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Diffstat (limited to 'HDF5Examples/FORTRAN/H5PAR/ph5_f90_subfiling.F90')
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diff --git a/HDF5Examples/FORTRAN/H5PAR/ph5_f90_subfiling.F90 b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_subfiling.F90 new file mode 100644 index 0000000..fc30717 --- /dev/null +++ b/HDF5Examples/FORTRAN/H5PAR/ph5_f90_subfiling.F90 @@ -0,0 +1,521 @@ +! +! Example of using HDF5's Subfiling VFD to write to an +! HDF5 file that is striped across multiple subfiles +! +! If the HDF5_NOCLEANUP environment variable is set, the +! files that this example creates will not be removed as +! the example finishes. +! +! In general, the current working directory in which compiling +! is done, is not suitable for parallel I/O and there is no +! standard pathname for parallel file systems. In some cases, +! the parallel file name may even need some parallel file type +! prefix such as: "pfs:/GF/...". Therefore, this example parses +! the HDF5_PARAPREFIX environment variable for a prefix, if one +! is needed. +! + +MODULE subf + + USE HDF5 + USE MPI + + CHARACTER(LEN=31), PARAMETER :: EXAMPLE_FILE = "h5_subfiling_default_example.h5" + CHARACTER(LEN=30), PARAMETER :: EXAMPLE_FILE2 = "h5_subfiling_custom_example.h5" + CHARACTER(LEN=33), PARAMETER :: EXAMPLE_FILE3 = "h5_subfiling_precreate_example.h5" + + CHARACTER(LEN=4), PARAMETER :: EXAMPLE_DSET_NAME = "DSET" + INTEGER , PARAMETER :: EXAMPLE_DSET_DIMS = 2 + + ! Have each MPI rank write 16MiB of data + INTEGER, PARAMETER :: EXAMPLE_DSET_NY = 4194304 + +CONTAINS + + ! Cleanup created files + + SUBROUTINE cleanup(filename, fapl_id) + + IMPLICIT NONE + INTEGER(HID_T) :: fapl_id + CHARACTER(*) :: filename + + LOGICAL :: do_cleanup + INTEGER :: status + + CALL get_environment_variable("HDF5_NOCLEANUP", STATUS=status) + !IF(status.EQ.0) CALL H5Fdelete_f(filename, fapl_id, status) + IF(status.EQ.0)THEN + OPEN(UNIT=15, IOSTAT=status, FILE=filename, STATUS='old') + IF(status .EQ. 0) CLOSE(15, STATUS='DELETE') + ENDIF + + END SUBROUTINE cleanup + + ! An example of using the HDF5 Subfiling VFD with + ! its default settings of 1 subfile per node, with + ! a stripe size of 32MiB + + SUBROUTINE subfiling_write_default(fapl_id, mpi_size, mpi_rank) + + IMPLICIT NONE + INTEGER(HID_T) :: fapl_id + INTEGER :: mpi_size + INTEGER :: mpi_rank + + INTEGER, DIMENSION(:), ALLOCATABLE, TARGET :: wdata + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: dset_dims + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: start + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: count + INTEGER(hid_t) :: file_id + INTEGER(hid_t) :: subfiling_fapl + INTEGER(hid_t) :: dset_id + INTEGER(hid_t) :: filespace + CHARACTER(LEN=512) :: filename, par_prefix + INTEGER :: status + INTEGER(SIZE_T) :: i + TYPE(C_PTR) :: f_ptr + + ! + ! Make a copy of the FAPL so we don't disturb + ! it for the other examples + ! + CALL H5Pcopy_f(fapl_id, subfiling_fapl, status) + + ! + ! Set Subfiling VFD on FAPL using default settings + ! (use IOC VFD, 1 IOC per node, 32MiB stripe size) + ! + ! Note that all of Subfiling's configuration settings + ! can be adjusted with environment variables as