Hi All,
I have time series data sets to write out as HDF5. I wondering whether below data flow is proper. Or is there any potential memory overwrite.
For instance, I am not sure whether H5Dwrite() performs the in-time (not delayed) I/O so that I can close the space_id and dataset_id right afterwards.
Also will "delete[] val_f" right after H5Dwrite() ruin the data on the disk? Is H5Fflush() redundant in this case? Thanks a lot.
//-------------
//initialize file_id, group_id...
for(int t=start_time_step; t<end_time_step; t++){
dim[0] = X;
dim[1] = Y;
float* val_f = new float[dim[0] * dim[1]];
/*assign data to float val_f[dim[0]*dim[1]]*/
for(int i=0; i<dim[0]; i++){
for(int j=0; j<dim[1]; j++){
val_f[i * dim[0] + j] = SomeFunction(i, j);
}
hid_t space_id = H5Screate_simple(2, dim, NULL);
hid_t dataset_id = H5Dcreate(group_id, "position", H5T_IEEE_F32BE, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
herr_t status = H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, space_id, H5S_ALL, H5P_DEFAULT, val_f);
if(status < 0){
std::cout << "H5Dwrite(position) failed. Aborting..." << std::endl;
exit(-1);
}
//H5Fflush(file_id, H5F_SCOPE_LOCAL);
H5Sclose(space_id);
H5Dclose(dataset_id);
delete[] val_f;
}
H5Gclose(group_id);
H5Fclose(file_id);
...
//-------------
Best,
xunlei
Hi Xunlei,
/ Hi All,
/>/ />/ Reporting a weird behavior involving H5Dcreate2(). The only difference
/>/ between 2 below code sections is using "pos" or "position" as the second
/>/ parameter of H5Dcreate2(). I am wondering whether "position" is a
/>/ reserved word/macro in HDF5. When using "position", all the elements
/>/ written in the .h5 file become -4.3160208E8. Please help.
/
There are no reserved names for objects in HDF5 files. This sort of behavior typically indicates a memory overwrite somewhere in the application. I suggest running it with valgrind to see if you can locate the problem.
Quincey
/ Best,
/>/ xunlei
/>/ />/ //---- below code writes INVALID data ----
/>/ /*allocate space, initialization, and etc.*/
/>/ ...
/>/ dim[0] = 100;
/>/ dim[1] = 3;
/>/ for(int j=0; j<dim[0]; j++){
/>/ val_f[ j] = ps[i][j].x;
/>/ val_f[ dim[0] + j] = ps[i][j].y;
/>/ val_f[2 * dim[0] + j] = ps[i][j].z;
/>/ }
/>/ />/ space_id = H5Screate_simple(2, dim, NULL);
/>/ dataset_id = H5Dcreate(group_frame_id, "position", H5T_IEEE_F32BE,
/>/ space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/>/ /* Write data to the dataset; */
/>/ status = H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, space_id, H5S_ALL,
/>/ H5P_DEFAULT, val_f);
/>/ />/ H5Sclose(space_id);
/>/ H5Dclose(dataset_id);
/>/ />/ //---- below code writes CORRECT data ----
/>/ /*allocate space, initialization, and etc.*/
/>/ ...
/>/ dim[0] = 100;
/>/ dim[1] = 3;
/>/ for(int j=0; j<dim[0]; j++){
/>/ val_f[ j] = ps[i][j].x;
/>/ val_f[ dim[0] + j] = ps[i][j].y;
/>/ val_f[2 * dim[0] + j] = ps[i][j].z;
/>/ }
/>/ />/ space_id = H5Screate_simple(2, dim, NULL);
/>/ dataset_id = H5Dcreate(group_frame_id, "pos", H5T_IEEE_F32BE, space_id,
/>/ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/>/ /* Write data to the dataset; */
/>/ status = H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, space_id, H5S_ALL,
/>/ H5P_DEFAULT, val_f);
/>/ />/ H5Sclose(space_id);
/>/ H5Dclose(dataset_id);
/>/ />/ />/ _______________________________________________
/>/ Hdf-forum is for HDF software users discussion.
/>/ Hdf-forum at hdfgroup.org <http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org>
/>/ http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org/
···
On Jan 10, 2010, at 4:43 PM, Xunlei Wu wrote: