Hi Jed, Attached is the example for your test.
This example uses H5Sset_none to tell H5Dwrite call that there will be no data. 4-th process HAS to participate we are in a collective mode. The code is ported and modified based on the C example from https://support.hdfgroup.org/ftp/HDF5/examples/parallel/coll_test.c The compiling flags in the makefile are same as those used in my own code. To compile the code, please run 'make all' To test the code, please run 'mpiexec -n 4 ./hdf5_zero_data'. Any number of processors larger than 4 should help to detect the problem. The code may crash on HDF5 1.12.0 but works fine on HDF5 1.10.x. The following platforms have been tested: Macos-Mojave + GNU-8.2 + HDF5-1.12.0 -> Works fine Ubuntu-16.04 + GNU-5.4 + HDF5-1.12.0 -> Crashes Ubuntu-16.04 + GNU-7.5 + HDF5-1.12.0 -> Crashes Ubuntu-16.04 + GNU-5.4 + HDF5-1.10.x -> Works fine Centos-7 + Intel2018 + HDF5-12.0 -> Works fine Possible error when code crashes At line 6686 of file H5_gen.F90 Fortran runtime error: Index '1' of dimension 1 of array 'buf' above upper bound of 0 Thanks, Danyang On 2020-06-12, 6:05 AM, "Jed Brown" <j...@jedbrown.org> wrote: Danyang Su <danyang...@gmail.com> writes: > Hi Jed, > > Thanks for your double check. > > The HDF 1.10.6 version also works. But versions from 1.12.x stop working. I'd suggest making a reduced test case in order to submit a bug report. This was the relevant change in PETSc for hdf5-1.12. https://gitlab.com/petsc/petsc/commit/806daeb7de397195b5132278177f4d5553f9f612 > Attached is the code section where I have problem. > > !c write the dataset collectively > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!! CODE CRASHES HERE IF SOME PROCESSORS HAVE NO DATA TO WRITE!!!! > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, hdf5_dsize, & > hdf5_ierr, file_space_id=filespace, & > mem_space_id=memspace, xfer_prp = xlist_id) > > Please let me know if there is something wrong in the code that causes the problem.
hdf5_zero_data.F90
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makefile
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