 1, 4, 2, 1, 6, 2 };
/* For testing the full selections in the slowest-growing end and in the middle dimensions */
int mem2_buffer[4][5][1][4][2][1][1][1];
hsize_t mem2_dims[8] = { 4, 5, 1, 4, 2, 1, 1, 1 };
hsize_t mem2_start[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
hsize_t mem2_count[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem2_stride[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem2_block[8] = { 4, 5, 1, 4, 2, 1, 1, 1 };
/* For testing two unadjacent full selections in the middle dimensions */
int mem3_buffer[1][5][3][1][1][3][6][1];
hsize_t mem3_dims[8] = { 1, 5, 3, 1, 1, 3, 6, 1 };
hsize_t mem3_start[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
hsize_t mem3_count[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem3_stride[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem3_block[8] = { 1, 5, 3, 1, 1, 3, 6, 1 };
/* For testing the full selections in the fastest-growing end and the slowest-growing end */
int mem4_buffer[4][5][1][1][1][1][6][2];
hsize_t mem4_dims[8] = { 4, 5, 1, 1, 1, 1, 6, 2 };
hsize_t mem4_start[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
hsize_t mem4_count[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem4_stride[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem4_block[8] = { 4, 5, 1, 1, 1, 1, 6, 2 };
/* For testing the full selections in the fastest-growing end and slowest-growing end,
* also in the middle dimensions */
int mem5_buffer[4][5][1][4][2][1][6][2];
hsize_t mem5_dims[8] = { 4, 5, 1, 4, 2, 1, 6, 2 };
hsize_t mem5_start[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
hsize_t mem5_count[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem5_stride[8] = { 1, 1, 1, 1, 1, 1, 1, 1 };
hsize_t mem5_block[8] = { 4, 5, 1, 4, 2, 1, 6, 2 };
/* Create and write the dataset */
sid = H5Screate_simple(8, da_dims, da_dims);
CHECK(sid, FAIL, "H5Screate_simple");
plid = H5Pcreate(H5P_DATASET_CREATE);
CHECK(plid, FAIL, "H5Pcreate");
if(is_chunked) {
ret = H5Pset_chunk(plid, 8, da_chunksize);
CHECK(ret, FAIL, "H5Pset_chunk");
}
/* Construct dataset's name */
memset(dset_name, 0, NAME_LEN);
strcat(dset_name, MULTI_ENDS_SEL_HYPER_DSET);
if(is_chunked)
strcat(dset_name, "_chunked");
did = H5Dcreate2(file, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, plid, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dcreate2");
for(i=0; i<4; i++)
for(j=0; j<5; j++)
for(k=0; k<3; k++)
for(l=0; l<4; l++)
for(m=0; m<2; m++)
for(n=0; n<3; n++)
for(p=0; p<6; p++) {
data_buf[i][j][k][l][m][n][p][0] = i*1000000 + j*100000 + k*10000 + l*1000 + m*100 + n*10 + p;
data_buf[i][j][k][l][m][n][p][1] = i*1000000 + j*100000 + k*10000 + l*1000 + m*100 + n*10 + p + 1;
}
ret = H5Dwrite(did, H5T_NATIVE_INT, sid, sid, H5P_DEFAULT, data_buf);
CHECK(ret, FAIL, "H5Dwrite");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
/* ****** Case 1: ******
* Testing the full selections in the fastest-growing end and in the middle dimensions*/
did = H5Dopen2(file, dset_name, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
/* Select the elements in the dataset */
ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, mem1_start, mem1_stride, mem1_count, mem1_block);
CHECK(ret, FAIL, "H5Sselect_hyperslab");
msid = H5Screate_simple(8, mem1_dims, mem1_dims);
CHECK(msid, FAIL, "H5Screate_simple");
ret = H5Sselect_all(msid);
CHECK(ret, FAIL, "H5Sselect_all");
ret = H5Dread(did, H5T_NATIVE_INT, msid, sid, H5P_DEFAULT, mem1_buffer);
CHECK(ret, FAIL, "H5Dread");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(msid);
CHECK(ret, FAIL, "H5Sclose");
for(i=0; i<4; i++)
for(j=0; j<2; j++)
for(k=0; k<6; k++)
for(l=0; l<2; l++)
if(data_buf[0][0][0][i][j][0][k][l] != mem1_buffer[0][0][0][i][j][0][k][l]) {
TestErrPrintf("%u: Read different values than written at index 0,0,0,%d,%d,0,%d,%d\n", __LINE__, i, j, k, l);
}
/* ****** Case 2: ******
* Testing the full selections in the slowest-growing end and in the middle dimensions*/
did = H5Dopen2(file, dset_name, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
/* Select the elements in the dataset */
ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, mem2_start, mem2_stride, mem2_count, mem2_block);
CHECK(ret, FAIL, "H5Sselect_hyperslab");
msid = H5Screate_simple(8, mem2_dims, mem2_dims);
CHECK(msid, FAIL, "H5Screate_simple");
ret = H5Sselect_all(msid);
CHECK(ret, FAIL, "H5Sselect_all");
ret = H5Dread(did, H5T_NATIVE_INT, msid, sid, H5P_DEFAULT, mem2_buffer);
CHECK(ret, FAIL, "H5Dread");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(msid);
CHECK(ret, FAIL, "H5Sclose");
for(i=0; i<4; i++)
for(j=0; j<5; j++)
for(k=0; k<4; k++)
for(l=0; l<2; l++)
if(data_buf[i][j][0][k][l][0][0][0] != mem2_buffer[i][j][0][k][l][0][0][0]) {
TestErrPrintf("%u: Read different values than written at index %d,%d,0,%d,%d,0,0,0\n", __LINE__, i, j, k, l);
}
/* ****** Case 3: ******
* Testing two unadjacent full selections in the middle dimensions */
did = H5Dopen2(file, dset_name, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
/* Select the elements in the dataset */
ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, mem3_start, mem3_stride, mem3_count, mem3_block);
CHECK(ret, FAIL, "H5Sselect_hyperslab");
msid = H5Screate_simple(8, mem3_dims, mem3_dims);
CHECK(msid, FAIL, "H5Screate_simple");
ret = H5Sselect_all(msid);
CHECK(ret, FAIL, "H5Sselect_all");
ret = H5Dread(did, H5T_NATIVE_INT, msid, sid, H5P_DEFAULT, mem3_buffer);
CHECK(ret, FAIL, "H5Dread");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(msid);
CHECK(ret, FAIL, "H5Sclose");
for(i=0; i<5; i++)
for(j=0; j<3; j++)
for(k=0; k<3; k++)
for(l=0; l<6; l++)
if(data_buf[0][i][j][0][0][k][l][0] != mem3_buffer[0][i][j][0][0][k][l][0]) {
TestErrPrintf("%u: Read different values than written at index 0,%d,%d,0,0,%d,%d,0\n", __LINE__, i, j, k, l);
}
/* ****** Case 4: ******
* Testing the full selections in the fastest-growing end and the slowest-growing end */
did = H5Dopen2(file, dset_name, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
/* Select the elements in the dataset */
ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, mem4_start, mem4_stride, mem4_count, mem4_block);
CHECK(ret, FAIL, "H5Sselect_hyperslab");
msid = H5Screate_simple(8, mem4_dims, mem4_dims);
CHECK(msid, FAIL, "H5Screate_simple");
ret = H5Sselect_all(msid);
CHECK(ret, FAIL, "H5Sselect_all");
ret = H5Dread(did, H5T_NATIVE_INT, msid, sid, H5P_DEFAULT, mem4_buffer);
CHECK(ret, FAIL, "H5Dread");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(msid);
CHECK(ret, FAIL, "H5Sclose");
for(i=0; i<4; i++)
for(j=0; j<5; j++)
for(k=0; k<6; k++)
for(l=0; l<2; l++)
if(data_buf[i][j][0][0][0][0][k][l] != mem4_buffer[i][j][0][0][0][0][k][l]) {
TestErrPrintf("%u: Read different values than written at index %d,%d,0,0,0,0,%d,%d\n", __LINE__, i, j, k, l);
}
/* ****** Case 5: ******
* Testing the full selections in the fastest-growing end and the slowest-growing end,
* and also in the middle dimensions */
did = H5Dopen2(file, dset_name, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
/* Select the elements in the dataset */
ret = H5Sselect_hyperslab(sid, H5S_SELECT_SET, mem5_start, mem5_stride, mem5_count, mem5_block);
CHECK(ret, FAIL, "H5Sselect_hyperslab");
msid = H5Screate_simple(8, mem5_dims, mem5_dims);
CHECK(msid, FAIL, "H5Screate_simple");
ret = H5Sselect_all(msid);
CHECK(ret, FAIL, "H5Sselect_all");
ret = H5Dread(did, H5T_NATIVE_INT, msid, sid, H5P_DEFAULT, mem5_buffer);
CHECK(ret, FAIL, "H5Dread");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(msid);
CHECK(ret, FAIL, "H5Sclose");
for(i=0; i<4; i++)
for(j=0; j<5; j++)
for(k=0; k<4; k++)
for(l=0; l<2; l++)
for(m=0; m<6; m++)
for(n=0; n<2; n++)
if(data_buf[i][j][0][k][l][0][m][n] != mem5_buffer[i][j][0][k][l][0][m][n]) {
TestErrPrintf("%u: Read different values than written at index %d,%d,0,%d,%d,0,%d,%d\n", __LINE__, i, j, k, l, m, n);
}
ret = H5Sclose(sid);
CHECK(ret, FAIL, "H5Sclose");
ret = H5Pclose(plid);
CHECK(ret, FAIL, "H5Pclose");
}
/*-------------------------------------------------------------------------
* Function: test_multi
*
* Purpose: Tests the file handle interface for MUTLI driver
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* Tuesday, Sept 24, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
test_multi(void)
{
hid_t file=(-1), fapl, fapl2=(-1), dset=(-1), space=(-1);
hid_t root, attr, aspace, atype;
hid_t access_fapl = -1;
char filename[1024];
int *fhandle2=NULL, *fhandle=NULL;
hsize_t file_size;
H5FD_mem_t mt, memb_map[H5FD_MEM_NTYPES];
hid_t memb_fapl[H5FD_MEM_NTYPES];
haddr_t memb_addr[H5FD_MEM_NTYPES];
const char *memb_name[H5FD_MEM_NTYPES];
char sv[H5FD_MEM_NTYPES][32];
hsize_t dims[2]={MULTI_SIZE, MULTI_SIZE};
hsize_t adims[1]={1};
char dname[]="dataset";
char meta[] = "this is some metadata on this file";
int i, j;
int buf[MULTI_SIZE][MULTI_SIZE];
TESTING("MULTI file driver");
/* Set file access property list for MULTI driver */
fapl = h5_fileaccess();
HDmemset(memb_map, 0, sizeof memb_map);
HDmemset(memb_fapl, 0, sizeof memb_fapl);
HDmemset(memb_name, 0, sizeof memb_name);
HDmemset(memb_addr, 0, sizeof memb_addr);
HDmemset(sv, 0, sizeof sv);
for(mt=H5FD_MEM_DEFAULT; mt<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) {
memb_fapl[mt] = H5P_DEFAULT;
memb_map[mt] = H5FD_MEM_SUPER;
}
memb_map[H5FD_MEM_DRAW] = H5FD_MEM_DRAW;
memb_map[H5FD_MEM_BTREE] = H5FD_MEM_BTREE;
memb_map[H5FD_MEM_GHEAP] = H5FD_MEM_GHEAP;
sprintf(sv[H5FD_MEM_SUPER], "%%s-%c.h5", 's');
memb_name[H5FD_MEM_SUPER] = sv[H5FD_MEM_SUPER];
memb_addr[H5FD_MEM_SUPER] = 0;
sprintf(sv[H5FD_MEM_BTREE], "%%s-%c.h5", 'b');
memb_name[H5FD_MEM_BTREE] = sv[H5FD_MEM_BTREE];
memb_addr[H5FD_MEM_BTREE] = HADDR_MAX/4;
sprintf(sv[H5FD_MEM_DRAW], "%%s-%c.h5", 'r');
memb_name[H5FD_MEM_DRAW] = sv[H5FD_MEM_DRAW];
memb_addr[H5FD_MEM_DRAW] = HADDR_MAX/2;
sprintf(sv[H5FD_MEM_GHEAP], "%%s-%c.h5", 'g');
memb_name[H5FD_MEM_GHEAP] = sv[H5FD_MEM_GHEAP];
memb_addr[H5FD_MEM_GHEAP] = (HADDR_MAX/4)*3;
if(H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name, memb_addr, TRUE) < 0)
TEST_ERROR;
h5_fixname(FILENAME[4], fapl, filename, sizeof filename);
if((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Test wrong ways to reopen multi files */
if(test_multi_opens(filename) < 0)
TEST_ERROR;
/* Reopen the file */
if((file=H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
/* Create and write data set */
if((space=H5Screate_simple(2, dims, NULL)) < 0)
TEST_ERROR;
/* Retrieve the access property list... */
if ((access_fapl = H5Fget_access_plist(file)) < 0)
TEST_ERROR;
/* Check that the driver is correct */
if(H5FD_MULTI != H5Pget_driver(access_fapl))
TEST_ERROR;
/* ...and close the property list */
if (H5Pclose(access_fapl) < 0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* Before any data is written, the raw data file is empty. So
* the file size is only the size of b-tree + HADDR_MAX/4.
