[cig-commits] r11540 - in cs/benchmark/cigma/trunk/src/h5io: . t
luis at geodynamics.org
luis at geodynamics.org
Mon Mar 24 17:17:50 PDT 2008
Author: luis
Date: 2008-03-24 17:17:49 -0700 (Mon, 24 Mar 2008)
New Revision: 11540
Removed:
cs/benchmark/cigma/trunk/src/h5io/Makefile
cs/benchmark/cigma/trunk/src/h5io/Makefile.dep
cs/benchmark/cigma/trunk/src/h5io/h5array.c
cs/benchmark/cigma/trunk/src/h5io/h5attr.c
cs/benchmark/cigma/trunk/src/h5io/h5dset.c
cs/benchmark/cigma/trunk/src/h5io/h5file.c
cs/benchmark/cigma/trunk/src/h5io/h5group.c
cs/benchmark/cigma/trunk/src/h5io/h5io.h
cs/benchmark/cigma/trunk/src/h5io/split.c
cs/benchmark/cigma/trunk/src/h5io/split.h
cs/benchmark/cigma/trunk/src/h5io/t/Makefile
cs/benchmark/cigma/trunk/src/h5io/t/test_h5dset.c
cs/benchmark/cigma/trunk/src/h5io/t/test_h5file.c
cs/benchmark/cigma/trunk/src/h5io/t/test_h5group.c
Log:
Removed obsolete h5io functions
Deleted: cs/benchmark/cigma/trunk/src/h5io/Makefile
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/Makefile 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/Makefile 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,38 +0,0 @@
-include ../../build/variables
-
-LIB = ../../lib/libh5io.a
-
-INCLUDES += $(HDF5_INCLUDES)
-CFLAGS = $(OPTIM) $(FLAGS) $(INCLUDES)
-
-SRC = \
- h5array.c \
- h5attr.c \
- h5dset.c \
- h5file.c \
- h5group.c \
- split.c \
-
-OBJ = $(SRC:.c=.o)
-
-.SUFFIXES: .o .c
-
-$(LIB): $(OBJ)
- $(AR) $(LIB) $(OBJ)
- $(RANLIB) $(LIB)
-
-.c.o:
- $(CC) $(CFLAGS) -c $<
-
-tests:
- cd t && make tests
-
-clean:
- rm -f *.o
- cd t && make clean
-
--include Makefile.dep
-depend:
- $(CC) -MM $(SRC) > Makefile.dep
-
-.PHONY: clean depend
Deleted: cs/benchmark/cigma/trunk/src/h5io/Makefile.dep
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/Makefile.dep 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/Makefile.dep 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,6 +0,0 @@
-h5array.o: h5array.c h5io.h
-h5attr.o: h5attr.c h5io.h
-h5dset.o: h5dset.c h5io.h
-h5file.o: h5file.c h5io.h
-h5group.o: h5group.c h5io.h split.h
-split.o: split.c split.h
Deleted: cs/benchmark/cigma/trunk/src/h5io/h5array.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/h5array.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/h5array.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,428 +0,0 @@
-#include <stdlib.h>
-#include "hdf5.h"
-#include "h5io.h"
-
-
-int h5io_array_init(h5array_t *array, hid_t type_id, int rank, int *shape, void *data)
-{
- int i;
-
- /* initialize dataspace */
- array->rank = rank;
- array->shape = (hsize_t *)malloc(rank * sizeof(hsize_t));
- if (shape != NULL)
- {
- for (i = 0; i < rank; i++)
- array->shape[i] = shape[i];
- }
- else
- {
- for (i = 0; i < rank; i++)
- array->shape[i] = 0;
- }
-
- /* initialize datatype */
- array->type_id = type_id;
-
- /* initialize data */
- array->data = data;
-
- return 0;
-}
-
-int h5io_array_free_dims(h5array_t *array)
-{
- free(array->shape);
- return 0;
-}
-
-int h5io_array_free_data(h5array_t *array)
-{
- if (array->data != NULL)
- {
- free(array->data);
- }
- return 0;
-}
-
-int h5io_array_free(h5array_t *array)
-{
- h5io_array_free_dims(array);
- h5io_array_free_data(array);
- return 0;
-}
-
-
-
-int h5io_array_npoints(h5array_t *array)
-{
- int i;
- int npoints = 1;
- for (i = 0; i < array->rank; i++)
- {
- npoints *= (int) array->shape[i];
- }
- return npoints;
-}
-
-int h5io_array_dim(h5array_t *array, int i)
-{
- if ((0 <= i) && (i < array->rank))
- {
- return (int)(array->shape[i]);
- }
- return 0;
-}
-
-void h5io_array_dims(h5array_t *array, int *rank, int **shape)
-{
- int i;
-
- *rank = array->rank;
- *shape = (int *)malloc((array->rank) * sizeof(int));
-
- for (i = 0; i < array->rank; i++)
- {
- (*shape)[i] = (int) array->shape[i];
- }
-}
-
-void h5io_array_dims1(h5array_t *array, int *n)
-{
- *n = array->shape[0];
-}
-
-void h5io_array_dims2(h5array_t *array, int *m, int *n)
-{
- *m = array->shape[0];
- *n = array->shape[1];
-}
-void h5io_array_dims3(h5array_t *array, int *l, int *m, int *n)
-{
- *l = array->shape[0];
- *m = array->shape[1];
- *n = array->shape[2];
-}
-
-
-
-hid_t h5io_array_open(h5array_t *array, hid_t loc_id, const char *name)
-{
- hid_t dataset_id;
- hid_t dataspace_id;
- herr_t status;
-
- dataset_id = H5Dopen(loc_id, name);
- if (dataset_id < 0)
- {
- return -1;
- }
-
- dataspace_id = H5Dget_space(dataset_id);
- if (dataspace_id < 0)
- {
- H5Dclose(dataset_id);
- return -2;
- }
-
- array->rank = H5Sget_simple_extent_ndims(dataspace_id);
-
- status = H5Sget_simple_extent_dims(dataspace_id, array->shape, NULL);
-
- status = H5Sclose(dataspace_id);
-
- return dataset_id;
-}
-
-
-hid_t h5io_array_create(h5array_t *array, hid_t loc_id, const char *name, const char *title)
-{
- hid_t dataspace_id;
- hid_t dataset_id;
- herr_t status;
-
- dataspace_id = H5Screate_simple(array->rank, array->shape, NULL);
- if (dataspace_id < 0)
- {
- return -1;
- }
-
- dataset_id = H5Dcreate(loc_id, name, array->type_id, dataspace_id, H5P_DEFAULT);
- if (dataset_id < 0)
- {
- H5Sclose(dataspace_id);
- return -2;
- }
-
- status = h5io_attr_set_str(dataset_id, "TITLE", title);
- status = h5io_attr_set_str(dataset_id, "CLASS", "ARRAY");
- status = h5io_attr_set_str(dataset_id, "FLAVOR", "numpy");
- status = h5io_attr_set_str(dataset_id, "VERSION", "2.3");
-
- status = H5Sclose(dataspace_id);
-
- return dataset_id;
-}
-
-
-int h5io_array_read(h5array_t *array, hid_t loc_id, const char *name)
-{
- int npoints;
- hid_t dataset_id;
- herr_t status;
-
- dataset_id = h5io_array_open(array, loc_id, name);
- if (dataset_id < 0)
- {
- return -1;
- }
-
- npoints = h5io_array_npoints(array);
-
- array->data = malloc(npoints * H5Tget_size(array->type_id));
- if (array->data == NULL)
- {
- H5Dclose(dataset_id);
- return -2;
- }
-
- status = H5Dread(dataset_id, array->type_id, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, array->data);
- if (status < 0)
- {
- H5Dclose(dataset_id);
