/*--------------------------------------------------------------------------*/
int openHDF5File(const char *name, int _iAppendMode)
{
hid_t file;
char *pathdest = getPathFilename(name);
char *currentpath = NULL;
char *filename = getFilenameWithExtension(name);
int ierr = 0;
void *oldclientdata = NULL;
/* Used to avoid stack trace to be displayed */
H5E_auto2_t oldfunc;
/* TO DO : remove when HDF5 will be fixed ... */
/* HDF5 does not manage no ANSI characters */
/* UGLY workaround :( */
/* We split path, move in this path, open file */
/* and return in previous place */
/* see BUG 6440 */
currentpath = scigetcwd(&ierr);
//prevent error msg to change directory to ""
if (strcmp(pathdest, "") != 0)
{
scichdir(pathdest);
}
/* Save old error handler */
H5Eget_auto2(H5E_DEFAULT, &oldfunc, &oldclientdata);
/* Turn off error handling */
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
if (_iAppendMode == 0)
{
//read only
file = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
}
else
{
//read write to append
file = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
}
/* The following test will display the backtrace in case of error */
/* Deactivated because displayed each time we call 'load' to open a non-HDF5 file */
/*if (file < 0)
{
H5Eprint(stderr);
}*/
/* Restore previous error handler */
H5Eset_auto2(H5E_DEFAULT, oldfunc, oldclientdata);
scichdir(currentpath);
FREE(currentpath);
FREE(filename);
FREE(pathdest);
return file;
}
/*
* Class: hdf_hdf5lib_exceptions_HDF5Library
* Method: H5error_off
* Signature: ()I
*
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5error_1off
(JNIEnv *env, jclass clss)
{
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
return 0;
} /* end Java_hdf_hdf5lib_H5_H5error_1off() */
//--------------------------------------------------------------------------
// Function: Exception::setAutoPrint
///\brief Turns on the automatic error printing.
///\param func - IN: Function to be called upon an error condition
///\param client_data - IN: Data passed to the error function
///\par Description
/// When the library is first initialized the auto printing
/// function, \a func, is set to the C API \c H5Eprint and
/// \a client_data is the standard error stream pointer, \c stderr.
/// Automatic stack traversal is always in the \c H5E_WALK_DOWNWARD
/// direction.
///\par
/// Users are encouraged to write their own more specific error
/// handlers
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void Exception::setAutoPrint( H5E_auto2_t& func, void* client_data )
{
// calls the C API routine H5Eset_auto to set the auto printing to
// the specified function.
herr_t ret_value = H5Eset_auto2( H5E_DEFAULT, func, client_data );
if( ret_value < 0 )
throw Exception( "Exception::setAutoPrint", "H5Eset_auto failed" );
}
//--------------------------------------------------------------------------
// Function: Exception::dontPrint
///\brief Turns off the automatic error printing from the C library.
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
void Exception::dontPrint()
{
// calls the C API routine H5Eset_auto with NULL parameters to turn
// off the automatic error printing.
herr_t ret_value = H5Eset_auto2( H5E_DEFAULT, NULL, NULL );
if( ret_value < 0 )
throw Exception( "Exception::dontPrint", "H5Eset_auto failed" );
}
/*-------------------------------------------------------------------------
* Function: h5_restore_err
*
* Purpose: Restore the default error handler.
*
* Return: N/A
*
* Programmer: Quincey Koziol
* Sept 10, 2015
*
*-------------------------------------------------------------------------
*/
void
h5_restore_err(void)
{
/* Restore the original error reporting routine */
HDassert(err_func != NULL);
H5Eset_auto2(H5E_DEFAULT, err_func, NULL);
err_func = NULL;
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose:
*
* Return: Success: zero
*
* Failure: non-zero
*
* Programmer: Robb Matzke
* Monday, September 28, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main(int argc, char *argv[])
{
hid_t xfer;
fill_t fill_style = FILL_ALL;
hbool_t use_cache = FALSE;
double splits[3];
int i, j, nerrors=0;
/* Default split ratios */
H5Eset_auto2(H5E_DEFAULT, display_error_cb, NULL);
if((xfer = H5Pcreate(H5P_DATASET_XFER)) < 0) goto error;
if(H5Pget_btree_ratios(xfer, splits+0, splits+1, splits+2) < 0) goto error;
if(H5Pclose(xfer) < 0) goto error;
/* Parse command-line options */
for(i = 1, j = 0; i < argc; i++) {
if (!strcmp(argv[i], "forward")) {
fill_style = FILL_FORWARD;
} else if (!strcmp(argv[i], "reverse")) {
fill_style = FILL_REVERSE;
} else if (!strcmp(argv[i], "inward")) {
fill_style = FILL_INWARD;
} else if (!strcmp(argv[i], "outward")) {
fill_style = FILL_OUTWARD;
} else if (!strcmp(argv[i], "random")) {
fill_style = FILL_RANDOM;
} else if (!strcmp(argv[i], "cache")) {
use_cache = TRUE;
} else if (j<3 && (isdigit(argv[i][0]) || '.'==argv[i][0])) {
splits[j++] = strtod(argv[i], NULL);
} else {
usage(argv[0]);
}
}
if (FILL_ALL==fill_style) {
printf("%-7s %8s\n", "Style", "Bytes/Chunk");
printf("%-7s %8s\n", "-----", "-----------");
nerrors += test(FILL_FORWARD, splits, FALSE, use_cache);
nerrors += test(FILL_REVERSE, splits, FALSE, use_cache);
nerrors += test(FILL_INWARD, splits, FALSE, use_cache);
nerrors += test(FILL_OUTWARD, splits, FALSE, use_cache);
nerrors += test(FILL_RANDOM, splits, FALSE, use_cache);
}
else {
if (use_cache) usage(argv[0]);
nerrors += test(fill_style, splits, TRUE, FALSE);
}
if (nerrors>0) goto error;
cleanup();
return 0;
error:
fprintf(stderr, "*** ERRORS DETECTED ***\n");
return 1;
}
static
void *tts_error_thread(void UNUSED *arg)
{
hid_t dataspace, datatype, dataset;
hsize_t dimsf[1]; /* dataset dimensions */
H5E_auto2_t old_error_cb;
void *old_error_client_data;
int value;
int ret;
/* preserve previous error stack handler */
H5Eget_auto2(H5E_DEFAULT, &old_error_cb, &old_error_client_data);
/* set each thread's error stack handler */
H5Eset_auto2(H5E_DEFAULT, error_callback, NULL);
/* define dataspace for dataset */
dimsf[0] = 1;
dataspace = H5Screate_simple(1, dimsf, NULL);
assert(dataspace >= 0);
/* define datatype for the data using native little endian integers */
datatype = H5Tcopy(H5T_NATIVE_INT);
assert(datatype >= 0);
H5Tset_order(datatype, H5T_ORDER_LE);
/* create a new dataset within the file */
dataset = H5Dcreate2(error_file, DATASETNAME, datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dataset >= 0) { /* not an error */
value = WRITE_NUMBER;
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &value);
H5Dclose(dataset);
} /* end if */
ret = H5Tclose(datatype);
assert(ret >= 0);
ret = H5Sclose(dataspace);
assert(ret >= 0);
/* turn our error stack handler off */
H5Eset_auto2(H5E_DEFAULT, old_error_cb, old_error_client_data);
return NULL;
}
/**
Traverse the path of an object in HDF5 file, checking existence of
groups in the path and creating them if required. */
hid_t HDF5DataWriter::getDataset(string path)
{
if (filehandle_ < 0){
return -1;
}
herr_t status = H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
// Create the groups corresponding to this path
string::size_type lastslash = path.find_last_of("/");
vector<string> pathTokens;
moose::tokenize(path, "/", pathTokens);
hid_t prev_id = filehandle_;
hid_t id = -1;
for ( unsigned int ii = 0; ii < pathTokens.size()-1; ++ii ){
// check if object exists
htri_t exists = H5Lexists(prev_id, pathTokens[ii].c_str(),
H5P_DEFAULT);
if (exists > 0){
// try to open existing group
id = H5Gopen2(prev_id, pathTokens[ii].c_str(), H5P_DEFAULT);
} else if (exists == 0) {
// If that fails, try to create a group
id = H5Gcreate2(prev_id, pathTokens[ii].c_str(),
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
if ((exists < 0) || (id < 0)){
// Failed to open/create a group, print the
// offending path (for debugging; the error is
// perhaps at the level of hdf5 or file system).
cerr << "Error: failed to open/create group: ";
for (unsigned int jj = 0; jj <= ii; ++jj){
cerr << "/" << pathTokens[jj];
}
cerr << endl;
prev_id = -1;
}
if (prev_id >= 0 && prev_id != filehandle_){
// Successfully opened/created new group, close the old group
status = H5Gclose(prev_id);
assert( status >= 0 );
}
prev_id = id;
}
string name = pathTokens[pathTokens.size()-1];
htri_t exists = H5Lexists(prev_id, name.c_str(), H5P_DEFAULT);
hid_t dataset_id = -1;
if (exists > 0){
dataset_id = H5Dopen2(prev_id, name.c_str(), H5P_DEFAULT);
} else if (exists == 0){
dataset_id = createDoubleDataset(prev_id, name);
} else {
cerr << "Error: H5Lexists returned "
<< exists << " for path \""
<< path << "\"" << endl;
}
return dataset_id;
}
void AMRreader::
init()
{
filename_="";
nblks_=0;
nrect_=nvert_=0;
blkxs_=blkdx_=datbuf_=NULL;
prebuf_=sndbuf_=tmpbuf_=NULL;
eos_=NULL;
// Turn off error message printing.
H5Eset_auto2(0,0,0);
}
int
main(int argc, char **argv)
{
miclass_t myclass = MI_CLASS_REAL;
mitype_t mytype = MI_TYPE_UNKNOWN;
misize_t mysize = 0;
char *myname = NULL;
mihandle_t volume = NULL;
/* Turn off automatic error reporting.
*/
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Check each file.
*/
while (--argc > 0) {
++argv;
if (micreate_volume(*argv, 0, NULL, MI_TYPE_INT, 0, NULL, &volume) < 0) { /*type 0 is equivalent to H5T_INTEGER */
fprintf(stderr, "Error opening %s\n", *argv);
}
else {
int i;
/* Repeat many times to expose resource leakage problems, etc.
