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-rw-r--r--testpar/t_mdset.c266
1 files changed, 222 insertions, 44 deletions
diff --git a/testpar/t_mdset.c b/testpar/t_mdset.c
index dab37e2..bfec845 100644
--- a/testpar/t_mdset.c
+++ b/testpar/t_mdset.c
@@ -6,11 +6,16 @@
#define SIZE 32
#define NDATASET 4
#define GROUP_DEPTH 128
-
+enum obj_type { is_group, is_dset };
+
void write_dataset(hid_t, hid_t, hid_t);
int read_dataset(hid_t, hid_t, hid_t);
void create_group_recursive(hid_t, hid_t, hid_t, int);
void recursive_read_group(hid_t, hid_t, hid_t, int);
+void write_attribute(hid_t, int, int);
+int read_attribute(hid_t, int, int);
+int check_value(DATATYPE *, DATATYPE *);
+void get_slab(hssize_t[], hsize_t[], hsize_t[], hsize_t[]);
/*
* Example of using PHDF5 to create ndatasets datasets. Each process write
@@ -25,7 +30,7 @@ void multiple_dset_write(char *filename, int ndatasets)
hsize_t count[DIM]={1,1};
double outme [SIZE][SIZE];
char dname [100];
-
+ herr_t ret;
MPI_Comm_rank (MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size (MPI_COMM_WORLD, &mpi_size);
@@ -47,7 +52,8 @@ void multiple_dset_write(char *filename, int ndatasets)
memspace = H5Screate_simple (DIM, chunk_dims, NULL);
filespace = H5Screate_simple (DIM, file_dims, NULL);
- H5Sselect_hyperslab (filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims);
+ ret = H5Sselect_hyperslab (filespace, H5S_SELECT_SET, chunk_origin, chunk_dims, count, chunk_dims);
+ VRFY((ret>=0), "mdata hyperslab selection");
for (n = 0; n < ndatasets; n++) {
sprintf (dname, "dataset %d", n);
@@ -78,7 +84,26 @@ void multiple_dset_write(char *filename, int ndatasets)
* it creates ngroups groups. Under the first group just created, it creates
* recursive subgroups of depth GROUP_DEPTH. In each created group, it
* generates NDATASETS datasets. Each process write a hyperslab of an array
- * into the file.
+ * into the file. The structure is like
+ *
+ * root group
+ * |
+ * ---------------------------- ... ... ------------------------
+ * | | | ... ... | |
+ * group0*+' group1*+' group2*+' ... ... group ngroups*+'
+ * |
+ * 1st_child_group*'
+ * |
+ * 2nd_child_group*'
+ * |
+ * :
+ * :
+ * |
+ * GROUP_DEPTHth_child_group*'
+ *
+ * * means the group has dataset(s).
+ * + means the group has attribute(s).
+ * ' means the datasets in the groups have attribute(s).
*/
void multiple_group_write(char *filename, int ngroups)
{
@@ -87,8 +112,8 @@ void multiple_group_write(char *filename, int ngroups)
char gname[64];
hid_t fid, gid, plist, memspace, filespace;
hssize_t chunk_origin[DIM];
- hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM]={1,1};
-
+ hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM];
+ herr_t ret1, ret2;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
@@ -98,29 +123,35 @@ void multiple_group_write(char *filename, int ngroups)
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist);
H5Pclose(plist);
-
- chunk_origin[0] = mpi_rank * (SIZE/mpi_size);
- chunk_origin[1] = 0;
- chunk_dims[0] = SIZE / mpi_size;
- chunk_dims[1] = SIZE;
-
- for(l=0; l<DIM; l++)
- file_dims[l] = SIZE;
+ /* decide the hyperslab according to process number. */
+ get_slab(chunk_origin, chunk_dims, count, file_dims);
- memspace = H5Screate_simple(DIM, chunk_dims, NULL);
+ /* select hyperslab in memory and file spaces. These two operations are
+ * identical since the datasets are the same. */
+ memspace = H5Screate_simple(DIM, file_dims, NULL);
+ ret1 = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin,
+ chunk_dims, count, chunk_dims);
filespace = H5Screate_simple(DIM, file_dims, NULL);
- H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims,
- count, chunk_dims);
-
+ ret2 = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin,
+ chunk_dims, count, chunk_dims);
+ VRFY((memspace>=0), "memspace");
+ VRFY((filespace>=0), "filespace");
+ VRFY((ret1>=0), "mgroup memspace selection");
+ VRFY((ret2>=0), "mgroup filespace selection");
+
/* creates ngroups groups under the root group, writes datasets in
* parallel. */
for(m = 0; m < ngroups; m++) {
- sprintf(gname, "/group%d", m);
+ sprintf(gname, "group%d", m);
gid = H5Gcreate(fid, gname, 0);
VRFY((gid > 0), gname);
-
+
+ /* create attribute for these groups. */
+ write_attribute(gid, is_group, m);
+