*/
if(file_size < HADDR_MAX/4 || file_size > HADDR_MAX/2)
TEST_ERROR;
if((dset=H5Dcreate2(file, dname, H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
for(i=0; i<MULTI_SIZE; i++)
for(j=0; j<MULTI_SIZE; j++)
buf[i][j] = i*10000+j;
if(H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
TEST_ERROR;
if((fapl2=H5Pcreate(H5P_FILE_ACCESS)) < 0)
TEST_ERROR;
if(H5Pset_multi_type(fapl2, H5FD_MEM_SUPER) < 0)
TEST_ERROR;
if(H5Fget_vfd_handle(file, fapl2, (void **)&fhandle) < 0)
TEST_ERROR;
if(*fhandle<0)
TEST_ERROR;
if(H5Pset_multi_type(fapl2, H5FD_MEM_DRAW) < 0)
TEST_ERROR;
if(H5Fget_vfd_handle(file, fapl2, (void **)&fhandle2) < 0)
TEST_ERROR;
if(*fhandle2<0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* After the data is written, the file size is huge because the
* beginning of raw data file is set at HADDR_MAX/2. It's supposed
* to be (HADDR_MAX/2 + 128*128*4)
*/
if(file_size < HADDR_MAX/2 || file_size > HADDR_MAX)
TEST_ERROR;
if(H5Sclose(space) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Pclose(fapl2) < 0)
TEST_ERROR;
/* Create and write attribute for the root group. */
if((root = H5Gopen2(file, "/", H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Attribute string. */
if((atype = H5Tcopy(H5T_C_S1)) < 0)
TEST_ERROR;
if(H5Tset_size(atype, strlen(meta) + 1) < 0)
TEST_ERROR;
if(H5Tset_strpad(atype, H5T_STR_NULLTERM) < 0)
TEST_ERROR;
/* Create and write attribute */
if((aspace = H5Screate_simple(1, adims, NULL)) < 0)
TEST_ERROR;
if((attr = H5Acreate2(root, "Metadata", atype, aspace, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
if(H5Awrite(attr, atype, meta) < 0)
TEST_ERROR;
/* Close IDs */
if(H5Tclose(atype) < 0)
TEST_ERROR;
if(H5Sclose(aspace) < 0)
TEST_ERROR;
if(H5Aclose(attr) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Sclose(space);
H5Dclose(dset);
H5Pclose(fapl);
H5Pclose(fapl2);
H5Fclose(file);
} H5E_END_TRY;
return -1;
}
/***********************************************************
**
** test_singleEnd_selElements(): Test element selection of only
** one block.
**
*************************************************************/
static void test_singleEnd_selElements(hid_t file, hbool_t is_chunked)
{
hid_t sid, plid, did, msid;
char dset_name[NAME_LEN]; /* Dataset name */
size_t elmts_numb;
herr_t ret; /* Generic error return */
int i, j, k;
hsize_t da_dims[4] = { 2, 3, 6, 2 };
hsize_t da_chunksize[4] = { 1, 3, 3, 2 };
/* For testing the full selection in the fastest-growing end */
int mem1_buffer[1][1][6][2];
hsize_t mem1_dims[4] = { 1, 1, 6, 2 };
hsize_t da_elmts1[12][4] = { {0, 0, 0, 0},
{0, 0, 0, 1},
{0, 0, 1, 0},
{0, 0, 1, 1},
{0, 0, 2, 0},
{0, 0, 2, 1},
{0, 0, 3, 0},
{0, 0, 3, 1},
{0, 0, 4, 0},
{0, 0, 4, 1},
{0, 0, 5, 0},
{0, 0, 5, 1} };
/* For testing the full selection in the slowest-growing end */
int mem2_buffer[2][3][1][1];
hsize_t mem2_dims[4] = { 2, 3, 1, 1 };
hsize_t da_elmts2[6][4] = { {0, 0, 0, 0},
{0, 1, 0, 0},
{0, 2, 0, 0},
{1, 0, 0, 0},
{1, 1, 0, 0},
{1, 2, 0, 0} };
/* For testing the full selection in the middle dimensions */
int mem3_buffer[1][3][6][1];
hsize_t mem3_dims[4] = { 1, 3, 6, 1 };
hsize_t da_elmts3[18][4] = { {0, 0, 0, 0},
{0, 0, 1, 0},
{0, 0, 2, 0},
{0, 0, 3, 0},
{0, 0, 4, 0},
{0, 0, 5, 0},
{0, 1, 0, 0},
{0, 1, 1, 0},
{0, 1, 2, 0},
{0, 1, 3, 0},
{0, 1, 4, 0},
{0, 1, 5, 0},
{0, 2, 0, 0},
{0, 2, 1, 0},
{0, 2, 2, 0},
{0, 2, 3, 0},
{0, 2, 4, 0},
{0, 2, 5, 0} };
/* Create and write the dataset */
sid = H5Screate_simple(4, da_dims, da_dims);
CHECK(sid, FAIL, "H5Screate_simple");
plid = H5Pcreate(H5P_DATASET_CREATE);
CHECK(plid, FAIL, "H5Pcreate");
if(is_chunked) {
ret = H5Pset_chunk(plid, 4, da_chunksize);
CHECK(ret, FAIL, "H5Pset_chunk");
}
/* Construct dataset's name */
memset(dset_name, 0, (size_t)NAME_LEN);
strcat(dset_name, SINGLE_END_DSET);
if(is_chunked)
strcat(dset_name, "_chunked");
did = H5Dcreate2(file, dset_name, H5T_NATIVE_INT, sid, H5P_DEFAULT, plid, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dcreate2");
/* Initialize the data to be written to file */
for(i=0; i<2; i++) {
for(j=0; j<3; j++) {
for(k=0; k<6; k++) {
da_buffer[i][j][k][0] = i*100 + j*10 + k;
da_buffer[i][j][k][1] = i*100 + j*10 + k + 1;
}
}
}
ret = H5Dwrite(did, H5T_NATIVE_INT, sid, sid, H5P_DEFAULT, da_buffer);
CHECK(ret, FAIL, "H5Dwrite");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
/* ****** Case 1: ******
* Testing the full selection in the fastest-growing end */
did = H5Dopen2(file, dset_name, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
/* Select the elements in the dataset */
elmts_numb = 12;
ret = H5Sselect_elements(sid, H5S_SELECT_SET, elmts_numb, (const hsize_t *)da_elmts1);
CHECK(ret, FAIL, "H5Sselect_elements");
/* Dataspace for memory buffer */
msid = H5Screate_simple(4, mem1_dims, mem1_dims);
CHECK(msid, FAIL, "H5Screate_simple");
ret = H5Sselect_all(msid);
CHECK(ret, FAIL, "H5Sselect_all");
ret = H5Dread(did, H5T_NATIVE_INT, msid, sid, H5P_DEFAULT, mem1_buffer);
CHECK(ret, FAIL, "H5Dread");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(msid);
CHECK(ret, FAIL, "H5Sclose");
for(i=0; i<6; i++)
for(j=0; j<2; j++)
if(da_buffer[0][0][i][j] != mem1_buffer[0][0][i][j]) {
TestErrPrintf("%u: Read different values than written at index 0,0,%d,%d\n", __LINE__, i, j);
}
/* ****** Case 2: ******
* Testing the full selection in the slowest-growing end */
did = H5Dopen2(file, dset_name, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
/* Select the elements in the dataset */
elmts_numb = 6;
ret = H5Sselect_elements(sid, H5S_SELECT_SET, elmts_numb, (const hsize_t *)da_elmts2);
CHECK(ret, FAIL, "H5Sselect_elements");
/* Dataspace for memory buffer */
msid = H5Screate_simple(4, mem2_dims, mem2_dims);
CHECK(msid, FAIL, "H5Screate_simple");
ret = H5Sselect_all(msid);
CHECK(ret, FAIL, "H5Sselect_all");
ret = H5Dread(did, H5T_NATIVE_INT, msid, sid, H5P_DEFAULT, mem2_buffer);
CHECK(ret, FAIL, "H5Dread");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(msid);
CHECK(ret, FAIL, "H5Sclose");
for(i=0; i<2; i++)
for(j=0; j<3; j++)
if(da_buffer[i][j][0][0] != mem2_buffer[i][j][0][0]) {
TestErrPrintf("%u: Read different values than written at index %d,%d,0,0, da_buffer = %d, mem2_buffer = %d\n", __LINE__, i, j, da_buffer[i][j][0][0], mem2_buffer[i][j][0][0]);
}
/* ****** Case 3: ******
* Testing the full selection in the middle dimensions */
did = H5Dopen2(file, dset_name, H5P_DEFAULT);
CHECK(did, FAIL, "H5Dopen");
/* Select the elements in the dataset */
elmts_numb = 18;
ret = H5Sselect_elements(sid, H5S_SELECT_SET, elmts_numb, (const hsize_t *)da_elmts3);
CHECK(ret, FAIL, "H5Sselect_elements");
/* Dataspace for memory buffer */
msid = H5Screate_simple(4, mem3_dims, mem3_dims);
CHECK(msid, FAIL, "H5Screate_simple");
ret = H5Sselect_all(msid);
CHECK(ret, FAIL, "H5Sselect_all");
ret = H5Dread(did, H5T_NATIVE_INT, msid, sid, H5P_DEFAULT, mem3_buffer);
CHECK(ret, FAIL, "H5Dread");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(msid);
CHECK(ret, FAIL, "H5Sclose");
for(i=0; i<3; i++)
for(j=0; j<6; j++)
if(da_buffer[0][i][j][0] != mem3_buffer[0][i][j][0]) {
TestErrPrintf("%u: Read different values than written at index 0,%d,%d,0\n", __LINE__, i, j);
}
ret = H5Sclose(sid);
CHECK(ret, FAIL, "H5Sclose");
ret = H5Pclose(plid);
CHECK(ret, FAIL, "H5Pclose");
}
bool Hdf5Dataset::saveMap(const VecVecDouble &pose_reach, const VecVecDouble &spheres, const VecDouble &ri, const double resolution)
{
if(!checkPath(this->path_))
{
createPath(this->path_);
}
const char *filepath = this->path_.c_str();
const char *name = this->filename_.c_str();
char fullpath[100];
strcpy(fullpath, filepath);
strcat(fullpath, name);
ROS_INFO("Saving map %s", this->filename_.c_str());
this->file_ = H5Fcreate(fullpath, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
this->group_poses_ = H5Gcreate(this->file_, "/Poses", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
this->group_spheres_ = H5Gcreate(this->file_, "/Spheres", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
ROS_INFO("Saving poses in reachability map");
const hsize_t ndims = 2;