*/
for (i = 0; i < 25000; i++) {
miget_data_type(volume, &mytype);
miget_data_type_size(volume, &mysize);
miget_data_class(volume, &myclass);
miget_space_name(volume, &myname);
mifree_name(myname);
}
miclose_volume(volume);
printf("file: %s type %d size %lld class %d\n", *argv,
mytype, mysize, myclass);
}
}
return (0);
}
void pyne::Material::from_hdf5(std::string filename, std::string datapath, int row, int protocol) {
// Turn off annoying HDF5 errors
herr_t status;
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
// Check that the file is there
if (!pyne::file_exists(filename))
throw pyne::FileNotFound(filename);
// Check to see if the file is in HDF5 format.
bool ish5 = H5Fis_hdf5(filename.c_str());
if (!ish5)
throw h5wrap::FileNotHDF5(filename);
//Set file access properties so it closes cleanly
hid_t fapl;
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG);
// Open the database
hid_t db = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, fapl);
bool datapath_exists = h5wrap::path_exists(db, datapath);
if (!datapath_exists)
throw h5wrap::PathNotFound(filename, datapath);
// Clear current content
comp.clear();
// Load via various protocols
if (protocol == 0)
_load_comp_protocol0(db, datapath, row);
else if (protocol == 1)
_load_comp_protocol1(db, datapath, row);
else
throw pyne::MaterialProtocolError();
// Close the database
status = H5Fclose(db);
// Renomalize the composition, just to be safe.
norm_comp();
};
/*-------------------------------------------------------------------------
* Function: h5_reset
*
* Purpose: Reset the library by closing it.
*
* Return: void
*
* Programmer: Robb Matzke
* Friday, November 20, 1998
*
*-------------------------------------------------------------------------
*/
void
h5_reset(void)
{
HDfflush(stdout);
HDfflush(stderr);
H5close();
/* Save current error stack reporting routine and redirect to our local one */
HDassert(err_func == NULL);
H5Eget_auto2(H5E_DEFAULT, &err_func, NULL);
H5Eset_auto2(H5E_DEFAULT, h5_errors, NULL);
/*
* I commented this chunk of code out because it's not clear what diagnostics
* were being output and under what circumstances, and creating this file
* is throwing off debugging some of the tests. I can't see any _direct_
* harm in keeping this section of code, but I can't see any _direct_
* benefit right now either. If we figure out under which circumstances
* diagnostics are being output, we should enable this behavior based on
* appropriate configure flags/macros. QAK - 2007/12/20
*/
#ifdef OLD_WAY
{
char filename[1024];
/*
* Cause the library to emit some diagnostics early so they don't
* interfere with other formatted output.
*/
sprintf(filename, "/tmp/h5emit-%05d.h5", HDgetpid());
H5E_BEGIN_TRY {
hid_t file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
hid_t grp = H5Gcreate2(file, "emit", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(grp);
H5Fclose(file);
HDunlink(filename);
} H5E_END_TRY;
}
#endif /* OLD_WAY */
}
/*
* Disable error stack printing when errors occur.
*/
void PrintErrorStackOff(void)
{
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
}
/*
* Enable error stack printing when errors occur.
*/
void PrintErrorStackOn(void)
{
H5Eset_auto2(H5E_DEFAULT, PrintErrorStackFunc, PrintErrorStackData);
}
/*-------------------------------------------------------------------------
* Function: test_error
*
* Purpose: Test error API functions
*
* Return: Success: 0
*
* Failure: -1
*
* Programmer: Raymond Lu
* July 10, 2003
*
*-------------------------------------------------------------------------
*/
static herr_t
test_error(hid_t file)
{
hid_t dataset, space;
hid_t estack_id;
hsize_t dims[2];
const char *FUNC_test_error = "test_error";
H5E_auto2_t old_func;
void *old_data;
HDfprintf(stderr, "\nTesting error API based on data I/O\n");
/* Create the data space */
dims[0] = DIM0;
dims[1] = DIM1;
if ((space = H5Screate_simple(2, dims, NULL))<0) TEST_ERROR;
/* Test H5E_BEGIN_TRY */
H5E_BEGIN_TRY {
dataset = H5Dcreate2(FAKE_ID, DSET_NAME, H5T_STD_I32BE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
} H5E_END_TRY;
/* Create the dataset */
if((dataset = H5Dcreate2(file, DSET_NAME, H5T_STD_I32BE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
H5Epush(H5E_DEFAULT, __FILE__, FUNC_test_error, __LINE__, ERR_CLS, ERR_MAJ_IO, ERR_MIN_CREATE,
"H5Dcreate2 failed");
goto error;
} /* end if */
/* Test enabling and disabling default printing */
if(H5Eget_auto2(H5E_DEFAULT, &old_func, &old_data) < 0)
TEST_ERROR;
if(old_data != NULL)
TEST_ERROR;
#ifdef H5_USE_16_API
if (old_func != (H5E_auto_t)H5Eprint)
TEST_ERROR;
#else /* H5_USE_16_API */
if (old_func != (H5E_auto2_t)H5Eprint2)
TEST_ERROR;
#endif /* H5_USE_16_API */
if(H5Eset_auto2(H5E_DEFAULT, NULL, NULL) < 0)
TEST_ERROR;
/* Make H5Dwrite fail, verify default print is disabled */
if(H5Dwrite(FAKE_ID, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, ipoints2) >= 0) {
H5Epush(H5E_DEFAULT, __FILE__, FUNC_test_error, __LINE__, ERR_CLS, ERR_MAJ_IO, ERR_MIN_WRITE,
"H5Dwrite shouldn't succeed");
goto error;
} /* end if */
if(H5Eset_auto2(H5E_DEFAULT, old_func, old_data) < 0)
TEST_ERROR;
/* Test saving and restoring the current error stack */
if(H5Dwrite(FAKE_ID, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, ipoints2) < 0) {
H5Epush(H5E_DEFAULT, __FILE__, FUNC_test_error, __LINE__, ERR_CLS, ERR_MAJ_IO, ERR_MIN_WRITE,
"H5Dwrite failed as supposed to");
estack_id = H5Eget_current_stack();
H5Dclose(dataset);
H5Sclose(space);
H5Eset_current_stack(estack_id);
goto error;
} /* end if */
/* In case program comes to this point, close dataset */
if(H5Dclose(dataset) < 0) TEST_ERROR;
TEST_ERROR;
error:
return -1;
} /* end test_error() */
/*-------------------------------------------------------------------------
* 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);
}
FCT_BGN()
{
int preserve = 0;
// MPI setup: MPI_Init and atexit(MPI_Finalize)
int world_size, world_rank;
MPI_Init(&argc, &argv);
atexit((void (*) ()) MPI_Finalize);
MPI_Comm_size(MPI_COMM_WORLD, &world_size);
MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
// Install the command line options defined above.
fctcl_install(my_cl_options);
// Retrieve and sanity check problem size options
preserve = fctcl_is("--preserve");
const int ncomponents = (int) strtol(
fctcl_val2("--ncomponents","2"), (char **) NULL, 10);
if (ncomponents < 1) {
fprintf(stderr, "\n--ncomponents=%d < 1\n", ncomponents);
MPI_Abort(MPI_COMM_WORLD, 1);
}
// Obtain default HDF5 error handler
H5E_auto2_t hdf5_handler;
void *hdf5_client_data;
H5Eget_auto2(H5E_DEFAULT, &hdf5_handler, &hdf5_client_data);
// Obtain default ESIO error handler
esio_error_handler_t * const esio_handler = esio_set_error_handler_off();
esio_set_error_handler(esio_handler);
// Fixture-related details
const char * const input_dir = getenv("ESIO_TEST_INPUT_DIR");
const char * const output_dir = getenv("ESIO_TEST_OUTPUT_DIR");
char * filetemplate = create_testfiletemplate(output_dir, __FILE__);
(void) input_dir; // Possibly unused
char * filename = NULL;
esio_handle state = NULL;
FCT_FIXTURE_SUITE_BGN(attribute_suite)
{
FCT_SETUP_BGN()
{
ESIO_MPICHKQ(MPI_Barrier(MPI_COMM_WORLD)); // Synchronize
// Restore HDF5/ESIO default error handling
H5Eset_auto2(H5E_DEFAULT, hdf5_handler, hdf5_client_data);
esio_set_error_handler(esio_handler);
// Rank 0 generates a unique filename and broadcasts it
int filenamelen;
if (world_rank == 0) {
filename = create_testfilename(filetemplate);
if (preserve) {
printf("\nfilename: %s\n", filename);
}
filenamelen = strlen(filename);
}
ESIO_MPICHKR(MPI_Bcast(&filenamelen, 1, MPI_INT,
0, MPI_COMM_WORLD));
if (world_rank > 0) {
filename = calloc(filenamelen + 1, sizeof(char));
}
ESIO_MPICHKR(MPI_Bcast(filename, filenamelen, MPI_CHAR,
0, MPI_COMM_WORLD));
fct_req(filename);
// Initialize ESIO state
state = esio_handle_initialize(MPI_COMM_WORLD);
fct_req(state);
}
FCT_SETUP_END();
FCT_TEARDOWN_BGN()
{
// Finalize ESIO state
esio_handle_finalize(state);
// Clean up the unique file and filename
if (world_rank == 0) {
if (!preserve) unlink(filename);
}
free(filename);
}
FCT_TEARDOWN_END();
// Test scalar-valued attributes, including overwrite details
FCT_TEST_BGN(attribute)
{
TYPE value;
// Open file
fct_req(0 == esio_file_create(state, filename, 1));
// Write zero to disk and flush the buffers
value = 0;
fct_req(0 == AFFIX(esio_attribute_write)(
state, "/", "attribute", &value));
fct_req(0 == esio_file_flush(state));
// Populate value with non-zero data
// TODO Vary this based on the rank?