- return -3;
- }
-
- status = H5Dclose(dataset_id);
-
- return 0;
-}
-
-
-
-int h5io_array_write(h5array_t *array, hid_t loc_id, const char *name)
-{
- hid_t dataspace_id;
- hid_t dataset_id;
- herr_t status;
-
- dataspace_id = H5Screate_simple(array->rank, array->shape, NULL);
- if (dataspace_id < 0)
- {
- return -1;
- }
-
- dataset_id = H5Dcreate(loc_id, name, array->type_id, dataspace_id,
- H5P_DEFAULT);
- if (dataset_id < 0)
- {
- H5Sclose(dataspace_id);
- return -2;
- }
-
- status = H5Dwrite(dataset_id, array->type_id, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, array->data);
- if (status < 0)
- {
- H5Sclose(dataspace_id);
- H5Dclose(dataset_id);
- return -3;
- }
-
- status = H5Sclose(dataspace_id);
- status = H5Dclose(dataset_id);
-
- return 0;
-}
-
-
-static herr_t h5io_hyperslab_init(h5array_t *array,
- hsize_t **offset, hsize_t **stride,
- hsize_t **count, hsize_t **block,
- int start, int end)
-{
- int i;
-
- *offset = NULL;
- *stride = NULL;
- *count = NULL;
- *block = NULL;
-
- if ((start < 0) || (start > end))
- {
- return -1;
- }
-
- if (start >= array->rank)
- {
- return -2;
- }
-
- if (array->rank == 0)
- {
- return -3;
- }
-
- *offset = (hsize_t *)malloc((array->rank) * sizeof(hsize_t));
- *stride = (hsize_t *)malloc((array->rank) * sizeof(hsize_t));
- *count = (hsize_t *)malloc((array->rank) * sizeof(hsize_t));
- *block = (hsize_t *)malloc((array->rank) * sizeof(hsize_t));
-
- /* first, select everything */
- for (i = 0; i < array->rank; i++)
- {
- (*offset)[i] = 0;
- (*block )[i] = array->shape[i];
- (*stride)[i] = 1;
- (*count )[i] = 1;
- }
-
- /* now, do the selection on the first dimension only */
- // TODO: add column to argument list
- (*offset)[0] = start;
- (*block )[0] = end - start;
-
- return 0;
-}
-
-static void h5io_hyperslab_free(hsize_t *offset, hsize_t *stride,
- hsize_t *count, hsize_t *block)
-{
- if (offset != NULL) free(offset);
- if (stride != NULL) free(stride);
- if (count != NULL) free(count);
- if (block != NULL) free(block);
-}
-
-
-
-int h5io_array_slice_read(h5array_t *array, hid_t dataset_id, int start, int end)
-{
- hsize_t *offset, *stride, *count, *block;
- hid_t memspace_id;
- hid_t filespace_id;
- herr_t status;
-
- status = h5io_hyperslab_init(array,
- &offset, &stride,
- &count, &block,
- start, end);
- if (status < 0)
- {
- return -1;
- }
-
- memspace_id = H5Screate_simple(array->rank, block, NULL);
- if (memspace_id < 0)
- {
- return -2;
- }
-
- filespace_id = H5Dget_space(dataset_id);
- if (filespace_id < 0)
- {
- H5Sclose(memspace_id);
- return -3;
- }
-
- if (array->data == NULL)
- {
- int i;
- int npoints = 1;
-
- for (i = 0; i < array->rank; i++)
- {
- npoints *= block[i];
- }
-
- array->data = malloc(npoints * H5Tget_size(array->type_id));
- if (array->data == NULL)
- {
- H5Sclose(memspace_id);
- H5Sclose(filespace_id);
- return -4;
- }
- }
-
- status = H5Sselect_hyperslab(filespace_id, H5S_SELECT_SET,
- offset, stride, count, block);
- if (status < 0)
- {
- H5Sclose(memspace_id);
- H5Sclose(filespace_id);
- return -5;
- }
-
- status = H5Dread(dataset_id, array->type_id, memspace_id, filespace_id,
- H5P_DEFAULT, array->data);
- if (status < 0)
- {
- H5Sclose(memspace_id);
- H5Sclose(filespace_id);
- return -5;
- }
-
- status = H5Sclose(memspace_id);
- status = H5Sclose(filespace_id);
-
- h5io_hyperslab_free(offset, stride, count, block);
-
- return 0;
-}
-
-int h5io_array_slice_write(h5array_t *array, hid_t dataset_id, int start, int end)
-{
- hsize_t *offset, *stride, *count, *block;
- hid_t memspace_id;
- hid_t filespace_id;
- herr_t status;
-
- status = h5io_hyperslab_init(array,
- &offset, &stride,
- &count, &block,
- start, end);
- if (status < 0)
- {
- return -1;
- }
-
- memspace_id = H5Screate_simple(array->rank, block, NULL);
- if (memspace_id < 0)
- {
- return -2;
- }
-
- filespace_id = H5Dget_space(dataset_id);
- if (filespace_id < 0)
- {
- H5Sclose(memspace_id);
- return -3;
- }
-
- status = H5Sselect_hyperslab(filespace_id, H5S_SELECT_SET,
- offset, stride, count, block);
- if (status < 0)
- {
- H5Sclose(memspace_id);
- H5Sclose(filespace_id);
- return -4;
- }
-
- status = H5Dwrite(dataset_id, array->type_id, memspace_id, filespace_id,
- H5P_DEFAULT, array->data);
- if (status < 0)
- {
- H5Sclose(memspace_id);
- H5Sclose(filespace_id);
- return -5;
- }
-
- status = H5Sclose(memspace_id);
- status = H5Sclose(filespace_id);
-
- h5io_hyperslab_free(offset, stride, count, block);
-
- return 0;
-}
-
Deleted: cs/benchmark/cigma/trunk/src/h5io/h5attr.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/h5attr.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/h5attr.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,549 +0,0 @@
-#include <stdlib.h>
-#include <string.h>
-#include "hdf5.h"
-#include "h5io.h"
-
-/****************************************************************************
- * Some of the following functions were based or taken from the H5ATTR.c *
- * source file in PyTables, which is a BSD-licensed python extension *
- * for accessing HDF5 files. *
- * *
- * The copyright notice is hereby retained. *
- * *
- * NCSA HDF *
- * Scientific Data Technologies *
- * National Center for Supercomputing Applications *
- * University of Illinois at Urbana-Champaign *
- * 605 E. Springfield, Champaign IL 61820 *
- * *
- * For conditions of distribution and use, see the accompanying *
- * hdf/COPYING file. *
- * *
- * Modified versions of H5LT for getting and setting attributes for open *
- * groups and leaves. *
- * F. Altet 2005/09/29 *
- * *
- ****************************************************************************/
-
-
-/*
- * attr_find_op - operator function used by h5io_attr_find
- *
- * (Pedro Vicente, pvn at ncsa.uiuc.edu - June 21, 2001)
- */
-static herr_t attr_find_op(hid_t loc_id, const char *name, void *op_data)
-{
- /* Define a default zero value for return. This will cause the
- * iterator to continue if the palette attribute is not found yet.
