Thank you for the validation, and for the suggestion to use H5Sselect_none(). That is probably the right thing for the dataspace. Not quite sure what to do about the memspace, though; the comment is correct that we crash if any of the dimensions is zero.
On Thu, Nov 9, 2017 at 8:34 AM, Jordan Henderson <jhender...@hdfgroup.org> wrote: > It seems you're discovering the issues right as I'm typing this! > > > I'm glad you were able to solve the issue with the hanging. I was starting > to suspect an issue with the MPI implementation but it's usually the last > thing on the list after inspecting the code itself. > > > As you've seen, it seems that PETSc is creating a NULL dataspace for the > ranks which are not contributing, instead of creating a Scalar/Simple > dataspace on all ranks and calling H5Sselect_none() for those that don't > participate. This would most likely explain the reason you saw the assertion > failure in the non-filtered case, as the legacy code probably was not > expecting to receive a NULL dataspace. On top of that, the NULL dataspace > seems like it is causing the parallel operation to break collective mode, > which is not allowed when filters are involved. I would need to do some > research as to why this happens before deciding whether it's more > appropriate to modify this in HDF5 or to have PETSc not use NULL dataspaces. > > > Avoiding deadlock from the final sort has been an issue I had to re-tackle a > few different times due to the nature of the code's complexity, but I will > investigate using the chunk offset as a secondary sort key and see if it > will run into problems in any other cases. Ideally, the chunk redistribution > might be updated in the future to involve all ranks in the operation instead > of just rank 0, also allowing for improvements to the redistribution > algorithm that may solve these problems, but for the time being this may be > sufficient. _______________________________________________ Hdf-forum is for HDF software users discussion. Hdf-forum@lists.hdfgroup.org http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