if(m != 0)
- write_dataset(memspace, filespace, gid);
+ write_dataset(memspace, filespace, gid);
+
H5Gclose(gid);
if(! ((m+1) % 10)) {
@@ -146,26 +177,31 @@ void multiple_group_write(char *filename, int ngroups)
void write_dataset(hid_t memspace, hid_t filespace, hid_t gid)
{
int i, j, n;
- int mpi_rank;
+ int mpi_rank, mpi_size;
char dname[32];
DATATYPE outme[SIZE][SIZE];
hid_t did;
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
for(n=0; n < NDATASET; n++) {
sprintf(dname, "dataset%d", n);
- did = H5Dcreate(gid, dname, H5T_NATIVE_DOUBLE, filespace,
+ did = H5Dcreate(gid, dname, H5T_NATIVE_INT, filespace,
H5P_DEFAULT);
VRFY((did > 0), dname);
for(i=0; i < SIZE; i++)
for(j=0; j < SIZE; j++)
- outme[i][j] = n*1000 + mpi_rank;
+ outme[i][j] = n*1000 + mpi_rank;
- H5Dwrite(did, H5T_NATIVE_DOUBLE, memspace, filespace, H5P_DEFAULT,
+ H5Dwrite(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT,
outme);
+
+ /* create attribute for these datasets.*/
+ write_attribute(did, is_dset, n);
+
H5Dclose(did);
}
}
@@ -212,7 +248,7 @@ void multiple_group_read(char *filename, int ngroups)
char gname[64];
hid_t plist, fid, gid, memspace, filespace;
hssize_t chunk_origin[DIM];
- hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM]={1,1};
+ hsize_t chunk_dims[DIM], file_dims[DIM], count[DIM];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
@@ -222,30 +258,33 @@ void multiple_group_read(char *filename, int ngroups)
fid = H5Fopen(filename, H5F_ACC_RDONLY, plist);
H5Pclose(plist);
- chunk_origin[0] = mpi_rank * (SIZE/mpi_size);
- chunk_origin[1] = 0;
- chunk_dims[0] = SIZE / mpi_size;
- chunk_dims[1] = SIZE;
+ /* decide hyperslab for each process */
+ get_slab(chunk_origin, chunk_dims, count, file_dims);
- for(l=0; l<DIM; l++)
- file_dims[l] = SIZE;
-
- memspace = H5Screate_simple(DIM, chunk_dims, NULL);
+ /* select hyperslab for memory and file space */
+ memspace = H5Screate_simple(DIM, file_dims, NULL);
+ H5Sselect_hyperslab(memspace, H5S_SELECT_SET, chunk_origin, chunk_dims,
+ count, chunk_dims);
filespace = H5Screate_simple(DIM, file_dims, NULL);
-
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, chunk_origin, chunk_dims,
count, chunk_dims);
/* open every group under root group. */
for(m=0; m<ngroups; m++) {
- sprintf(gname, "/group%d", m);
+ sprintf(gname, "group%d", m);
gid = H5Gopen(fid, gname);
VRFY((gid > 0), gname);
/* check the data. */
if(m != 0)
if( error_num = read_dataset(memspace, filespace, gid) )
- nerrors += error_num;
+ nerrors += error_num;
+
+ /* check attribute.*/
+ error_num = 0;
+ if( error_num = read_attribute(gid, is_group, m) )
+ nerrors += error_num;
+
H5Gclose(gid);
if(!((m+1)%10))
@@ -270,27 +309,40 @@ void multiple_group_read(char *filename, int ngroups)
*/
int read_dataset(hid_t memspace, hid_t filespace, hid_t gid)
{
- int i, j, n, mpi_rank, vrfy_errors=0;
+ int i, j, n, mpi_rank, mpi_size, attr_errors=0, vrfy_errors=0;
char dname[32];
- DATATYPE outdata[SIZE][SIZE], indata[SIZE][SIZE];
+ DATATYPE *outdata, *indata;
hid_t did;
hsize_t block[DIM]={SIZE,SIZE};
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
+
+ indata = (DATATYPE*)malloc(SIZE*SIZE*sizeof(DATATYPE));
+ outdata = (DATATYPE*)malloc(SIZE*SIZE*sizeof(DATATYPE));
for(n=0; n<NDATASET; n++) {
sprintf(dname, "dataset%d", n);
did = H5Dopen(gid, dname);
VRFY((did>0), dname);
- H5Dread(did, H5T_NATIVE_DOUBLE, memspace, filespace, H5P_DEFAULT,
+ H5Dread(did, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT,
indata);
+ /* this is the original value */
for(i=0; i<SIZE; i++)
- for(j=0; j<SIZE; j++)
- outdata[i][j] = n*1000 + mpi_rank;
-
- vrfy_errors = dataset_vrfy(NULL, NULL, NULL, block, indata, outdata);
+ for(j=0; j<SIZE; j++) {
+ *outdata = n*1000 + mpi_rank;
+ outdata++;
+ }
+ outdata -= SIZE*SIZE;
+
+ /* compare the original value(outdata) to the value in file(indata).*/
+ vrfy_errors = check_value(indata, outdata);
+
+ /* check attribute.*/
+ if( attr_errors = read_attribute(did, is_dset, n) )
+ vrfy_errors += attr_errors;
H5Dclose(did);
}
@@ -324,3 +376,129 @@ void recursive_read_group(hid_t memspace, hid_t filespace, hid_t gid,
H5Gclose(child_gid);
}
}
+
+/* Create and write attribute for a group or a dataset. For groups, attribute
+ * is a scalar datum; for dataset, it is a one-dimensional array.
