r7799

Dependencies

  • Intel Parallel Studio XE 2017 Update 1 Cluster Editon >= 17.0.1
  • mpich2 >= 3.2
  • NetCDF-C >= 4.5.0
  • NetCDF Fortran
  • hdf5 >= 1.8.19
  • zlib >= 1.2.11
  • szip >= 2.1
  • libtool >= 2.4.6
  • autconf >= 2.69

Installation

Load the needed modules or add the to the path

  1. Download the repository
$ cd cd /home/mgomezzul/apps/delft3d/intel
$ svn checkout https://svn.oss.deltares.nl/repos/delft3d/tags/8799 delft3d_8850
  1. For installation, the following steps must be done:
$ cd delft3d_8850/src
$ ./build.sh -intel18 -64bit -c "--build=x86_64-redhat-linux"

Module

    #%Module1.0####################################################################
##
## module load delft3d/8799_intel-18.0.2
##
## /share/apps/modules/delft3d/8799_intel-18.0.2
##
## Written by Mateo Gómez-Zuluaga
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using Delft3D 8799\
          \nin the shared directory /share/apps/delft3d/8799/intel-18.0.2\
          \nbuilded with Intel Compiler 18.0.2, MPICH2-3.2.1, NetCDF 4.6.1, \
          \nNetCDF 4.4.4 and HDF5-1.8.20."
}

module-whatis "(Name________) delft3d"
module-whatis "(Version_____) 8799"
module-whatis "(Compilers___) intel-18.0.2"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) netcdf-4.6.1, netcdf-fortran-4.4.4, hdf5-1.8.20"

# for Tcl script use only
set         topdir        /share/apps/delft3d/8799/intel-18.0.2
set         version       8799
set         sys           x86_64-redhat-linux

conflict delft3d
module load netcdf/4.6.1_intel-18.0.2
module load mpich2/3.2.1_intel-18.0.2

setenv              D3D_HOME                $topdir
setenv              ARCH                    lnx64

prepend-path        PATH                    $topdir/bin

prepend-path        LD_LIBRARY_PATH         $topdir/lib
prepend-path        LIBRARY_PATH            $topdir/lib
prepend-path        LD_RUN_PATH             $topdir/lib

prepend-path    LD_LIBRARY_PATH         $topdir/lnx64/dimr/bin
prepend-path    LIBRARY_PATH            $topdir/lnx64/dimr/bin
prepend-path    LD_RUN_PATH             $topdir/lnx64/dimr/bin

prepend-path        PATH                    $topdir/lnx64/flow2d3d/bin
prepend-path        LD_LIBRARY_PATH         $topdir/lnx64/flow2d3d/bin
prepend-path        LIBRARY_PATH            $topdir/lnx64/flow2d3d/bin
prepend-path        LD_RUN_PATH             $topdir/lnx64/flow2d3d/bin

prepend-path        PATH                    $topdir/lnx64/part/bin
prepend-path        LD_LIBRARY_PATH         $topdir/lnx64/part/bin
prepend-path        LIBRARY_PATH            $topdir/lnx64/part/bin
prepend-path        LD_RUN_PATH             $topdir/lnx64/part/bin

prepend-path        LD_LIBRARY_PATH         $topdir/lnx64/plugins/bin
prepend-path        LIBRARY_PATH            $topdir/lnx64/plugins/bin
prepend-path        LD_RUN_PATH             $topdir/lnx64/plugins/bin

prepend-path        PATH                    $topdir/lnx64/scripts

prepend-path        LD_LIBRARY_PATH         $topdir/lnx64/shared
prepend-path        LIBRARY_PATH            $topdir/lnx64/shared
prepend-path        LD_RUN_PATH             $topdir/lnx64/shared

prepend-path        PATH                    $topdir/lnx64/swan/bin
prepend-path        PATH                    $topdir/lnx64/swan/scripts
prepend-path        LD_LIBRARY_PATH         $topdir/lnx64/swan/bin
prepend-path        LIBRARY_PATH            $topdir/lnx64/swan/bin
prepend-path        LD_RUN_PATH             $topdir/lnx64/swan/bin

prepend-path        PATH                    $topdir/lnx64/waq/bin
prepend-path        LD_LIBRARY_PATH         $topdir/lnx64/waq/bin
prepend-path        LIBRARY_PATH            $topdir/lnx64/waq/bin
prepend-path        LD_RUN_PATH             $topdir/lnx64/waq/bin

prepend-path        PATH                    $topdir/lnx64/wave/bin
prepend-path        LD_LIBRARY_PATH         $topdir/lnx64/wave/bin
prepend-path        LIBRARY_PATH            $topdir/lnx64/wave/bin
prepend-path        LD_RUN_PATH             $topdir/lnx64/wave/bin

Use mode

#!/bin/bash

#SBATCH --partition=longjobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --time=4:00:00
#SBATCH --job-name=delft3d_271
#SBATCH -o test_%N_%j.out      # File to which STDOUT will be written
#SBATCH -e test_%N_%j.err      # File to which STDERR will be written

export SBATCH_EXPORT=NONE
export OMP_NUM_THREADS=16
export OMP_NUM_THREADS_SWAN=$SLURM_NTASKS
#export NHOSTS=$SLURM_JOB_NUM_NODES
#export NSLOTS=$SLURM_NTASKS

module load delft3d/8799_intel-18.0.2

# Specify the config file to be used here
argfile=config_d_hydro.xml
mdwfile=271.mdw

# Run in parallel Flow
mpirun -np 1 d_hydro.exe $argfile &

# Run in combination Wave
wave.exe $mdwfile 1

Author

  • Mateo Gómez Zuluaga