// Read string attribute <attr_name> given by address <path>
char AH5_read_str_attr(hid_t loc_id, const char *path, char *attr_name, char **rdata)
{
hid_t attr_id, filetype, memtype;
size_t sdim;
char success = AH5_FALSE;
if (AH5_path_valid(loc_id, path) || strcmp(path, ".") == 0)
if (H5Aexists_by_name(loc_id, path, attr_name, H5P_DEFAULT) > 0)
{
attr_id = H5Aopen_by_name(loc_id, path, attr_name, H5P_DEFAULT, H5P_DEFAULT);
filetype = H5Aget_type(attr_id);
sdim = H5Tget_size(filetype);
sdim++; // make a space for null terminator
*rdata = (char *) malloc(sdim * sizeof(char));
memtype = H5Tcopy(H5T_C_S1);
H5Tset_size(memtype, sdim);
if (H5Aread(attr_id, memtype, *rdata) >= 0)
success = AH5_TRUE;
else
free(*rdata);
H5Tclose(memtype);
H5Tclose(filetype);
H5Aclose(attr_id);
}
if (!success)
*rdata = NULL;
return success;
}
// read a complex float attribute
float_complex read_complex_attribute(hid_t loc_id, const char* path,
const char* name)
{
float_complex value;
float *buf;
hid_t attr_id, real_type_id;
;
hsize_t *dims;
herr_t status;
status = H5Aexists_by_name(loc_id, path, name, H5P_DEFAULT);
if (status < 0)
{
printf("attribut %s does not exist \n", name);
}
real_type_id = create_real_type_id();
attr_id = H5Aopen_by_name(loc_id, path, name, H5P_DEFAULT, H5P_DEFAULT);
status = H5Aread(attr_id, real_type_id, buf);
if (status < 0)
{
printf("Can't read attribute : %s\n", name);
}
value.re = buf[0]; value.im=buf[1];
return value;
}
// Read integer attribute <attr_name> given by address <path>
char AH5_read_int_attr(hid_t loc_id, const char *path, char *attr, int *rdata)
{
char success = AH5_FALSE;
if (AH5_path_valid(loc_id, path))
if (H5Aexists_by_name(loc_id, path, attr, H5P_DEFAULT) > 0)
if (H5LTget_attribute_int(loc_id, path, attr, rdata) >= 0)
success = AH5_TRUE;
if(!success)
*rdata = 0;
return success;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aexists_by_name
* Signature: (JLjava/lang/String;Ljava/lang/String;J)Z
*/
JNIEXPORT jboolean JNICALL
Java_hdf_hdf5lib_H5_H5Aexists_1by_1name
(JNIEnv *env, jclass clss, jlong loc_id, jstring obj_name, jstring attr_name, jlong lapl_id)
{
htri_t bval = JNI_FALSE;
const char *aName;
const char *attrName;
PIN_JAVA_STRING_TWO(obj_name, aName, attr_name, attrName);
if (aName != NULL && attrName != NULL) {
bval = H5Aexists_by_name((hid_t)loc_id, aName, attrName, (hid_t)lapl_id);
UNPIN_JAVA_STRING_TWO(obj_name, aName, attr_name, attrName);
if (bval > 0)
bval = JNI_TRUE;
else if (bval < 0)
h5libraryError(env);
}
return (jboolean)bval;
} /* end Java_hdf_hdf5lib_H5_H5Aexists_1by_1name */
// Read complex attribute <attr_name> given by address <path>
char AH5_read_cpx_attr(hid_t loc_id, const char* path, char* attr_name, AH5_complex_t *rdata)
{
hid_t attr_id, type_id;
float buf[2];
char success = AH5_FALSE;
if (AH5_path_valid(loc_id, path))
if (H5Aexists_by_name(loc_id, path, attr_name, H5P_DEFAULT) > 0)
{
attr_id = H5Aopen_by_name(loc_id, path, attr_name, H5P_DEFAULT, H5P_DEFAULT);
type_id = AH5_H5Tcreate_cpx_memtype();
if (H5Aread(attr_id, type_id, buf) >= 0)
{
*rdata = AH5_set_complex(buf[0], buf[1]);
success = AH5_TRUE;
}
H5Tclose(type_id);
H5Aclose(attr_id);
}
if (!success)
*rdata = AH5_set_complex(0, 0);
return success;
}
// Read all optional attributes