const hsize_t ncols = 10;
int posSize =pose_reach.size();
int chunk_size;
int PY = 10;
if (posSize % 2)
{
chunk_size = (posSize / 2) + 1;
}
else
{
chunk_size = (posSize / 2);
}
// Create Dataspace
hsize_t dims[ndims] = {0, ncols}; // Starting with an empty buffer
hsize_t max_dims[ndims] = {H5S_UNLIMITED, ncols}; // Creating dataspace
hid_t file_space = H5Screate_simple(ndims, dims, max_dims);
// Create Dataset Property list
hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CHUNKED);
hsize_t chunk_dims[ndims] = {chunk_size, ncols};
H5Pset_chunk(plist, ndims, chunk_dims);
// Create the datset
this->poses_dataset_ = H5Dcreate(this->group_poses_, "poses_dataset", H5T_NATIVE_FLOAT, file_space, H5P_DEFAULT, plist, H5P_DEFAULT);
// Closing resources
H5Pclose(plist);
H5Sclose(file_space);
// Creating the first buffer
hsize_t nlines = chunk_size;
float *buffer = new float[nlines * ncols];
float **dset1_data = new float *[nlines];
for (hsize_t i = 0; i < nlines; ++i)
{
dset1_data[i] = &buffer[i * ncols];
}
// Data for the first chunk
for (int i = 0; i < chunk_size; i++)
{
for (int j = 0; j < PY; j++)
{
dset1_data[i][j] = pose_reach[i][j];
}
}
// Memory dataspace indicating size of the buffer
dims[0] = chunk_size;
dims[1] = ncols;
hid_t mem_space = H5Screate_simple(ndims, dims, NULL);
// Extending dataset
dims[0] = chunk_size;
dims[1] = ncols;
H5Dset_extent(this->poses_dataset_, dims);
// Selecting hyperslab on the dataset
file_space = H5Dget_space(this->poses_dataset_);
hsize_t start[2] = {0, 0};
hsize_t count[2] = {chunk_size, ncols};
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
// Writing buffer to the dataset
H5Dwrite(this->poses_dataset_, H5T_NATIVE_FLOAT, mem_space, file_space, H5P_DEFAULT, buffer);
// Closing file dataspace
H5Sclose(file_space);
// Data for the Second chunk
for (int i = chunk_size; i < posSize; i++)
{
for (int j = 0; j < PY; j++)
{
dset1_data[i - chunk_size][j] = pose_reach[i][j];
}
}
// Resizing new memory dataspace indicating new size of the buffer
dims[0] = posSize - chunk_size;
dims[1] = ncols;
H5Sset_extent_simple(mem_space, ndims, dims, NULL);
// Extend dataset
dims[0] = posSize;
dims[1] = ncols;
H5Dset_extent(this->poses_dataset_, dims);
// Selecting hyperslab
file_space = H5Dget_space(this->poses_dataset_);
start[0] = chunk_size;
start[1] = 0;
count[0] = posSize - chunk_size;
count[1] = ncols;
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
// Writing buffer to dataset
H5Dwrite(this->poses_dataset_, H5T_NATIVE_FLOAT, mem_space, file_space, H5P_DEFAULT, buffer);
// Closing all the resources
delete[] dset1_data;
delete[] buffer;
// Creating Sphere dataset
ROS_INFO("Saving spheres in Reachability map");
hid_t sphere_dataspace;
const int SX = spheres.size();
const int SY = 4;
hsize_t dims2[2]; // dataset dimensions
dims2[0] = SX;
dims2[1] = SY;
double dset2_data[SX][SY];
for(int i=0;i<spheres.size();++i)
{
for(int j=0;j<spheres[i].size();++j)
{
dset2_data[i][j] = spheres[i][j];
}
for (int j = 3; j < SY; j++)
{
dset2_data[i][j] = ri[i];
}
}
sphere_dataspace = H5Screate_simple(2, dims2, NULL);
this->sphere_dataset_ = H5Dcreate2(this->group_spheres_, "sphere_dataset", H5T_NATIVE_DOUBLE,
sphere_dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(this->sphere_dataset_, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset2_data);
// Creating attribute
hsize_t attr_dims;
float attr_data[1];
attr_data[0] = resolution;
attr_dims = 1;
sphere_dataspace = H5Screate_simple(1, &attr_dims, NULL);
this->attr_ = H5Acreate2(this->sphere_dataset_, "Resolution", H5T_NATIVE_FLOAT, sphere_dataspace,
H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(this->attr_, H5T_NATIVE_FLOAT, attr_data);
//H5Aclose(this->attr_);
// Closing all
H5Sclose(sphere_dataspace);
H5Sclose(file_space);
H5Sclose(mem_space);
close();
}
/*-------------------------------------------------------------------------
* Function: test_multi_compat
*
* Purpose: Tests the backward compatibility for MULTI driver.
* See if we can open files created with v1.6 library.
* The source file was created by the test/file_handle.c
* of the v1.6 library. This test verifies the fix for
* Issue 2598. In v1.6 library, there was EOA for the whole
* MULTI file saved in the super block. We took it out in
* v1.8 library because it's meaningless for the MULTI file.
* v1.8 library saves the EOA for the metadata file, instead.
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* 21 June 2011
*
*-------------------------------------------------------------------------
*/
static herr_t
test_multi_compat(void)
{
hid_t file=(-1), fapl, fapl2=(-1), dset=(-1), space=(-1);
hid_t access_fapl = -1;
char newname[1024];
char filename_s[1024], newname_s[1024];
char filename_r[1024], newname_r[1024];
int *fhandle2=NULL, *fhandle=NULL;
H5FD_mem_t mt, memb_map[H5FD_MEM_NTYPES];
hid_t memb_fapl[H5FD_MEM_NTYPES];
haddr_t memb_addr[H5FD_MEM_NTYPES];
const char *memb_name[H5FD_MEM_NTYPES];
char sv[H5FD_MEM_NTYPES][32];
hsize_t dims[2]={MULTI_SIZE, MULTI_SIZE};
char dname[]="dataset2";
int i, j;
int buf[MULTI_SIZE][MULTI_SIZE];
TESTING("MULTI file driver backward compatibility");
/* Set file access property list for MULTI driver */
fapl = h5_fileaccess();
HDmemset(memb_map, 0, sizeof memb_map);
HDmemset(memb_fapl, 0, sizeof memb_fapl);
HDmemset(memb_name, 0, sizeof memb_name);
HDmemset(memb_addr, 0, sizeof memb_addr);
HDmemset(sv, 0, sizeof sv);
for(mt=H5FD_MEM_DEFAULT; mt<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt))
memb_map[mt] = H5FD_MEM_SUPER;
memb_map[H5FD_MEM_DRAW] = H5FD_MEM_DRAW;
memb_fapl[H5FD_MEM_SUPER] = H5P_DEFAULT;
sprintf(sv[H5FD_MEM_SUPER], "%%s-%c.h5", 's');
memb_name[H5FD_MEM_SUPER] = sv[H5FD_MEM_SUPER];
memb_addr[H5FD_MEM_SUPER] = 0;
memb_fapl[H5FD_MEM_DRAW] = H5P_DEFAULT;
sprintf(sv[H5FD_MEM_DRAW], "%%s-%c.h5", 'r');
memb_name[H5FD_MEM_DRAW] = sv[H5FD_MEM_DRAW];
memb_addr[H5FD_MEM_DRAW] = HADDR_MAX/2;
if(H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name, memb_addr, TRUE)<0)
TEST_ERROR;
h5_fixname(FILENAME[9], fapl, newname, sizeof newname);
/* Make copy for the data file in the build directory, to protect the
* original file in the source directory */
sprintf(filename_s, "%s-%c.h5", MULTI_COMPAT_BASENAME, 's');
sprintf(newname_s, "%s-%c.h5", FILENAME[9], 's');
h5_make_local_copy(filename_s, newname_s);
sprintf(filename_r, "%s-%c.h5", MULTI_COMPAT_BASENAME, 'r');
sprintf(newname_r, "%s-%c.h5", FILENAME[9], 'r');
h5_make_local_copy(filename_r, newname_r);
/* Reopen the file for read only. Verify 1.8 library can open file
* created with 1.6 library. */
if((file=H5Fopen(newname, H5F_ACC_RDONLY, fapl)) < 0)
TEST_ERROR;
if((dset = H5Dopen2(file, DSET1_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Make sure we can reopen the file for read and write */
if((file=H5Fopen(newname, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
if((dset = H5Dopen2(file, DSET1_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Reopen the file for adding another dataset. The new EOA for metadata file
* should be written to the file */
if((file=H5Fopen(newname, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
/* Create and write data set */
if((space=H5Screate_simple(2, dims, NULL)) < 0)
TEST_ERROR;
if((dset=H5Dcreate2(file, DSET2_NAME, H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
for(i=0; i<MULTI_SIZE; i++)
for(j=0; j<MULTI_SIZE; j++)
buf[i][j] = i*10000+j;
if(H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Sclose(space) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Reopen the file for read only again. Verify the library can handle
* the EOA correctly */
if((file=H5Fopen(newname, H5F_ACC_RDONLY, fapl)) < 0)
TEST_ERROR;
if((dset = H5Dopen2(file, DSET1_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if((dset = H5Dopen2(file, DSET2_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Sclose(space);
H5Dclose(dset);
H5Pclose(fapl);
H5Fclose(file);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* test_compress
*
* Ensures that a FL packet table can be compressed.