well + ! in this case. + ! + + CALL H5Pset_fapl_subfiling_f(subfiling_fapl, status) + + ! + ! OPTIONAL: Set alignment of objects in HDF5 file to + ! be equal to the Subfiling stripe size. + ! Choosing a Subfiling stripe size and HDF5 + ! object alignment value that are some + ! multiple of the disk block size can + ! generally help performance by ensuring + ! that I/O is well-aligned and doesn't + ! excessively cross stripe boundaries. + ! + ! Note that this option can substantially + ! increase the size of the resulting HDF5 + ! files, so it is a good idea to keep an eye + ! on this. + ! + + CALL H5Pset_alignment_f(subfiling_fapl, 0_HSIZE_T, 33554432_HSIZE_T, status) ! ALIGN to default 32MiB stripe size + + ! Parse any parallel prefix and create filename + par_prefix(:) = "" + CALL get_environment_variable("HDF5_PARAPREFIX", VALUE=par_prefix, STATUS=status) + filename = TRIM(par_prefix)//EXAMPLE_FILE + + ! Create a new file collectively + CALL H5Fcreate_f(filename, H5F_ACC_TRUNC_F, file_id, status, access_prp = subfiling_fapl) + + ! Create the dataspace for the dataset. The second + ! dimension varies with the number of MPI ranks + ! while the first dimension is fixed. + + dset_dims(1) = EXAMPLE_DSET_NY + dset_dims(2) = mpi_size + CALL H5Screate_simple_f(EXAMPLE_DSET_DIMS, dset_dims, filespace, status) + + ! Create the dataset with default properties + + CALL H5Dcreate_f(file_id, EXAMPLE_DSET_NAME, H5T_NATIVE_INTEGER, filespace, dset_id, status) + ! Each MPI rank writes from a contiguous memory + ! region to the hyperslab in the file + + start(1) = 0 + start(2) = mpi_rank + count(1) = dset_dims(1) + count(2) = 1 + CALL H5Sselect_hyperslab_f(filespace, H5S_SELECT_SET_F, start, count, status) + + ! Initialize data buffer + ALLOCATE(wdata(COUNT(1)*COUNT(2))) + DO i = 1, COUNT(1)*COUNT(2) + wdata(i) = mpi_rank + ENDDO + + ! Write to dataset + f_ptr = C_LOC(wdata) + CALL H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER, f_ptr, status, mem_space_id=H5S_BLOCK_F, file_space_id=filespace) + + ! Close/release resources. + DEALLOCATE(wdata) + CALL H5Dclose_f(dset_id, status) + CALL H5Sclose_f(filespace, status) + + CALL H5Fclose_f(file_id, status) + + CALL cleanup(EXAMPLE_FILE, subfiling_fapl) + + CALL H5Pclose_f(subfiling_fapl, status) + + END SUBROUTINE subfiling_write_default + + ! + ! An example of using the HDF5 Subfiling VFD with + ! custom settings + ! + + SUBROUTINE subfiling_write_custom(fapl_id, mpi_size, mpi_rank) + + IMPLICIT NONE + INTEGER(HID_T) :: fapl_id + INTEGER :: mpi_size + INTEGER :: mpi_rank + + INTEGER, DIMENSION(:), ALLOCATABLE, TARGET :: wdata + + TYPE(H5FD_subfiling_config_t) :: subf_config + TYPE(H5FD_ioc_config_t) :: ioc_config + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: dset_dims + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: start + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: count + INTEGER(hid_t) :: file_id + INTEGER(hid_t) :: subfiling_fapl + INTEGER(hid_t) :: dset_id + INTEGER(hid_t) :: filespace + CHARACTER(LEN=512) :: filename, par_prefix + INTEGER :: status + INTEGER(SIZE_T) :: i + TYPE(C_PTR) :: f_ptr + + ! Make a copy of the FAPL so we don't disturb + ! it for the other examples + + CALL