Hi Jed, These three extra arguments in h5dcreate_f are optional so I am not sure if these three arguments cause the problem. The error is from h5dwrite_f where all the arguments are provided.
I will try to see if I can reproduce the problem in C. Thanks, Danyang On 2020-06-13, 1:39 PM, "Jed Brown" <j...@jedbrown.org> wrote: Can you reproduce in C? You're missing three extra arguments that exist in the Fortran interface. https://support.hdfgroup.org/HDF5/doc/RM/RM_H5D.html#Dataset-Create Danyang Su <danyang...@gmail.com> writes: > 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. > > !c > !c This example uses H5Sset_none to tell H5Dwrite call that > !c there will be no data. 4-th process HAS to participate since > !c we are in a collective mode. > !c > !c The code is ported and modified based on the C example > !c from https://support.hdfgroup.org/ftp/HDF5/examples/parallel/coll_test.c > !c by Danyang Su on June 12, 2020. > !c > !c To compile the code, please run 'make all' > !c To test the code, please run 'mpiexec -n 4 ./hdf5_zero_data' > !c > !c IMPORTNANT NOTE > !c The code may crash on HDF5 1.12.0 but works fine on HDF5 1.10.x. > !c > !c The following platforms have been tested: > !c Macos-Mojave + GNU-8.2 + HDF5-1.12.0 -> Works fine > !c Ubuntu-16.04 + GNU-5.4 + HDF5-1.12.0 -> Crashes > !c Ubuntu-16.04 + GNU-7.5 + HDF5-1.12.0 -> Crashes > !c Ubuntu-16.04 + GNU-5.4 + HDF5-1.10.x -> Works fine > !c Centos-7 + Intel2018 + HDF5-12.0 -> Works fine > !c > !c Possible error when code crashes > !c At line 6686 of file H5_gen.F90 > !c Fortran runtime error: Index '1' of dimension 1 of array 'buf' above upper bound of 0 > !c > > program hdf5_zero_data > > > #include <petsc/finclude/petscsys.h> > > use petscsys > use hdf5 > > implicit none > > character(len=10), parameter :: h5File_Name = "SDS_row.h5" > character(len=8), parameter :: DatasetName = "IntArray" > integer, parameter :: nx = 8, ny = 5, ndim = 2 > > integer :: i > integer :: hdf5_ierr ! HDF5 error code > PetscErrorCode :: ierr > > integer(HID_T) :: file_id ! File identifier > integer(HID_T) :: dset_id ! Dataset identifier > integer(HID_T) :: space_id ! Space identifier > integer(HID_T) :: plist_id ! Property list identifier > integer(HID_T) :: FileSpace ! File identifier > integer(HID_T) :: MemSpace ! Dataset identifier > > integer(HSIZE_T) :: dimsf(2) ! Dataset dimensions > integer(HSIZE_T) :: hcount(2) ! hyperslab selection parameters > integer(HSIZE_T) :: offset(2) ! hyperslab selection parameters > > integer, allocatable :: data(:) ! Dataset to write > > integer :: mpi_size, mpi_rank; > > !c Initialize MPI. > call PetscInitialize(Petsc_Null_Character,ierr) > CHKERRQ(ierr) > call MPI_Comm_rank(Petsc_Comm_World,mpi_rank,ierr) > CHKERRQ(ierr) > call MPI_Comm_size(Petsc_Comm_World,mpi_size,ierr) > CHKERRQ(ierr) > > !c initialize fortran interface > call h5open_f(hdf5_ierr) > > !c Set up file access property list with parallel I/O access. > call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdf5_ierr) > call h5pset_fapl_mpio_f(plist_id, Petsc_Comm_World, & > MPI_INFO_NULL, hdf5_ierr) > > !c Create a new file collectively and release property list identifier. > call h5fcreate_f(h5File_Name, H5F_ACC_TRUNC_F, file_id, & > hdf5_ierr, access_prp = plist_id) > call h5pclose_f(plist_id, hdf5_ierr) > > !c Create the dataspace for the dataset. > dimsf(1) = nx > dimsf(2) = ny > call h5screate_simple_f(ndim, dimsf, FileSpace, hdf5_ierr) > > !c Create the dataset with default properties and close filespace. > call h5dcreate_f(file_id, DatasetName, H5T_NATIVE_INTEGER, & > FileSpace, dset_id, hdf5_ierr) > call h5sclose_f(FileSpace, hdf5_ierr) > > !c Each process defines dataset in memory and writes it to the hyperslab > !c in the file. > if (mpi_rank == 3) then > hcount(1) = 0 > hcount(2) = dimsf(2) > else > hcount(1) = dimsf(1)/mpi_size > hcount(2) = dimsf(2) > end if > > offset(1) = mpi_rank*hcount(1) > offset(2) = 0 > call h5screate_simple_f(ndim, hcount, MemSpace, hdf5_ierr) > > if (mpi_rank == 3) then > call h5sselect_none_f(MemSpace,hdf5_ierr) > end if > > !c Select hyperslab in the file. > call h5dget_space_f(dset_id,FileSpace,hdf5_ierr) > call h5sselect_hyperslab_f(FileSpace, H5S_SELECT_SET_F, & > offset, hcount, hdf5_ierr) > > if (mpi_rank == 3) then > call h5sselect_none_f(FileSpace,hdf5_ierr) > end if > > !c Initialize data buffer. > if (mpi_rank == 3) then > allocate(data(0)) > write(*,*) 'Null data space for processor ',mpi_rank > else > allocate(data(hcount(1)*hcount(2))) > write(*,*) 'Data space for processor ',mpi_rank, 'size',size(data) > do i = 1, hcount(1)*hcount(2) > data(i) = mpi_rank+10 > end do > end if > > !c Create property list for collective dataset write. > call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdf5_ierr) > call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, & > hdf5_ierr) > !c write the dataset collectively > call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, data, hcount, & > hdf5_ierr, file_space_id=FileSpace, & > mem_space_id=MemSpace, xfer_prp = plist_id) > > !c free data. > deallocate(data) > > !c Close/release resources. > call h5dclose_f(dset_id, hdf5_ierr) > call h5sclose_f(FileSpace, hdf5_ierr) > call h5sclose_f(MemSpace, hdf5_ierr) > call h5pclose_f(plist_id, hdf5_ierr) > call h5fclose_f(file_id, hdf5_ierr) > > call PetscFinalize(ierr) > CHKERRQ(ierr) > > return > > end program hdf5_zero_data