- */
- int ret = 0;
-
- char *attr_name = (char *)op_data;
-
- /* Shut the compiler up */
- loc_id = loc_id;
-
- /*
- * Define a positive value for return value if the attribute was
- * found. This will cause the iterator to immediately return that
- * positive value, indicating short-circuit success
- */
-
- if (strcmp(name, attr_name) == 0)
- {
- ret = 1;
- }
-
- return ret;
-}
-
-
-
-/*
- * h5io_attr_find - Inquires if an attribute named attr_name exists attached
- * to the object loc_id. This function uses H5Aiterate with the operator
- * function attr_find_op.
- *
- * Success: The return value of the first operator that returns
- * non-zero, or zero if all members were processed with no
- * operator returning non-zero.
- *
- * Failure: Negative if something goes wrong within the library,
- * or the negative value returned by one of the operators.
- *
- * (Pedro Vicente, pvn at ncsa.uiuc.edu - June 21, 2001)
- */
-herr_t h5io_attr_find(hid_t loc_id, const char *attr_name)
-{
- unsigned int attr_num;
- herr_t ret;
-
- attr_num = 0;
- ret = H5Aiterate(loc_id, &attr_num, attr_find_op, (void *)attr_name);
-
- return ret;
-}
-
-
-/* h5io_attr_set - Sets an attribute named attr_name.
- * On success it returns 0, while on failure it returns -1.
- * (Pedro Vicente, pvn at ncsa.uiuc.edu - July 25, 2001)
- */
-herr_t h5io_attr_set(hid_t obj_id, const char *attr_name, hid_t type_id, const void *data)
-{
- hid_t space_id, attr_id;
- herr_t status;
-
- int has_attr;
-
- /* Create the data space for the attribute. */
- space_id = H5Screate(H5S_SCALAR);
- if (space_id < 0)
- {
- goto out;
- }
-
- /* Verify if the attribute already exists. */
- has_attr = h5io_attr_find(obj_id, attr_name);
- if (has_attr == 1)
- {
- /* The attribute already exists. Delete it. */
- status = H5Adelete(obj_id, attr_name);
- if (status < 0)
- {
- goto out;
- }
- }
-
- /* Create the attribute. */
- attr_id = H5Acreate(obj_id, attr_name, type_id, space_id, H5P_DEFAULT);
- if (attr_id < 0)
- {
- goto out;
- }
-
- /* Write the attribute data. */
- status = H5Awrite(attr_id, type_id, data);
- if (status < 0)
- {
- goto out;
- }
-
- /* Close the attribute. */
- status = H5Aclose(attr_id);
- if (status < 0)
- {
- goto out;
- }
-
- /* Close the data space. */
- status = H5Sclose(space_id);
- if (status < 0)
- {
- goto out;
- }
-
- return 0;
-
-out:
- return -1;
-}
-
-
-/*
- * h5io_attr_get - reads an attribute named attr_name with the memory
- * type type_id. On success it returns 0, while on failure it returns -1.
- *
- * (Pedro Vicente, pvn at ncsa.uiuc.edu - September 19, 2002)
- */
-herr_t h5io_attr_get(hid_t obj_id, const char *attr_name, hid_t type_id, void *data)
-{
- hid_t attr_id;
- herr_t status;
-
- attr_id = H5Aopen_name(obj_id, attr_name);
- if (attr_id < 0)
- {
- return -1;
- }
-
- status = H5Aread(attr_id, type_id, data);
- if (status < 0)
- {
- goto out;
- }
-
- status = H5Aclose(attr_id);
- if (status < 0)
- {
- return -1;
- }
-
- return 0;
-
-out:
- H5Aclose(attr_id);
- return -1;
-}
-
-
-
-/*
- * h5io_attr_get_dims - Gets the dimensionality of an attribute.
- * On success it returns 0, while on failure it returns -1.
- *
- * (Pedro Vicente, pvn at ncsa.uiuc.edu - September 4, 2001)
- */
-herr_t h5io_attr_get_dims(hid_t obj_id, const char *attr_name, int *rank, hsize_t *dims)
-{
- hid_t attr_id;
- hid_t space_id;
- herr_t status;
-
- /* Open the attribute */
- attr_id = H5Aopen_name(obj_id, attr_name);
- if (attr_id < 0)
- {
- return -1;
- }
-
- /* Get the dataspace handle */
- space_id = H5Aget_space(attr_id);
- if (space_id < 0)
- {
- goto out;
- }
-
- /* Get the number of dimensions */
- *rank = H5Sget_simple_extent_ndims(space_id);
- if (*rank < 0)
- {
- goto out;
- }
-
- /* Get dimensions */
- status = H5Sget_simple_extent_dims(space_id, dims, NULL);
- if (status < 0)
- {
- goto out;
- }
-
- /* Terminate access to the dataspace */
- status = H5Sclose(space_id);
- if (status < 0)
- {
- goto out;
- }
-
- /* End access to the attribute */
- status = H5Aclose(attr_id);
- if (status < 0)
- {
- goto out;
- }
-
- return 0;
-
-out:
- H5Aclose(attr_id);
- return -1;
-}
-
-/*
- * h5io_attr_set_str - Creates and writes a string attribute named attr_name
- * and attahes it to the object specified by obj_id. If the attribute already
- * exists, it is overwritten. On success it returns 0, while on failure
- * it returns -1.
- *
- * (Pedro Vicente, pvn at ncsa.uiuc.edu - July 23, 2001)
- */
-herr_t h5io_attr_set_str(hid_t obj_id,
- const char *attr_name,
- const char *attr_data)
-{
- hid_t attr_type;
- hid_t attr_size;
- hid_t attr_space_id;
- hid_t attr_id;
- int has_attr;
- herr_t status;
-
- /* Create the attribute */
- attr_type = H5Tcopy(H5T_C_S1);
- if (attr_type < 0)
- {
- goto out;
- }
-
- attr_size = strlen(attr_data) + 1; /* extra null term */
-
- status = H5Tset_size(attr_type, (size_t)attr_size);
- if (status < 0)
- {
- goto out;
- }
-
- status = H5Tset_strpad(attr_type, H5T_STR_NULLTERM);
- if (status < 0)
- {
- goto out;
- }
-
- attr_space_id = H5Screate(H5S_SCALAR);
- if (status < 0)
- {
- goto out;
- }
-
- /* Verify if the attribute already exists */
- has_attr = h5io_attr_find(obj_id, attr_name);
-
- /* If the attribute already exists, delete it */
- if (has_attr == 1)
- {
- status = H5Adelete(obj_id, attr_name);
- if (status < 0)
- {
- goto out;
- }
- }
-
- /* Create the attribute. */
- attr_id = H5Acreate(obj_id, attr_name, attr_type, attr_space_id,
- H5P_DEFAULT);
- if (attr_id < 0)
- {
- goto out;
- }
-
- /* Write the attribute data. */
- status = H5Awrite(attr_id, attr_type, attr_data);
- if (status < 0)
- {
- goto out;
- }
-
- status = H5Aclose(attr_id);
- if (status < 0)
- {
- goto out;
- }
-
- status = H5Sclose(attr_space_id);
- if (status < 0)
- {
- goto out;
- }
-
- status = H5Tclose(attr_type);
- if (status < 0)
- {
- goto out;
- }
-
- return 0;
-
-out:
- return -1;
-}
-
-
-
-/*
- * h5io_attr_get_str - Reads a string attribute named attr_name.
