Apparently this has been reported before as a problem with PETSc/HDF5 integration: https://lists.mcs.anl.gov/pipermail/petsc-users/2012-January/011980.html
On Thu, Nov 9, 2017 at 8:37 AM, Michael K. Edwards <m.k.edwa...@gmail.com> wrote: > 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
