Adding scripts and input files for a test case

.gitignore

@@ -17,3 +17,5 @@
 configure.wrf*
 *.backup
 *.f90
+#added for macOS environment (KSA)
+**/.DS_Store

testcases/conus_12-km/namelist_v4.5.2_conus12km_restart.input

@@ -0,0 +1,107 @@
+ &time_control
+ run_days                            = 5,
+ run_hours                           = 0,
+ run_minutes                         = 0,
+ run_seconds                         = 0, 
+ start_year                          = 2008,
+ start_month                         = 07,
+ start_day                           = 15,
+ start_hour                          = 00,
+ start_minute                        = 00,
+ start_second                        = 00,
+ end_year                            = 2008,
+ end_month                           = 07,
+ end_day                             = 21,
+ end_hour                            = 00,
+ end_minute                          = 00,
+ end_second                          = 00,
+ interval_seconds                    = 21600
+ input_from_file                     = .true.,
+ history_interval_m                  = 360,
+ frames_per_outfile                  = 1,
+ restart                             = .true.,
+ restart_interval                    = 7200,
+ io_form_history                     = 11,
+ io_form_restart                     = 11,
+ io_form_input                       = 11,
+ io_form_boundary                    = 11,
+ debug_level                         = 0,
+ nocolons                            = .true.,
+ override_restart_timers             = .true.,
+ /
+
+ &domains
+ perturb_input                       = .false.
+ time_step                           = 72,
+ time_step_fract_num                 = 0,
+ time_step_fract_den                 = 1,
+ max_dom                             = 1,
+ s_we                                = 1,
+ e_we                                = 425,
+ e_sn                                = 300,
+ e_vert                              = 50,
+ dx                                  = 12000,
+ dy                                  = 12000,
+ grid_id                             = 1,
+ parent_id                           = 0,
+ i_parent_start                      = 0,
+ j_parent_start                      = 0,
+ parent_grid_ratio                   = 1,
+ parent_time_step_ratio              = 1,
+ feedback                            = 1,
+ smooth_option                       = 0
+ num_metgrid_levels                  = 34,
+ num_metgrid_soil_levels             = 4,
+ numtiles                            = 4,
+ nproc_x                             = 8,
+ nproc_y                             = 24, 
+ /
+
+ &physics
+ physics_suite                       = 'conus'
+ mp_physics                          = -1,
+ ra_lw_physics                       = -1,
+ ra_sw_physics                       = -1,
+ radt                                = 12,
+ sf_sfclay_physics                   = -1,
+ sf_surface_physics                  = -1,
+ bl_pbl_physics                      = -1,
+ bldt                                = 0,
+ cu_physics                          = -1,
+ cudt                                = 0,
+ isfflx                              = 1,
+ ifsnow                              = 0,
+ icloud                              = 1,
+ surface_input_source                = 1,
+ num_soil_layers                     = 1,
+ maxiens                             = 1,
+ maxens                              = 1,
+ maxens2                             = 1,
+ maxens3                             = 1,
+ ensdim                              = 1,
+ /
+
+ &dynamics
+ w_damping                           = 1,
+ diff_opt                            = 1,
+ km_opt                              = 4,
+ khdif                               = 0,
+ kvdif                               = 0,
+ non_hydrostatic                     = .true.,
+ moist_adv_opt                       = 1,
+ scalar_adv_opt                      = 1,
+ use_baseparam_fr_nml = .t.
+ /
+
+ &bdy_control
+ spec_bdy_width                      = 5,
+ spec_zone                           = 1,
+ relax_zone                          = 4,
+ specified                           = .true., 
+ nested                              = .false.,
+ /
+
+ &namelist_quilt
+ nio_tasks_per_group = 0,
+ nio_groups = 1,
+ /