- * On success it returns 0, while on failure it returns -1.
- *
- * (Francesc Altet, faltet at carabos.com - February 23, 2005)
- */
-herr_t h5io_attr_get_str(hid_t obj_id, const char *attr_name, char **data)
-{
- hid_t attr_id;
- hid_t attr_type;
- size_t type_size;
- herr_t status;
-
- *data = NULL;
-
- attr_id = H5Aopen_name(obj_id, attr_name);
- if (attr_id < 0)
- {
- return -1;
- }
-
- attr_type = H5Aget_type(attr_id);
- if (attr_type < 0)
- {
- goto out;
- }
-
- /* Get the size */
- type_size = H5Tget_size(attr_type);
- if (type_size < 0)
- {
- goto out;
- }
-
- /* Malloc enough space for the string, plus 1 for the trailing '\0' */
- *data = (char *)malloc((type_size + 1) * sizeof(char));
-
- status = H5Aread(attr_id, attr_type, *data);
- if (status < 0)
- {
- goto out;
- }
-
- /* Set the last character to \0 in case we are dealing with
- * space padded strings.
- */
- (*data)[type_size] = '\0';
-
- /* TODO: check that following statement doesn't fail */
- status = H5Tclose(attr_type);
- if (status < 0)
- {
- goto out;
- }
-
- status = H5Aclose(attr_id);
- if (status < 0)
- {
- return -1;
- }
-
- return 0;
-
-out:
-
- if (attr_type != 0)
- H5Tclose(attr_type);
-
- H5Aclose(attr_id);
-
- if (*data)
- free(*data);
-
- return -1;
-}
-
-
-
-/*
- * h5io_attr_set_array - write an array attribute. Returns 0 on success,
- * and -1 on failure. (July 25, 2001)
- */
-herr_t h5io_attr_set_array(hid_t obj_id,
- const char *attr_name,
- size_t rank,
- hsize_t *dims,
- hid_t type_id,
- const void *data)
-{
- hid_t space_id, attr_id;
- herr_t status;
-
- int has_attr;
-
- /* Create the data space for the attribute. */
- space_id = H5Screate_simple(rank, dims, NULL);
- if (space_id < 0)
- {
- goto out;
- }
-
- /* Verify if the attribute already exists. */
- has_attr = h5io_attr_find(obj_id, attr_name);
- if (has_attr == 1)
- {
- /* The attribute already exists. Delete it. */
- status = H5Adelete(obj_id, attr_name);
- if (status < 0)
- {
- goto out;
- }
- }
-
- /* Create the attribute. */
- attr_id = H5Acreate(obj_id, attr_name, type_id, space_id, H5P_DEFAULT);
- if (attr_id < 0)
- {
- goto out;
- }
-
- /* Write the attribute data. */
- status = H5Awrite(attr_id, type_id, data);
- if (status < 0)
- {
- goto out;
- }
-
- /* Close the dataspace. */
- status = H5Sclose(space_id);
- if (status < 0)
- {
- goto out;
- }
-
- return 0;
-
-out:
- return -1;
-}
-
-herr_t h5io_attr_set_array1(hid_t obj_id,
- const char *attr_name,
- hsize_t dim,
- hid_t type_id,
- const void *data)
-{
- return h5io_attr_set_array(obj_id, attr_name, 1, &dim, type_id, data);
-}
-
-herr_t h5io_attr_set_array1_of_ints(hid_t obj_id,
- const char *attr_name,
- hsize_t dim,
- const int *data)
-{
- return h5io_attr_set_array(obj_id, attr_name, 1, &dim, H5T_NATIVE_INT, data);
-}
-
-herr_t h5io_attr_set_array1_of_floats(hid_t obj_id,
- const char *attr_name,
- hsize_t dim,
- const float *data)
-{
- return h5io_attr_set_array(obj_id, attr_name, 1, &dim, H5T_NATIVE_FLOAT, data);
-}
-
-herr_t h5io_attr_set_array1_of_doubles(hid_t obj_id,
- const char *attr_name,
- hsize_t dim,
- const double *data)
-{
- return h5io_attr_set_array(obj_id, attr_name, 1, &dim, H5T_NATIVE_DOUBLE, data);
-}
-
-
-herr_t h5io_attr_set_int(hid_t obj_id, const char *attr_name, int n)
-{
- return h5io_attr_set(obj_id, attr_name, H5T_NATIVE_INT, &n);
-}
-
-herr_t h5io_attr_set_long(hid_t obj_id, const char *attr_name, long n)
-{
- return h5io_attr_set(obj_id, attr_name, H5T_NATIVE_LONG, &n);
-}
-
-herr_t h5io_attr_set_llong(hid_t obj_id, const char *attr_name, long long n)
-{
- return h5io_attr_set(obj_id, attr_name, H5T_NATIVE_LLONG, &n);
-}
-
-herr_t h5io_attr_set_float(hid_t obj_id, const char *attr_name, float x)
-{
- return h5io_attr_set(obj_id, attr_name, H5T_NATIVE_FLOAT, &x);
-}
-
-herr_t h5io_attr_set_double(hid_t obj_id, const char *attr_name, double x)
-{
- return h5io_attr_set(obj_id, attr_name, H5T_NATIVE_DOUBLE, &x);
-}
Deleted: cs/benchmark/cigma/trunk/src/h5io/h5dset.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/h5dset.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/h5dset.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,245 +0,0 @@
-#include <stdlib.h>
-#include "hdf5.h"
-#include "h5io.h"
-
-
-hid_t h5io_dset_create(hid_t loc_id, const char *name, const char *title,
- hid_t type_id, int rank, int *shape)
-{
- hid_t dataset_id;
- hid_t dataspace_id;
- herr_t status;
-
- if (rank > 0)
- {
- hsize_t *dims;
- int i;
- dims = (hsize_t *)malloc(rank * sizeof(hsize_t));
- for (i = 0; i < rank; i++)
- {
- dims[i] = shape[i];
- }
-
- dataspace_id = H5Screate_simple(rank, dims, NULL);
- if (dataspace_id < 0)
- {
- free(dims);
- return -1;
- }
- free(dims);
- }
- else
- {
- return -3;
- }
-
- dataset_id = H5Dcreate(loc_id, name, type_id, dataspace_id, H5P_DEFAULT);
- if (dataset_id < 0)
- {
- H5Sclose(dataspace_id);
- return -2;
- }
-
- status = h5io_attr_set_str(dataset_id, "TITLE", title);
- status = h5io_attr_set_str(dataset_id, "CLASS", "ARRAY");
- status = h5io_attr_set_str(dataset_id, "FLAVOR", "numpy");
- status = h5io_attr_set_str(dataset_id, "VERSION", "2.3");
-
- status = H5Sclose(dataspace_id);
-
- return dataset_id;
-}
-
-
-hid_t h5io_dset_open(hid_t loc_id, const char *name,
- hid_t *type_id, int *rank, int *shape, int *npoints)
-{
- hid_t dataset_id;
- hid_t dataspace_id;
- herr_t status;
-
- dataset_id = H5Dopen(loc_id, name);
- if (dataset_id < 0)
- {
- return -1;
- }
-
- if (type_id != NULL)
- {
- *type_id = H5Dget_type(dataset_id);
- }
-
- if ((rank != NULL) || (shape != NULL) || (npoints != NULL))
- {
- dataspace_id = H5Dget_space(dataset_id);
-
- if (rank != NULL)
- {
- *rank = H5Sget_simple_extent_ndims(dataspace_id);
- }
-
- // TODO: think about the shape[] array. should we allocate
- // it here instead of copying it to a fixed array?
