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Fix selection npoints in dset multi read/write
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@mattjala
mattjala committed Jun 30, 2023
1 parent cd619bf commit 698b497
Showing 1 changed file with 39 additions and 18 deletions.
57 changes: 39 additions & 18 deletions src/rest_vol_dataset.c
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ const char *external_storage_keys[] = {"externalStorage", (const char *)0}
#define NUM_MAX_HOST_CONNS 25
#define BACKOFF_INITIAL_DURATION 10000000 /* 10,000,000 ns -> 0.01 sec */
#define BACKOFF_SCALE_FACTOR 1.5
#define BACKOFF_MAX_BEFORE_FAIL 4000000000 /* 4,000,000,000 ns -> 4 sec */
#define BACKOFF_MAX_BEFORE_FAIL 3000000000 /* 30,000,000,000 ns -> 30 sec */

/* Default sizes for strings formed when dealing with turning a
* representation of an HDF5 dataspace and a selection within one into JSON
Expand Down Expand Up @@ -436,7 +436,7 @@ RV_dataset_read(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spac
curl_off_t *post_len_arr = NULL;
RV_object_t **datasets = (RV_object_t **)dset;
H5T_class_t dtype_class;
hssize_t mem_select_npoints, file_select_npoints;
hssize_t *mem_select_npoints, *file_select_npoints;
hid_t *mem_space_id = NULL, *file_space_id = NULL;
hbool_t is_transfer_binary = FALSE;
htri_t is_variable_str;
Expand Down Expand Up @@ -512,6 +512,12 @@ RV_dataset_read(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spac
if ((post_len_arr = calloc(count, sizeof(H5S_sel_type *))) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failed to allocate memory for post lengths");

if ((file_select_npoints = calloc(count, sizeof(hsize_t))) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failed to allocate memory for file selection npoints");

if ((mem_select_npoints = calloc(count, sizeof(hsize_t))) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failed to allocate memory for memory selection npoints");

/* Copy mspace and fspace arrays to local copy, to avoid modifying user's arrays */
if ((mem_space_id = calloc(count, sizeof(hid_t *))) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
Expand Down Expand Up @@ -555,7 +561,7 @@ RV_dataset_read(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spac
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set up non global curl write data: %s",
curl_err_buf);

mem_space_id[i] = _mem_space_id[i];
mem_space_id[i] = _mem_space_id[i];
file_space_id[i] = _file_space_id[i];
}

Expand Down Expand Up @@ -626,17 +632,17 @@ RV_dataset_read(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spac
} /* end else */

/* Verify that the number of selected points matches */
if ((mem_select_npoints = H5Sget_select_npoints(mem_space_id[i])) < 0)
if ((mem_select_npoints[i] = H5Sget_select_npoints(mem_space_id[i])) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "memory dataspace is invalid");
if ((file_select_npoints = H5Sget_select_npoints(file_space_id[i])) < 0)
if ((file_select_npoints[i] = H5Sget_select_npoints(file_space_id[i])) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "file dataspace is invalid");
if (mem_select_npoints != file_select_npoints)
if (mem_select_npoints[i] != file_select_npoints[i])
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL,
"memory selection num points != file selection num points");

#ifdef RV_CONNECTOR_DEBUG
printf("-> %lld points selected in file dataspace\n", file_select_npoints);
printf("-> %lld points selected in memory dataspace\n\n", mem_select_npoints);
printf("-> %lld points selected in file dataspace\n", file_select_npoints[i]);
printf("-> %lld points selected in memory dataspace\n\n", mem_select_npoints[i]);
#endif

/* Setup the host header */
Expand Down Expand Up @@ -857,11 +863,15 @@ RV_dataset_read(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spac

/* Scatter the read data out to the supplied read buffer according to the
* mem_type_id and mem_space_id given */
read_data_size = (size_t)file_select_npoints * dtype_size;
read_data_size = (size_t)file_select_npoints[handle_index] * dtype_size;
struct response_read_info resp_info;
resp_info.response_buf = &response_buffers[handle_index];
resp_info.read_size = &read_data_size;

#ifdef RV_CONNECTOR_DEBUG
printf(" Attempting to scatter data from read #%zu\n", handle_index);
#endif

if (H5Dscatter(dataset_read_scatter_op, &resp_info, mem_type_id[handle_index],
mem_space_id[handle_index], buf[handle_index]) < 0)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
Expand All @@ -871,7 +881,7 @@ RV_dataset_read(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spac
if (H5T_STD_REF_OBJ == mem_type_id[handle_index]) {
/* Convert the received binary buffer into a buffer of rest_obj_ref_t's */
if (RV_convert_buffer_to_obj_refs(
response_buffers[handle_index].buffer, (size_t)file_select_npoints,
response_buffers[handle_index].buffer, (size_t)file_select_npoints[handle_index],
(rv_obj_ref_t **)&obj_ref_buf, &read_data_size) < 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTCONVERT, FAIL,
"can't convert ref string/s to object ref array");
Expand Down Expand Up @@ -954,6 +964,7 @@ RV_dataset_read(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spac

if (host_header_arr && host_header_arr[i])
RV_free(host_header_arr[i]);

