forked from NOAA-EMC/GSI
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
2b1d706
commit 3cbe71f
Showing
6 changed files
with
257 additions
and
23 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| help([[ | ||
| ]]) | ||
|
|
||
|
|
||
| local PrgEnv_intel_ver=os.getenv("PrgEnv_intel_ver") or "8.1.0" | ||
| local intel_ver=os.getenv("intel_ver") or "19.1.3.304" | ||
| local craype_ver=os.getenv("craype_ver") or "2.7.8" | ||
| local cray_mpich_ver=os.getenv("cray_mpich_ver") or "8.1.7" | ||
| local cmake_ver= os.getenv("cmake_ver") or "3.20.2" | ||
| local python_ver=os.getenv("python_ver") or "3.8.6" | ||
| local prod_util_ver=os.getenv("prod_util_ver") or "2.0.10" | ||
|
|
||
| local netcdf_ver=os.getenv("netcdf_ver") or "4.7.4" | ||
| local bufr_ver=os.getenv("bufr_ver") or "11.7.0" | ||
| local bacio_ver=os.getenv("bacio_ver") or "2.4.1" | ||
| local w3emc_ver=os.getenv("w3emc_ver") or "2.9.2" | ||
| local sp_ver=os.getenv("sp_ver") or "2.3.3" | ||
| local ip_ver=os.getenv("ip_ver") or "3.3.3" | ||
| local sigio_ver=os.getenv("sigio_ver") or "2.3.2" | ||
| local sfcio_ver=os.getenv("sfcio_ver") or "1.4.1" | ||
| local nemsio_ver=os.getenv("nemsio_ver") or "2.5.4" | ||
| local wrf_io_ver=os.getenv("wrf_io_ver") or "1.2.0" | ||
| local ncio_ver=os.getenv("ncio_ver") or "1.1.2" | ||
| local crtm_ver=os.getenv("crtm_ver") or "2.4.0" | ||
| local ncdiag_ver=os.getenv("ncdiag_ver") or "1.1.1" | ||
|
|
||
| load("PrgEnv-intel") | ||
| load("intel") | ||
| load("craype") | ||
| load("cray-mpich") | ||
| load(pathJoin("cmake", cmake_ver)) | ||
| load(pathJoin("python", python_ver)) | ||
| load(pathJoin("prod_util", prod_util_ver)) | ||
| load(pathJoin("netcdf", netcdf_ver)) | ||
| load(pathJoin("bufr", bufr_ver)) | ||
| load(pathJoin("bacio", bacio_ver)) | ||
| load(pathJoin("w3emc", w3emc_ver)) | ||
| load(pathJoin("sp", sp_ver)) | ||
| load(pathJoin("ip", ip_ver)) | ||
| load(pathJoin("sigio", sigio_ver)) | ||
| load(pathJoin("sfcio", sfcio_ver)) | ||
| load(pathJoin("nemsio", nemsio_ver)) | ||
| load(pathJoin("wrf_io", wrf_io_ver)) | ||
| load(pathJoin("ncio", ncio_ver)) | ||
| load(pathJoin("crtm", crtm_ver)) | ||
| load(pathJoin("ncdiag",ncdiag_ver)) | ||
|
|
||
| pushenv("GSI_BINARY_SOURCE_DIR", "/lfs/h2/emc/global/noscrub/emc.global/FIX/fix/gsi/20230911") | ||
|
|
||
| whatis("Description: GSI environment on WCOSS2 Acorn") |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,171 @@ | ||
| #!/bin/sh --login | ||
| set -x | ||
| echo "starting sub_acorn" | ||
| usage="\ | ||
| Usage: $0 [options] executable [args] | ||
| where the options are: | ||
| -a account account (default: none) | ||
| -b binding run smt binding or not (default:NO) | ||
| -d dirin initial directory (default: cwd) | ||
| -e envars copy comma-separated environment variables | ||
| -g group group name | ||
| -i append standard input to command file | ||
| -j jobname specify jobname (default: executable basename) | ||
| -m machine machine on which to run (default: current) | ||
| -n write command file to stdout rather than submitting it | ||
| -o output specify output file (default: jobname.out) | ||
| -p procs[/nodes[/ppreq] | ||
| number of MPI tasks and optional nodes or Bblocking and | ||
| ppreq option (N or S) (defaults: serial, Bunlimited, S) | ||
| -q queue[/qpreq] queue name and optional requirement, e.g. dev/P | ||
| (defaults: 1 if serial or dev if parallel and none) | ||
| (queue 3 or 4 is dev or prod with twice tasks over ip) | ||
| (options: P=parallel, B=bigmem, b=batch) | ||
| -r rmem[/rcpu] resources memory and cpus/task (default: '1024 mb', 1) | ||
| -t timew wall time limit in [[hh:]mm:]ss format (default: 900) | ||
| -u userid userid to run under (default: self) | ||
| -v verbose mode | ||
| -w when when to run, in yyyymmddhh[mm], +hh[mm], thh[mm], or | ||
| Thh[mm] (full, incremental, today or tomorrow) format | ||
| (default: now) | ||
| Function: This command submits a job to the batch queue." | ||
| subcmd="$*" | ||
| stdin=NO | ||
| nosub=NO | ||
| account="" | ||