H5Pcopy_f(fapl_id, subfiling_fapl, status) + + ! Get a default Subfiling and IOC configuration + CALL h5pget_fapl_subfiling_f(subfiling_fapl, subf_config, status) + CALL h5pget_fapl_ioc_f(subfiling_fapl,ioc_config, status) + + ! Set Subfiling configuration to use a 1MiB + ! stripe size and the SELECT_IOC_EVERY_NTH_RANK + ! selection method. By default, without a setting + ! in the H5FD_SUBFILING_IOC_SELECTION_CRITERIA + ! environment variable, this will use every MPI + ! rank as an I/O concentrator. + + subf_config%shared_cfg%stripe_size = 1048576 + subf_config%shared_cfg%ioc_selection = SELECT_IOC_EVERY_NTH_RANK_F + + ! Set IOC configuration to use 2 worker threads + ! per IOC instead of the default setting and + ! update IOC configuration with new subfiling + ! configuration. + + ioc_config%thread_pool_size = 2 + + ! Set our new configuration on the IOC + ! FAPL used for Subfiling + + CALL H5Pset_fapl_ioc_f(subf_config%ioc_fapl_id, status, ioc_config) + + ! Finally, set our new Subfiling configuration + ! on the original FAPL + + CALL H5Pset_fapl_subfiling_f(subfiling_fapl, status, subf_config) + ! + ! OPTIONAL: Set alignment of objects in HDF5 file to + ! be equal to the Subfiling stripe size. + ! Choosing a Subfiling stripe size and HDF5 + ! object alignment value that are some + ! multiple of the disk block size can + ! generally help performance by ensuring + ! that I/O is well-aligned and doesn't + ! excessively cross stripe boundaries. + ! + ! Note that this option can substantially + ! increase the size of the resulting HDF5 + ! files, so it is a good idea to keep an eye + ! on this. + ! + + CALL H5Pset_alignment_f(subfiling_fapl, 0_HSIZE_T, 33554432_HSIZE_T, status) ! ALIGN to default 32MiB stripe size + + ! Parse any parallel prefix and create filename + par_prefix(:) = "" + CALL get_environment_variable("HDF5_PARAPREFIX", VALUE=par_prefix, STATUS=status) + filename = TRIM(par_prefix)//EXAMPLE_FILE + + ! Create a new file collectively + CALL H5Fcreate_f(filename, H5F_ACC_TRUNC_F, file_id, status, access_prp = subfiling_fapl) + + ! Create the dataspace for the dataset. The second + ! dimension varies with the number of MPI ranks + ! while the first dimension is fixed. + + dset_dims(1) = EXAMPLE_DSET_NY + dset_dims(2) = mpi_size + CALL H5Screate_simple_f(EXAMPLE_DSET_DIMS, dset_dims, filespace, status) + + ! Create the dataset with default properties + + CALL H5Dcreate_f(file_id, EXAMPLE_DSET_NAME, H5T_NATIVE_INTEGER, filespace, dset_id, status) + ! Each MPI rank writes from a contiguous memory + ! region to the hyperslab in the file + + start(1) = 0 + start(2) = mpi_rank + count(1) = dset_dims(1) + count(2) = 1 + CALL H5Sselect_hyperslab_f(filespace, H5S_SELECT_SET_F, start, count, status) + + ! Initialize data buffer + ALLOCATE(wdata(COUNT(1)*COUNT(2))) + DO i = 1, COUNT(1)*COUNT(2) + wdata(i) = mpi_rank + ENDDO + + ! Write to dataset + f_ptr = C_LOC(wdata) + CALL H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER, f_ptr, status, mem_space_id=H5S_BLOCK_F, file_space_id=filespace) + + ! Close/release resources. + DEALLOCATE(wdata) + CALL H5Dclose_f(dset_id, status) + CALL H5Sclose_f(filespace, status) + + CALL H5Fclose_f(file_id, status) + + CALL cleanup(EXAMPLE_FILE, subfiling_fapl) + + CALL H5Pclose_f(subfiling_fapl, status) + + END SUBROUTINE subfiling_write_custom + + ! + ! An example of pre-creating an HDF5 file on MPI rank + ! 