value = 5678;
// Overwrite zeros on disk with test data
fct_req(0 == AFFIX(esio_attribute_write)(
state, "/", "attribute", &value));
// Clear storage in memory
value = 0;
{ // Ensure we can retrieve the size correctly
int count;
fct_req(0 == esio_attribute_sizev(
state, "/", "attribute", &count));
fct_chk_eq_int(count, 1);
}
// Close the file
fct_req(0 == esio_file_close(state));
// Reopen the file using normal HDF5 APIs on root processor
// Ensure we can retrieve the data by other means
if (world_rank == 0) {
TYPE data;
const hid_t file_id
= H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
fct_req(0 <= AFFIX(H5LTget_attribute)(file_id, "/",
"attribute",
&data));
#ifdef __INTEL_COMPILER
#pragma warning(push,disable:1572)
#endif
fct_chk(data == 5678);
#ifdef __INTEL_COMPILER
#pragma warning(pop)
#endif
fct_req(0 <= H5Fclose(file_id));
}
// Re-read the file in a distributed manner and verify contents
fct_req(0 == esio_file_open(state, filename, 0));
fct_req(0 == AFFIX(esio_attribute_read)(
state, "/", "attribute", &value));
#ifdef __INTEL_COMPILER
#pragma warning(push,disable:1572)
#endif
fct_chk(value == 5678);
#ifdef __INTEL_COMPILER
#pragma warning(pop)
#endif
// Check that non-existent attribute yields quiet ESIO_NOTFOUND
fct_chk(ESIO_NOTFOUND == esio_attribute_sizev(
state, "/", "nonexistent", NULL));
fct_req(0 == esio_file_close(state));
}
FCT_TEST_END();
// Test vector-like attributes
FCT_TEST_BGN(attribute)
{
TYPE *value;
// Allocate storage
value = calloc(ncomponents, sizeof(TYPE));
fct_req(value);
// Open file
fct_req(0 == esio_file_create(state, filename, 1));
// Populate test data
for (int i = 0; i < ncomponents; ++i) {
value[i] = (TYPE) i + 5678;
}
// Write attribute to file
fct_req(0 == AFFIX(esio_attribute_writev)(
state, "/", "attribute", value, ncomponents));
{ // Ensure we can retrieve the size correctly
int count;
fct_req(0 == esio_attribute_sizev(
state, "/", "attribute", &count));
fct_chk_eq_int(count, ncomponents);
}
// Close the file
fct_req(0 == esio_file_close(state));
// Free the temporary
free(value);
// Reopen the file using normal HDF5 APIs on root processor
// Examine the contents to ensure it matches
if (world_rank == 0) {
value = calloc(ncomponents, sizeof(TYPE));
fct_req(value);
const hid_t file_id
= H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
fct_req(0 <= AFFIX(H5LTget_attribute)(file_id, "/",
"attribute", value));
for (int i = 0; i < ncomponents; ++i) {
#ifdef __INTEL_COMPILER
#pragma warning(push,disable:1572)
#endif
fct_chk(i + 5678 == value[i]);
#ifdef __INTEL_COMPILER
#pragma warning(pop)
#endif
}
fct_req(0 <= H5Fclose(file_id));
free(value);
}
// Re-read the file in a distributed manner and verify contents
value = calloc(ncomponents, sizeof(TYPE));
fct_req(value);
fct_req(0 == esio_file_open(state, filename, 0));
fct_req(0 == AFFIX(esio_attribute_readv)(
state, "/", "attribute", value, ncomponents));
for (int i = 0; i < ncomponents; ++i) {
#ifdef __INTEL_COMPILER
#pragma warning(push,disable:1572)
#endif
fct_chk(i + 5678 == value[i]);
#ifdef __INTEL_COMPILER
#pragma warning(pop)
#endif
}
free(value);
fct_req(0 == esio_file_close(state));
}
FCT_TEST_END();
}
FCT_FIXTURE_SUITE_END();
free(filetemplate);
}
inline SilenceHDF5()
: _client_data(0)
{
H5Eget_auto2(H5E_DEFAULT, &_func, &_client_data);
H5Eset_auto2(H5E_DEFAULT, 0, 0);
}
FCT_BGN()
{
int preserve = 0;
// MPI setup: MPI_Init and atexit(MPI_Finalize)
int world_size, world_rank;
MPI_Init(&argc, &argv);
atexit((void (*) ()) MPI_Finalize);
MPI_Comm_size(MPI_COMM_WORLD, &world_size);
MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
// Install the command line options defined above.
fctcl_install(my_cl_options);
// Retrieve options
preserve = fctcl_is("--preserve");
// Obtain default HDF5 error handler
H5E_auto2_t hdf5_handler;
void *hdf5_client_data;
H5Eget_auto2(H5E_DEFAULT, &hdf5_handler, &hdf5_client_data);
// Obtain default ESIO error handler
esio_error_handler_t * const esio_handler = esio_set_error_handler_off();
esio_set_error_handler(esio_handler);
// Fixture-related details
const char * const input_dir = getenv("ESIO_TEST_INPUT_DIR");
const char * const output_dir = getenv("ESIO_TEST_OUTPUT_DIR");
char * filetemplate = create_testfiletemplate(output_dir, __FILE__);
char * filename = NULL;
esio_handle handle = NULL;
FCT_FIXTURE_SUITE_BGN(esio_file)
{
FCT_SETUP_BGN()
{
ESIO_MPICHKQ(MPI_Barrier(MPI_COMM_WORLD)); // Synchronize
// Restore HDF5/ESIO default error handling
H5Eset_auto2(H5E_DEFAULT, hdf5_handler, hdf5_client_data);
esio_set_error_handler(esio_handler);
// Rank 0 generates a unique filename and broadcasts it
int filenamelen;
if (world_rank == 0) {
filename = create_testfilename(filetemplate);
if (preserve) {
printf("\nfilename: %s\n", filename);
}
filenamelen = strlen(filename);
}
ESIO_MPICHKR(MPI_Bcast(&filenamelen, 1, MPI_INT,
0, MPI_COMM_WORLD));
if (world_rank > 0) {
filename = calloc(filenamelen + 1, sizeof(char));
}
ESIO_MPICHKR(MPI_Bcast(filename, filenamelen, MPI_CHAR,
0, MPI_COMM_WORLD));
fct_req(filename);
// Initialize ESIO handle
handle = esio_handle_initialize(MPI_COMM_WORLD);
fct_req(handle);
// Check that the handle correctly reports world_size
int size;
fct_req(ESIO_SUCCESS == esio_handle_comm_size(handle, &size));
fct_chk_eq_int(world_size, size);
// Check that the handle correctly reports world_rank
int rank;
fct_req(ESIO_SUCCESS == esio_handle_comm_rank(handle, &rank));
fct_chk_eq_int(world_rank, rank);
}
FCT_SETUP_END();
FCT_TEARDOWN_BGN()
{
// Finalize ESIO handle
esio_handle_finalize(handle);
// Clean up the unique file and filename
if (world_rank == 0) {
if (!preserve) unlink(filename);
}
free(filename);
}
FCT_TEARDOWN_END();
FCT_TEST_BGN(success_code)
{
fct_chk_eq_int(0, ESIO_SUCCESS); // Success is zero
fct_chk(!ESIO_SUCCESS); // Not success is true
}
FCT_TEST_END();
FCT_TEST_BGN(file_create_and_open)
{
// No open file so esio_file_path is empty
fct_req(NULL == esio_file_path(handle));
// Create with overwrite should always work
fct_req(0 == esio_file_create(handle, filename, 1 /* o/w */));
// Flush flush flush should always work
fct_req(0 == esio_file_flush(handle));
fct_req(0 == esio_file_flush(handle));
fct_req(0 == esio_file_flush(handle));
// Check that esio_file_path points to a valid canonical location
struct stat statbuf;
char *file_path = esio_file_path(handle);
fct_req(file_path != NULL);
fct_chk_startswith_str(file_path, "/"); // Absolute?
fct_req(0 == stat(file_path, &statbuf));
free(file_path);
// Close the file
fct_req(0 == esio_file_close(handle));
// Double closure should silently succeed
fct_req(0 == esio_file_close(handle));
// No open file so esio_file_path is empty
fct_req(NULL == esio_file_path(handle));
// Create without overwrite should fail
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
esio_set_error_handler_off();
fct_req(0 != esio_file_create(handle, filename, 0 /* no o/w */));
esio_set_error_handler(esio_handler);
H5Eset_auto2(H5E_DEFAULT, hdf5_handler, hdf5_client_data);
// Remove the file and create without overwrite should succeed
ESIO_MPICHKQ(MPI_Barrier(MPI_COMM_WORLD)); // Synchronize
if (world_rank == 0) {
fct_req(0 == unlink(filename));
}
ESIO_MPICHKQ(MPI_Barrier(MPI_COMM_WORLD)); // Synchronize
fct_req(0 == esio_file_create(handle, filename, 0 /* no o/w */));
// Close the file
fct_req(0 == esio_file_close(handle));
// Ensure we can open in read-only mode
fct_req(0 == esio_file_open(handle, filename, 0 /* read-only */));
// Close the file
fct_req(0 == esio_file_close(handle));
// Ensure we can open in read-write mode
fct_req(0 == esio_file_open(handle, filename, 1 /* read-write */));
// Close the file
fct_req(0 == esio_file_close(handle));
}
FCT_TEST_END();
FCT_TEST_BGN(file_clone)
{
// Dynamically create the empty.h5 source filename per input_dir
if (input_dir == NULL && world_rank == 0) {
fprintf(stderr, "\nESIO_TEST_INPUT_DIR not in environment!\n");
}
fct_req(NULL != input_dir /* check ESIO_TEST_INPUT_DIR set */);
int srcfilelen = strlen(input_dir);
fct_req(srcfilelen > 0);
srcfilelen += strlen("/empty.h5");
srcfilelen += 1;
char * srcfile = calloc(srcfilelen, 1);
fct_req(NULL != srcfile);
fct_req(NULL != strcat(srcfile, input_dir));
fct_req(NULL != strcat(srcfile, "/empty.h5"));
// Clone with overwrite should always work
fct_req(0 == esio_file_clone(handle, srcfile, filename, 1));
// Close the file
fct_req(0 == esio_file_close(handle));
// Create without overwrite should fail
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
esio_set_error_handler_off();
fct_req(0 != esio_file_clone(handle, srcfile, filename, 0));
esio_set_error_handler(esio_handler);
H5Eset_auto2(H5E_DEFAULT, hdf5_handler, hdf5_client_data);
// Remove the file and create without overwrite should succeed
ESIO_MPICHKQ(MPI_Barrier(MPI_COMM_WORLD)); // Synchronize
if (world_rank == 0) {
fct_req(0 == unlink(filename));
}
ESIO_MPICHKQ(MPI_Barrier(MPI_COMM_WORLD)); // Synchronize
fct_req(0 == esio_file_clone(handle, srcfile, filename, 0));
// Close the file
fct_req(0 == esio_file_close(handle));
// Deallocate the srcfile name
free(srcfile);
}
FCT_TEST_END();
// Much of this functionality is covered in restart_helpers.c
// and restart_rename.{sh,c}. This covers only the public API's
// most basic usage.