}

curl_multi_cleanup(curl_multi_handle);
Expand All @@ -971,6 +982,8 @@ RV_dataset_read(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spac
RV_free(failed_handles_to_retry);
RV_free(current_backoff_duration);
RV_free(time_of_fail);
RV_free(file_select_npoints);
RV_free(mem_select_npoints);
PRINT_ERROR_STACK;

return ret_value;
Expand All @@ -997,7 +1010,7 @@ RV_dataset_write(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spa
upload_info *uinfo_arr = NULL;
H5T_class_t dtype_class;
curl_off_t *write_len = NULL;
hssize_t mem_select_npoints, file_select_npoints;
hssize_t *mem_select_npoints, *file_select_npoints;
hid_t *mem_space_id = NULL, *file_space_id = NULL;
hbool_t is_transfer_binary = FALSE;
htri_t is_variable_str;
Expand Down Expand Up @@ -1067,6 +1080,12 @@ RV_dataset_write(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spa
if ((file_space_id = calloc(count, sizeof(hid_t *))) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"failed to allocate memory for file space pointers");

if ((file_select_npoints = calloc(count, sizeof(hsize_t))) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failed to allocate memory for file selection npoints");

if ((mem_select_npoints = calloc(count, sizeof(hsize_t))) == NULL)
FUNC_GOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failed to allocate memory for memory selection npoints");

/* Initialize arrays */
for (size_t i = 0; i < count; i++) {
Expand Down Expand Up @@ -1196,17 +1215,17 @@ RV_dataset_write(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spa
} /* end else */

/* Verify that the number of selected points matches */
if ((mem_select_npoints = H5Sget_select_npoints(mem_space_id[i])) < 0)
if ((mem_select_npoints[i] = H5Sget_select_npoints(mem_space_id[i])) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "memory dataspace is invalid");
if ((file_select_npoints = H5Sget_select_npoints(file_space_id[i])) < 0)
if ((file_select_npoints[i] = H5Sget_select_npoints(file_space_id[i])) < 0)
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "file dataspace is invalid");
if (mem_select_npoints != file_select_npoints)
if (mem_select_npoints[i] != file_select_npoints[i])
FUNC_GOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL,
"memory selection num points != file selection num points");

#ifdef RV_CONNECTOR_DEBUG
printf("-> %lld points selected in file dataspace\n", file_select_npoints);
printf("-> %lld points selected in memory dataspace\n\n", mem_select_npoints);
printf("-> %lld points selected in file dataspace\n", file_select_npoints[i]);
printf("-> %lld points selected in memory dataspace\n\n", mem_select_npoints[i]);
#endif

/* Setup the size of the data being transferred and the data buffer itself (for non-simple
Expand All @@ -1218,12 +1237,12 @@ RV_dataset_write(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spa
if (0 == (dtype_size = H5Tget_size(mem_type_id[i])))
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_BADVALUE, FAIL, "memory datatype is invalid");

write_body_len = (size_t)file_select_npoints * dtype_size;
write_body_len = (size_t)file_select_npoints[i] * dtype_size;
} /* end if */
else {
if (H5T_STD_REF_OBJ == mem_type_id[i]) {
/* Convert the buffer of rest_obj_ref_t's to a binary buffer */
if (RV_convert_obj_refs_to_buffer((const rv_obj_ref_t *)buf[i], (size_t)file_select_npoints,
if (RV_convert_obj_refs_to_buffer((const rv_obj_ref_t *)buf[i], (size_t)file_select_npoints[i],
&(write_bodies[i]), &write_body_len) < 0)
FUNC_GOTO_ERROR(H5E_DATATYPE, H5E_CANTCONVERT, FAIL,
"can't convert object ref/s to ref string/s");
Expand Down Expand Up @@ -1570,6 +1589,8 @@ RV_dataset_write(size_t count, void *dset[], hid_t mem_type_id[], hid_t _mem_spa
RV_free(failed_handles_to_retry);
RV_free(current_backoff_duration);
RV_free(time_of_fail);
RV_free(mem_select_npoints);
RV_free(file_select_npoints);
PRINT_ERROR_STACK;

return ret_value;
Expand Down

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