0 when using the HDF5 Subfiling VFD. In this case, + ! the subfiling stripe count must be set so that rank + ! 0 knows how many subfiles to pre-create. + + SUBROUTINE subfiling_write_precreate(fapl_id, mpi_size, mpi_rank) + + IMPLICIT NONE + INTEGER(HID_T) :: fapl_id + INTEGER :: mpi_size + INTEGER :: mpi_rank + + INTEGER, DIMENSION(:), ALLOCATABLE, TARGET :: wdata + TYPE(H5FD_subfiling_config_t) :: subf_config + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: dset_dims + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: start + INTEGER(hsize_t), DIMENSION(1:EXAMPLE_DSET_DIMS) :: count + INTEGER(hid_t) :: file_id + INTEGER(hid_t) :: subfiling_fapl + INTEGER(hid_t) :: dset_id + INTEGER(hid_t) :: filespace + CHARACTER(LEN=512) :: filename, par_prefix + INTEGER :: status + INTEGER(SIZE_T) :: i + TYPE(C_PTR) :: f_ptr + + ! Make a copy of the FAPL so we don't disturb + ! it for the other examples + + CALL H5Pcopy_f(fapl_id, subfiling_fapl, status) + + ! Get a default Subfiling and IOC configuration + CALL h5pget_fapl_subfiling_f(subfiling_fapl, subf_config, status) + + ! + ! Set the Subfiling stripe count so that rank + ! 0 knows how many subfiles the logical HDF5 + ! file should consist of. In this case, use + ! 5 subfiles with a default stripe size of + ! 32MiB. + + subf_config%shared_cfg%stripe_count = 5 + ! + ! OPTIONAL: Set alignment of objects in HDF5 file to + ! be equal to the Subfiling stripe size. + ! Choosing a Subfiling stripe size and HDF5 + ! object alignment value that are some + ! multiple of the disk block size can + ! generally help performance by ensuring + ! that I/O is well-aligned and doesn't + ! excessively cross stripe boundaries. + ! + ! Note that this option can substantially + ! increase the size of the resulting HDF5 + ! files, so it is a good idea to keep an eye + ! on this. + ! + + CALL H5Pset_alignment_f(subfiling_fapl, 0_HSIZE_T, 1048576_HSIZE_T, status) ! Align to custom 1MiB stripe size + + ! Parse any parallel prefix and create filename + par_prefix(:) = "" + CALL get_environment_variable("HDF5_PARAPREFIX", VALUE=par_prefix, STATUS=status) + filename = TRIM(par_prefix)//EXAMPLE_FILE + + ! Set dataset dimensionality + dset_dims(1) = EXAMPLE_DSET_NY + dset_dims(2) = mpi_size + + IF (mpi_rank .EQ. 0) THEN + ! + ! Make sure only this rank opens the file + ! + CALL H5Pset_mpi_params_f(subfiling_fapl, MPI_COMM_SELF, MPI_INFO_NULL, status) + + ! + ! Set the Subfiling VFD on our FAPL using + ! our custom configuration + ! + CALL H5Pset_fapl_subfiling_f(subfiling_fapl, status, subf_config); + + ! + ! Create a new file on rank 0 + ! + CALL H5Fcreate_f(filename, H5F_ACC_TRUNC_F, file_id, status, access_prp = subfiling_fapl) + + ! Create the dataspace for the dataset. The second + ! dimension varies with the number of MPI ranks + ! while the first dimension is fixed. + ! + CALL H5Screate_simple_f(EXAMPLE_DSET_DIMS, dset_dims, filespace, status) + + ! Create the dataset with default properties + + CALL H5Dcreate_f(file_id, EXAMPLE_DSET_NAME, H5T_NATIVE_INTEGER, filespace, dset_id, status) + + ! Initialize