FCT_TEST_BGN(file_close_restart)
{
struct stat statbuf;
// Form template and expected file paths from temporary filename
char *template = malloc(strlen(filename) + 2);
fct_req(template);
inline ~SilenceHDF5() { H5Eset_auto2(H5E_DEFAULT, _func, _client_data); }
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: h5watch
*
* Return: Success: 0
* Failure: 1
*
* Programmer: Vailin Choi; August 2010
*
*-------------------------------------------------------------------------
*/
int
main(int argc, const char *argv[])
{
char drivername[50];
char *fname = NULL;
char *dname = NULL;
void *edata;
H5E_auto2_t func;
char *x;
hid_t fid = -1;
hid_t fapl = -1;
/* Set up tool name and exit status */
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
/* parse command line options */
parse_command_line(argc, argv);
if(argc <= opt_ind) {
error_msg("missing dataset name\n");
usage(h5tools_getprogname());
leave(EXIT_FAILURE);
}
/* Mostly copied from tools/h5ls coding & modified accordingly */
/*
* [OBJECT] is specified as
* [<filename>/<path_to_dataset>/<dsetname>]
*
* Example: ../dir1/foo/bar/dset
* \_________/\______/
* file obj
*
* The dichotomy is determined by calling H5Fopen() repeatedly until it
* succeeds. The first call uses the entire name and each subsequent call
* chops off the last component. If we reach the beginning of the name
* then there must have been something wrong with the file (perhaps it
* doesn't exist).
*/
if((fname = HDstrdup(argv[opt_ind])) == NULL) {
error_msg("memory allocation failed (file %s:line %d)\n",
__FILE__, __LINE__);
h5tools_setstatus(EXIT_FAILURE);
}
/* Create a copy of file access property list */
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
return -1;
/* Set to use the latest library format */
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
return -1;
do {
while(fname && *fname) {
fid = h5tools_fopen(fname, H5F_ACC_RDONLY|H5F_ACC_SWMR_READ, fapl, NULL, drivername, sizeof drivername);
if(fid >= 0) {
HDfprintf(stdout, "Opened \"%s\" with %s driver.\n", fname, drivername);
break; /*success*/
} /* end if */
/* Shorten the file name; lengthen the object name */
x = dname;
dname = HDstrrchr(fname, '/');
if(x)
*x = '/';
if(!dname)
break;
*dname = '\0';
} /* end while */
/* Try opening the file again if somehow unstable */
} while(g_retry-- > 0 && fid == FAIL);
if(fid < 0) {
error_msg("unable to open file \"%s\"\n", fname);
if(fname) HDfree(fname);
if(fapl >= 0) H5Pclose(fapl);
leave(EXIT_FAILURE);
}
if(!dname) {
error_msg("no dataset specified\n");
h5tools_setstatus(EXIT_FAILURE);
} else {
*dname = '/';
x = dname;
if((dname = HDstrdup(dname)) == NULL) {
error_msg("memory allocation failed (file %s:line %d)\n",
__FILE__, __LINE__);
h5tools_setstatus(EXIT_FAILURE);
} else {
*x = '\0';
/* Validate dataset */
if(check_dataset(fid, dname) < 0)
h5tools_setstatus(EXIT_FAILURE);
/* Validate input "fields" */
else if(g_list_of_fields && *g_list_of_fields)
if(process_cmpd_fields(fid, dname) < 0)
h5tools_setstatus(EXIT_FAILURE);
}
}
/* If everything is fine, start monitoring the datset */
if(h5tools_getstatus() != EXIT_FAILURE)
if(monitor_dataset(fid, dname) < 0)
h5tools_setstatus(EXIT_FAILURE);
/* Free spaces */
if(fname) HDfree(fname);
if(dname) HDfree(dname);
if(g_list_of_fields) HDfree(g_list_of_fields);
if(g_listv) {
H5LD_clean_vector(g_listv);
HDfree(g_listv);
}
if(g_dup_fields) HDfree(g_dup_fields);
/* Close the file access property list */
if(fapl >= 0 && H5Pclose(fapl) < 0) {
error_msg("unable to close file access property list\n");
h5tools_setstatus(EXIT_FAILURE);
}
/* Close the file */
if(H5Fclose(fid) < 0) {
error_msg("unable to close file\n");
h5tools_setstatus(EXIT_FAILURE);
}
H5Eset_auto2(H5E_DEFAULT, func, edata);
/* exit */
leave(h5tools_getstatus());
} /* main() */
/*-------------------------------------------------------------------------
* Function: check_dataset
*
* Purpose: To check whether a dataset can be monitored:
A chunked dataset with unlimited or max. dimension setting
*
* Return: Non-negative on success: dataset can be monitored
* Negative on failure: dataset cannot be monitored
*
* Programmer: Vailin Choi; August 2010
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
check_dataset(hid_t fid, char *dsetname)
{
hid_t did=-1; /* Dataset id */
hid_t dcp=-1; /* Dataset creation property */
hid_t sid=-1; /* Dataset's dataspace id */
int ndims; /* # of dimensions in the dataspace */
unsigned u; /* Local index variable */
hsize_t cur_dims[H5S_MAX_RANK]; /* size of dataspace dimensions */
hsize_t max_dims[H5S_MAX_RANK]; /* maximum size of dataspace dimensions */
hbool_t unlim_max_dims = FALSE; /* whether dataset has unlimited or max. dimension setting */
void *edata;
H5E_auto2_t func;
herr_t ret_value = SUCCEED; /* Return value */
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Open the dataset */
if((did = H5Dopen2(fid, dsetname, H5P_DEFAULT)) < 0) {
error_msg("unable to open dataset \"%s\"\n", dsetname);
ret_value = FAIL;
goto done;
}
/* Get dataset's creation property list */
if((dcp = H5Dget_create_plist(did)) < 0) {
error_msg("unable to get dataset's creation property list\"%s\"\n", dsetname);
ret_value = FAIL;
goto done;
}
/* Query dataset's layout; the layout should be chunked */
if(H5Pget_layout(dcp) != H5D_CHUNKED) {
error_msg("\"%s\" should be a chunked dataset\n", dsetname);
ret_value = FAIL;
goto done;
}
HDmemset(cur_dims, 0, sizeof cur_dims);
HDmemset(max_dims, 0, sizeof max_dims);
/* Get dataset's dataspace */
if((sid = H5Dget_space(did)) < 0) {
error_msg("can't get dataset's dataspace\"%s\"\n", dsetname);
ret_value = FAIL;
goto done;
}
/* Get dimension size of dataset's dataspace */
if((ndims = H5Sget_simple_extent_dims(sid, cur_dims, max_dims)) < 0) {
error_msg("can't get dataspace dimensions for dataset \"%s\"\n", dsetname);
ret_value = FAIL;
goto done;
}
/* Check whether dataset has unlimited dimension or max. dimension setting */
for(u = 0; u < (unsigned)ndims; u++)
if(max_dims[u] == H5S_UNLIMITED || cur_dims[u] != max_dims[u]) {
unlim_max_dims = TRUE;
break;
}
if(!unlim_max_dims) {
error_msg("\"%s\" should have unlimited or max. dimension setting\n", dsetname);
ret_value = FAIL;
}
done:
H5Eset_auto2(H5E_DEFAULT, func, edata);
/* Closing */
H5E_BEGIN_TRY
H5Sclose(sid);
H5Pclose(dcp);
H5Dclose(did);
H5E_END_TRY
return(ret_value);
} /* check_dataset() */
int main(int argc,char *argv[]) {
struct options opts = {
0,
1,
0,
0,
-1,
1,
0,
-1,
1,
NULL,
};
getopts(argc,argv,&opts);
H5Eset_auto2(H5E_DEFAULT,NULL,NULL);
hid_t fid = H5Fopen(opts.filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if(fid < 0) {
fprintf(stderr,"Failed to open %s.\n",opts.filename);
return fid;
}
if(opts.info) {
// count the number of trials in the file
hid_t trial;
int num_trials = 0;
std::stringstream trial_name;
for(;;) {
trial_name.str("");
trial_name << "/Trial" << num_trials+1;
if((trial = H5Gopen(fid,trial_name.str().c_str(),H5P_DEFAULT)) < 0)
break;
else {
print_trial_info(trial,++num_trials);
H5Gclose(trial);
}
}
H5Fclose(fid);
return 0;
}
std::stringstream data_name;
data_name << "/Trial" << opts.trial << "/Synchronous Data/Channel Data";
hid_t table = H5Dopen(fid,data_name.str().c_str(),H5P_DEFAULT);
if(table < 0) {
fprintf(stderr,"Requested trial #%d does not exist.\n",opts.trial);
return table;
}
hsize_t ncols = H5Tget_size(H5Dget_type(table))/sizeof(double);
H5Dclose(table);
table = H5PTopen(fid,data_name.str().c_str());
hsize_t nrows;
H5PTget_num_packets(table,&nrows);
// validate column and row ranges
if(opts.cols_end == -1 || opts.cols_end >= ncols)
opts.cols_end = ncols-1;
if(opts.rows_end == -1 || opts.rows_end >= nrows)
opts.rows_end = nrows-1;
opts.cols_end -= (opts.cols_end-opts.cols_start)%opts.cols_step;
opts.rows_end -= (opts.rows_end-opts.rows_start)%opts.rows_step;
if((opts.cols_start-opts.cols_end)*opts.cols_step > 0)
opts.cols_step *= -1;
if((opts.rows_start-opts.rows_end)*opts.rows_step > 0)
opts.rows_step *= -1;
int row_idx = opts.rows_start;
do {
H5PTset_index(table,row_idx);
double data[ncols];
H5PTget_next(table,1,data);
int col_idx = opts.cols_start;
do {
if(opts.binary) {
write(1,data+col_idx,sizeof(double));
} else {
printf("%e ",data[col_idx]);
}
if(col_idx == opts.cols_end)
break;
col_idx += opts.cols_step;
} while(1);
if(!opts.binary)
printf("\n");
if(row_idx == opts.rows_end)
break;
row_idx += opts.rows_step;
} while(1);
H5PTclose(table);
H5Fclose(fid);
return 0;
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: HDF5 user block jammer
*
* Return: Success: 0
* Failure: 1
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main (int argc, const char *argv[])
{
int ufid = -1;
int h5fid = -1;
int ofid = -1;
void *edata;
H5E_auto2_t func;
hid_t ifile = -1;
hid_t plist = -1;
herr_t status;
htri_t testval;
hsize_t usize;
hsize_t h5fsize;
hsize_t startub;
hsize_t where;
hsize_t newubsize;
off_t fsize;
h5_stat_t sbuf;
h5_stat_t sbuf2;
int res;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
parse_command_line (argc, argv);
if (ub_file == NULL) {
/* no user block */
error_msg("missing arguemnt for -u <user_file>.\n");
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
testval = H5Fis_hdf5 (ub_file);
if (testval > 0) {
error_msg("-u <user_file> cannot be HDF5 file, but it appears to be an HDF5 file.\n");
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
if (input_file == NULL) {
error_msg("missing arguemnt for -i <HDF5 file>.\n");
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
testval = H5Fis_hdf5 (input_file);
if (testval <= 0) {
error_msg("Input HDF5 file \"%s\" is not HDF5 format.\n", input_file);
help_ref_msg(stderr);
leave (EXIT_FAILURE);
}
ifile = H5Fopen (input_file, H5F_ACC_RDONLY, H5P_DEFAULT);
if (ifile < 0) {
error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
leave (EXIT_FAILURE);
}
plist = H5Fget_create_plist (ifile);
if (plist < 0) {
error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
H5Fclose(ifile);
leave (EXIT_FAILURE);
}
status = H5Pget_userblock (plist, &usize);
if (status < 0) {
error_msg("Can't get user block for file \"%s\"\n", input_file);