- // after all, even the rank is unknown before opening
- // a dataset. note that the type would then have to
- // change to "int **shape"
- if (shape != NULL)
- {
- int i;
- hsize_t *dims;
-
- dims = (hsize_t *)malloc((*rank) * sizeof(hsize_t));
- status = H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
- for (i = 0; i < *rank; i++)
- {
- shape[i] = (int)dims[i];
- }
- free(dims);
- }
-
- if (npoints != NULL)
- {
- *npoints = H5Sget_simple_extent_npoints(dataspace_id);
- }
-
- status = H5Sclose(dataspace_id);
- }
-
- return dataset_id;
-}
-
-
-
-int h5io_dset_read(hid_t loc_id, const char *name,
- hid_t type_id, int rank, int *shape, void **data)
-{
- int dset_rank;
- int dset_npts;
- hid_t dataset_id;
- herr_t status;
-
- dataset_id = h5io_dset_open(loc_id, name, NULL, &dset_rank, shape, &dset_npts);
- if (dataset_id < 0)
- {
- return -1;
- }
- if (rank != dset_rank)
- {
- H5Dclose(dataset_id);
- return -2;
- }
-
- *data = malloc(dset_npts * H5Tget_size(type_id));
- if (*data == NULL)
- {
- H5Dclose(dataset_id);
- return -3;
- }
-
- status = H5Dread(dataset_id, type_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, *data);
- if (status < 0)
- {
- H5Dclose(dataset_id);
- return -4;
- }
-
- status = H5Dclose(dataset_id);
-
- return 0;
-}
-
-int h5io_dset_read1(hid_t loc_id,
- const char *name,
- hid_t type_id,
- void **data, int *n)
-{
- return h5io_dset_read(loc_id, name, type_id, 1, n, data);
-}
-
-int h5io_dset_read2(hid_t loc_id,
- const char *name,
- hid_t type_id,
- void **data, int *m, int *n)
-{
- int shape[2];
- int ret;
-
- ret = h5io_dset_read(loc_id, name, type_id, 2, shape, data);
-
- *m = shape[0];
- *n = shape[1];
-
- return ret;
-}
-
-int h5io_dset_read3(hid_t loc_id,
- const char *name,
- hid_t type_id,
- void **data, int *l, int *m, int *n)
-{
- int shape[3];
- int ret;
-
- ret = h5io_dset_read(loc_id, name, type_id, 3, shape, data);
-
- *l = shape[0];
- *m = shape[1];
- *n = shape[2];
-
- return ret;
-}
-
-
-int h5io_dset_write(hid_t loc_id, const char *name, const char *title,
- hid_t type_id, int rank, int *shape, void *data)
-{
- hid_t dataset_id;
- herr_t status;
-
- dataset_id = h5io_dset_create(loc_id, name, title, type_id, rank, shape);
- if (dataset_id < 0)
- {
- return -1;
- }
-
- status = H5Dwrite(dataset_id, type_id, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, data);
- if (status < 0)
- {
- H5Dclose(dataset_id);
- return -2;
- }
-
- H5Dclose(dataset_id);
- return 0;
-}
-
-int h5io_dset_write1(hid_t loc_id,
- const char *name,
- const char *title,
- hid_t type_id,
- void *data, int n)
-{
- return h5io_dset_write(loc_id, name, title, type_id, 1, &n, data);
-}
-
-int h5io_dset_write2(hid_t loc_id,
- const char *name,
- const char *title,
- hid_t type_id,
- void *data, int m, int n)
-{
- int dims[2] = {m,n};
- return h5io_dset_write(loc_id, name, title, type_id, 2, dims, data);
-}
-
-int h5io_dset_write3(hid_t loc_id,
- const char *name,
- const char *title,
- hid_t type_id,
- void *data, int l, int m, int n)
-{
- int dims[3] = {l,m,n};
- return h5io_dset_write(loc_id, name, title, type_id, 3, dims, data);
-}
-
Deleted: cs/benchmark/cigma/trunk/src/h5io/h5file.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/h5file.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/h5file.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,157 +0,0 @@
-#include <string.h>
-#include "hdf5.h"
-#include "h5io.h"
-
-
-hid_t h5io_file_create(const char *filename, const char *mode)
-{
- hid_t file_id;
- hid_t root;
- herr_t status;
-
- if (strcmp(mode, "w") == 0)
- {
- /* Create file by truncating (i.e. overwriting previous file) */
- file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
- }
- else if (strcmp(mode, "x") == 0)
- {
- /* Create file exclusively (i.e. fail if it already exists) */
- file_id = H5Fcreate(filename, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
- }
- else
- {
- return -1;
- }
-
- if (file_id < 0)
- {
- return -2;
- }
-
- root = H5Gopen(file_id, "/");
- status = h5io_attr_set_str(root, "TITLE", "Cigma file"); // TODO: add title to argument list
- status = h5io_attr_set_str(root, "CLASS", "GROUP");
- status = h5io_attr_set_str(root, "VERSION", "1.0");
- status = h5io_attr_set_str(root, "PYTABLES_FORMAT_VERSION", "1.5");
- status = H5Gclose(root);
-
- return file_id;
-}
-
-
-hid_t h5io_file_open(const char *filename, const char *mode)
-{
- /*
- * Open file for reading. Fail if file doesn't exist.
- */
- if (strcmp(mode, "r") == 0)
- {
- hid_t file_id;
-
- /* Open file in read-only mode */
- file_id = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
-
- /* Check for failure */
- if (file_id < 0)
- {
- return -1;
- }
-
- return file_id;
- }
-
- /*
- * Open file for writing. If file exists, it is truncated.
- */
- if (strcmp(mode, "w") == 0)
- {
- hid_t file_id;
-
- file_id = h5io_file_create(filename, "w");
-
- if (file_id < 0)
- {
- return -2;
- }
-
- return file_id;
- }
-
- /*
- * Open file for reading and writing. Fail if file doesn't exist.
- */
- if (strcmp(mode, "rw") == 0)
- {
- hid_t file_id;
-
- /* Open file in read-write mode */
- file_id = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
-
- if (file_id < 0)
- {
- return -3;
- }
-
- return file_id;
- }
-
- /*
- * Open file for reading and writing. Create the file if necessary.