* This test creates a file named TEST_COMPRESS_FILE
*
*-------------------------------------------------------------------------
*/
static int
test_compress(void)
{
hid_t fid1 = -1;
herr_t err;
hid_t table = -1;
hid_t part_t = -1;
hid_t dset_id = -1;
hid_t plist_id = -1;
size_t c;
size_t num_elems = 1;
unsigned filter_vals[1];
particle_t readPart;
hsize_t count;
TESTING("packet table compression");
/* Create a file. */
if((fid1 = H5Fcreate(TEST_COMPRESS_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) TEST_ERROR;
/* Create a datatype for the particle struct */
part_t = make_particle_type();
assert(part_t != -1);
/* Create a new table with compression level 8 */
table = H5PTcreate_fl(fid1, "Compressed Test Dataset", part_t, (hsize_t)80, 8);
if( H5PTis_valid(table) < 0) TEST_ERROR;
/* We can now use this table exactly the same way we use a normal uncompressed
* packet table, and it should pass the same tests. */
/* Add many particles */
for(c = 0; c < BIG_TABLE_SIZE ; c+=8)
{
/* Append eight particles at once*/
err = H5PTappend(table, (size_t)8, &(testPart[0]));
if( err < 0) TEST_ERROR;
}
/* Count the number of packets in the table */
err = H5PTget_num_packets(table, &count);
if( err < 0) TEST_ERROR;
if( count != BIG_TABLE_SIZE ) TEST_ERROR;
/* Read particles to ensure that all of them were written correctly */
for(c = 0; c < BIG_TABLE_SIZE; c++)
{
err = H5PTget_next(table, 1, &readPart);
if(err < 0) TEST_ERROR;
/* Ensure that particles were read correctly */
if( cmp_par(c % 8, 0, testPart, &readPart) != 0) TEST_ERROR;
}
/* Close the table */
err = H5PTclose(table);
if( err < 0) TEST_ERROR;
/* Open the packet table as a regular dataset and make sure that the
* compression filter is set.
*/
dset_id = H5Dopen2(fid1, "Compressed Test Dataset", H5P_DEFAULT);
if( dset_id < 0) TEST_ERROR;
plist_id = H5Dget_create_plist(dset_id);
if( plist_id < 0) TEST_ERROR;
err = H5Pget_filter_by_id2(plist_id, H5Z_FILTER_DEFLATE, NULL, &num_elems,
filter_vals, 0, NULL, NULL);
if( err < 0) TEST_ERROR;
/* The compression level should be 8, the value we passed in */
if(filter_vals[0] != 8) TEST_ERROR;
/* Clean up */
err = H5Pclose(plist_id);
if( err < 0) TEST_ERROR;
err = H5Dclose(dset_id);
if( err < 0) TEST_ERROR;
/* Create a new table without compression. */
table = H5PTcreate_fl(fid1, "Uncompressed Dataset", part_t, (hsize_t)80, -1);
if(table < 0) TEST_ERROR;
/* Close the packet table */
err = H5PTclose(table);
if( err < 0) TEST_ERROR;
/* Open the packet table as a regular dataset and make sure that the
* compression filter is not set.
*/
dset_id = H5Dopen2(fid1, "Uncompressed Dataset", H5P_DEFAULT);
if( dset_id < 0) TEST_ERROR;
plist_id = H5Dget_create_plist(dset_id);
if( plist_id < 0) TEST_ERROR;
H5E_BEGIN_TRY {
err = H5Pget_filter_by_id2(plist_id, H5Z_FILTER_DEFLATE, NULL, &num_elems,
filter_vals, 0, NULL, NULL);
if( err >= 0) TEST_ERROR;
} H5E_END_TRY
/* Clean up */
err = H5Pclose(plist_id);
if( err < 0) TEST_ERROR;
err = H5Dclose(dset_id);
if( err < 0) TEST_ERROR;
/* Close the datatype and the file */
err = H5Tclose(part_t);
if( err < 0) TEST_ERROR;
err = H5Fclose(fid1);
if( err < 0) TEST_ERROR;
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(plist_id);
H5Dclose(dset_id);
H5Tclose(part_t);
H5PTclose(table);
H5Fclose(fid1);
} H5E_END_TRY
H5_FAILED();
return -1;
}
/*-------------------------------------------------------------------------
* Function: test_direct
*
* Purpose: Tests the file handle interface for DIRECT I/O driver
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* Wednesday, 20 September 2006
*
*-------------------------------------------------------------------------
*/
static herr_t
test_direct(void)
{
#ifdef H5_HAVE_DIRECT
hid_t file=(-1), fapl, access_fapl = -1;
hid_t dset1=-1, dset2=-1, space1=-1, space2=-1;
char filename[1024];
int *fhandle=NULL;
hsize_t file_size;
hsize_t dims1[2], dims2[1];
size_t mbound;
size_t fbsize;
size_t cbsize;
int *points, *check, *p1, *p2;
int wdata2[DSET2_DIM] = {11,12,13,14};
int rdata2[DSET2_DIM];
int i, j, n;
#endif /*H5_HAVE_DIRECT*/
TESTING("DIRECT I/O file driver");
#ifndef H5_HAVE_DIRECT
SKIPPED();
return 0;
#else /*H5_HAVE_DIRECT*/
/* Set property list and file name for Direct driver. Set memory alignment boundary
* and file block size to 512 which is the minimum for Linux 2.6. */
fapl = h5_fileaccess();
if(H5Pset_fapl_direct(fapl, MBOUNDARY, FBSIZE, CBSIZE) < 0)
TEST_ERROR;
h5_fixname(FILENAME[5], fapl, filename, sizeof filename);
/* Verify the file access properties */
if(H5Pget_fapl_direct(fapl, &mbound, &fbsize, &cbsize) < 0)
TEST_ERROR;
if(mbound != MBOUNDARY || fbsize != FBSIZE || cbsize != CBSIZE)
TEST_ERROR;
if(H5Pset_alignment(fapl, (hsize_t)THRESHOLD, (hsize_t)FBSIZE) < 0)
TEST_ERROR;
H5E_BEGIN_TRY {
file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
} H5E_END_TRY;
if(file<0) {
H5Pclose (fapl);
SKIPPED();
printf(" Probably the file system doesn't support Direct I/O\n");
return 0;
}
/* Retrieve the access property list... */
if ((access_fapl = H5Fget_access_plist(file)) < 0)
TEST_ERROR;
/* Check that the driver is correct */
if(H5FD_DIRECT != H5Pget_driver(access_fapl))
TEST_ERROR;
/* ...and close the property list */
if (H5Pclose(access_fapl) < 0)
TEST_ERROR;
/* Check file handle API */
if(H5Fget_vfd_handle(file, H5P_DEFAULT, (void **)&fhandle) < 0)
TEST_ERROR;
if(*fhandle<0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* There is no guarantee of the number of metadata allocations, but it's
* 4 currently and the size of the file should be between 3 & 4 file buffer
* sizes..
