add file operator for sim_cleanup

- it can be chosen between copy or moving the files in the clean-up stage
- the choice is based on expid.conf; section sim_clean_general; variable to control file_op_mode

Author: s-poll

ctl/sim_ctl/sim_cleanup.sh

@@ -6,6 +6,18 @@ echo "###"
 echo "# Cleanup Simulation"
 echo "###"
 
+parse_config_file ${conf_file} "sim_clean_general"
+
+file_op_mode=${file_op_mode:-"copy"}
+
+file_op() {
+    if [ "$file_op_mode" = "move" ]; then
+        mv -v "$@"
+    else
+        cp -v "$@"
+    fi
+}
+
 simout_dir=${out_dir}/${caseid}${modelid}_${dateymd}
 simrst_dir=${rst_dir}/${caseid}${dateymd}
 
@@ -19,87 +31,87 @@ echo "Moving model output to simout and storing restart files"
 
 mkdir -p "${simout_dir}/log" "${simout_dir}/nml" "${simout_dir}/rst" "${simout_dir}/bin"
 
-cp ${tsmp2_env} ${simout_dir}/bin/
+file_op ${tsmp2_env} ${simout_dir}/bin/
 
 if [[ "${MODEL_ID}" == *-* ]]; then
-  cp -v ${sim_dir}/namcouple ${simout_dir}/nml/
+  file_op ${sim_dir}/namcouple ${simout_dir}/nml/
 fi # MODEL_ID oasis
 
 if [[ "${modelid}" == *icon* ]]; then
   # Namelist
-  cp -v ${sim_dir}/NAMELIST_icon ${simout_dir}/nml/
-  cp -v ${sim_dir}/icon_master.namelist ${simout_dir}/nml/
+  file_op ${sim_dir}/NAMELIST_icon ${simout_dir}/nml/
+  file_op ${sim_dir}/icon_master.namelist ${simout_dir}/nml/
 
   # Model output
   mkdir -p ${simout_dir}/out/icon
-  cp -v ${sim_dir}/ICON_out_* ${simout_dir}/out/icon
+  file_op ${sim_dir}/ICON_out_* ${simout_dir}/out/icon
 
   # Model log
-  cp -v ${sim_dir}/nml.atmo.log ${simout_dir}/log/
-  cp -v ${sim_dir}/*.dat ${simout_dir}/log/
+  file_op ${sim_dir}/nml.atmo.log ${simout_dir}/log/
+  file_op ${sim_dir}/*.dat ${simout_dir}/log/
 
   # Restart
   mkdir -p ${simout_dir}/rst/icon ${simrst_dir}/icon
-  cp -v ${sim_dir}/${expid}_restart_ATMO_*.nc  ${simout_dir}/rst/icon
-  cp -v ${sim_dir}/${expid}_restart_ATMO_*.nc  ${simrst_dir}/icon # save twice as simout is archived
+  file_op ${sim_dir}/${expid}_restart_ATMO_*.nc  ${simout_dir}/rst/icon
+  file_op ${sim_dir}/${expid}_restart_ATMO_*.nc  ${simrst_dir}/icon # save twice as simout is archived
 
   # copy binary
-  cp -v icon ${simout_dir}/bin/
+  file_op icon ${simout_dir}/bin/
 
 fi # icon
 
 if [[ "${modelid}" == *clm* ]]; then
   # Namelist
-  cp -v ${sim_dir}/*_in ${simout_dir}/nml/
-  cp -v ${sim_dir}/datm.* ${simout_dir}/nml/
+  file_op ${sim_dir}/*_in ${simout_dir}/nml/
+  file_op ${sim_dir}/datm.* ${simout_dir}/nml/
 
   # Model output
   mkdir -p ${simout_dir}/out/eclm
-  cp -v ${sim_dir}/eCLM_*.clm2.h* ${simout_dir}/out/eclm
+  file_op ${sim_dir}/eCLM_*.clm2.h* ${simout_dir}/out/eclm
 