char AH5_read_opt_attrs(hid_t loc_id, const char *path, AH5_opt_attrs_t *opt_attrs, char mandatory_attrs[][AH5_ATTR_LENGTH], size_t nb_mandatory_attrs)
{
char success = AH5_FALSE, is_mandatory;
H5O_info_t object_info;
hsize_t i, j, k = 0;
hid_t attr_id, type_id, memtype;
float buf[2];
hsize_t nb_present_mandatory_attrs = 0;
char temp_name[AH5_ATTR_LENGTH];
if (AH5_path_valid(loc_id, path))
{
// Check presence of all mandatory attributes
for (i = 0; i < (hsize_t) nb_mandatory_attrs; i++)
if (H5Aexists_by_name(loc_id, path, mandatory_attrs[i], H5P_DEFAULT) > 0)
nb_present_mandatory_attrs++;
H5Oget_info_by_name(loc_id, path, &object_info, H5P_DEFAULT);
opt_attrs->nb_instances = object_info.num_attrs - nb_present_mandatory_attrs;
if (opt_attrs->nb_instances > 0)
opt_attrs->instances = (AH5_attr_instance_t *) malloc ((size_t) opt_attrs->nb_instances * sizeof(AH5_attr_instance_t));
for (i = 0; i < object_info.num_attrs; i++)
{
is_mandatory = AH5_FALSE;
attr_id = H5Aopen_by_idx(loc_id, path, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, i, H5P_DEFAULT, H5P_DEFAULT);
H5Aget_name(attr_id, AH5_ATTR_LENGTH, temp_name);
for (j = 0; j < nb_mandatory_attrs; j++)
if (strcmp(temp_name, mandatory_attrs[j]) == 0)
is_mandatory = AH5_TRUE;
if (!is_mandatory)
{
opt_attrs->instances[k].name = strdup(temp_name);
type_id = H5Aget_type(attr_id);
opt_attrs->instances[k].type = H5Tget_class(type_id);
H5Tclose(type_id);
switch (opt_attrs->instances[k].type)
{
case H5T_INTEGER:
opt_attrs->instances[k].value.i = 0;
if (H5Aread(attr_id, H5T_NATIVE_INT, &(opt_attrs->instances[k].value.i)) >= 0)
success = AH5_TRUE;
break;
case H5T_FLOAT:
opt_attrs->instances[k].value.f = 0;
if (H5Aread(attr_id, H5T_NATIVE_FLOAT, &(opt_attrs->instances[k].value.f)) >= 0)
success = AH5_TRUE;
break;
case H5T_COMPOUND:
opt_attrs->instances[k].value.c = AH5_set_complex(0, 0);
type_id = AH5_H5Tcreate_cpx_memtype();
if (H5Aread(attr_id, type_id, buf) >= 0)
{
opt_attrs->instances[k].value.c = AH5_set_complex(buf[0], buf[1]);
success = AH5_TRUE;
}
H5Tclose(type_id);
break;
case H5T_STRING:
opt_attrs->instances[k].value.s = NULL;
memtype = H5Tcopy(H5T_C_S1);
H5Tset_size(memtype, AH5_ATTR_LENGTH);
opt_attrs->instances[k].value.s = (char *) malloc(AH5_ATTR_LENGTH * sizeof(char));
if (H5Aread(attr_id, memtype, opt_attrs->instances[k].value.s) >= 0)
success = AH5_TRUE;
H5Tclose(memtype);
break;
default:
opt_attrs->instances[k].type = H5T_NO_CLASS;
printf("***** WARNING: Unsupported type of attribute \"%s@%s\". *****\n\n", path, opt_attrs->instances[k].name);
break;
}
k++;
}
H5Aclose(attr_id);
}
}
if (!success)
{
opt_attrs->instances = NULL;
opt_attrs->nb_instances = 0;
}
return success;
}
/*-------------------------------------------------------------------------
* Function: read_records
*
* Purpose: For a given dataset, checks to make sure that the stated
* and actual sizes are the same. If they are not, then
* we have an inconsistent dataset due to a SWMR error.
*
* Parameters: const char *filename
* The SWMR test file's name.
*
* unsigned verbose
* Whether verbose console output is desired.
*
* unsigned long nrecords
* The total number of records to read.
*
* unsigned poll_time
* The amount of time to sleep (s).