*/
if(file_size < (FBSIZE * 3) || file_size >= (FBSIZE * 4))
TEST_ERROR;
/* Allocate aligned memory for data set 1. For data set 1, everything is aligned including
* memory address, size of data, and file address. */
if(posix_memalign(&points, (size_t)FBSIZE, (size_t)(DSET1_DIM1*DSET1_DIM2*sizeof(int)))!=0)
TEST_ERROR;
if(posix_memalign(&check, (size_t)FBSIZE, (size_t)(DSET1_DIM1*DSET1_DIM2*sizeof(int)))!=0)
TEST_ERROR;
/* Initialize the dset1 */
p1 = points;
for(i = n = 0; i < DSET1_DIM1; i++)
for(j = 0; j < DSET1_DIM2; j++)
*p1++ = n++;
/* Create the data space1 */
dims1[0] = DSET1_DIM1;
dims1[1] = DSET1_DIM2;
if((space1 = H5Screate_simple(2, dims1, NULL)) < 0)
TEST_ERROR;
/* Create the dset1 */
if((dset1 = H5Dcreate2(file, DSET1_NAME, H5T_NATIVE_INT, space1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Write the data to the dset1 */
if(H5Dwrite(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, points) < 0)
TEST_ERROR;
if(H5Dclose(dset1) < 0)
TEST_ERROR;
if((dset1 = H5Dopen2(file, DSET1_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Read the data back from dset1 */
if(H5Dread(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, check) < 0)
TEST_ERROR;
/* Check that the values read are the same as the values written */
p1 = points;
p2 = check;
for(i = 0; i < DSET1_DIM1; i++)
for(j = 0; j < DSET1_DIM2; j++)
if(*p1++ != *p2++) {
H5_FAILED();
printf(" Read different values than written in data set 1.\n");
printf(" At index %d,%d\n", i, j);
TEST_ERROR;
} /* end if */
/* Create the data space2. For data set 2, memory address and data size are not aligned. */
dims2[0] = DSET2_DIM;
if((space2 = H5Screate_simple(1, dims2, NULL)) < 0)
TEST_ERROR;
/* Create the dset2 */
if((dset2 = H5Dcreate2(file, DSET2_NAME, H5T_NATIVE_INT, space2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Write the data to the dset1 */
if(H5Dwrite(dset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata2) < 0)
TEST_ERROR;
if(H5Dclose(dset2) < 0)
TEST_ERROR;
if((dset2 = H5Dopen2(file, DSET2_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Read the data back from dset1 */
if(H5Dread(dset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata2) < 0)
TEST_ERROR;
/* Check that the values read are the same as the values written */
for(i = 0; i < DSET2_DIM; i++)
if(wdata2[i] != rdata2[i]) {
H5_FAILED();
printf(" Read different values than written in data set 2.\n");
printf(" At index %d\n", i);
TEST_ERROR;
} /* end if */
if(H5Sclose(space1) < 0)
TEST_ERROR;
if(H5Dclose(dset1) < 0)
TEST_ERROR;
if(H5Sclose(space2) < 0)
TEST_ERROR;
if(H5Dclose(dset2) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
if(points)
free(points);
if(check)
free(check);
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose (fapl);
H5Sclose(space1);
H5Dclose(dset1);
H5Sclose(space2);
H5Dclose(dset2);
H5Fclose(file);
} H5E_END_TRY;
return -1;
#endif /*H5_HAVE_DIRECT*/
}
int
main()
{
printf("\n*** Checking HDF5 memory use.\n");
printf("*** checking HDF5 memory use writing along unlimited dimension...");
{
#define NDIMS1 1
#define NUM_DATASETS 10000
#define CHUNKSIZE 1
hid_t fapl_id, fcpl_id;
hid_t datasetid[NUM_DATASETS];
hid_t fileid, grpid, spaceid, plistid;
hsize_t chunksize[NDIMS1], dimsize[NDIMS1], maxdimsize[NDIMS1];
char var_name[STR_LEN + 1];
int v;
/* Create file, setting latest_format in access propertly list
* and H5P_CRT_ORDER_TRACKED in the creation property list. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
if (H5Pset_link_creation_order(fcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0) ERR;
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Open root group. */
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
/* Create 1 D data space with unlimited dimension. */
dimsize[0] = 0;
maxdimsize[0] = H5S_UNLIMITED;
if ((spaceid = H5Screate_simple(NDIMS1, dimsize, maxdimsize)) < 0) ERR;
/* Create property list. */
if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
/* Set up chunksizes. */
chunksize[0] = CHUNKSIZE;
if (H5Pset_chunk(plistid, NDIMS1, chunksize) < 0)ERR;
/* Create the variables. */
for (v = 0; v < NUM_DATASETS; v++)
{
sprintf(var_name, "var_%d", v);
/* printf("creating var %s\n", var_name);*/
if ((datasetid[v] = H5Dcreate(grpid, var_name, H5T_NATIVE_INT,
spaceid, plistid)) < 0) ERR_RET;
}
/* Close the datasets. */
for (v = 0; v < NUM_DATASETS; v++)
if (H5Dclose(datasetid[v]) < 0) ERR_RET;
/* Close everything. */
if (H5Pclose(fapl_id) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0)
ERR;
/* Now reopen the file and check. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
/* if ((datasetid = H5Dopen1(grpid, SIMPLE_VAR_NAME)) < 0) ERR; */
/* if ((spaceid = H5Dget_space(datasetid)) < 0) */
/* if (H5Sget_simple_extent_dims(spaceid, fdims, fmaxdims) > 0) ERR; */
/* if (H5Dread(datasetid, H5T_NATIVE_INT, H5S_ALL, */
/* spaceid, H5P_DEFAULT, data_in) < 0) ERR; */
/* /\* Check the data. *\/ */
/* for (x = 0; x < NX; x++) */
/* for (y = 0; y < NY; y++) */
/* if (data_in[x][y] != data_out[x][y]) ERR_RET; */
if (H5Pclose(fapl_id) < 0 ||
/* H5Dclose(datasetid) < 0 ||
H5Sclose(spaceid) < 0 ||*/
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0)
ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
/*-------------------------------------------------------------------------
* Function: test_core
*
* Purpose: Tests the file handle interface for CORE driver
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* Tuesday, Sept 24, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
test_core(void)
{
hid_t file=(-1), fapl, access_fapl = -1;
char filename[1024];
void *fhandle=NULL;
hsize_t file_size;
int *points, *check, *p1, *p2;
hid_t dset1=-1, space1=-1;
hsize_t dims1[2];
int i, j, n;
TESTING("CORE file driver");
/* Set property list and file name for CORE driver */
fapl = h5_fileaccess();
if(H5Pset_fapl_core(fapl, (size_t)CORE_INCREMENT, TRUE) < 0)
TEST_ERROR;
h5_fixname(FILENAME[1], fapl, filename, sizeof filename);
if((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR;
/* Retrieve the access property list... */
if ((access_fapl = H5Fget_access_plist(file)) < 0)
TEST_ERROR;
/* Check that the driver is correct */
if(H5FD_CORE != H5Pget_driver(access_fapl))
TEST_ERROR;
/* ...and close the property list */
if (H5Pclose(access_fapl) < 0)
TEST_ERROR;
if(H5Fget_vfd_handle(file, H5P_DEFAULT, &fhandle) < 0)
TEST_ERROR;
if(fhandle==NULL)
{
printf("fhandle==NULL\n");
TEST_ERROR;
}
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* There is no garantee the size of metadata in file is constant.
* Just try to check if it's reasonable. Why is this 4KB?
*/
if(file_size<2*KB || file_size>6*KB)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Open the file with backing store off for read and write.
* Changes won't be saved in file. */
if(H5Pset_fapl_core(fapl, (size_t)CORE_INCREMENT, FALSE) < 0)
TEST_ERROR;
if((file=H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
/* Allocate memory for data set. */
points=(int*)malloc(DSET1_DIM1*DSET1_DIM2*sizeof(int));
check=(int*)malloc(DSET1_DIM1*DSET1_DIM2*sizeof(int));
/* Initialize the dset1 */
p1 = points;
for(i = n = 0; i < DSET1_DIM1; i++)
for(j = 0; j < DSET1_DIM2; j++)
*p1++ = n++;
/* Create the data space1 */
dims1[0] = DSET1_DIM1;
dims1[1] = DSET1_DIM2;
if((space1 = H5Screate_simple(2, dims1, NULL)) < 0)
TEST_ERROR;
/* Create the dset1 */
if((dset1 = H5Dcreate2(file, DSET1_NAME, H5T_NATIVE_INT, space1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Write the data to the dset1 */
if(H5Dwrite(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, points) < 0)
TEST_ERROR;
if(H5Dclose(dset1) < 0)
TEST_ERROR;
if((dset1 = H5Dopen2(file, DSET1_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Read the data back from dset1 */
if(H5Dread(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, check) < 0)
TEST_ERROR;
/* Check that the values read are the same as the values written */
p1 = points;
p2 = check;
for(i = 0; i < DSET1_DIM1; i++)
for(j = 0; j < DSET1_DIM2; j++)
if(*p1++ != *p2++) {
H5_FAILED();
printf(" Read different values than written in data set 1.\n");
printf(" At index %d,%d\n", i, j);
TEST_ERROR;
} /* end if */
if(H5Dclose(dset1) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Open the file with backing store on for read and write.
* Changes will be saved in file. */
if(H5Pset_fapl_core(fapl, (size_t)CORE_INCREMENT, TRUE) < 0)
TEST_ERROR;
if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
/* Create the dset1 */
if((dset1 = H5Dcreate2(file, DSET1_NAME, H5T_NATIVE_INT, space1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Write the data to the dset1 */
if(H5Dwrite(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, points) < 0)
TEST_ERROR;
if(H5Dclose(dset1) < 0)
TEST_ERROR;
if((dset1 = H5Dopen2(file, DSET1_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR;
/* Reallocate memory for reading buffer. */
if(check)
free(check);
check = (int*)malloc(DSET1_DIM1 * DSET1_DIM2 * sizeof(int));
/* Read the data back from dset1 */
if(H5Dread(dset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, check) < 0)
TEST_ERROR;
/* Check that the values read are the same as the values written */
p1 = points;
p2 = check;
for(i = 0; i < DSET1_DIM1; i++)
for(j = 0; j < DSET1_DIM2; j++)
if(*p1++ != *p2++) {
H5_FAILED();
printf(" Read different values than written in data set 1.\n");
printf(" At index %d,%d\n", i, j);
TEST_ERROR;
} /* end if */
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* There is no garantee the size of metadata in file is constant.
