HDF5 Extended Tests and Examples

HDF5 Extended Tests and Examples

Benchmark Description

This HDF5 example shows how to write a “chunked” dataset into a HDF5 file. Each process writes a “chunk” of data to a dataset.

Command line Options

command-line arguments
 -gridPoints_x         number of grid points in x-direction
 -gridPoints_y         number of grid points in y-direction
 -nProcs_x             number of MPI ranks in x-direction
 -nProcs_y             number of MPI ranks in y-direction
 -path                 path to the output directory (default: ./)
 -help                 print this help message

Example Output

  1, 1, 1, 1, 3, 3, 3, 3,
  1, 1, 1, 1, 3, 3, 3, 3,
  1, 1, 1, 1, 3, 3, 3, 3,
  2, 2, 2, 2, 4, 4, 4, 4,
  2, 2, 2, 2, 4, 4, 4, 4,
  2, 2, 2, 2, 4, 4, 4, 4

Resources

• https://support.hdfgroup.org/documentation/hdf5/latest/_intro_par_h_d_f5.html
• https://support.hdfgroup.org/documentation/hdf5/latest/_learn_basics.html
• https://support.hdfgroup.org/documentation/hdf5/latest/_getting_started.html

Build Environment

module use /opt/cray/pals/lmod/modulefiles/core
module load cray-pals
module swap PrgEnv-cray PrgEnv-gnu
module load cray-hdf5-parallel/1.14.3.1

make

Makefile

PROJECT = hdf5_example
PROJECT_DIR = $(shell pwd)
SRC_DIR = $(PROJECT_DIR)/src
BIN_DIR = $(PROJECT_DIR)/bin
INCLUDE_DIR =$(PROJECT_DIR)/include
SRC_FILES := mod_globals.f90 mod_mpi.f90 mod_parse_commandline.f90 mod_helpers.f90 mod_hdf5_io.f90 hdf5_example.f90
HDF5_INCLUDE_DIR = ${HDF5_ROOT}/include
HDF5_LIBRARY_DIR = ${HDF5_ROOT}/lib
HDF5_LIBS = -lhdf5 -lhdf5_fortran
FCFLAGS = -g -Wall
DEBUGGING = T
READFILE = T
PP_FLAGS = -cpp
FC = ftn

# ==============================================================================
FLAGS += $(PP_FLAGS)
FLAGS += $(FCFLAGS)

.PHONY: clean all lib

#all:

all:
    echo ${HDF5_INCLUDE_DIR} ,${HDF5_LIB_DIR}
    mkdir -p $(BIN_DIR) $(INCLUDE_DIR)
    cd $(SRC_DIR); \
    $(FC) $(FLAGS) -I${HDF5_INCLUDE_DIR} -L${HDF5_LIBRARY_DIR} ${HDF5_LIBS} $(SRC_FILES) -o $(PROJECT); \
    mv $(PROJECT) $(BIN_DIR); \
    mv *.mod $(INCLUDE_DIR) ; \

clean:
    rm -rf $(BIN_DIR) $(INCLUDE_DIR)

Execution Script

#!/bin/bash

#PBS -N bm035_Cray_HDF5
#PBS -l select=4:node_type=mi300a:mpiprocs=4
#PBS -l walltime=00:20:00
#PBS -q test 

module use /opt/cray/pals/lmod/modulefiles/core
module load cray-pals
module swap PrgEnv-cray PrgEnv-gnu
module load cray-hdf5-parallel/1.14.3.1

NPROCS=16
GRIDPOINTS_X=100000
GRIDPOINTS_Y=10000
NPROCS_X=4
NPROCS_Y=4
EXEDIR=/zhome/academic/HLRS/hlrs/hpchppof/hunter/hunter_acceptance/Benchmarks_Performance/bm035_Cray_HDF5/bin
OUTPUT_DIR=/lustre/hpe/ws12/ws12.a/ws/hpchppof-hunter_acceptance/bm035_Cray_HDF5

mpirun -np ${NPROCS} --ppn 4 ${EXEDIR}/hdf5_example -gridPoints_x ${GRIDPOINTS_X} -gridPoints_y ${GRIDPOINTS_Y} -nProcs_x ${NPROCS_X} -nProcs_y ${NPROCS_Y} -path ${OUTPUT_DIR}

Execution Results

Commandline arguments: 
 gridPoints_x:                      100000
 gridPoints_y:                       10000
 nProcs_x:                      4
 nProcs_y:                      4
 Path:               /lustre/hpe/ws12/ws12.a/ws/hpchppof-hunter_acceptance/bm035_Cray_HDF5

--------------- MPI-IO Hints ---------------
                    romio_cb_pfr = disable
               romio_cb_fr_types = aar
                        cb_align = 2
                  cb_buffer_size = 16777216
           romio_cb_fr_alignment = 1
           romio_cb_ds_threshold = 0
               romio_cb_alltoall = automatic
                   romio_cb_read = automatic
                  romio_cb_write = automatic
               romio_no_indep_rw = false
                  romio_ds_write = automatic
              ind_wr_buffer_size = 524288
                   romio_ds_read = disable
              ind_rd_buffer_size = 4194304
                       direct_io = false
                 striping_factor = 8
                   striping_unit = 4194304
             overstriping_factor = 0
     romio_lustre_start_iodevice = -1
     aggregator_placement_stride = -1
               abort_on_rw_error = disable
                  cb_config_list = *:*
                        cb_nodes = 8
           romio_filesystem_type = CRAY ADIO:
--------------------------------------------

--------------------HDF5 Benchmark --------------------
Number of MPI processes             :        16
Number of gridpoints in x-direction :    100000
Number of gridpoints in y-direction :     10000
Total I/O amount in MiB             :      7629.39
Time in sec                         :         3.43
I/O bandwidth in MiB/s              :      2226.91