In this page, We describe how to install and use FLASH code on OCTOPUS.
 

Download Software

Please downloade FLASH code from this page. User registration required.
FLASH code(Flash Center, University Chicago)
 

Preparing compile

For compiling FLASH code, please set OpenMPI and install HDF5 and PnetCDF, HYPRE.
 

    setting OpenMPI

      You should compule FLASH code and other relative software by OpenMPI and GNU compuler. Please set it by the following command before compile.

      BASE=/octfs/apl/HPC-X/hpcx-v2.2.0-gcc-MLNX_OFED_LINUX-4.2-1.2.0.0-redhat7.3-x86_64
      source ${BASE}/hpcx-init.sh
      hpcx_load

      Please see the following page for how to use OpenMPI.
      How to use OpenMPI
       

    install HDF5

    1. Download hdf5-1.8.20 from the following page

    2. Please extract tar ball.

      tar xvzf hdf5-1.8.20.tar.gz

     

    3. make,make install

      cd hdf5-1.8.20
      ./configure --prefix=/octfs/work/(your group name)/(your user ID)/HDF5/ --enable-fortran CC=mpicc F9X=mpif90 --enable-parallel
      make
      make install

       

    Install PnetCDF

    1. Downloade PnetCDF-1.9.0 from the following page.

    2. Please extract tar ball.

      tar xvzf parallel-netcdf-1.9.0.tar.gz

     

    3. make,make install

      cd parallel-netcdf-1.9.0
      ./configure --prefix=/octfs/work/(your group name)/(your user ID)/PnetCDF/
      make
      make install

       

     

    HYPRE install

    1. Download HYPRE-2.11.2 from the following page.

    2. Please extract tar ball.

      tar -xzvf hypre-2.11.2.tar.gz

     

    3. make,make install

      cd hypre-2.11.2/src
      ./configure --prefix=/octfs/work/(your group name)/(your user ID)/HYPRE/ CC=mpicc F9X=mpif90
      make
      make install

       

how to complile

    In this items, we descrive how to compule LaserSlab Simulation on FLASH code4.5.
    Please see the following official manual as well.
    FLASH code support page
     
    1.Please extract FLASH code.
     

    2.execute "setup script"

    cd FLASH4.5/
    ./setup -auto LaserSlab

     

    3.modify Makefile

    cd object
    vi Makefile.h

    Please modify as the following

    MPI_PATH = /octfs/apl/HPC-X/hpcx-v2.2.0-gcc-MLNX_OFED_LINUX-4.2-1.2.0.0-redhat7.3-x86_64/ompi/
    HDF5_PATH = /octfs/work/(your group name)/(your user ID)/HDF5
    NCMPI_PATH = /octfs/work/(your group name)/(your user ID)/PnetCDF
    HYPRE_PATH = /octfs/work/(your group name)/(your user ID)/HYPRE

    * please check your group name by "id -gn" command.

     

    4.set LD_LIBRARY_PATH

    export LD_LIBRARY_PATH=/octfs/work/(your group name)/(your user ID)/HDF5/lib:$LD_LIBRARY_PATH
    export LD_LIBRARY_PATH=/octfs/work/(your group name)/(your user ID)/PnetCDF/lib:$LD_LIBRARY_PATH
    export LD_LIBRARY_PATH=/octfs/work/(your group name)/(your user ID)/HYPRE/lib:$LD_LIBRARY_PATH

     

    5.make

    make

    If you re-compile, please execute "make" command after executing "make clean". When compiling success, you get "flash4" execution file.

     

how to execute

    We permit only batch request for executing FLASH code.
     

    batch script

    The following example is a job script FRASH code executes on 96 porcess(4 nodes, 24 proccess per node).
     

     

    how to run batch request

    % qsub flash.sh