* Just try to check if it's reasonable. */
if(file_size<64*KB || file_size>256*KB)
TEST_ERROR;
if(H5Sclose(space1) < 0)
TEST_ERROR;
if(H5Dclose(dset1) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
if(points)
free(points);
if(check)
free(check);
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose (fapl);
H5Fclose(file);
} H5E_END_TRY;
return -1;
}
int
main()
{
printf("\n*** Checking HDF5 dimscales detach.\n");
printf("*** Creating a file with two vars with one dimension scale...");
{
hid_t fileid, grpid, spaceid, var1_id, var2_id, dimscaleid, cparmsid;
hid_t fcpl_id, fapl_id, create_propid, access_propid;
hsize_t dims[NDIMS] = {DIM_LEN};
char dimscale_wo_var[STR_LEN];
float data = 42;
/* Create file. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if (H5Pset_cache(fapl_id, 0, CHUNK_CACHE_NELEMS, CHUNK_CACHE_SIZE,
CHUNK_CACHE_PREEMPTION) < 0) ERR;
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_18, H5F_LIBVER_18) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
if (H5Pclose(fcpl_id) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create dimension scale. */
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
if ((spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
if ((dimscaleid = H5Dcreate1(grpid, DIMSCALE_NAME, H5T_IEEE_F32BE,
spaceid, create_propid)) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5Pclose(create_propid) < 0) ERR;
sprintf(dimscale_wo_var, "%s%10d", DIM_WITHOUT_VARIABLE, DIM_LEN);
if (H5DSset_scale(dimscaleid, dimscale_wo_var) < 0) ERR;
/* Create a variable that uses this dimension scale. */
if ((access_propid = H5Pcreate(H5P_DATASET_ACCESS)) < 0) ERR;
if (H5Pset_chunk_cache(access_propid, CHUNK_CACHE_NELEMS,
CHUNK_CACHE_SIZE, CHUNK_CACHE_PREEMPTION) < 0) ERR;
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_fill_value(create_propid, H5T_NATIVE_FLOAT, &data) < 0) ERR;
if (H5Pset_layout(create_propid, H5D_CONTIGUOUS) < 0) ERR;
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
if ((spaceid = H5Screate_simple(NDIMS, dims, dims)) < 0) ERR;
if ((var1_id = H5Dcreate2(grpid, VAR1_NAME, H5T_NATIVE_FLOAT, spaceid,
H5P_DEFAULT, create_propid, access_propid)) < 0) ERR;
if (H5Pclose(create_propid) < 0) ERR;
if (H5Pclose(access_propid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5DSattach_scale(var1_id, dimscaleid, 0) < 0) ERR;
/* Create another variable that uses this dimension scale. */
if ((access_propid = H5Pcreate(H5P_DATASET_ACCESS)) < 0) ERR;
if (H5Pset_chunk_cache(access_propid, CHUNK_CACHE_NELEMS,
CHUNK_CACHE_SIZE, CHUNK_CACHE_PREEMPTION) < 0) ERR;
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_fill_value(create_propid, H5T_NATIVE_FLOAT, &data) < 0) ERR;
if (H5Pset_layout(create_propid, H5D_CONTIGUOUS) < 0) ERR;
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
if ((spaceid = H5Screate_simple(NDIMS, dims, dims)) < 0) ERR;
if ((var2_id = H5Dcreate2(grpid, VAR2_NAME, H5T_NATIVE_FLOAT, spaceid,
H5P_DEFAULT, create_propid, access_propid)) < 0) ERR;
if (H5Pclose(create_propid) < 0) ERR;
if (H5Pclose(access_propid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5DSattach_scale(var2_id, dimscaleid, 0) < 0) ERR;
/* Now detach the scales and remove the dimscale. This doesn't
* work if I reverse the order of the statements. */
if (H5DSdetach_scale(var2_id, dimscaleid, 0) < 0) ERR;
if (H5DSdetach_scale(var1_id, dimscaleid, 0) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(var1_id) < 0) ERR;
if (H5Dclose(dimscaleid) < 0) ERR;
if (H5Gclose(grpid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
/* /\* Now read the file and check it. *\/ */
/* { */
/* hid_t fileid, spaceid = 0, datasetid = 0; */
/* hsize_t num_obj, i; */
/* int obj_class; */
/* char obj_name[STR_LEN + 1]; */
/* char dimscale_name[STR_LEN+1]; */
/* htri_t is_scale; */
/* char label[STR_LEN+1]; */
/* int num_scales; */
/* hsize_t dims[1], maxdims[1]; */
/* H5G_stat_t statbuf; */
/* HDF5_OBJID_T dimscale_obj, vars_dimscale_obj; */
/* struct nc_hdf5_link_info link_info; */
/* hsize_t idx = 0; */
/* /\* Open the file. *\/ */
/* if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR; */
/* if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR; */
/* /\* Loop through objects in the root group. *\/ */
/* if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR; */
/* for (i = 0; i < num_obj; i++) */
/* { */
/* if (H5Literate(grpid, H5_INDEX_CRT_ORDER, H5_ITER_INC, */
/* &idx, visit_link, (void *)&link_info) < 0) ERR; */
/* printf("Encountered: HDF5 object link_info.name %s\n", link_info.name); */
/* /\* Deal with object based on its obj_class. *\/ */
/* switch(link_info.obj_type) */
/* { */
/* case H5I_GROUP: */
/* break; */
/* case H5I_DATASET: */
/* /\* Open the dataset. *\/ */
/* if ((datasetid = H5Dopen1(fileid, link_info.name)) < 0) ERR; */
/* if ((spaceid = H5Dget_space(datasetid)) < 0) ERR; */
/* if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR; */
/* if (maxdims[0] != DIM_LEN) ERR; */
/* if (H5Sclose(spaceid) < 0) ERR; */
/* /\* Is this a dimscale? *\/ */
/* if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR; */
/* if (is_scale && strcmp(link_info.name, DIMSCALE_NAME)) ERR; */
/* if (is_scale) */
/* { */
/* /\* A dimscale comes with a NAME attribute, in */
/* * addition to its real name. *\/ */
/* if (H5DSget_scale_name(datasetid, dimscale_name, STR_LEN) < 0) ERR; */
/* if (strcmp(dimscale_name, dimscale_wo_var)) ERR; */
/* /\* fileno and objno uniquely identify an object and a */
/* * HDF5 file. *\/ */
/* if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR; */
/* dimscale_obj.fileno[0] = statbuf.fileno[0]; */
/* dimscale_obj.objno[0] = statbuf.objno[0]; */
/* dimscale_obj.fileno[1] = statbuf.fileno[1]; */
/* dimscale_obj.objno[1] = statbuf.objno[1]; */
/* /\*printf("scale statbuf.fileno = %d statbuf.objno = %d\n", */
/* statbuf.fileno, statbuf.objno);*\/ */
/* } */
/* else */
/* { */
/* /\* Here's how to get the number of scales attached */
/* * to the dataset's dimension 0. *\/ */
/* if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR; */
/* if (num_scales != 1) ERR; */
/* /\* Go through all dimscales for this var and learn about them. *\/ */
/* if (H5DSiterate_scales(datasetid, 0, NULL, alien_visitor, */
/* &vars_dimscale_obj) < 0) ERR; */
/* /\*printf("vars_dimscale_obj.fileno = %d vars_dimscale_obj.objno = %d\n", */
/* vars_dimscale_obj.fileno, vars_dimscale_obj.objno);*\/ */
/* /\* if (vars_dimscale_obj.fileno[0] != dimscale_obj.fileno[0] || *\/ */
/* /\* vars_dimscale_obj.objno[0] != dimscale_obj.objno[0] || *\/ */
/* /\* vars_dimscale_obj.fileno[1] != dimscale_obj.fileno[1] || *\/ */
/* /\* vars_dimscale_obj.objno[1] != dimscale_obj.objno[1]) ERR; *\/ */
/* /\* There's also a label for dimension 0. *\/ */
/* if (H5DSget_label(datasetid, 0, label, STR_LEN) < 0) ERR; */
/* /\*printf("found non-scale dataset %s, label %s\n", link_info.name, label);*\/ */
/* } */
/* if (H5Dclose(datasetid) < 0) ERR; */
/* break; */
/* case H5I_DATATYPE: */
/* break; */
/* default: */
/* printf("Unknown object!"); */
/* ERR; */
/* } */
/* } */
/* /\* Close up the shop. *\/ */
/* if (H5Fclose(fileid) < 0) ERR; */
/* }*/
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
/*-------------------------------------------------------------------------
* Function: test_family
*
* Purpose: Tests the file handle interface for FAMILY driver
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* Tuesday, Sept 24, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
test_family(void)
{
hid_t file=(-1), fapl, fapl2=(-1), space=(-1), dset=(-1);
hid_t access_fapl = -1;
char filename[1024];
char dname[]="dataset";
unsigned int i, j;
int *fhandle=NULL, *fhandle2=NULL;
int buf[FAMILY_NUMBER][FAMILY_SIZE];
hsize_t dims[2]={FAMILY_NUMBER, FAMILY_SIZE};
hsize_t file_size;
TESTING("FAMILY file driver");
/* Set property list and file name for FAMILY driver */
fapl = h5_fileaccess();
if(H5Pset_fapl_family(fapl, (hsize_t)FAMILY_SIZE, H5P_DEFAULT) < 0)
TEST_ERROR;
h5_fixname(FILENAME[2], fapl, filename, sizeof filename);
if((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Test different wrong ways to reopen family files where there's only
* one member file existing. */
if(test_family_opens(filename, fapl) < 0)
TEST_ERROR;
/* Reopen the file with default member file size */
if(H5Pset_fapl_family(fapl, (hsize_t)H5F_FAMILY_DEFAULT, H5P_DEFAULT) < 0)
TEST_ERROR;
if((file=H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* The file size is supposed to be about 800 bytes right now. */
if(file_size < (KB / 2) || file_size > KB)
TEST_ERROR;
/* Create and write dataset */
if((space=H5Screate_simple(2, dims, NULL)) < 0)
TEST_ERROR;
/* Retrieve the access property list... */
if ((access_fapl = H5Fget_access_plist(file)) < 0)
TEST_ERROR;
/* Check that the driver is correct */
if(H5FD_FAMILY != H5Pget_driver(access_fapl))
TEST_ERROR;
/* ...and close the property list */
if (H5Pclose(access_fapl) < 0)
TEST_ERROR;
if((dset=H5Dcreate2(file, dname, H5T_NATIVE_INT, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
for(i=0; i<FAMILY_NUMBER; i++)
for(j=0; j<FAMILY_SIZE; j++)
buf[i][j] = i*10000+j;
if(H5Dwrite(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
TEST_ERROR;
/* check file handle API */
if((fapl2=H5Pcreate(H5P_FILE_ACCESS)) < 0)
TEST_ERROR;
if(H5Pset_family_offset(fapl2, (hsize_t)0) < 0)
TEST_ERROR;
if(H5Fget_vfd_handle(file, fapl2, (void **)&fhandle) < 0)
TEST_ERROR;
if(*fhandle<0)
TEST_ERROR;
if(H5Pset_family_offset(fapl2, (hsize_t)(FAMILY_SIZE*2)) < 0)
TEST_ERROR;
if(H5Fget_vfd_handle(file, fapl2, (void **)&fhandle2) < 0)
TEST_ERROR;
if(*fhandle2<0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* Some data has been written. The file size should be bigger(18KB+976
* bytes if int size is 4 bytes) now. */
if(sizeof(int)<=4) {
if(file_size<18*KB || file_size>20*KB)
TEST_ERROR;
} else if(sizeof(int)>=8) {
if(file_size<32*KB || file_size>40*KB)
TEST_ERROR;
}
if(H5Sclose(space) < 0)
TEST_ERROR;
if(H5Dclose(dset) < 0)
TEST_ERROR;
if(H5Pclose(fapl2) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
/* Test different wrong ways to reopen family files when there're multiple
* member files existing. */
if(test_family_opens(filename, fapl) < 0)
TEST_ERROR;
/* Reopen the file with correct member file size. */
if(H5Pset_fapl_family(fapl, (hsize_t)FAMILY_SIZE, H5P_DEFAULT) < 0)
TEST_ERROR;
if((file=H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Sclose(space);
H5Dclose(dset);
H5Pclose (fapl2);
H5Fclose(file);
} H5E_END_TRY;
return -1;
}
int
main()
{
printf("\n*** Checking HDF5 dimscales some more.\n");
printf("*** Creating a file with one var with one dimension scale...");