H5Pclose(plist);
H5Fclose(ifile);
leave (EXIT_FAILURE);
}
H5Pclose(plist);
H5Fclose(ifile);
ufid = HDopen(ub_file, O_RDONLY, 0);
if(ufid < 0) {
error_msg("unable to open user block file \"%s\"\n", ub_file);
leave (EXIT_FAILURE);
}
res = HDfstat(ufid, &sbuf);
if(res < 0) {
error_msg("Can't stat file \"%s\"\n", ub_file);
HDclose (ufid);
leave (EXIT_FAILURE);
}
fsize = (off_t)sbuf.st_size;
h5fid = HDopen(input_file, O_RDONLY, 0);
if(h5fid < 0) {
error_msg("unable to open HDF5 file for read \"%s\"\n", input_file);
HDclose (ufid);
leave (EXIT_FAILURE);
}
res = HDfstat(h5fid, &sbuf2);
if(res < 0) {
error_msg("Can't stat file \"%s\"\n", input_file);
HDclose (h5fid);
HDclose (ufid);
leave (EXIT_FAILURE);
}
h5fsize = (hsize_t)sbuf2.st_size;
if (output_file == NULL) {
ofid = HDopen (input_file, O_WRONLY, 0);
if (ofid < 0) {
error_msg("unable to open output file \"%s\"\n", output_file);
HDclose (h5fid);
HDclose (ufid);
leave (EXIT_FAILURE);
}
}
else {
ofid = HDopen (output_file, O_WRONLY | O_CREAT | O_TRUNC, 0644);
if (ofid < 0) {
error_msg("unable to create output file \"%s\"\n", output_file);
HDclose (h5fid);
HDclose (ufid);
leave (EXIT_FAILURE);
}
}
newubsize = compute_user_block_size ((hsize_t) fsize);
startub = usize;
if (usize > 0) {
if (do_clobber == TRUE) {
/* where is max of the current size or the new UB */
if (usize > newubsize) {
newubsize = usize;
}
startub = 0; /*blast the old */
}
else {
/* add new ub to current ublock, pad to new offset */
newubsize += usize;
newubsize = compute_user_block_size ((hsize_t) newubsize);
}
}
/* copy the HDF5 from starting at usize to starting at newubsize:
* makes room at 'from' for new ub */
/* if no current ub, usize is 0 */
copy_some_to_file (h5fid, ofid, usize, newubsize, (ssize_t) (h5fsize - usize));
/* copy the old ub to the beginning of the new file */
if (!do_clobber) {
where = copy_some_to_file (h5fid, ofid, (hsize_t) 0, (hsize_t) 0, (ssize_t) usize);
}
/* copy the new ub to the end of the ub */
where = copy_some_to_file (ufid, ofid, (hsize_t) 0, startub, (ssize_t) - 1);
/* pad the ub */
where = write_pad (ofid, where);
if(ub_file)
HDfree (ub_file);
if(input_file)
HDfree (input_file);
if(output_file)
HDfree (output_file);
if(ufid >= 0)
HDclose (ufid);
if(h5fid >= 0)
HDclose (h5fid);
if(ofid >= 0)
HDclose (ofid);
return h5tools_getstatus();
}
/*------------------------------------------------------------------------- * Function: main * * Usage: debug FILENAME [OFFSET] * * Return: Success: exit (0) * * Failure: exit (non-zero) * * Programmer: Robb Matzke * [email protected] * Jul 18 1997 * *------------------------------------------------------------------------- */ int main(int argc, char *argv[]) { hid_t fid, fapl, dxpl; H5F_t *f; haddr_t addr = 0, extra = 0, extra2 = 0, extra3 = 0, extra4 = 0; uint8_t sig[H5F_SIGNATURE_LEN]; size_t u; H5E_auto2_t func; void *edata; herr_t status = SUCCEED; if(argc == 1) { HDfprintf(stderr, "Usage: %s filename [signature-addr [extra]]\n", argv[0]); HDexit(1); } /* end if */ /* Initialize the library */ if(H5open() < 0) { HDfprintf(stderr, "cannot initialize the library\n"); HDexit(1); } /* end if */ /* Disable error reporting */ H5Eget_auto2(H5E_DEFAULT, &func, &edata); H5Eset_auto2(H5E_DEFAULT, NULL, NULL); /* * Open the file and get the file descriptor. */ dxpl = H5AC_ind_read_dxpl_id; if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { HDfprintf(stderr, "cannot create file access property list\n"); HDexit(1); } /* end if */ if(HDstrchr(argv[1], '%')) if(H5Pset_fapl_family (fapl, (hsize_t)0, H5P_DEFAULT) < 0) { fprintf(stderr, "cannot set file access property list\n"); HDexit(1); } if((fid = H5Fopen(argv[1], H5F_ACC_RDONLY, fapl)) < 0) { HDfprintf(stderr, "cannot open file\n"); HDexit(1); } /* end if */ if(NULL == (f = (H5F_t *)H5I_object(fid))) { HDfprintf(stderr, "cannot obtain H5F_t pointer\n"); HDexit(2); } /* end if */ /* Ignore metadata tags while using h5debug */ if(H5AC_ignore_tags(f) < 0) { HDfprintf(stderr, "cannot ignore metadata tags\n"); HDexit(1); } /* * Parse command arguments. */ if(argc > 2) addr = (haddr_t)HDstrtoll(argv[2], NULL, 0); if(argc > 3) extra = (haddr_t)HDstrtoll(argv[3], NULL, 0); if(argc > 4) extra2 = (haddr_t)HDstrtoll(argv[4], NULL, 0); if(argc > 5) extra3 = (haddr_t)HDstrtoll(argv[5], NULL, 0); if(argc > 6) extra4 = (haddr_t)HDstrtoll(argv[6], NULL, 0); /* * Read the signature at the specified file position. */ HDfprintf(stdout, "Reading signature at address %a (rel)\n", addr); if(H5F_block_read(f, H5FD_MEM_SUPER, addr, sizeof(sig), dxpl, sig) < 0) { HDfprintf(stderr, "cannot read signature\n"); HDexit(3); } if(!HDmemcmp(sig, H5F_SIGNATURE, (size_t)H5F_SIGNATURE_LEN)) { /* * Debug the file's super block. */ status = H5F_debug(f, stdout, 0, VCOL); } else if(!HDmemcmp(sig, H5HL_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a local heap. */ status = H5HL_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL); } else if(!HDmemcmp (sig, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a global heap collection. */ status = H5HG_debug (f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL); } else if(!HDmemcmp(sig, H5G_NODE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a symbol table node. */ /* Check for extra parameters */ if(extra == 0) { HDfprintf(stderr, "\nWarning: Providing the group's local heap address will give more information\n"); HDfprintf(stderr, "Symbol table node usage:\n"); HDfprintf(stderr, "\th5debug <filename> <Symbol table node address> <address of local heap>\n\n"); } /* end if */ status = H5G_node_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra); } else if(!HDmemcmp(sig, H5B_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a B-tree. B-trees are debugged through the B-tree * subclass. The subclass identifier is the byte immediately * after the B-tree signature. */ H5B_subid_t subtype = (H5B_subid_t)sig[H5_SIZEOF_MAGIC]; unsigned ndims; uint32_t dim[H5O_LAYOUT_NDIMS]; switch(subtype) { case H5B_SNODE_ID: /* Check for extra parameters */ if(extra == 0) { HDfprintf(stderr, "\nWarning: Providing the group's local heap address will give more information\n"); HDfprintf(stderr, "B-tree symbol table node usage:\n"); HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <address of local heap>\n\n"); HDexit(4); } /* end if */ status = H5G_node_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra); break; case H5B_CHUNK_ID: /* Check for extra parameters */ if(extra == 0) { HDfprintf(stderr, "ERROR: Need number of dimensions of chunk in order to dump chunk B-tree node\n"); HDfprintf(stderr, "B-tree chunked storage node usage:\n"); HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n"); HDexit(4); } /* end if */ /* Build array of chunk dimensions */ ndims = (unsigned)extra; dim[0] = (uint32_t)extra2; if(ndims > 1) dim[1] = (uint32_t)extra3; if(ndims > 2) dim[2] = (uint32_t)extra4; /* Check for dimension error */ if(ndims > 3) { HDfprintf(stderr, "ERROR: Only 3 dimensions support currently (fix h5debug)\n"); HDfprintf(stderr, "B-tree chunked storage node usage:\n"); HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n"); HDexit(4); } /* end for */ for(u = 0; u < ndims; u++) if(0 == dim[u]) { HDfprintf(stderr, "ERROR: Chunk dimensions should be >0\n"); HDfprintf(stderr, "B-tree chunked storage node usage:\n"); HDfprintf(stderr, "\th5debug <filename> <B-tree node address> <# of dimensions> <slowest chunk dim>...<fastest chunk dim>\n"); HDexit(4); } /* end if */ /* Set the last dimension (the element size) to zero */ dim[ndims] = 0; status = H5D_btree_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, ndims, dim); break; case H5B_NUM_BTREE_ID: default: HDfprintf(stderr, "Unknown v1 B-tree subtype %u\n", (unsigned)(subtype)); HDexit(4); } } else if(!HDmemcmp(sig, H5B2_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a v2 B-tree header. */ const H5B2_class_t *cls = get_H5B2_class(sig); HDassert(cls); if((cls == H5D_BT2 || cls == H5D_BT2_FILT) && extra == 0) { HDfprintf(stderr, "ERROR: Need v2 B-tree header address and object header address containing the layout message in order to dump header\n"); HDfprintf(stderr, "v2 B-tree hdr usage:\n"); HDfprintf(stderr, "\th5debug <filename> <v2 B-tree header address> <object header address>\n"); HDexit(4); } /* end if */ status = H5B2__hdr_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, (haddr_t)extra); } else if(!HDmemcmp(sig, H5B2_INT_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a v2 B-tree internal node. */ const H5B2_class_t *cls = get_H5B2_class(sig); HDassert(cls); /* Check for enough valid parameters */ if((cls == H5D_BT2 || cls == H5D_BT2_FILT) && (extra == 0 || extra2 == 0 || extra3 == 0 || extra4 == 0)) { fprintf(stderr, "ERROR: Need v2 B-tree header address, the node's number of records, depth, and object header address containing the layout message in order to dump internal node\n"); fprintf(stderr, "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n"); fprintf(stderr, "v2 B-tree internal node usage:\n"); fprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> <number of records> <depth> <object header address>\n"); HDexit(4); } else if(extra == 0 || extra2 == 0 || extra3 == 0) { HDfprintf(stderr, "ERROR: Need v2 B-tree header address and the node's number of records and depth in order to dump internal node\n"); HDfprintf(stderr, "NOTE: Leaf nodes are depth 0, the internal nodes above them are depth 1, etc.