- */
- if (strcmp(mode, "rw+") == 0)
- {
- hid_t file_id;
-
- /* See http://hdf.ncsa.uiuc.edu/HDF5/doc/Errors.html */
- herr_t (*old_func)(void *);
- void *old_client_data;
-
- /* Save old error handler */
- H5Eget_auto(&old_func, &old_client_data);
-
- /* Turn off error handling */
- H5Eset_auto(NULL, NULL);
-
- /* Open file in read-write mode -- errors supprssed */
- file_id = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
-
- /* Restore error handler */
- H5Eset_auto(old_func, old_client_data);
-
- /* If opening the file failed, try to create it */
- if (file_id < 0)
- {
- file_id = h5io_file_create(filename, "w");
- if (file_id < 0)
- {
- return -4;
- }
- }
-
- return file_id;
- }
-
- /*
- * Exclusively open file for writing. Fail if file already exists.
- */
- if (strcmp(mode, "x") == 0)
- {
- hid_t file_id;
-
- file_id = h5io_file_create(filename, "x");
-
- if (file_id < 0)
- {
- return -5;
- }
-
- return file_id;
- }
-
- /*
- * Invalid mode was provided.
- */
- return -6;
-}
-
Deleted: cs/benchmark/cigma/trunk/src/h5io/h5group.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/h5group.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/h5group.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,113 +0,0 @@
-#include "hdf5.h"
-#include "h5io.h"
-#include "split.h"
-#include <string.h>
-
-hid_t h5io_group_create(hid_t loc_id, const char *name)
-{
- hid_t group_id;
- herr_t status;
-
- group_id = H5Gcreate(loc_id, name, 0);
- if (group_id < 0)
- {
- return -1;
- }
-
- status = h5io_attr_set_str(group_id, "TITLE", "");
- status = h5io_attr_set_str(group_id, "CLASS", "GROUP");
- status = h5io_attr_set_str(group_id, "VERSION", "1.0");
- status = h5io_attr_set_str(group_id, "PYTABLES_FORMAT_VERSION", "1.5");
-
- return group_id;
-}
-
-
-hid_t h5io_group_open(hid_t loc_id, const char *name)
-{
- return H5Gopen(loc_id, name);
-}
-
-
-hid_t h5io_group_touch(hid_t loc_id, const char *name)
-{
- hid_t group_id;
-
- group_id = H5Gopen(loc_id, name);
-
- if (group_id < 0)
- {
- group_id = h5io_group_create(loc_id, name);
- if (group_id < 0)
- {
- return -1;
- }
- }
-
- return group_id;
-}
-
-
-hid_t h5io_group_touch_path(hid_t loc_id, const char *path)
-{
- hid_t group_id;
-
- /*
- * Temporarily disabling error messages:
- * see http://hdf.ncsa.uiuc.edu/HDF5/doc/Errors.html
- */
- herr_t (*old_func)(void *);
- void *old_client_data;
-
- /* Save old error handler */
- H5Eget_auto(&old_func, &old_client_data);
-
- /* Turn off error handling */
- H5Eset_auto(NULL, NULL);
-
- /* Attempt to open the group */
- group_id = H5Gopen(loc_id, path);
-
- if (group_id < 0)
- {
- herr_t status;
- hid_t parent_id;
- hid_t child_id;
- char **names;
- int i,n;
-
- split(path, strlen(path), &names, &n, '/');
-
- /* first parent */
- parent_id = h5io_group_touch(loc_id, names[0]);
- if (parent_id < 0)
- {
- H5Eset_auto(old_func, old_client_data);
- split_free(names, n);
- return -1;
- }
-
- for (i = 1; i < n; i++)
- {
- /* get child id */
- child_id = h5io_group_touch(parent_id, names[i]);
- if (child_id < 0)
- {
- H5Eset_auto(old_func, old_client_data);
- split_free(names, n);
- return -2;
- }
- /* move to next parent */
- status = H5Gclose(parent_id);
- parent_id = child_id;
- }
-
- /* return last group */
- group_id = parent_id;
- }
-
- /* Restore previous error handler */
- H5Eset_auto(old_func, old_client_data);
-
- return group_id;
-}
Deleted: cs/benchmark/cigma/trunk/src/h5io/h5io.h
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/h5io.h 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/h5io.h 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,144 +0,0 @@
-#ifndef __H5IO_H__
-#define __H5IO_H__
-
-#include "hdf5.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
-/****************************************************************************
- * File and group interface *
- ****************************************************************************/
-hid_t h5io_file_create(const char *filename, const char *mode);
-hid_t h5io_file_open(const char *filename, const char *mode);
-
-hid_t h5io_group_create(hid_t loc_id, const char *name);
-hid_t h5io_group_open(hid_t loc_id, const char *name);
-
-hid_t h5io_group_touch(hid_t loc_id, const char *name);
-hid_t h5io_group_touch_path(hid_t loc_id, const char *path);
-
-
-
-/****************************************************************************
- * Attribute interface *
- ****************************************************************************/
-
-herr_t h5io_attr_find(hid_t loc_id, const char *attr_name);
-herr_t h5io_attr_set(hid_t obj_id, const char *attr_name, hid_t type_id, const void *data);
-herr_t h5io_attr_get(hid_t obj_id, const char *attr_name, hid_t type_id, void *data);
-herr_t h5io_attr_get_dims(hid_t obj_id, const char *attr_name, int *rank, hsize_t *dims);
-
-herr_t h5io_attr_set_str(hid_t obj_id, const char *attr_name, const char *attr_data);
-herr_t h5io_attr_get_str(hid_t obj_id, const char *attr_name, char **data);
-
-herr_t h5io_attr_set_int(hid_t obj_id, const char *attr_name, int n);
-herr_t h5io_attr_set_long(hid_t obj_id, const char *attr_name, long n);
-herr_t h5io_attr_set_llong(hid_t obj_id, const char *attr_name, long long n);
-herr_t h5io_attr_set_float(hid_t obj_id, const char *attr_name, float x);
-herr_t h5io_attr_set_double(hid_t obj_id, const char *attr_name, double x);
-
-herr_t h5io_attr_set_array(hid_t obj_id, const char *attr_name,
- size_t rank, hsize_t *dims, hid_t type_id, const void *data);
-
-herr_t h5io_attr_set_array1(hid_t obj_id, const char *attr_name,
- hsize_t dim, hid_t type_id, const void *data);
-
-herr_t h5io_attr_set_array1_of_ints(hid_t obj_id, const char *attr_name,
- hsize_t dim, const int *data);
-
-herr_t h5io_attr_set_array1_of_floats(hid_t obj_id, const char *attr_name,
- hsize_t dim, const float *data);
-
-herr_t h5io_attr_set_array1_of_doubles(hid_t obj_id, const char *attr_name,
- hsize_t dim, const double *data);
-
-/****************************************************************************
- * Dataset interface *
- ****************************************************************************/
-
-hid_t h5io_dset_create(hid_t loc_id, const char *name, const char *title,
- hid_t type_id, int rank, int *shape);
-
-hid_t h5io_dset_open(hid_t loc_id, const char *name,
- hid_t *type_id, int *rank, int *shape, int *npoints);