{
hid_t fileid, spaceid, datasetid, dimscaleid, cparmsid;
hsize_t dims[NDIMS] = {DIM1_LEN}, maxdims[NDIMS] = {H5S_UNLIMITED};
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
/* Create the space that will be used both for the dimscale and
* the 1D dataset that will attach it. */
if ((spaceid = H5Screate_simple(NDIMS, dims, maxdims)) < 0) ERR;
/* Modify dataset creation properties, i.e. enable chunking. */
dims[0] = 1;
if ((cparmsid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(cparmsid, NDIMS, dims) < 0) ERR;
/* Create our dimension scale, as an unlimited dataset. */
if ((dimscaleid = H5Dcreate(fileid, DIMSCALE_NAME, H5T_NATIVE_INT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSset_scale(dimscaleid, NAME_ATTRIBUTE) < 0) ERR;
/* Create a variable which uses it. */
if ((datasetid = H5Dcreate(fileid, VAR1_NAME, H5T_NATIVE_INT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSattach_scale(datasetid, dimscaleid, 0) < 0) ERR;
if (H5DSset_label(datasetid, 0, DIMSCALE_LABEL) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(dimscaleid) < 0 ||
H5Dclose(datasetid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking that one var, one dimscale file can be read...");
{
hid_t fileid, spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
char dimscale_name[NC_MAX_NAME+1];
htri_t is_scale;
char label[NC_MAX_NAME+1];
int num_scales;
hsize_t dims[1], maxdims[1];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj, vars_dimscale_obj;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/*printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n",
obj_class, obj_name);*/
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* This should be an unlimited dataset. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if (maxdims[0] != H5S_UNLIMITED) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale && strcmp(obj_name, DIMSCALE_NAME)) ERR;
if (is_scale)
{
/* A dimscale comes with a NAME attribute, in
* addition to its real name. */
if (H5DSget_scale_name(datasetid, dimscale_name, NC_MAX_NAME) < 0) ERR;
if (strcmp(dimscale_name, NAME_ATTRIBUTE)) ERR;
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj.fileno[0] = statbuf.fileno[0];
dimscale_obj.objno[0] = statbuf.objno[0];
dimscale_obj.fileno[1] = statbuf.fileno[1];
dimscale_obj.objno[1] = statbuf.objno[1];
/*printf("statbuf.fileno = %d statbuf.objno = %d\n",
statbuf.fileno, statbuf.objno);*/
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
if (H5DSiterate_scales(datasetid, 0, NULL, alien_visitor,
&vars_dimscale_obj) < 0) ERR;
/*printf("vars_dimscale_obj.fileno = %d vars_dimscale_obj.objno = %d\n",
vars_dimscale_obj.fileno, vars_dimscale_obj.objno);*/
if (vars_dimscale_obj.fileno[0] != dimscale_obj.fileno[0] ||
vars_dimscale_obj.objno[0] != dimscale_obj.objno[0] ||
vars_dimscale_obj.fileno[1] != dimscale_obj.fileno[1] ||
vars_dimscale_obj.objno[1] != dimscale_obj.objno[1]) ERR;
/* There's also a label for dimension 0. */
if (H5DSget_label(datasetid, 0, label, NC_MAX_NAME) < 0) ERR;
/*printf("found non-scale dataset %s, label %s\n", obj_name, label);*/
}
if (H5Dclose(datasetid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Sclose(spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a file with one var with two dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define DIMS_2 2
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME "pres"
hid_t fileid, lat_spaceid, lon_spaceid, pres_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid;
hsize_t dims[DIMS_2];
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_2, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these two dimscales. */
if ((pres_datasetid = H5Dcreate(fileid, PRES_NAME, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking that one var, two dimscales file can be read...");
{
#define NDIMS2 2
hid_t fileid, spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t dims[NDIMS2], maxdims[NDIMS2];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[2], vars_dimscale_obj[2];
int dimscale_cnt = 0;
int d, ndims;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
if (ndims > NDIMS2) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a file with one var with two unlimited dimension scales...");
{
#define U1_LEN 3
#define U2_LEN 2
#define DIMS2 2
#define U1_NAME "u1"
#define U2_NAME "u2"
#define VNAME "v1"
hid_t fapl_id, fcpl_id, grpid, plistid, plistid2;
hid_t fileid, lat_spaceid, lon_spaceid, pres_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid;
hsize_t dims[DIMS2], maxdims[DIMS2], chunksize[DIMS2] = {10, 10};
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[2], vars_dimscale_obj[2];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = 0;
maxdims[0] = H5S_UNLIMITED;
if ((lat_spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
if ((lon_spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = 0;
dims[1] = 0;
maxdims[0] = H5S_UNLIMITED;
maxdims[1] = H5S_UNLIMITED;
if ((pres_spaceid = H5Screate_simple(DIMS2, dims, maxdims)) < 0) ERR;
/* Set up the dataset creation property list for the two dimensions. */
if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(plistid, 1, chunksize) < 0) ERR;
if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate(grpid, U1_NAME, H5T_NATIVE_INT,
lat_spaceid, plistid)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate(grpid, U2_NAME, H5T_NATIVE_INT,
lon_spaceid, plistid)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
/* Set up the dataset creation property list for the variable. */
if ((plistid2 = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(plistid2, DIMS2, chunksize) < 0) ERR;
if (H5Pset_attr_creation_order(plistid2, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
/* Create a variable which uses these two dimscales. */
if ((pres_datasetid = H5Dcreate(grpid, VNAME, H5T_NATIVE_DOUBLE, pres_spaceid,
plistid2)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
/* Close down the show. */
if (H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Pclose(plistid) < 0 ||
H5Pclose(plistid2) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i = 0; i < num_obj; i++)
{
/*Get the type (i.e. group, dataset, etc.), and the name of
the object. */
if ((obj_class = H5Gget_objtype_by_idx(grpid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(grpid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(grpid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Check the dimension lengths. */
{
hid_t spaceid1;
hsize_t h5dimlen[DIMS2], h5dimlenmax[DIMS2];
int dataset_ndims;
/* Check U1. */
if ((datasetid = H5Dopen1(grpid, U1_NAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 1 || h5dimlen[0] != 0 || h5dimlenmax[0] != H5S_UNLIMITED) ERR;
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
/* Check U2. */
if ((datasetid = H5Dopen1(grpid, U2_NAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 1 || h5dimlen[0] != 0 || h5dimlenmax[0] != H5S_UNLIMITED) ERR;
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
/* Check V1. */
if ((datasetid = H5Dopen1(grpid, VNAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 0 || h5dimlen[1] != 0 ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* All done. */
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
}
/* Write two hyperslabs. */
{
#define NUM_VALS 3
hid_t file_spaceid, mem_spaceid;
hsize_t h5dimlen[DIMS2], h5dimlenmax[DIMS2], xtend_size[DIMS2] = {1, NUM_VALS};
hsize_t start[DIMS2] = {0, 0};
hsize_t count[DIMS2] = {1, NUM_VALS};
double value[NUM_VALS];
int dataset_ndims;
int i;
/* Set up phony data. */
for (i = 0; i < NUM_VALS; i++)
value[i] = (float)i;
/* Open the dataset, check its dimlens. */
if ((datasetid = H5Dopen1(grpid, VNAME)) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 0 || h5dimlen[1] != 0 ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Extend the size of the dataset. */
if (H5Dextend(datasetid, xtend_size) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
/* Check the size. */
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 1 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Set up the file and memory spaces. */
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, NULL, count, NULL) < 0) ERR;
if ((mem_spaceid = H5Screate_simple(DIMS2, count, NULL)) < 0) ERR;
/* Write a slice of data. */
if (H5Dwrite(datasetid, H5T_NATIVE_DOUBLE, mem_spaceid, file_spaceid,
H5P_DEFAULT, value) < 0)
/* Check the size. */
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 1 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Extend the size of the dataset for the second slice. */
xtend_size[0]++;
if (H5Dextend(datasetid, xtend_size) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
/* Set up the file and memory spaces for a second slice. */
start[0]++;
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, NULL, count, NULL) < 0) ERR;
if ((mem_spaceid = H5Screate_simple(DIMS2, count, NULL)) < 0) ERR;
/* Write a second slice of data. */
if (H5Dwrite(datasetid, H5T_NATIVE_DOUBLE, mem_spaceid, file_spaceid,
H5P_DEFAULT, value) < 0)
/* Check the size again. */
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 2 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* All done. */
if (H5Dclose(datasetid) ||
H5Sclose(mem_spaceid) ||
H5Sclose(file_spaceid)) ERR;
}
/* Close up the shop. */
if (H5Sclose(spaceid)) ERR;
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking dimension scales with attached dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define TIME_LEN 5
#define LEN_LEN 10
#define DIMS_3 3
#define NUM_DIMSCALES1 4
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME1 "z_pres"
#define TIME_NAME "time"
#define LEN_NAME "u_len"
hid_t fileid, lat_spaceid, lon_spaceid, time_spaceid, pres_spaceid, len_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid, time_dimscaleid, len_dimscaleid;
hid_t fapl_id, fcpl_id;
hsize_t dims[DIMS_3];
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t maxdims[DIMS_3];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[NUM_DIMSCALES1], vars_dimscale_obj[NUM_DIMSCALES1];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = TIME_LEN;
if ((time_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LEN_LEN;
if ((len_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
dims[2] = TIME_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_3, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate1(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate1(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
if ((time_dimscaleid = H5Dcreate1(fileid, TIME_NAME, H5T_NATIVE_INT,
time_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(time_dimscaleid, NULL) < 0) ERR;