   # Model log
-  cp -v ${sim_dir}/logs/${SLURM_JOB_ID}.comp_*.log ${simout_dir}/log/
-  cp -v ${sim_dir}/timing/model_timing_stats ${simout_dir}/log/
+  file_op ${sim_dir}/logs/${SLURM_JOB_ID}.comp_*.log ${simout_dir}/log/
+  file_op ${sim_dir}/timing/model_timing_stats ${simout_dir}/log/
 
   # Restart
   mkdir -p ${simout_dir}/rst/eclm ${simrst_dir}/eclm
-  cp -v ${sim_dir}/eCLM_*.clm2.r* ${simout_dir}/rst/eclm
-  cp -v ${sim_dir}/eCLM_*.clm2.r* ${simrst_dir}/eclm # save twice as simout is archived
+  file_op ${sim_dir}/eCLM_*.clm2.r* ${simout_dir}/rst/eclm
+  file_op ${sim_dir}/eCLM_*.clm2.r* ${simrst_dir}/eclm # save twice as simout is archived
 
   # Copy binary
-  cp -v eclm ${simout_dir}/bin/
+  file_op eclm ${simout_dir}/bin/
 
 fi # clm
 
 if [[ "${modelid}" == *parflow* ]]; then
 
   # Namelist
-  cp -v ${sim_dir}/coup_oas.tcl ${simout_dir}/nml/
+  file_op ${sim_dir}/coup_oas.tcl ${simout_dir}/nml/
 
   # Model output
   mkdir -p ${simout_dir}/out/parflow
-  cp -v ${sim_dir}/*.out.?????.nc ${simout_dir}/out/parflow
+  file_op ${sim_dir}/*.out.?????.nc ${simout_dir}/out/parflow
 
   # Model log
-  cp -v ${sim_dir}/*out.kinsol.log ${simout_dir}/log/
-  cp -v ${sim_dir}/*out.log ${simout_dir}/log/
-  cp -v ${sim_dir}/*out.timing* ${simout_dir}/log/
+  file_op ${sim_dir}/*out.kinsol.log ${simout_dir}/log/
+  file_op ${sim_dir}/*out.log ${simout_dir}/log/
+  file_op ${sim_dir}/*out.timing* ${simout_dir}/log/
 
   # Restart
   mkdir -p ${simout_dir}/rst/parflow ${simrst_dir}/parflow
   pflnout=$(echo "( ((${simlenhr}/${pfloutfrq}) + ${pfloutmfilt} -1) / ${pfloutmfilt})" | bc)
   pflnlast=$(printf "%05d" $(echo "1 + (${pflnout} -1) * ${pfloutmfilt}" | bc))
 #  cp -v $(ls -1 ${sim_dir}/*.out.?????.nc | tail -1) ${simout_dir}/rst/parflow
   # save twice as simout is archived
-  cp -v ${sim_dir}/${EXP_ID}.out.${pflnlast}.nc ${simout_dir}/rst/parflow
-  cp -v ${sim_dir}/${EXP_ID}.out.${pflnlast}.nc ${simrst_dir}/parflow/${EXP_ID}.out.$(date -u -d "${datep1}" +%Y%m%d%H%M%S).nc # 2nd copy
+  file_op ${sim_dir}/${EXP_ID}.out.${pflnlast}.nc ${simout_dir}/rst/parflow
+  file_op ${sim_dir}/${EXP_ID}.out.${pflnlast}.nc ${simrst_dir}/parflow/${EXP_ID}.out.$(date -u -d "${datep1}" +%Y%m%d%H%M%S).nc # 2nd copy
 
   # Copy binary
-  cp -v parflow ${simout_dir}/bin/
+  file_op parflow ${simout_dir}/bin/
 
 fi # parflow
 
-cp -v ${sim_dir}/slm_multiprog_mapping.conf ${simout_dir}/log/
+file_op ${sim_dir}/slm_multiprog_mapping.conf ${simout_dir}/log/
 
 # sim logs
 mv ${log_dir}/${SLURM_JOB_NAME}_${SLURM_JOB_ID}.{err,out} ${simout_dir}/log/.