\n"); HDfprintf(stderr, "v2 B-tree internal node usage:\n"); HDfprintf(stderr, "\th5debug <filename> <internal node address> <v2 B-tree header address> <number of records> <depth>\n"); HDexit(4); } /* end if */ status = H5B2__int_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (unsigned)extra3, (haddr_t)extra4); } else if(!HDmemcmp(sig, H5B2_LEAF_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a v2 B-tree leaf node. */ const H5B2_class_t *cls = get_H5B2_class(sig); HDassert(cls); /* Check for enough valid parameters */ if((cls == H5D_BT2 || cls == H5D_BT2_FILT) && (extra == 0 || extra2 == 0 || extra3 == 0 )) { fprintf(stderr, "ERROR: Need v2 B-tree header address, number of records, and object header address containing the layout message in order to dump leaf node\n"); fprintf(stderr, "v2 B-tree leaf node usage:\n"); fprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records> <object header address>\n"); HDexit(4); } else if(extra == 0 || extra2 == 0) { HDfprintf(stderr, "ERROR: Need v2 B-tree header address and number of records in order to dump leaf node\n"); HDfprintf(stderr, "v2 B-tree leaf node usage:\n"); HDfprintf(stderr, "\th5debug <filename> <leaf node address> <v2 B-tree header address> <number of records>\n"); HDexit(4); } /* end if */ status = H5B2__leaf_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, (haddr_t)extra3); } else if(!HDmemcmp(sig, H5HF_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a fractal heap header. */ status = H5HF_hdr_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL); } else if(!HDmemcmp(sig, H5HF_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a fractal heap direct block. */ /* Check for enough valid parameters */ if(extra == 0 || extra2 == 0) { HDfprintf(stderr, "ERROR: Need fractal heap header address and size of direct block in order to dump direct block\n"); HDfprintf(stderr, "Fractal heap direct block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <direct block address> <heap header address> <size of direct block>\n"); HDexit(4); } /* end if */ status = H5HF_dblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra, (size_t)extra2); } else if(!HDmemcmp(sig, H5HF_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a fractal heap indirect block. */ /* Check for enough valid parameters */ if(extra == 0 || extra2 == 0) { HDfprintf(stderr, "ERROR: Need fractal heap header address and number of rows in order to dump indirect block\n"); HDfprintf(stderr, "Fractal heap indirect block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <indirect block address> <heap header address> <number of rows>\n"); HDexit(4); } /* end if */ status = H5HF_iblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra, (unsigned)extra2); } else if(!HDmemcmp(sig, H5FS_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a free space header. */ status = H5FS_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL); } else if(!HDmemcmp(sig, H5FS_SINFO_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug free space serialized sections. */ /* Check for enough valid parameters */ if(extra == 0 || extra2 == 0) { HDfprintf(stderr, "ERROR: Need free space header address and client address in order to dump serialized sections\n"); HDfprintf(stderr, "Free space serialized sections usage:\n"); HDfprintf(stderr, "\th5debug <filename> <serialized sections address> <free space header address> <client address>\n"); HDexit(4); } /* end if */ status = H5FS_sects_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, extra, extra2); } else if(!HDmemcmp(sig, H5SM_TABLE_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug shared message master table. */ status = H5SM_table_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, (unsigned) UFAIL, (unsigned) UFAIL); } else if(!HDmemcmp(sig, H5SM_LIST_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug shared message list index. */ /* Check for enough valid parameters */ if(extra == 0) { HDfprintf(stderr, "ERROR: Need shared message header address in order to shared message list\n"); HDfprintf(stderr, "Shared message list usage:\n"); HDfprintf(stderr, "\th5debug <filename> <shared message list address> <shared message header address>\n"); HDexit(4); } /* end if */ status = H5SM_list_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, (haddr_t)extra); } else if(!HDmemcmp(sig, H5EA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug an extensible aray header. */ const H5EA_class_t *cls = get_H5EA_class(sig); HDassert(cls); /* Check for enough valid parameters */ if(extra == 0) { HDfprintf(stderr, "ERROR: Need object header address containing the layout message in order to dump header\n"); HDfprintf(stderr, "Extensible array header block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <Extensible Array header address> <object header address>\n"); HDexit(4); } /* end if */ status = H5EA__hdr_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra); } else if(!HDmemcmp(sig, H5EA_IBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug an extensible aray index block. */ const H5EA_class_t *cls = get_H5EA_class(sig); HDassert(cls); /* Check for enough valid parameters */ if(extra == 0 || extra2 == 0) { HDfprintf(stderr, "ERROR: Need extensible array header address and object header address containing the layout message in order to dump index block\n"); HDfprintf(stderr, "Extensible array index block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <index block address> <array header address> <object header address\n"); HDexit(4); } /* end if */ status = H5EA__iblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, extra2); } else if(!HDmemcmp(sig, H5EA_SBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug an extensible aray super block. */ const H5EA_class_t *cls = get_H5EA_class(sig); HDassert(cls); /* Check for enough valid parameters */ if(extra == 0 || extra2 == 0 || extra3 == 0) { HDfprintf(stderr, "ERROR: Need extensible array header address, super block index and object header address containing the layout message in order to dump super block\n"); HDfprintf(stderr, "Extensible array super block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <super block address> <array header address> <super block index> <object header address>\n"); HDexit(4); } /* end if */ status = H5EA__sblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, (unsigned)extra2, extra3); } else if(!HDmemcmp(sig, H5EA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug an extensible aray data block. */ const H5EA_class_t *cls = get_H5EA_class(sig); HDassert(cls); /* Check for enough valid parameters */ if(extra == 0 || extra2 == 0 || extra3 == 0) { HDfprintf(stderr, "ERROR: Need extensible array header address, # of elements in data block and object header address containing the layout message in order to dump data block\n"); HDfprintf(stderr, "Extensible array data block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <data block address> <array header address> <# of elements in data block> <object header address\n"); HDexit(4); } /* end if */ status = H5EA__dblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, (size_t)extra2, extra3); } else if(!HDmemcmp(sig, H5FA_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a fixed array header. */ const H5FA_class_t *cls = get_H5FA_class(sig); HDassert(cls); /* Check for enough valid parameters */ if(extra == 0) { HDfprintf(stderr, "ERROR: Need object header address containing the layout message in order to dump header\n"); HDfprintf(stderr, "Fixed array header block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <Fixed Array header address> <object header address>\n"); HDexit(4); } /* end if */ status = H5FA__hdr_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra); } else if(!HDmemcmp(sig, H5FA_DBLOCK_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug a fixed array data block. */ const H5FA_class_t *cls = get_H5FA_class(sig); HDassert(cls); /* Check for enough valid parameters */ if(extra == 0 || extra2 == 0) { HDfprintf(stderr, "ERROR: Need fixed array header address and object header address containing the layout message in order to dump data block\n"); HDfprintf(stderr, "fixed array data block usage:\n"); HDfprintf(stderr, "\th5debug <filename> <data block address> <array header address> <object header address>\n"); HDexit(4); } /* end if */ status = H5FA__dblock_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL, cls, extra, extra2); } else if(!HDmemcmp(sig, H5O_HDR_MAGIC, (size_t)H5_SIZEOF_MAGIC)) { /* * Debug v2 object header (which have signatures). */ status = H5O_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL); } else if(sig[0] == H5O_VERSION_1) { /* * This could be a v1 object header. Since they don't have a signature * it's a somewhat "ify" detection. */ status = H5O_debug(f, H5AC_ind_read_dxpl_id, addr, stdout, 0, VCOL); } else { /* * Got some other unrecognized signature. */ printf("%-*s ", VCOL, "Signature:"); for (u = 0; u < sizeof(sig); u++) { if (sig[u] > ' ' && sig[u] <= '~' && '\\' != sig[u]) HDputchar(sig[u]); else if ('\\' == sig[u]) { HDputchar('\\'); HDputchar('\\'); } else printf("\\%03o", sig[u]); } HDputchar('\n'); HDfprintf(stderr, "unknown signature\n"); HDexit(4); } /* end else */ /* Check for an error when dumping information */ if(status < 0) { HDfprintf(stderr, "An error occurred!\n"); H5Eprint2(H5E_DEFAULT, stderr); HDexit(5); } /* end if */ H5Pclose(fapl); H5Fclose(fid); H5Eset_auto2(H5E_DEFAULT, func, edata); return 0; } /* main() */
int
main(int argc, const char *argv[])
{
iter_t iter;
const char *fname = NULL;
hid_t fid;
struct handler_t *hand;
H5F_info_t finfo;
/* Disable error reporting */
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
hand = parse_command_line (argc, argv);
if(!hand) {
error_msg(progname, "unable to parse command line arguments \n");
leave(EXIT_FAILURE);
} /* end if */
fname = argv[opt_ind];
printf("Filename: %s\n", fname);
fid = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
if(fid < 0) {
error_msg(progname, "unable to open file \"%s\"\n", fname);
leave(EXIT_FAILURE);
} /* end if */
/* Initialize iter structure */
iter_init(&iter, fid);
/* Get storge info for SOHM's btree/list/heap and superblock extension */
if(H5Fget_info(fid, &finfo) < 0)
warn_msg(progname, "Unable to retrieve SOHM info\n");
else {
iter.super_ext_size = finfo.super_ext_size;
iter.SM_hdr_storage_size = finfo.sohm.hdr_size;
iter.SM_index_storage_size = finfo.sohm.msgs_info.index_size;
iter.SM_heap_storage_size = finfo.sohm.msgs_info.heap_size;
} /* end else */
/* Walk the objects or all file */
if(display_object) {
unsigned u;
u = 0;
