Add a very simple hdf5 exercise for exploration

parallel-io/README.md

@@ -1,5 +1,6 @@
 # Parallel I/O exercises
 
 - [Parallel I/O with Posix](posix)
-- [HDF5 example](hdf5)
+- [HDF5-writerank](hdf5-writerank)
+- [HDF5-write-read](hdf5-writeread)
 

parallel-io/hdf5-writerank/README.md

@@ -0,0 +1,12 @@
+## HDF5-writerank exercise
+
+Explore the HDF5 codes ([hdf5-writerank.c](hdf5-writerank.c) or [hdf5-writerank.f90](hdf5-writerank.f90)) and try to compile them.
+
+On Lumi, you will need to load the module `cray-hdf5-parallel` before you 
+can compile the code:
+
+```
+module load cray-hdf5-parallel
+```
+
+After compiling, try running the program with some number of MPI ranks. After this, try using the `h5dump` and `h5ls`  commands to check the values in the HDF5 file that is produced by running the example. Do you understand what the program does and what are the values in the file (as shown by `h5dump`)?

parallel-io/hdf5-writerank/hdf5-writerank.F90

@@ -0,0 +1,42 @@
+program hdf5_writerank
+    use mpi
+    use hdf5
+    implicit none
+    ! Declare vars
+    integer :: err, myproc, numprocs
+    integer(hid_t) :: plist, file, dataspace, dataset, memspace
+    integer(hsize_t) :: counts(1)
+    ! Initialize MPI
+    call mpi_init(err)
+    call mpi_comm_rank(MPI_COMM_WORLD, myproc, err)
+    call mpi_comm_size(MPI_COMM_WORLD, numprocs, err)
+
+    ! Initialize Fortran HDF5 interface
+    call h5open_f(err)
+    ! Create a new property list for file acccess
+    call h5pcreate_f(H5P_FILE_ACCESS_F, plist, err)
+    ! Store MPI IO communicator info to the file access property list
+    call h5pset_fapl_mpio_f(plist, MPI_COMM_WORLD, MPI_INFO_NULL, err)
+    ! Create a new HDF5 file named "parallel_out.h5"
+    call h5fcreate_f("parallel_out.h5", H5F_ACC_TRUNC_F, file, err, access_prp=plist)
+    ! Create a new simple dataspace for the file and open for access
+    call h5screate_simple_f(1, int([numprocs], hsize_t), dataspace, err)
+    ! creates a new dataset named "MPI_RANKS" for 'file'
+    call h5dcreate_f(file, "MPI_RANKS", H5T_NATIVE_INTEGER, dataspace, dataset, err)
+    ! Number of blocks to be included in the hyperslab region
+    counts(1) = 1
+    ! Select a hyperslab region of the file dataspace
+    call h5sselect_hyperslab_f(dataspace, H5S_SELECT_SET_F, int([myproc], hsize_t), counts, err)
+    ! Create a new simple dataspace for the memory buffer and open for access
+    call h5screate_simple_f(1, counts, memspace, err)
+    ! Each rank writes its own rank number (partially constructing 'dataset') into a file
+    call h5dwrite_f(dataset, H5T_NATIVE_INTEGER, [myproc], int([numprocs], hsize_t), err, memspace, dataspace, H5P_DEFAULT_F)
+
+    ! Close all handles
+    call h5dclose_f(dataset, err)
+    call h5sclose_f(dataspace, err)
+    call h5fclose_f(file, err)
+    call h5pclose_f(plist, err)
+    call h5close_f(err)
+    call mpi_finalize(err)
+end program hdf5_writerank

parallel-io/hdf5-writerank/hdf5-writerank.c

@@ -0,0 +1,38 @@
+#include "hdf5.h"
+#include <mpi.h>
+
+int main(int argc, char **argv) {
+
+    // Initialize MPI
+    int myproc, numprocs;
+    MPI_Init(&argc, &argv);
+    MPI_Comm_rank(MPI_COMM_WORLD, &myproc);
+    MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
+
+    // Create a new property list for file acccess
+    hid_t plist = H5Pcreate(H5P_FILE_ACCESS);
+    // Store MPI IO communicator info to the file access property list
+    H5Pset_fapl_mpio(plist, MPI_COMM_WORLD, MPI_INFO_NULL);
+    // Create a new HDF5 file named "parallel_out.h5"
+    hid_t file = H5Fcreate("parallel_out.h5", H5F_ACC_TRUNC, H5P_DEFAULT, plist);
+    // Create a new simple dataspace for the file and open for access
+    hid_t dataspace = H5Screate_simple(1, (const hsize_t[]){numprocs}, NULL);
+    // creates a new dataset named "MPI_RANKS" for 'file'
+    hid_t dataset = H5Dcreate(file, "MPI_RANKS", H5T_NATIVE_INT, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    // Number of blocks to be included in the hyperslab region
+    hsize_t count[] = {1};
+    // Select a hyperslab region of the file dataspace
+    H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, (const hsize_t[]){myproc}, NULL, count, NULL);
+    // Create a new simple dataspace for the memory buffer and open for access
+    hid_t memspace = H5Screate_simple(1, count, NULL);
+    // Each rank writes its own rank number (partially constructing 'dataset') into a file
+    H5Dwrite(dataset, H5T_NATIVE_INT, memspace, dataspace, H5P_DEFAULT, &myproc);
+
+    // Close all handles and return
+    H5Dclose(dataset);
+    H5Sclose(dataspace);
+    H5Fclose(file);
+    H5Pclose(plist);
+    MPI_Finalize();
+    return 0;
+}