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Merge pull request #27 from desihub/fuji-guadalupe
Updates for fuji and guadalupe
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| #!/bin/bash | ||
| if [[ $# < 1 ]]; then | ||
| echo "SPECPROD is required!" | ||
| exit 1 | ||
| fi | ||
| if [[ $# < 2 ]]; then | ||
| echo "DIRECTORY is required!" | ||
| exit 1 | ||
| fi | ||
| export SPECPROD=$1 | ||
| directory=$2 | ||
| [[ -z "${DESI_SPECTRO_REDUX}" ]] && export DESI_SPECTRO_REDUX=/global/cfs/cdirs/desi/spectro/redux | ||
| for d in ${DESI_SPECTRO_REDUX}/${SPECPROD}/${directory}/*; do | ||
| n=$(basename ${d}) | ||
| job_name=redux_${SPECPROD}_$(tr '/' '_' <<<${directory})_${n} | ||
| cat > ${job_name}.sh <<EOT | ||
| #!/bin/bash | ||
| #SBATCH --account=desi | ||
| #SBATCH --qos=xfer | ||
| #SBATCH --time=12:00:00 | ||
| #SBATCH --mem=10GB | ||
| #SBATCH --job-name=${job_name} | ||
| #SBATCH --licenses=cfs | ||
| cd ${DESI_SPECTRO_REDUX}/${SPECPROD}/${directory} | ||
| hsi mkdir -p desi/spectro/redux/${SPECPROD}/${directory} | ||
| htar -cvf desi/spectro/redux/${SPECPROD}/${directory}/${job_name}.tar -H crc:verify=all ${n} | ||
| [[ \$? == 0 ]] && mv -v /global/homes/d/desi/jobs/${job_name}.sh /global/homes/d/desi/jobs/done | ||
| EOT | ||
| chmod +x ${job_name}.sh | ||
| done |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| #!/bin/bash | ||
| # | ||
| module load esslurm | ||
| function usage() { | ||
| local execName=$(basename $0) | ||
| ( | ||
| echo "${execName} [-h] [-j JOBS] [-m JOBS] [-s SECONDS] [-t] [-v] PREFIX" | ||
| echo "" | ||
| echo "Submit jobs that match PREFIX." | ||
| echo "" | ||
| echo " -h = Print this message and exit." | ||
| echo " -j JOBS = Fill the queue up to JOBS jobs (default 12)." | ||
| echo " -m JOBS = Submit no more that JOBS jobs total (default is all matching jobs)." | ||
| echo " -s SECONDS = Sleep between submission batches (default 60)." | ||
| echo " -t = Test mode. Do not actually make any changes. Implies -v." | ||
| echo " -v = Verbose mode. Print extra information." | ||
| # echo " -V = Version. Print a version string and exit." | ||
| ) >&2 | ||
| } | ||
| max_jobs=12 | ||
| total_jobs='' | ||
| sleepy_time=60 | ||
| verbose=false | ||
| test=false | ||
| while getopts hj:m:s:tv argname; do | ||
| case ${argname} in | ||
| h) usage; exit 0 ;; | ||
| j) max_jobs=${OPTARG} ;; | ||
| m) total_jobs=${OPTARG} ;; | ||
| s) sleepy_time=${OPTARG} ;; | ||
| t) test=true; verbose=true ;; | ||
| v) verbose=true ;; | ||
| *) usage; exit 1 ;; | ||
| esac | ||
| done | ||
| shift $((OPTIND-1)) | ||
| if (( $# < 1 )); then | ||
| echo "ERROR: PREFIX required!" | ||
| exit 1 | ||
| fi | ||
| prefix=$1 | ||
| available_jobs=($(ls ${prefix}*)) | ||
| if [[ -n "${total_jobs}" ]]; then | ||
| n_available=${total_jobs} | ||
| else | ||
| n_available=${#available_jobs[*]} | ||
| fi | ||
| j=0 | ||
| while true; do | ||
| echo -n "INFO: " | ||
| date | ||
| foo=$(squeue -u ${USER} | wc -l) | ||
| n_jobs=$(( foo - 1 )) | ||
| if (( n_jobs < max_jobs )); then | ||
| n_submitted=0 | ||
| while (( j < n_available && n_submitted + n_jobs < max_jobs )); do | ||
| ${verbose} && echo "DEBUG: sbatch ${available_jobs[${j}]}" | ||
| ${test} || sbatch ${available_jobs[${j}]} | ||
| n_submitted=$(( n_submitted + 1 )) | ||
| j=$(( j + 1 )) | ||
| done | ||
| echo "INFO: Submitted ${n_submitted} jobs." | ||
| ${verbose} && echo "DEBUG: Job index is ${j}." | ||
| fi | ||
| if (( j == n_available)); then | ||
| echo "INFO: All jobs submitted." | ||
| break | ||
| fi | ||
| ${verbose} && echo "DEBUG: sleep ${sleepy_time}" | ||
| sleep ${sleepy_time} | ||
| done |
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