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Setting up the Run Script

The GSI run script ush/comgsi_run_regional.ksh, which is provided with the source code, must be customized to the local environment. These changes include things such as the analysis time and date, the path to files, and MPI specific information, which are necessary for running all of tutorial cases.

For this tutorial, start by copying the original run script to a working copy
cd ${PATH of working directory}/run
cp ${PATH}/comGSIv3.7_EnKFv1.3/ush/comgsi_run_regional.ksh run_gsi_regional.ksh_basic
This will be used as the template for all the later scripts used in the regional practice.

Make the following modifications to the script run_gsi_regional.ksh_basic

• On top of the scripts, add an appropriate batch script. For example on Cheyenne:

#PBS -A PXXXXXXXX
#PBS -l walltime=00:20:00
#PBS -N basic
#PBS -l select=1:ncpus=4:mpiprocs=4
#PBS -q premium
#PBS -o out.basic
#PBS -j oe



• Set the variable GSIPROC to 4
• Set the variable ARCH to LINUX_PBS, as an example value appropriate for Linux with PBS.
• In the case set up section of the script, set the environment variables to values appropriate for your environment on your machine. For example:
• ANAL_TIME=2018081212
• JOB_DIR=/gpfs/fs1/p/ral/jntp/mhu/gsi/v37/run
• RUN_NAME=basic
• OBS_ROOT=/glade/p/ral/jntp/DAtask/case_data/2018081212/obs
• BK_ROOT=/glade/p/ral/jntp/DAtask/case_data/2018081212/bkg
• GSI_ROOT=/gpfs/fs1/p/ral/jntp/mhu/gsi/v37/comGSIv3.7_EnKFv1.3
• CRTM_ROOT=/glade/p/ral/jntp/DAtask/case_data/CRTM_2.2.3
• ENS_ROOT=/glade/p/ral/jntp/DAtask/case_data/2018081212/gfsens
• HH=`echo $ANAL_TIME | cut -c9-10`
• GSI_EXE=${JOB_DIR}/gsi.x #assume you have a copy of gsi.x here
• WORK_ROOT=${JOB_DIR}/${RUN_NAME}
• FIX_ROOT=${GSI_ROOT}/fix
• GSI_NAMELIST=${GSI_ROOT}/ush/comgsi_namelist.sh
• PREPBUFR=${OBS_ROOT}/rap.t${HH}z.prepbufr.tm00
• BK_FILE=${BK_ROOT}/wrfout_d01_2018-08-12_12:00:00
This example is only for ARW core background files.


• Still in case set up setion, leave the following settings as default:

  if_hybrid=No     # Yes, or, No -- case sensitive !
  if_4DEnVar=No    # Yes, or, No -- case sensitive (set if_hybrid=Yes first)!
  if_observer=No   # Yes, or, No -- case sensitive !
  if_nemsio=No     # Yes, or, No -- case sensitive !
  if_oneob=No      # Yes, or, No -- case sensitive !

  bk_core=ARW
  bkcv_option=NAM
  if_clean=clean



• Search Section # Link to the radiance data, look for the list of observations and comment the links to the BUFR file under this section:
# ln -s ${srcobsfile[$ii]} ${gsiobsfile[$ii]}