| binding="NO" | ||
| dirin="" | ||
| envars="" | ||
| group="" | ||
| jobname="" | ||
| machine="" | ||
| output="" | ||
| procs=0 | ||
| nodes="" | ||
| ppreq="" | ||
| queue="" | ||
| qpreq="" | ||
| rmem="1024" | ||
| rcpu="1" | ||
| timew="900" | ||
| userid="" | ||
| verbose=NO | ||
| when="" | ||
| while getopts a:b:d:e:g:ij:m:no:p:q:r:t:u:vw: opt;do | ||
| case $opt in | ||
| a) account="$OPTARG";; | ||
| b) binding="$OPTARG";; | ||
| d) dirin="$OPTARG";; | ||
| e) envars="$OPTARG";; | ||
| g) group="$OPTARG";; | ||
| i) stdin=YES;; | ||
| j) jobname=$OPTARG;; | ||
| m) machine="$OPTARG";; | ||
| n) nosub=YES;; | ||
| o) output=$OPTARG;; | ||
| p) procs=$(echo $OPTARG/|cut -d/ -f1);nodes=$(echo $OPTARG/|cut -d/ -f2);ppreq=$(echo $OPTARG/|cut -d/ -f3);; | ||
| q) queue=$(echo $OPTARG/|cut -d/ -f1);qpreq=$(echo $OPTARG/|cut -d/ -f2);; | ||
| r) rmem=$(echo $OPTARG/|cut -d/ -f1);rcpu=$(echo $OPTARG/|cut -d/ -f2);; | ||
| t) timew=$OPTARG;; | ||
| u) userid=$OPTARG;; | ||
| v) verbose=YES;; | ||
| w) when=$OPTARG;; | ||
| \?) echo $0: invalid option >&2;echo "$usage" >&2;exit 1;; | ||
| esac | ||
| done | ||
| shift $(($OPTIND-1)) | ||
| if [[ $# -eq 0 ]];then | ||
| echo $0: missing executable name >&2;echo "$usage" >&2;exit 1 | ||
| fi | ||
| exec=$1 | ||
| if [[ ! -s $exec ]]&&which $exec >/dev/null 2>&1;then | ||
| exec=$(which $exec) | ||
| fi | ||
| shift | ||
| args="$*" | ||
| bn=$(basename $exec) | ||
| export jobname=${jobname:-$bn} | ||
| output=${output:-$jobname.out} | ||
| myuser=$LOGNAME | ||
| myhost=$(hostname) | ||
|
|
||
| DATA=/lfs/h2/emc/stmp/$LOGNAME/tmp | ||
| mkdir -p $DATA | ||
|
|
||
| queue=${queue:-dev} | ||
| timew=${timew:-01:20:00} | ||
| task_node=${task_node:-$procs} | ||
| size=$((nodes*task_node)) | ||
| envars=$envars | ||
| threads=${rcpu:-1} | ||
| ncpus=$((procs*threads)) | ||
|
|
||
| export TZ=GMT | ||
| cfile=$DATA/sub$$ | ||
| > $cfile | ||
| echo "#!/bin/bash" >> $cfile | ||
| echo "" >> $cfile | ||
| echo "#PBS -o $output" >> $cfile | ||
| echo "#PBS -N $jobname" >> $cfile | ||
| echo "#PBS -q $queue" >> $cfile | ||
| echo "#PBS -l walltime=$timew" >> $cfile | ||
| echo "#PBS -l select=$nodes:mpiprocs=$procs:ompthreads=$threads:ncpus=$ncpus" >> $cfile | ||
| echo "#PBS -l place=vscatter:exclhost" >> $cfile | ||
| echo "#PBS -j oe" >> $cfile | ||
| echo "#PBS -A "$accnt >> $cfile | ||
|
|
||
| echo "" >> $cfile | ||
| echo "export OMP_NUM_THREADS=$threads" >> $cfile | ||
| echo "export ntasks=$(( $nodes * $procs ))" >> $cfile | ||
| echo "export ppn=$procs" >> $cfile | ||
| echo "export threads=$threads" >> $cfile | ||
| echo "" >> $cfile | ||
| echo ". "$(awk '{ print $1, $2, $3, $4, $5, $6, $7, $8, $9 }' $regdir/regression_var.out) >>$cfile | ||
| echo "" >> $cfile | ||
|
|
||
| echo "module reset" >> $cfile | ||
| echo "module use $modulefiles" >> $cfile | ||
| echo "module load gsi_acorn.intel" >> $cfile | ||
| echo "module load envvar/1.0" >> $cfile | ||
| echo "module load cray-pals/1.2.2" >> $cfile | ||
| echo "module -t list 2>&1 | while read line;do module show $line 2>&1 | sed -n -e '2p';done | sort" >> $cfile | ||
| echo "module avail" >> $cfile | ||
|
|
||
| echo "" >> $cfile | ||
|
|
||
| cat $exec >> $cfile | ||
|
|
||
| if [[ $nosub = YES ]];then | ||
| cat $cfile | ||
| exit | ||
| elif [[ $verbose = YES ]];then | ||
| set -x | ||
| cat $cfile | ||
| fi | ||
|
|
||
| if [[ $stdin = YES ]];then | ||
| cat | ||
| fi >>$cfile | ||
| if [[ $nosub = YES ]];then | ||
| cat $cfile | ||
| exit | ||
| elif [[ $verbose = YES ]];then | ||
| set -x | ||
| cat $cfile | ||
| fi | ||
| qsub=${qsub:-qsub} | ||
|
|
||
| ofile=$DATA/subout$$ | ||
| >$ofile | ||
| chmod 777 $ofile | ||
| $qsub -V $cfile >$ofile | ||
| rc=$? | ||
| cat $ofile | ||
| if [[ -w $SUBLOG ]];then | ||
| jobn=$(grep -i submitted $ofile|head -n1|cut -d\" -f2) | ||
| date -u +"%Y%m%d%H%M%S : $subcmd : $jobn" >>$SUBLOG | ||
| fi | ||
| ##rm $cfile $ofile | ||
| ##[[ $MKDATA = YES ]] && rmdir $DATA | ||
| echo "ending sub_acorn" | ||
| exit $rc |