-
-
-int h5io_dset_read(hid_t loc_id, const char *name,
- hid_t type_id, int rank, int *shape, void **data);
-
-int h5io_dset_read1(hid_t loc_id, const char *name,
- hid_t type_id, void **data, int *n);
-
-int h5io_dset_read2(hid_t loc_id, const char *name,
- hid_t type_id, void **data, int *m, int *n);
-
-int h5io_dset_read3(hid_t loc_id, const char *name,
- hid_t type_id, void **data, int *l, int *m, int *n);
-
-
-int h5io_dset_write(hid_t loc_id, const char *name, const char *title,
- hid_t type_id, int rank, int *shape, void *data);
-
-int h5io_dset_write1(hid_t loc_id, const char *name, const char *title,
- hid_t type_id, void *data, int n);
-
-int h5io_dset_write2(hid_t loc_id, const char *name, const char *title,
- hid_t type_id, void *data, int m, int n);
-
-int h5io_dset_write3(hid_t loc_id, const char *name, const char *title,
- hid_t type_id, void *data, int l, int m, int n);
-
-
-int h5io_dset_slice_read3(hid_t loc_id,
- const char *name,
- hid_t type_id,
- int rank, hsize_t *dims, void *data,
- int start, int end);
-
-int h5io_dset_slice_write3(hid_t loc_id,
- const char *name,
- const char *title,
- hid_t type_id,
- int start, int end);
-
-/****************************************************************************
- * Array interface *
- ****************************************************************************/
-
-typedef struct {
- int rank;
- hsize_t *shape;
- hid_t type_id;
- void *data;
-} h5array_t;
-
-int h5io_array_init(h5array_t *array, hid_t type_id, int rank, int *shape, void *data);
-int h5io_array_free_dims(h5array_t *array);
-int h5io_array_free_data(h5array_t *array);
-int h5io_array_free(h5array_t *array);
-
-int h5io_array_npoints(h5array_t *array);
-int h5io_array_dim(h5array_t *array, int i);
-void h5io_array_dims(h5array_t *array, int *rank, int **shape);
-void h5io_array_dims1(h5array_t *array, int *n);
-void h5io_array_dims2(h5array_t *array, int *m, int *n);
-void h5io_array_dims3(h5array_t *array, int *l, int *m, int *n);
-
-hid_t h5io_array_open(h5array_t *array, hid_t loc_id, const char *name);
-hid_t h5io_array_create(h5array_t *array, hid_t loc_id, const char *name, const char *title);
-
-int h5io_array_read(h5array_t *array, hid_t loc_id, const char *name);
-int h5io_array_write(h5array_t *array, hid_t loc_id, const char *name);
-
-int h5io_array_slice_read(h5array_t *array, hid_t dataset_id, int start, int end);
-int h5io_array_slice_write(h5array_t *array, hid_t dataset_id, int start, int end);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* __H5IO_H__ */
Deleted: cs/benchmark/cigma/trunk/src/h5io/split.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/split.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/split.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,184 +0,0 @@
-#include <stdlib.h>
-#include <string.h>
-#include <assert.h>
-#include "split.h"
-
-/*
- * Data structure for our basic string tokenizer. Basically, the strategy
- * is to copy the desired string into our buffer, where we can zero out
- * the separator characters in-place. Using a struct allows us to avoid
- * defining global variables like in the version of split.c from the project
- * http://www.nongnu.org/uri/ on which this code is inspired.
- */
-
-typedef struct {
- char separator; /* separator character */
- char **tokens; /* tokens array */
- int token_count; /* real size of tokens array */
- int max_token_count; /* size of tokens array */
- char *buffer; /* buffer string */
- int buffer_length; /* length of buffer string */
-} strtok_t;
-
-
-
-/*
- * In this section, we define the methods for our string tokenizer
- * object. Namely, a constructor, a destructor, and then the actual
- * routine to split the string.
- */
-static void strtok_init(strtok_t *st, char sep)
-{
- /* remember the separator character */
- st->separator = sep;
-
- /* starting up with 0 tokens */
- st->token_count = 0;
-
- /* setup the initial array sizes */
- st->buffer_length = 512; /* 512 chars in buffer */
- st->max_token_count = 16; /* 16 tokens in array */
-
- /* allocate enough tokens and initialize buffer */
- st->buffer = (char *)malloc(st->buffer_length * sizeof(char));
- st->tokens = (char **)malloc(st->max_token_count * sizeof(char *));
-
- return;
-}
-
-static void strtok_free(strtok_t *st)
-{
- if (st != NULL)
- {
- free(st->buffer);
- free(st->tokens);
- }
-}
-
-static void strtok_split(strtok_t *st, const char *s, int len)
-{
- /* Quick validation */
- assert(st->separator != '\0');
-
- /*
- * First, check whether our buffer is large enough to manipulate
- * the string s, and if not, reallocate enough memory.
- */
- if (st->buffer_length < len)
- {
- st->buffer_length = (len < 512) ? 512 : len+1;
- st->buffer = (char *)realloc(st->buffer, st->buffer_length * sizeof(char));
- }
-
- /*
- * Next, copy the string s into our buffer and tokenize it in-place.
- * Essentially, zero out the locations where we find the separator
- * character, while remembering the beginning of each string.
- */
- memcpy(st->buffer, s, len);
- st->buffer[len] = '\0';
- {
- char *first, *p;
- int index, last;
-
- first = st->buffer;
- last = st->buffer_length - 1;
-
- /* remove trailing separators */
- while (last >= 0 && st->buffer[last] == st->separator)
- {
- st->buffer[last] = '\0';
- last--;
- }
-
- /* remove leading separators */
- while(*first == st->separator)
- {
- first++;
- }
-
- /* store first token */
- index = 0;
- st->tokens[index++] = first;
-
- /* keep tokenizing the buffer */
- for (p = strchr(first, st->separator);
- p != NULL;
- p = strchr(p, st->separator))
- {
- /* separator found -- zero it out */
- *p = '\0';
-
- /* make p point to next char */
- p++;
-
- /* store the next token */
- if ((*p != st->separator) && (*p != '\0'))
- {
- st->tokens[index++] = p;
-
- /* check whether we need to expand our tokens array,
- * to make room for the next batch of tokens */
- if (index >= (st->max_token_count))
- {
- st->max_token_count += 16;
- st->tokens = (char **)realloc(st->tokens,
- st->max_token_count * sizeof(char *));
- }
- }
- }
-
- /* store the final count */
- st->token_count = index;
- }
-
- return;
-}
-
-
-
-/*
- * Finally, we provide a public interface to our string tokenizer.
- * The caller subsumes the responsibility of freeing the newly allocated
- * list, as well as each individual string in that list.