data buffer + ALLOCATE(wdata(dset_dims(1)*dset_dims(2))) + DO i = 1, dset_dims(1)*dset_dims(2) + wdata(i) = i + ENDDO + + ! + ! Rank 0 writes to the whole dataset + ! + f_ptr = C_LOC(wdata) + CALL H5Dwrite_f(dset_id, H5T_NATIVE_INTEGER, f_ptr, status, mem_space_id=H5S_BLOCK_F, file_space_id=filespace) + + ! + ! Close/release resources. + ! + DEALLOCATE(wdata) + CALL H5Dclose_f(dset_id, status) + CALL H5Sclose_f(filespace, status) + + CALL H5Fclose_f(file_id, status) + ENDIF + + CALL MPI_Barrier(MPI_COMM_WORLD, status) + + ! + ! Use all MPI ranks to re-open the file and + ! read back the dataset that was created + ! + CALL H5Pset_mpi_params_f(subfiling_fapl, MPI_COMM_WORLD, MPI_INFO_NULL, status) + + ! + ! Use the same subfiling configuration as rank 0 + ! used to create the file + ! + CALL H5Pset_fapl_subfiling_f(subfiling_fapl, status, subf_config) + + ! + ! Re-open the file on all ranks + ! + + CALL H5Fopen_f(filename, H5F_ACC_RDONLY_F, file_id, status, access_prp=subfiling_fapl) + + ! + ! Open the dataset that was created + ! + CALL H5Dopen_f(file_id, EXAMPLE_DSET_NAME, dset_id, status) + + ! + ! Initialize data buffer + ! + + ALLOCATE(wdata(dset_dims(1)*dset_dims(2))) + ! + ! Read the dataset on all ranks + ! + f_ptr = C_LOC(wdata) + CALL H5Dread_f(dset_id, H5T_NATIVE_INTEGER, f_ptr, status, mem_space_id=H5S_BLOCK_F, file_space_id=H5S_ALL_F) + + DEALLOCATE(wdata) + + CALL H5Dclose_f(dset_id, status) + CALL H5Fclose_f(file_id, status) + + CALL cleanup(EXAMPLE_FILE, subfiling_fapl) + + CALL H5Pclose_f(subfiling_fapl, status) + + END SUBROUTINE subfiling_write_precreate + +END MODULE subf + +PROGRAM main + + USE SUBF + IMPLICIT NONE + + INTEGER :: comm = MPI_COMM_WORLD + INTEGER :: info = MPI_INFO_NULL + INTEGER(HID_T) :: fapl_id + INTEGER :: mpi_size + INTEGER :: mpi_rank + INTEGER :: required + INTEGER :: provided + INTEGER :: status + + ! HDF5 Subfiling VFD requires MPI_Init_thread with MPI_THREAD_MULTIPLE + required = MPI_THREAD_MULTIPLE + provided = 0 + CALL mpi_init_thread(required, provided, status) + IF (provided .NE. required) THEN + WRITE(*,*) "MPI doesn't support MPI_Init_thread with MPI_THREAD_MULTIPLE *FAILED*" + CALL MPI_Abort(comm, -1, status) + ENDIF + + CALL MPI_Comm_size(comm, mpi_size, status) + CALL MPI_Comm_rank(comm, mpi_rank, status) + + ! + ! Initialize HDF5 library and Fortran interfaces. + ! + CALL h5open_f(status) + + ! + ! Set up File Access Property List with MPI + ! parameters for the Subfiling VFD to use + CALL h5pcreate_f(H5P_FILE_ACCESS_F, fapl_id, status) + CALL H5Pset_mpi_params_f(fapl_id, comm, info, status) + + ! Use Subfiling VFD with default settings + CALL subfiling_write_default(fapl_id, mpi_size, mpi_rank) + + ! Use Subfiling VFD with custom settings + CALL subfiling_write_custom(fapl_id, mpi_size, mpi_rank) + + ! Use Subfiling VFD to precreate the HDF5 file on MPI rank + CALL subfiling_write_precreate(fapl_id, mpi_size, mpi_rank) + + CALL H5Pclose_f(fapl_id, status) + ! + ! Close FORTRAN interfaces and HDF5 library. + ! + CALL h5close_f(status) + + IF(mpi_rank .EQ. 0) WRITE(*,"(A)") "PHDF5 example finished with no errors" + + CALL MPI_Finalize(status) + +END PROGRAM main |