Here is my context: I compute velocities in a 3D mesh. This mesh is divide in subdomain (cubes) for every MPI job. I can dump all the domain thanks to parallel hdf5 routines.
But, I would like to dump also a slice of this domain via parallel hdf5 (I mean, I want to use a collective write). In this case, the slice is only included in a few subdomains. So, for the other subdomains/mpi job, the dimensions of their hyperslab part are null.
For a collective I/O, all mpi-job must to pass through the CALL h5dwrite_f(...,...,data,dims,...). Some mpi-job (in fact, a lot!) have data and dims equal to zero.
My code crashs! HDF5 complains about
"H5Screate_simple(): zero sized dimension for non-unlimited dimension"
How can I handle this without create a smaller communicator??
On Jun 15, 2011, at 4:44 PM, Stéphane Backaert wrote:
Hello!
Here is my context: I compute velocities in a 3D mesh. This mesh is divide in subdomain (cubes) for every MPI job. I can dump all the domain thanks to parallel hdf5 routines.
But, I would like to dump also a slice of this domain via parallel hdf5 (I mean, I want to use a collective write). In this case, the slice is only included in a few subdomains. So, for the other subdomains/mpi job, the dimensions of their hyperslab part are null.
For a collective I/O, all mpi-job must to pass through the CALL h5dwrite_f(...,...,data,dims,...). Some mpi-job (in fact, a lot!) have data and dims equal to zero.
My code crashs! HDF5 complains about
"H5Screate_simple(): zero sized dimension for non-unlimited dimension"
How can I handle this without create a smaller communicator??
I believe that we have addressed this limitation with the 1.8.7 release. Can you give that a try?
Yes, it have been addressed!
Unfortunately, the hdf5 library on the cluster I have to use is older. The solution is to add an "if(data ==null) h5sselect_none(fspace_id) or h5sselect_none(mspace_id) " before the h5dwrite.
I found this trick on this forum...
Thanks!
Stephane
···
On 20 juin 2011, at 22:55, Quincey Koziol wrote:
Hi Stephane,
On Jun 15, 2011, at 4:44 PM, Stéphane Backaert wrote:
Hello!
Here is my context: I compute velocities in a 3D mesh. This mesh is divide in subdomain (cubes) for every MPI job. I can dump all the domain thanks to parallel hdf5 routines.
But, I would like to dump also a slice of this domain via parallel hdf5 (I mean, I want to use a collective write). In this case, the slice is only included in a few subdomains. So, for the other subdomains/mpi job, the dimensions of their hyperslab part are null.
For a collective I/O, all mpi-job must to pass through the CALL h5dwrite_f(...,...,data,dims,...). Some mpi-job (in fact, a lot!) have data and dims equal to zero.
My code crashs! HDF5 complains about
"H5Screate_simple(): zero sized dimension for non-unlimited dimension"
How can I handle this without create a smaller communicator??
I believe that we have addressed this limitation with the 1.8.7 release. Can you give that a try?