while(hand[u].obj) {
if (h5trav_visit(fid, hand[u].obj, TRUE, TRUE, obj_stats, lnk_stats, &iter) < 0)
warn_msg(progname, "Unable to traverse object \"%s\"\n", hand[u].obj);
else
print_statistics(hand[u].obj, &iter);
u++;
} /* end while */
} /* end if */
else {
if (h5trav_visit(fid, "/", TRUE, TRUE, obj_stats, lnk_stats, &iter) < 0)
warn_msg(progname, "Unable to traverse objects/links in file \"%s\"\n", fname);
else
print_statistics("/", &iter);
} /* end else */
if (hand) free(hand);
if(H5Fclose(fid) < 0) {
error_msg(progname, "unable to close file \"%s\"\n", fname);
leave(EXIT_FAILURE);
}
leave(EXIT_SUCCESS);
}
/*-------------------------------------------------------------------------
* Function: main
*
* Modifications:
* 2/2010; Vailin Choi
* Get the size of user block
*
*-------------------------------------------------------------------------
*/
int
main(int argc, const char *argv[])
{
iter_t iter;
const char *fname = NULL;
hid_t fid = -1;
hid_t fcpl;
struct handler_t *hand = NULL;
H5F_info_t finfo;
int i;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable error reporting */
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
if((hand = parse_command_line(argc, argv))==NULL) {
goto done;
}
fname = argv[opt_ind];
printf("Filename: %s\n", fname);
HDmemset(&iter, 0, sizeof(iter));
fid = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
if(fid < 0) {
error_msg("unable to open file \"%s\"\n", fname);
h5tools_setstatus(EXIT_FAILURE);
goto done;
} /* end if */
/* Initialize iter structure */
iter.fid = fid;
if(H5Fget_filesize(fid, &iter.filesize) < 0)
warn_msg("Unable to retrieve file size\n");
HDassert(iter.filesize != 0);
/* Get storge info for file-level structures */
if(H5Fget_info(fid, &finfo) < 0)
warn_msg("Unable to retrieve file info\n");
else {
iter.super_ext_size = finfo.super_ext_size;
iter.SM_hdr_storage_size = finfo.sohm.hdr_size;
iter.SM_index_storage_size = finfo.sohm.msgs_info.index_size;
iter.SM_heap_storage_size = finfo.sohm.msgs_info.heap_size;
} /* end else */
if((fcpl = H5Fget_create_plist(fid)) < 0)
warn_msg("Unable to retrieve file creation property\n");
if(H5Pget_userblock(fcpl, &iter.ublk_size) < 0)
warn_msg("Unable to retrieve userblock size\n");
/* Walk the objects or all file */
if(display_object) {
unsigned u;
u = 0;
while(hand[u].obj) {
if (h5trav_visit(fid, hand[u].obj, TRUE, TRUE, obj_stats, lnk_stats, &iter) < 0)
warn_msg("Unable to traverse object \"%s\"\n", hand[u].obj);
else
print_statistics(hand[u].obj, &iter);
u++;
} /* end while */
} /* end if */
else {
if (h5trav_visit(fid, "/", TRUE, TRUE, obj_stats, lnk_stats, &iter) < 0)
warn_msg("Unable to traverse objects/links in file \"%s\"\n", fname);
else
print_statistics("/", &iter);
} /* end else */
done:
if(hand) {
for (i = 0; i < argc; i++)
if(hand[i].obj) {
free(hand[i].obj);
hand[i].obj=NULL;
}
free(hand);
hand = NULL;
/* Free iter structure */
iter_free(&iter);
if(fid >= 0 && H5Fclose(fid) < 0) {
error_msg("unable to close file \"%s\"\n", fname);
h5tools_setstatus(EXIT_FAILURE);
}
}
leave(h5tools_getstatus());
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: Create group(s) in an HDF5 file
*
* Programmer: Quincey Koziol, 2/13/2007
*
*-------------------------------------------------------------------------
*/
int
main(int argc, const char *argv[])
{
hid_t fid; /* HDF5 file ID */
hid_t fapl_id; /* File access property list ID */
hid_t lcpl_id; /* Link creation property list ID */
size_t curr_group; /* Current group to create */
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable the HDF5 library's error reporting */
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
/* Parse command line */
HDmemset(¶ms, 0, sizeof(params));
if(parse_command_line(argc, argv, ¶ms) < 0) {
error_msg("unable to parse command line arguments\n");
leave(EXIT_FAILURE);
} /* end if */
/* Create file access property list */
if((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
error_msg("Could not create file access property list\n");
leave(EXIT_FAILURE);
} /* end if */
/* Check for creating groups with new format version */
if(params.latest) {
/* Set the "use the latest version of the format" bounds */
if(H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
error_msg("Could not set property for using latest version of the format\n");
leave(EXIT_FAILURE);
} /* end if */
/* Display some output if requested */
if(params.verbose)
printf("%s: Creating groups with latest version of the format\n", h5tools_getprogname());
} /* end if */
/* Attempt to open an existing HDF5 file first */
fid = h5tools_fopen(params.fname, H5F_ACC_RDWR, fapl_id, NULL, NULL, 0);
/* 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 < 0)
fid = H5Fcreate(params.fname, H5F_ACC_EXCL, H5P_DEFAULT, fapl_id);
/* Test for error in opening file */
if(fid < 0) {
error_msg("Could not open output file '%s'\n", params.fname);
leave(EXIT_FAILURE);
} /* end if */
/* Create link creation property list */
if((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) {
error_msg("Could not create link creation property list\n");
leave(EXIT_FAILURE);
} /* end if */
/* Check for creating intermediate groups */
if(params.parents) {
/* Set the intermediate group creation property */
if(H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) {
error_msg("Could not set property for creating parent groups\n");
leave(EXIT_FAILURE);
} /* end if */
/* Display some output if requested */
if(params.verbose)
printf("%s: Creating parent groups\n", h5tools_getprogname());
} /* end if */
/* Loop over creating requested groups */
for(curr_group = 0; curr_group < params.ngroups; curr_group++) {
hid_t gid; /* Group ID */
/* Attempt to create a group */
if((gid = H5Gcreate2(fid, params.groups[curr_group], lcpl_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
error_msg("Could not create group '%s'\n", params.groups[curr_group]);
leave(EXIT_FAILURE);
} /* end if */
/* Close the group */
if(H5Gclose(gid) < 0) {
error_msg("Could not close group '%s'??\n", params.groups[curr_group]);
leave(EXIT_FAILURE);
} /* end if */
/* Display some output if requested */
if(params.verbose)
printf("%s: created group '%s'\n", h5tools_getprogname(), params.groups[curr_group]);
} /* end for */
/* Close link creation property list */
if(H5Pclose(lcpl_id) < 0) {
error_msg("Could not close link creation property list\n");
leave(EXIT_FAILURE);
} /* end if */
/* Close file */
if(H5Fclose(fid) < 0) {
error_msg("Could not close output file '%s'??\n", params.fname);
leave(EXIT_FAILURE);
} /* end if */
/* Close file access property list */
if(H5Pclose(fapl_id) < 0) {
error_msg("Could not close file access property list\n");
leave(EXIT_FAILURE);
} /* end if */
/* Shut down h5tools lib */
h5tools_close();
leave(EXIT_SUCCESS);
} /* end main() */
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: HDF5 user block unjammer
*
* Return: Success: 0
* Failure: 1
*
* Programmer:
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
main(int argc, const char *argv[])
{
void *edata;
H5E_auto2_t func;
hid_t ifile = -1;
hid_t plist = -1;
off_t fsize;
hsize_t usize;
htri_t testval;
herr_t status;
int res;
h5_stat_t sbuf;
h5tools_setprogname(PROGRAMNAME);
h5tools_setstatus(EXIT_SUCCESS);
/* Disable error reporting */
H5Eget_auto2(H5E_DEFAULT, &func, &edata);
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
/* Initialize h5tools lib */
h5tools_init();
if(EXIT_FAILURE == parse_command_line(argc, argv))
goto done;
if (input_file == NULL) {
/* no user block */
error_msg("missing arguemnt for HDF5 file input.\n");
help_ref_msg(stderr);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
testval = H5Fis_hdf5(input_file);
if (testval <= 0) {
error_msg("Input HDF5 file \"%s\" is not HDF\n", input_file);
help_ref_msg (stderr);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
ifile = H5Fopen(input_file, H5F_ACC_RDONLY , H5P_DEFAULT);
if (ifile < 0) {
error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
plist = H5Fget_create_plist(ifile);
if (plist < 0) {
error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
status = H5Pget_userblock(plist, & usize);
if (status < 0) {
error_msg("Can't get user block for file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
status = H5Pclose(plist);
HDassert(status >= 0);
status = H5Fclose(ifile);
HDassert(status >= 0);
if (usize == 0) {
/* no user block to remove: message? */
error_msg("\"%s\" has no user block: no change to file\n", input_file);
h5tools_setstatus(EXIT_SUCCESS);
goto done;
}
res = HDfstat(HDfileno(rawinstream), &sbuf);
if(res < 0) {
error_msg("Can't stat file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
fsize = sbuf.st_size;
if (do_delete && (ub_file != NULL)) {
error_msg("??\"%s\"\n", ub_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
if (output_file == NULL) {
error_msg("unable to open output HDF5 file \"%s\"\n", input_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
/* copy from 0 to 'usize - 1' into ufid */
if (!do_delete) {
if(copy_to_file(rawinstream, rawoutstream, 0, (ssize_t) usize) < 0) {
error_msg("unable to copy user block to output file \"%s\"\n", ub_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
}
/* copy from usize to end of file into h5fid,
* starting at end of user block if present */
if(copy_to_file(rawinstream, rawdatastream, (ssize_t) usize, (ssize_t)(fsize - (ssize_t)usize)) < 0) {
error_msg("unable to copy hdf5 data to output file \"%s\"\n", output_file);
h5tools_setstatus(EXIT_FAILURE);
goto done;
}
done:
if(input_file)
HDfree(input_file);
if(output_file)
HDfree(output_file);
if(ub_file) {
HDfree(ub_file);
}
h5tools_close();
return h5tools_getstatus();
}
void pyne::Material::write_hdf5(std::string filename, std::string datapath,
std::string nucpath, float row, int chunksize) {
int row_num = (int) row;
// Turn off annoying HDF5 errors
H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
//Set file access properties so it closes cleanly
hid_t fapl;
fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(fapl,H5F_CLOSE_STRONG);
// Create new/open datafile.
hid_t db;
if (pyne::file_exists(filename)) {
bool ish5 = H5Fis_hdf5(filename.c_str());
if (!ish5)
throw h5wrap::FileNotHDF5(filename);
db = H5Fopen(filename.c_str(), H5F_ACC_RDWR, fapl);
}
else
db = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
//
// Read in nuclist if available, write it out if not
//
bool nucpath_exists = h5wrap::path_exists(db, nucpath);
std::vector<int> nuclides;
int nuc_size;
hsize_t nuc_dims[1];
if (nucpath_exists) {
nuclides = h5wrap::h5_array_to_cpp_vector_1d<int>(db, nucpath, H5T_NATIVE_INT);
nuc_size = nuclides.size();
nuc_dims[0] = nuc_size;
} else {
nuclides = std::vector<int>();
for (pyne::comp_iter i = comp.begin(); i != comp.end(); i++)
nuclides.push_back(i->first);
nuc_size = nuclides.size();
// Create the data if it doesn't exist
int nuc_data [nuc_size];
for (int n = 0; n != nuc_size; n++)
nuc_data[n] = nuclides[n];
nuc_dims[0] = nuc_size;
hid_t nuc_space = H5Screate_simple(1, nuc_dims, NULL);
hid_t nuc_set = H5Dcreate2(db, nucpath.c_str(), H5T_NATIVE_INT, nuc_space,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(nuc_set, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, nuc_data);
H5Fflush(db, H5F_SCOPE_GLOBAL);
};
//
// Write out the data itself to the file
//
hid_t data_set, data_space, data_hyperslab;
int data_rank = 1;
hsize_t data_dims[1] = {1};
hsize_t data_max_dims[1] = {H5S_UNLIMITED};
hsize_t data_offset[1] = {0};
size_t material_struct_size = sizeof(pyne::material_struct) + sizeof(double)*nuc_size;
hid_t desc = H5Tcreate(H5T_COMPOUND, material_struct_size);
hid_t comp_values_array_type = H5Tarray_create2(H5T_NATIVE_DOUBLE, 1, nuc_dims);
// make the data table type
H5Tinsert(desc, "mass", HOFFSET(pyne::material_struct, mass), H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "density", HOFFSET(pyne::material_struct, density),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "atoms_per_molecule", HOFFSET(pyne::material_struct, atoms_per_mol),
H5T_NATIVE_DOUBLE);
H5Tinsert(desc, "comp", HOFFSET(pyne::material_struct, comp),
comp_values_array_type);
material_struct * mat_data = new material_struct[material_struct_size];
(*mat_data).mass = mass;
(*mat_data).density = density;
(*mat_data).atoms_per_mol = atoms_per_molecule;
for (int n = 0; n != nuc_size; n++) {
if (0 < comp.count(nuclides[n]))
(*mat_data).comp[n] = comp[nuclides[n]];
else
(*mat_data).comp[n] = 0.0;
};
// get / make the data set
bool datapath_exists = h5wrap::path_exists(db, datapath);
if (datapath_exists) {
data_set = H5Dopen2(db, datapath.c_str(), H5P_DEFAULT);
data_space = H5Dget_space(data_set);
data_rank = H5Sget_simple_extent_dims(data_space, data_dims, data_max_dims);
// Determine the row size.
if (std::signbit(row))
row_num = data_dims[0] + row; // careful, row is negative
if (data_dims[0] <= row_num) {
// row == -0, extend to data set so that we can append, or
// row_num is larger than current dimension, resize to accomodate.
data_dims[0] = row_num + 1;
H5Dset_extent(data_set, data_dims);
}
data_offset[0] = row_num;
} else {
// Get full space
data_space = H5Screate_simple(1, data_dims, data_max_dims);
// Make data set properties to enable chunking
hid_t data_set_params = H5Pcreate(H5P_DATASET_CREATE);
hsize_t chunk_dims[1] ={chunksize};
H5Pset_chunk(data_set_params, 1, chunk_dims);
H5Pset_deflate(data_set_params, 1);
material_struct * data_fill_value = new material_struct[material_struct_size];
(*data_fill_value).mass = -1.0;
(*data_fill_value).density= -1.0;
(*data_fill_value).atoms_per_mol = -1.0;
for (int n = 0; n != nuc_size; n++)
(*data_fill_value).comp[n] = 0.0;
H5Pset_fill_value(data_set_params, desc, &data_fill_value);
// Create the data set
data_set = H5Dcreate2(db, datapath.c_str(), desc, data_space, H5P_DEFAULT,
data_set_params, H5P_DEFAULT);
H5Dset_extent(data_set, data_dims);
// Add attribute pointing to nuc path
hid_t nuc_attr_type = H5Tcopy(H5T_C_S1);
H5Tset_size(nuc_attr_type, nucpath.length());
hid_t nuc_attr_space = H5Screate(H5S_SCALAR);
hid_t nuc_attr = H5Acreate2(data_set, "nucpath", nuc_attr_type, nuc_attr_space,
H5P_DEFAULT, H5P_DEFAULT);
H5Awrite(nuc_attr, nuc_attr_type, nucpath.c_str());
H5Fflush(db, H5F_SCOPE_GLOBAL);
// Remember to de-allocate
delete[] data_fill_value;
};
// Get the data hyperslab
data_hyperslab = H5Dget_space(data_set);
hsize_t data_count[1] = {1};
H5Sselect_hyperslab(data_hyperslab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
// Get a memory space for writing
hid_t mem_space = H5Screate_simple(1, data_count, data_max_dims);
// Write the row...
H5Dwrite(data_set, desc, mem_space, data_hyperslab, H5P_DEFAULT, mat_data);
// Close out the Dataset
H5Fflush(db, H5F_SCOPE_GLOBAL);
H5Dclose(data_set);
H5Sclose(data_space);
H5Tclose(desc);
//
// Write out the metadata to the file
//
std::string attrpath = datapath + "_metadata";
hid_t metadatapace, attrtype, metadataet, metadatalab, attrmemspace;
int attrrank;
attrtype = H5Tvlen_create(H5T_NATIVE_CHAR);
// get / make the data set
bool attrpath_exists = h5wrap::path_exists(db, attrpath);
if (attrpath_exists) {
metadataet = H5Dopen2(db, attrpath.c_str(), H5P_DEFAULT);
metadatapace = H5Dget_space(metadataet);
attrrank = H5Sget_simple_extent_dims(metadatapace, data_dims, data_max_dims);
if (data_dims[0] <= row_num) {
// row == -0, extend to data set so that we can append, or
// row_num is larger than current dimension, resize to accomodate.
data_dims[0] = row_num + 1;
H5Dset_extent(metadataet, data_dims);
}
data_offset[0] = row_num;
} else {
hid_t metadataetparams;
hsize_t attrchunkdims [1];
// Make data set properties to enable chunking
metadataetparams = H5Pcreate(H5P_DATASET_CREATE);
attrchunkdims[0] = chunksize;
H5Pset_chunk(metadataetparams, 1, attrchunkdims);
H5Pset_deflate(metadataetparams, 1);
hvl_t attrfillvalue [1];
attrfillvalue[0].len = 3;
attrfillvalue[0].p = (char *) "{}\n";
H5Pset_fill_value(metadataetparams, attrtype, &attrfillvalue);
// make dataset
metadatapace = H5Screate_simple(1, data_dims, data_max_dims);
metadataet = H5Dcreate2(db, attrpath.c_str(), attrtype, metadatapace,
H5P_DEFAULT, metadataetparams, H5P_DEFAULT);
H5Dset_extent(metadataet, data_dims);
};
// set the attr string
hvl_t attrdata [1];
Json::FastWriter writer;
std::string metadatatr = writer.write(metadata);
attrdata[0].p = (char *) metadatatr.c_str();
attrdata[0].len = metadatatr.length();
// write the attr
metadatalab = H5Dget_space(metadataet);
H5Sselect_hyperslab(metadatalab, H5S_SELECT_SET, data_offset, NULL, data_count, NULL);
attrmemspace = H5Screate_simple(1, data_count, data_max_dims);
H5Dwrite(metadataet, attrtype, attrmemspace, metadatalab, H5P_DEFAULT, attrdata);
// close attr data objects
H5Fflush(db, H5F_SCOPE_GLOBAL);
H5Dclose(metadataet);
H5Sclose(metadatapace);
H5Tclose(attrtype);
// Close out the HDF5 file
H5Fclose(db);
// Remember the milk!
// ...by which I mean to deallocate
delete[] mat_data;
};