+ */
+void write_attribute(hid_t obj_id, int this_type, int num)
+{
+ hid_t sid, aid;
+ hsize_t dspace_dims[1]={8};
+ int i, mpi_rank, attr_data[8], dspace_rank=1;
+ char attr_name[32];
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+
+ if(this_type == is_group) {
+ sprintf(attr_name, "Group Attribute %d", num);
+ sid = H5Screate(H5S_SCALAR);
+ aid = H5Acreate(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT);
+ if(MAINPROCESS)
+ H5Awrite(aid, H5T_NATIVE_INT, &num);
+ H5Aclose(aid);
+ H5Sclose(sid);
+ }
+ else if(this_type == is_dset) {
+ sprintf(attr_name, "Dataset Attribute %d", num);
+ for(i=0; i<8; i++)
+ attr_data[i] = i;
+ sid = H5Screate_simple(dspace_rank, dspace_dims, NULL);
+ aid = H5Acreate(obj_id, attr_name, H5T_NATIVE_INT, sid, H5P_DEFAULT);
+ if(MAINPROCESS)
+ H5Awrite(aid, H5T_NATIVE_INT, attr_data);
+ H5Aclose(aid);
+ H5Sclose(sid);
+ }
+
+}
+
+/* Read and verify attribute for group or dataset. */
+int read_attribute(hid_t obj_id, int this_type, int num)
+{
+ hid_t aid;
+ hsize_t group_block[2]={1,1}, dset_block[2]={1, 8};
+ int i, mpi_rank, in_num, in_data[8], out_data[8], vrfy_errors = 0;
+ char attr_name[32];
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+
+ if(this_type == is_group) {
+ sprintf(attr_name, "Group Attribute %d", num);
+ aid = H5Aopen_name(obj_id, attr_name);
+ if(MAINPROCESS) {
+ H5Aread(aid, H5T_NATIVE_INT, &in_num);
+ vrfy_errors = dataset_vrfy(NULL, NULL, NULL, group_block,
+ &in_num, &num);
+ }
+ H5Aclose(aid);
+ }
+ else if(this_type == is_dset) {
+ sprintf(attr_name, "Dataset Attribute %d", num);
+ for(i=0; i<8; i++)
+ out_data[i] = i;
+ aid = H5Aopen_name(obj_id, attr_name);
+ if(MAINPROCESS) {
+ H5Aread(aid, H5T_NATIVE_INT, in_data);
+ vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data,
+ out_data);
+ }
+ H5Aclose(aid);
+ }
+
+ return vrfy_errors;
+}
+
+/* This functions compares the original data with the read-in data for its
+ * hyperslab part only by process ID. */
+int check_value(DATATYPE *indata, DATATYPE *outdata)
+{
+ int mpi_rank, mpi_size, i, j, err_num=0;
+ hssize_t chunk_origin[DIM];
+ hsize_t chunk_dims[DIM], count[DIM];
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
+
+ get_slab(chunk_origin, chunk_dims, count, NULL);
+
+ indata += chunk_origin[0]*SIZE;
+ outdata += chunk_origin[0]*SIZE;
+ for(i=chunk_origin[0]; i<(chunk_origin[0]+chunk_dims[0]); i++)
+ for(j=chunk_origin[1]; j<(chunk_origin[1]+chunk_dims[1]); j++) {
+ if( *indata != *outdata )
+ if(err_num++ < MAX_ERR_REPORT || verbose)
+ printf("Dataset Verify failed at [%d][%d](row %d, col%d): expect %d, got %d\n", i, j, i, j, *outdata, *indata);
+ }
+ if(err_num > MAX_ERR_REPORT && !verbose)
+ printf("[more errors ...]\n");
+ if(err_num)
+ printf("%d errors found in check_value\n", err_num);
+ return err_num;
+}
+
+/* Decide the portion of data chunk in dataset by process ID. */
+void get_slab(hssize_t chunk_origin[], hsize_t chunk_dims[], hsize_t count[],
+ hsize_t file_dims[])
+{
+ int mpi_rank, mpi_size;
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
+
+ if(chunk_origin != NULL) {
+ chunk_origin[0] = mpi_rank * (SIZE/mpi_size);
+ chunk_origin[1] = 0;
+ }
+ if(chunk_dims != NULL) {
+ chunk_dims[0] = SIZE/mpi_size;
+ chunk_dims[1] = SIZE;
+ }
+ if(file_dims != NULL)
+ file_dims[0] = file_dims[1] = SIZE;
+ if(count != NULL)
+ count[0] = count[1] = 1;
+}
+
+/*=============================================================================
+ * End of t_mdset.c
+ *===========================================================================*/