*
* unsigned reopen_count
*
*
* Return: Success: 0
* Failure: -1
*
*-------------------------------------------------------------------------
*/
static int
read_records(const char *filename, unsigned verbose, unsigned long nrecords,
unsigned poll_time, unsigned reopen_count)
{
hid_t fid; /* File ID */
hid_t aid; /* Attribute ID */
time_t start_time; /* Starting time */
hid_t mem_sid; /* Memory dataspace ID */
symbol_t record; /* The record to add to the dataset */
unsigned seed; /* Seed for random number generator */
unsigned iter_to_reopen = reopen_count; /* # of iterations until reopen */
unsigned long u; /* Local index variable */
hid_t fapl;
HDassert(filename);
HDassert(poll_time != 0);
/* Create file access property list */
if((fapl = h5_fileaccess()) < 0)
return -1;
H5Pset_fclose_degree(fapl, H5F_CLOSE_SEMI);
/* Emit informational message */
if(verbose)
HDfprintf(stderr, "Opening file: %s\n", filename);
/* Open the file */
if((fid = H5Fopen(filename, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, fapl)) < 0)
return -1;
/* Seed the random number generator with the attribute in the file */
if((aid = H5Aopen(fid, "seed", H5P_DEFAULT)) < 0)
return -1;
if(H5Aread(aid, H5T_NATIVE_UINT, &seed) < 0)
return -1;
if(H5Aclose(aid) < 0)
return -1;
HDsrandom(seed);
/* Reset the record */
/* (record's 'info' field might need to change for each record written, also) */
HDmemset(&record, 0, sizeof(record));
/* Create a dataspace for the record to read */
if((mem_sid = H5Screate(H5S_SCALAR)) < 0)
return -1;
/* Emit informational message */
if(verbose)
HDfprintf(stderr, "Reading records\n");
/* Get the starting time */
start_time = HDtime(NULL);
/* Read records */
for(u = 0; u < nrecords; u++) {
symbol_info_t *symbol = NULL; /* Symbol (dataset) */
htri_t attr_exists; /* Whether the sequence number attribute exists */
unsigned long file_u; /* Attribute sequence number (writer's "u") */
/* Get a random dataset, according to the symbol distribution */
symbol = choose_dataset();
/* Fill in "nrecords" field. Note that this depends on the writer
* using the same algorithm and "nrecords" */
symbol->nrecords = nrecords / 5;
/* Wait until we can read the dataset */
do {
/* Check if sequence attribute exists */
if((attr_exists = H5Aexists_by_name(fid, symbol->name, "seq", H5P_DEFAULT)) < 0)
return -1;
if(attr_exists) {
/* Read sequence number attribute */
if((aid = H5Aopen_by_name(fid, symbol->name, "seq", H5P_DEFAULT, H5P_DEFAULT)) < 0)
return -1;
if(H5Aread(aid, H5T_NATIVE_ULONG, &file_u) < 0)
return -1;
if(H5Aclose(aid) < 0)
return -1;
/* Check if sequence number is at least u - if so, this should
* guarantee that this record has been written */
if(file_u >= u)
break;
} /* end if */
/* Check for timeout */
if(HDtime(NULL) >= (time_t)(start_time + (time_t)TIMEOUT)) {
HDfprintf(stderr, "Reader timed out\n");
return -1;
} /* end if */
/* Pause */
HDsleep(poll_time);
/* Retrieve and print the collection of metadata read retries */
if(print_metadata_retries_info(fid) < 0)
HDfprintf(stderr, "Warning: could not obtain metadata retries info\n");
/* Reopen the file */
if(H5Fclose(fid) < 0)
return -1;
if((fid = H5Fopen(filename, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, fapl)) < 0)
return -1;
iter_to_reopen = reopen_count;
} while(1);
/* Emit informational message */
if(verbose)
HDfprintf(stderr, "Checking dataset %lu\n", u);
/* Check dataset */
if(check_dataset(fid, verbose, symbol, &record, mem_sid) < 0)
return -1;
HDmemset(&record, 0, sizeof(record));
/* Check for reopen */
iter_to_reopen--;
if(iter_to_reopen == 0) {
/* Emit informational message */
if(verbose)
HDfprintf(stderr, "Reopening file: %s\n", filename);
/* Retrieve and print the collection of metadata read retries */
if(print_metadata_retries_info(fid) < 0)
HDfprintf(stderr, "Warning: could not obtain metadata retries info\n");
/* Reopen the file */
if(H5Fclose(fid) < 0)
return -1;
if((fid = H5Fopen(filename, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, fapl)) < 0)
return -1;
iter_to_reopen = reopen_count;
} /* end if */
} /* end while */
/* Retrieve and print the collection of metadata read retries */
if(print_metadata_retries_info(fid) < 0)
HDfprintf(stderr, "Warning: could not obtain metadata retries info\n");
/* Close file */
if(H5Fclose(fid) < 0)
return -1;
/* Close the memory dataspace */
if(H5Sclose(mem_sid) < 0)
return -1;
return 0;
} /* end read_records() */