- */
-void split(const char *str, int len,
- char ***split_list, int *split_count, char sep)
-{
- int i;
- strtok_t tok;
-
- /* guard against NULL separator */
- if (sep == '\0')
- {
- *split_list = NULL;
- *split_count = 0;
- return;
- }
-
- strtok_init(&tok, sep);
- strtok_split(&tok, str, len);
-
- *split_list = (char **)malloc(tok.token_count * sizeof(char *));
- *split_count = tok.token_count;
-
- for (i = 0; i < tok.token_count; i++)
- {
- (*split_list)[i] = strdup(tok.tokens[i]);
- }
-
- strtok_free(&tok);
-}
-
-void split_free(char **split_list, int split_count)
-{
- int i;
- if (split_list != NULL)
- {
- for (i = 0; i < split_count; i++)
- {
- free(split_list[i]);
- }
- free(split_list);
- }
-}
Deleted: cs/benchmark/cigma/trunk/src/h5io/split.h
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/split.h 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/split.h 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,15 +0,0 @@
-#ifndef __SPLIT_H__
-#define __SPLIT_H__
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-void split(const char *str, int len,
- char ***split_list, int *split_count, char sep);
-
-void split_free(char **split_list, int split_count);
-
-#ifdef __cplusplus
-}
-#endif
-#endif /* __SPLIT_H__ */
Deleted: cs/benchmark/cigma/trunk/src/h5io/t/Makefile
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/t/Makefile 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/t/Makefile 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,31 +0,0 @@
-include ../../../build/variables
-
-H5IO_LIB = ../../../lib/libh5io.a
-
-INCLUDES += $(HDF5_INCLUDES)
-LIBS += $(CIGMA_LIBS)
-LIBS += -lh5io
-LIBS += -lhdf5
-LDFLAGS += -L../../../lib
-LDFLAGS += $(HDF5_LDFLAGS)
-
-OPTIM += -fno-strict-aliasing
-FLAGS += $(INCLUDES)
-
-CFLAGS = $(OPTIM) $(FLAGS) $(LDFLAGS)
-
-TESTS = \
- test_h5file \
- test_h5group \
- test_h5dset \
-
-tests: $(TESTS)
-
-test_%: test_%.c $(H5IO_LIB)
- $(CC) $(CFLAGS) $< -o $@ $(LIBS)
-
-clean:
- rm -f test_io.h5
- rm -f $(TESTS)
-
-.PHONY: clean
Deleted: cs/benchmark/cigma/trunk/src/h5io/t/test_h5dset.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/t/test_h5dset.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/t/test_h5dset.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,78 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include "../h5io.h"
-
-int main(int argc, char *argv[])
-{
- char *filename = "test_io.h5";
-
- hid_t file_id;
- herr_t status;
- int ierr;
-
- /* Open the file */
- file_id = h5io_file_open(filename, "w");
- if (file_id < 0)
- {
- fprintf(stderr, "Could not access '%s'\n", filename);
- return -1;
- }
-
- /* Create a dataset */
- {
- int array[15] = { 1, 2, 3, 4, 5,
- 6, 7, 8, 8, 10,
- 11, 12, 13, 14, 15};
-
- ierr = h5io_dset_write2(file_id, "/myarray", "My integer array",
- H5T_NATIVE_INT, array, 3, 5);
-
- if (ierr < 0)
- {
- fprintf(stderr, "Could not write /myarray\n");
- return -2;
- }
- }
-
- /* Open the file again and try to read the dataset we just wrote */
- {
- int m,n;
- int *myarray;
- hid_t file2;
-
- file2 = h5io_file_open(filename, "rw");
- if (file2 < 0)
- {
- fprintf(stderr, "Could not open '%s' for reading!\n", filename);
- return -3;
- }
-
- ierr = h5io_dset_read2(file2, "/myarray", H5T_NATIVE_INT,
- (void **)&myarray, &m, &n);
- if (ierr < 0)
- {
- fprintf(stderr, "Could not read /myarray\n");
- return -4;
- }
-
- {
- int i,j;
- for (i = 0; i < m; i++)
- {
- for (j = 0; j < n; j++)
- {
- printf("%2d\t", myarray[i*n + j]);
- }
- printf("\n");
- }
- }
-
- free(myarray);
- status = H5Fclose(file2);
- }
-
- /* Clean up */
- status = H5Fclose(file_id);
-
- return 0;
-}
Deleted: cs/benchmark/cigma/trunk/src/h5io/t/test_h5file.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/t/test_h5file.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/t/test_h5file.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,24 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include "hdf5.h"
-#include "../h5io.h"
-
-int main(int argc, char *argv[])
-{
- hid_t file_id;
- herr_t status;
-
- char *filename = "test_io.h5";
-
- file_id = h5io_file_create(filename, "w");
- if (file_id < 0)
- {
- fprintf(stderr, "Error: failed to create file '%s'\n", filename);
- return EXIT_FAILURE;
- }
- printf("Created file '%s'\n", filename);
-
- status = H5Fclose(file_id);
-
- return EXIT_SUCCESS;
-}
Deleted: cs/benchmark/cigma/trunk/src/h5io/t/test_h5group.c
===================================================================
--- cs/benchmark/cigma/trunk/src/h5io/t/test_h5group.c 2008-03-24 17:24:26 UTC (rev 11539)
+++ cs/benchmark/cigma/trunk/src/h5io/t/test_h5group.c 2008-03-25 00:17:49 UTC (rev 11540)
@@ -1,82 +0,0 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include "hdf5.h"
-#include "../h5io.h"
-
-int main(int argc, char *argv[])
-{
- hid_t file_id;
- char *filename = "test_io.h5";
-
- /* groups */
- hid_t model_id;
- hid_t geometry_id;
- hid_t topology_id;
- hid_t solutions_id;
-
- hid_t snapshot0;
- hid_t snapshot1;
- hid_t snapshot2;
-
- hid_t foobarbaz0;
- hid_t foobarbaz1;
- hid_t foobarbaz2;
-
-
- /* error handling */
- herr_t status;
-
- /* open test file, creating it if necessary */
- file_id = h5io_file_open(filename, "rw+");
- if (file_id < 0)
- {
- fprintf(stderr, "Error: failed to open file '%s'\n", filename);
- return EXIT_FAILURE;
- }
-
- #define CHKERR(id) \
- {\
- fprintf(stderr, "Checking " #id "\n");\
- if ((id) < 0)\
- {\
- fprintf(stderr, "Failed to create " #id " (%d)\n", (id));\
- H5Fclose(file_id);\
- return EXIT_FAILURE;\
- }\
- }
-
- model_id = h5io_group_create(file_id, "/model"); CHKERR(model_id);
- geometry_id = h5io_group_create(model_id, "geometry"); CHKERR(geometry_id);
- topology_id = h5io_group_create(model_id, "topology"); CHKERR(topology_id);
- solutions_id = h5io_group_create(file_id, "/model/solutions"); CHKERR(solutions_id);
-
- snapshot0 = h5io_group_touch_path(solutions_id, "snapshot0"); CHKERR(snapshot0);
- snapshot1 = h5io_group_touch_path(model_id, "solutions/snapshot1"); CHKERR(snapshot1);
- snapshot2 = h5io_group_touch_path(file_id, "/model/solutions/snapshot2"); CHKERR(snapshot2);
-
- foobarbaz0 = h5io_group_touch_path(file_id, "/foo/bar/baz"); CHKERR(foobarbaz0);
- foobarbaz1 = h5io_group_touch_path(model_id, "foo/bar/baz"); CHKERR(foobarbaz1);
- foobarbaz2 = h5io_group_touch_path(model_id, "/geometry/foo/bar/baz"); CHKERR(foobarbaz2);
-
- /* touch an existing path */
- H5Gclose(foobarbaz2);
- foobarbaz2 = h5io_group_touch_path(model_id, "/geometry/foo/bar/baz"); CHKERR(foobarbaz2);
-
- /* clean up */
- H5Gclose(model_id);
- H5Gclose(geometry_id);
- H5Gclose(topology_id);
- H5Gclose(solutions_id);
-
- H5Gclose(snapshot0);
- H5Gclose(snapshot1);
- H5Gclose(snapshot2);
-
- H5Gclose(foobarbaz0);
- H5Gclose(foobarbaz1);
- H5Gclose(foobarbaz2);
-
- status = H5Fclose(file_id);
-
- return EXIT_SUCCESS;
-}
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