if ((len_dimscaleid = H5Dcreate1(fileid, LEN_NAME, H5T_NATIVE_INT,
len_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(len_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these three dimscales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME1, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, time_dimscaleid, 2) < 0) ERR;
/* Attach a dimscale to a dimscale. Unfortunately, HDF5 does not
* allow this. Woe is me. */
/*if (H5DSattach_scale(time_dimscaleid, len_dimscaleid, 0) < 0) ERR;*/
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(time_dimscaleid) < 0 ||
H5Dclose(len_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(time_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Sclose(len_spaceid) < 0 ||
H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking cration ordering of datasets which are also dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define TIME_LEN 5
#define LEN_LEN 10
#define DIMS_3 3
#define NUM_DIMSCALES2 4
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME1 "z_pres"
#define TIME_NAME "time"
#define LEN_NAME "u_len"
hid_t fileid, lat_spaceid, lon_spaceid, time_spaceid, pres_spaceid, len_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid, time_dimscaleid, len_dimscaleid;
hid_t fapl_id, fcpl_id;
hsize_t dims[DIMS_3];
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t maxdims[DIMS_3];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[NUM_DIMSCALES2], vars_dimscale_obj[NUM_DIMSCALES2];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = TIME_LEN;
if ((time_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LEN_LEN;
if ((len_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
dims[2] = TIME_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_3, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate1(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate1(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
if ((time_dimscaleid = H5Dcreate1(fileid, TIME_NAME, H5T_NATIVE_INT,
time_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(time_dimscaleid, NULL) < 0) ERR;
if ((len_dimscaleid = H5Dcreate1(fileid, LEN_NAME, H5T_NATIVE_INT,
len_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(len_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these three dimscales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME1, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, time_dimscaleid, 2) < 0) ERR;
/* Attach a dimscale to a dimscale. Unfortunately, HDF5 does not
* allow this. Woe is me. */
/*if (H5DSattach_scale(time_dimscaleid, len_dimscaleid, 0) < 0) ERR;*/
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(time_dimscaleid) < 0 ||
H5Dclose(len_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(time_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Sclose(len_spaceid) < 0 ||
H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
/*-------------------------------------------------------------------------
* Function: test_sec2
*
* Purpose: Tests the file handle interface for SEC2 driver
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* Tuesday, Sept 24, 2002
*
*-------------------------------------------------------------------------
*/
static herr_t
test_sec2(void)
{
hid_t file = -1;
hid_t fapl = -1;
hid_t access_fapl = -1;
char filename[1024];
int *fhandle = NULL;
hsize_t file_size = 0;
TESTING("SEC2 file driver");
/* Set property list and file name for SEC2 driver. */
fapl = h5_fileaccess();
if(H5Pset_fapl_sec2(fapl) < 0)
TEST_ERROR;
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR;
/* Retrieve the access property list... */
if((access_fapl = H5Fget_access_plist(file)) < 0)
TEST_ERROR;
/* Check that the driver is correct */
if(H5FD_SEC2 != H5Pget_driver(access_fapl))
TEST_ERROR;
/* ...and close the property list */
if(H5Pclose(access_fapl) < 0)
TEST_ERROR;
/* Check file handle API */
if(H5Fget_vfd_handle(file, H5P_DEFAULT, (void **)&fhandle) < 0)
TEST_ERROR;
if(*fhandle < 0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* There is no guarantee the size of metadata in file is constant.
* Just try to check if it's reasonable. It's 2KB right now.
*/
if(file_size < 1 * KB || file_size > 4 * KB)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(fapl);
H5Fclose(file);
} H5E_END_TRY;
return -1;
}
int
main (void)
{
hid_t file, src_space, vspace,
dset; /* Handles */
hid_t dcpl;
herr_t status;
hsize_t vdsdims[3] = {VDSDIM0, VDSDIM1, VDSDIM2},
vdsdims_max[3] = {H5S_UNLIMITED, VDSDIM1, VDSDIM1},
dims[3] = {DIM0, DIM1, DIM2},
start[3], /* Hyperslab parameters */
stride[3],
count[3],
block[3];
hsize_t start_out[3], /* Hyperslab parameter out */
stride_out[3],
count_out[3],
block_out[3];
int i;
H5D_layout_t layout; /* Storage layout */
size_t num_map; /* Number of mappings */
ssize_t len; /* Length of the string; also a return value */
char *filename;
char *dsetname;
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create VDS dataspace. */
vspace = H5Screate_simple (RANK, vdsdims, vdsdims_max);
/* Create dataspaces for the source dataset. */
src_space = H5Screate_simple (RANK, dims, NULL);
/* Create VDS creation property */
dcpl = H5Pcreate (H5P_DATASET_CREATE);
/* Initialize hyperslab values */
start[0] = 0;
start[1] = 0;
start[2] = 0;
stride[0] = DIM0;
stride[1] = 1;
stride[2] = 1;
count[0] = H5S_UNLIMITED;
count[1] = 1;
count[2] = 1;
block[0] = DIM0;
block[1] = DIM1;
block[2] = DIM2;
/*
* Build the mappings
*
*/
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, stride, count, block);
status = H5Pset_virtual (dcpl, vspace, "f-%b.h5", "/A", src_space);
/* Create a virtual dataset */
dset = H5Dcreate2 (file, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT,
dcpl, H5P_DEFAULT);
status = H5Sclose (vspace);
status = H5Sclose (src_space);
status = H5Dclose (dset);
status = H5Fclose (file);
/*
* Now we begin the read section of this example.
*/
/*
* Open file and dataset using the default properties.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen2 (file, DATASET, H5P_DEFAULT);
/*
* Get creation property list and mapping properties.
*/
dcpl = H5Dget_create_plist (dset);
/*
* Get storage layout.
*/
layout = H5Pget_layout (dcpl);
if (H5D_VIRTUAL == layout)
printf(" Dataset has a virtual layout \n");
else
printf(" Wrong layout found \n");
/*
* Find number of mappings.
*/
status = H5Pget_virtual_count (dcpl, &num_map);
printf(" Number of mappings is %d\n", (int)num_map);
/*
* Get mapping parameters for each mapping.
*/
for (i = 0; i < (int)num_map; i++) {
printf(" Mapping %d \n", i);
printf(" Selection in the virtual dataset \n");
/* Get selection in the virttual dataset */
vspace = H5Pget_virtual_vspace (dcpl, (size_t)i);
if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) {
if (H5Sis_regular_hyperslab(vspace)) {
status = H5Sget_regular_hyperslab (vspace, start_out, stride_out, count_out, block_out);
printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], (unsigned long long)start_out[1], (unsigned long long)start_out[2]);
printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], (unsigned long long)count_out[1], (unsigned long long)count_out[2]);
printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], (unsigned long long)block_out[1], (unsigned long long)block_out[2]);
}
}
/* Get source file name */
len = H5Pget_virtual_filename (dcpl, (size_t)i, NULL, 0);
filename = (char *)malloc((size_t)len*sizeof(char)+1);
H5Pget_virtual_filename (dcpl, (size_t)i, filename, len+1);
printf(" Source filename %s\n", filename);
/* Get source dataset name */
len = H5Pget_virtual_dsetname (dcpl, (size_t)i, NULL, 0);
dsetname = (char *)malloc((size_t)len*sizeof(char)+1);
H5Pget_virtual_dsetname (dcpl, (size_t)i, dsetname, len+1);
printf(" Source dataset name %s\n", dsetname);
/* Get selection in the source dataset */
printf(" Selection in the source dataset ");
src_space = H5Pget_virtual_srcspace (dcpl, (size_t)i);
if(H5Sget_select_type(src_space) == H5S_SEL_ALL) {
printf("H5S_ALL \n");
}
/* EIP read data back */
H5Sclose(vspace);
H5Sclose(src_space);
free(filename);
free(dsetname);
}
/*
* Close and release resources.
*/
status = H5Pclose (dcpl);
status = H5Dclose (dset);
status = H5Fclose (file);
return 0;
}
/*-------------------------------------------------------------------------
* Function: test_filter_write_failure
*
* Purpose: Tests the library's behavior when a mandate filter returns
* failure. There're only 5 chunks with each of them having
* 2 integers. The filter will fail in the last chunk. The
* dataset should release all resources even though the last
* chunk can't be flushed to file. The file should close
* successfully.
*
* Return:
* Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* 25 August 2010
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
test_filter_write(char *file_name, hid_t my_fapl)
{
char filename[1024];
hid_t file = -1;
hid_t dataset=-1; /* dataset ID */
hid_t sid=-1; /* dataspace ID */
hid_t dcpl=-1; /* dataset creation property list ID */
hsize_t dims[1]={DIM}; /* dataspace dimension - 10*/
hsize_t chunk_dims[1]={FILTER_CHUNK_DIM}; /* chunk dimension - 2*/
int nfilters; /* number of filters in DCPL */
unsigned flags; /* flags for filter */
int points[DIM]; /* Data */
int rbuf[DIM]; /* Data */
herr_t ret; /* generic return value */
int i;
TESTING("data writing when a mandatory filter fails");
/* Create file */
if((file = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, my_fapl)) < 0) TEST_ERROR
/* create the data space */
if((sid = H5Screate_simple(1, dims, NULL)) < 0) TEST_ERROR
/* Create dcpl and register the filter */
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) TEST_ERROR
if(H5Pset_chunk(dcpl, 1, chunk_dims) < 0) TEST_ERROR
if(H5Zregister (H5Z_FAIL_TEST) < 0) TEST_ERROR
/* Check that the filter was registered */
if(TRUE != H5Zfilter_avail(H5Z_FILTER_FAIL_TEST)) FAIL_STACK_ERROR
/* Enable the filter as mandatory */
if(H5Pset_filter(dcpl, H5Z_FILTER_FAIL_TEST, 0, (size_t)0, NULL) < 0)
TEST_ERROR
/* create a dataset */
if((dataset = H5Dcreate2(file, DSET_NAME, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0) TEST_ERROR
/* Initialize the write buffer */
for(i = 0; i < DIM; i++)
points[i] = i;
/* Write data */
if(H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, sid, H5P_DEFAULT, points) < 0) TEST_ERROR
/* clean up objects used for this test */
if(H5Pclose (dcpl) < 0) TEST_ERROR
if(H5Sclose (sid) < 0) TEST_ERROR
/* Dataset closing should fail */
H5E_BEGIN_TRY {
ret = H5Dclose (dataset);
} H5E_END_TRY;
if(ret >= 0) {
H5_FAILED();
puts(" Dataset is supposed to fail because the chunk can't be flushed to file.");
TEST_ERROR
}