testcases/conus_12-km/readme.md

@@ -0,0 +1,49 @@
+# CONUS12km benchmark case
+
+## Source
+
+Original files were downloaded from NCAR MMM website:
+
+https://www2.mmm.ucar.edu/wrf/users/benchmark/benchdata_v422.html
+
+## Files
+
+The following three files + tar.gz archive file provide everything needed to run the test case.
+
+Only thing a user needs to do is to run the shell script `setup_rundir_WRF.sh`
+
+- `namelist_v4.5.2_conus12km_restart.input`: wrf namelist for the test case
+- `sub_wrf_pm_testcase.sh` : an example batch script to run a test case on Perlmutter
+- `setup_rundir_WRF.sh` : createa a directory to run the test simulation, copy input files, and submit a job after editing (sed) a copy of `sub_wrf_pm_testcase.sh` batch script. 
+- Initial and boundary conditions, and look-up tables for various model modules/kernels are archived and 
+stored in a publicly available space under WRF-SIG repository. The `setup_rundir_WRF.sh` script downloads this file
+by wget command.
+
+### setup_rundir_WRF.sh
+
+Edit the following three lines and then execute.
+```
+casename="codee_test01"  #identifier for the new simulation
+
+#email address to receive notifications from the slurm system
+myemail="Koichi.Sakaguchi@pnnl.gov" 
+
+#directory where we run wrf.exe and writes output
+rundir="/pscratch/sd/k/ksa/simulation/WRF/WRFSIG/${casename}" 
+
+```
+
+## Test Case
+
+The original CONUS12km case runs only for one hour to simulate a strong winter storm case.
+
+For more robust statistics and higher sensitivity to source code changes, the simulation period is extended
+to 5 days (can be as long as 10 days) and to the summer season (July) in 2008; this time period is chosen
+just for the convenience of K. Sakaguchi, who uses this period for his own research). 
+In the summer the influence of lateral boundary forcing 
+(e.g., winds coming in from the west) is weaker than in the winter, therefore processes originated 
+locally (within the model domain) have more impact. 
+So changes in the model executable would appear sooner and stronger.
+
+The 5-day simulation typically ends within 15 minutes using 194 MPI tasks, 4 threads in each task, 
+on 3 CPU nodes of Perlmutter. 

testcases/conus_12-km/setup_rundir_WRF.sh

@@ -0,0 +1,45 @@
+#! /bin/bash
+set -e
+
+#edit these lines ----------------------------------------
+
+casename="codee_test01"  #identifier for the new simulation
+
+#email address to receive notifications from the slurm system
+myemail="Koichi.Sakaguchi@pnnl.gov" 
+
+#directory where we run wrf.exe and writes output
+rundir="/pscratch/sd/k/ksa/simulation/WRF/WRFSIG/${casename}" 
+
+# -------------------
+scriptdir=$(pwd)
+
+mkdir -p ${rundir}
+
+cd ${rundir}
+pwd
+
+#get input files from NERSC's WRFSIG CFS space through Science Gateway service
+echo "downloading input file archive"
+
+wget https://portal.nersc.gov/cfs/m4232pub/testcase_input/testcase_input_conus12km_v4.5.2.tar.gz
+
+echo "expanding the input file arhive"
+
+tar -zxf testcase_input_conus12km_v4.5.2.tar.gz
+
+echo "finished copying the input files"
+
+
+rm -rf ${rundir}/namelist.input #remove the default namelist.input file
+#copy WRF namelist
+cp ${scriptdir}/namelist_v4.5.2_conus12km_restart.input ${rundir}/namelist.input
+
+#copy sbatch script
+cp ${scriptdir}/sub_wrf_pm_testcase.sh ${rundir}/sub_testcase.sh
+
+#edit the email address and job name in the sbatch script
+sed -i "s/elvis@nersc.gov/${myemail}/" sub_testcase.sh
+sed -i "s/elvis_test01/${casename}/" sub_testcase.sh
+
+sbatch sub_testcase.sh

testcases/conus_12-km/sub_wrf_pm_testcase.sh

@@ -0,0 +1,43 @@
+#!/bin/bash 
+#SBATCH -N 3
+#SBATCH -q debug
+#SBATCH -t 00:30:00
+#SBATCH -J elvis_test01
+#SBATCH -A m4232
+#SBATCH --mail-type=END,FAIL
+#SBATCH --mail-user=elvis@nersc.gov
+#SBATCH -L scratch,cfs
+#SBATCH -C cpu
+#SBATCH --tasks-per-node=64
+##SBATCH -S 4
+
+ntile=4  #number of OpenMP threads per MPI task
+
+#Modules --------------------------------------------------------------------
+module load contrib
+module load wrf/4.5.2
+
+#if to run with a wrf executable from modified source codes:
+#1. don't load the wrf module
+#2. the modified executable (wrf.exe) has to be placed in the rundir 
+
+#OpenMP settings:
+export OMP_NUM_THREADS=$ntile
+export OMP_PLACES=threads
+export OMP_PROC_BIND=spread
+
+#run simulation
+srun -n 192 -c 4 --cpu_bind=cores wrf.exe  #3 nodes
+
+#capture error code
+srunval=$?
+
+#rename and save the process 0 out and err files
+cp rsl.error.0000 rsl.error_0_$SLURM_JOB_ID
+cp rsl.out.0000 rsl.out_0_$SLURM_JOB_ID
+
+if [ $srunval -ne 0 ]; then
+    echo "run failed"
+    exit 10
+fi
+