diff --git a/create_lanes.sh b/create_lanes.sh index fc84fc3..f310dd7 100755 --- a/create_lanes.sh +++ b/create_lanes.sh @@ -1,122 +1,124 @@ #!/bin/bash set -euo pipefail # Script made from the page # https://docs.ycrc.yale.edu/clusters-at-yale/guides/cryosparc/ script_path=$(dirname "$0") # relative script_path=$(cd "${script_path}" && pwd) # absolutized and normalized install_path="$HOME"/cryosparc # set up some more paths db_path=${install_path}/database worker_path=${install_path}/cryosparc2_worker # Usage usage () { echo "Usage:" echo " -p install path : prefix for installation [${install_path}] " echo " -v : be verbose" echo " -h : print this notice" echo "" } VERBOSE=false # Parse options while getopts ":p:vh" opt; do case $opt in p) install_path="${OPTARG}" ;; v) VERBOSE=true ;; h) usage OPTIND=1 exit 0 ;; \?) echo "Invalid option: -$OPTARG" >&2 usage OPTIND=1 exit 1 ;; :) echo "Option -$OPTARG requires an argument." >&2 usage OPTIND=1 exit 1 ;; esac done # Reset OPTIND to allow the next invocation to work OPTIND=1 message() { if $VERBOSE then echo "${1}" fi } echo "[Info] Starting the master if needed" if [ $(${install_path}/cryosparc_master/bin/cryosparcm.sh status | grep -c "CryoSPARC is not running") -eq 1 ]; then ${install_path}/cryosparc_master/bin/cryosparcm.sh start fi user_name=$(whoami) user_accounts=$(sacctmgr show assoc where user=${user_name} format=Account%100 -P | grep -v Account) mkdir -p ${install_path}/site_configs && cd ${install_path}/site_configs for _account in $user_accounts; do if [ $(sacctmgr show assoc where account=${_account} format=ParentName%100 -P | grep -v "Par Name" | grep -c courses) -eq 0 ]; then _worker_name=${HOSTNAME}-${_account} max_wall=$(sacctmgr show assoc where account=${_account} format=MaxWall -P | grep -v MaxWall | head -1) for mem in 90 180 360 720; do mkdir -p ${install_path}/site_configs/${_worker_name}_${mem}gb && cd ${install_path}/site_configs/${_worker_name}_${mem}gb cat << EOF > cluster_info.json { "name": "${_worker_name}_${mem}gb", "worker_bin_path": "${install_path}/cryosparc_worker/bin/cryosparcw", "cache_path": "/tmp/{{ cryosparc_username }}/cryosparc_cache", "cache_reserve_mb": 10000, "cache_quota_mb": 1000000, "send_cmd_tpl": "{{ command }}", "qsub_cmd_tpl": "sbatch {{ script_path_abs }}", "qstat_cmd_tpl": "squeue -j {{ cluster_job_id }}", "qdel_cmd_tpl": "scancel {{ cluster_job_id }}", "qinfo_cmd_tpl": "sinfo" } EOF cat << EOF > cluster_script.sh #!/bin/bash -l #SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }} -#SBATCH -n {{ num_cpu }} -#SBATCH --gres gpu:{{ num_gpu }} +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=1 +#SBATCH --cpus-per-task={{ num_cpu }} +#SBATCH --gres=gpu:{{ num_gpu }} #SBATCH --mem ${mem}GB #SBATCH --time ${max_wall} #SBATCH -o {{ job_dir_abs }}/slurm.out #SBATCH -e {{ job_dir_abs }}/slurm.err #SBATCH -A ${_account} module load gcc cuda/11.0.2 python mkdir -p /tmp/${USER} ln -sf \${TMPDIR} /tmp/${USER}/cryosparc_cache {{ run_cmd }} EOF ${install_path}/cryosparc_master/bin/cryosparcm cluster connect done fi done #${install_path}/cryosparc_master/bin/cryosparcm.sh stop diff --git a/create_reserved_lanes.sh b/create_reserved_lanes.sh index 816c836..e406a2d 100755 --- a/create_reserved_lanes.sh +++ b/create_reserved_lanes.sh @@ -1,119 +1,121 @@ #!/bin/bash set -euo pipefail # Script made from the page # https://docs.ycrc.yale.edu/clusters-at-yale/guides/cryosparc/ script_path=$(dirname "$0") # relative script_path=$(cd "${script_path}" && pwd) # absolutized and normalized install_path="$HOME"/cryosparc # set up some more paths db_path=${install_path}/database worker_path=${install_path}/cryosparc2_worker # Usage usage () { echo "Usage:" echo " -p install path : prefix for installation [${install_path}] " echo " -v : be verbose" echo " -h : print this notice" echo "" } VERBOSE=false read -p "Enter group account at SCITAS: " hpc_account read -p "Enter reservation name: " reservation_name # Parse options while getopts ":p:vh" opt; do case $opt in p) install_path="${OPTARG}" ;; v) VERBOSE=true ;; h) usage OPTIND=1 exit 0 ;; \?) echo "Invalid option: -$OPTARG" >&2 usage OPTIND=1 exit 1 ;; :) echo "Option -$OPTARG requires an argument." >&2 usage OPTIND=1 exit 1 ;; esac done # Reset OPTIND to allow the next invocation to work OPTIND=1 message() { if $VERBOSE then echo "${1}" fi } echo "[Info] Starting the master if needed" if [ $(${install_path}/cryosparc_master/bin/cryosparcm.sh status | grep -c "CryoSPARC is not running") -eq 1 ]; then ${install_path}/cryosparc_master/bin/cryosparcm.sh start fi cd ${install_path}/site_configs for _account in $hpc_account; do if [ $(sacctmgr show assoc where account=${_account} format=ParentName%100 -P | grep -v "Par Name" | grep -c courses) -eq 0 ]; then _worker_name=${HOSTNAME}-${_account}-reserved max_wall=$(sacctmgr show assoc where account=${_account} format=MaxWall -P | grep -v MaxWall | head -1) for mem in 90; do mkdir -p ${install_path}/site_configs/${_worker_name}_${mem}gb && cd ${install_path}/site_configs/${_worker_name}_${mem}gb cat << EOF > cluster_info.json { "name": "${_worker_name}_${mem}gb", "worker_bin_path": "${install_path}/cryosparc_worker/bin/cryosparcw", "cache_path": "/tmp/{{ cryosparc_username }}/cryosparc_cache", "cache_reserve_mb": 10000, "cache_quota_mb": 1000000, "send_cmd_tpl": "{{ command }}", "qsub_cmd_tpl": "sbatch {{ script_path_abs }}", "qstat_cmd_tpl": "squeue -j {{ cluster_job_id }}", "qdel_cmd_tpl": "scancel {{ cluster_job_id }}", "qinfo_cmd_tpl": "sinfo" } EOF cat << EOF > cluster_script.sh #!/bin/bash -l #SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }} -#SBATCH -n {{ num_cpu }} -#SBATCH --gres gpu:{{ num_gpu }} +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=1 +#SBATCH --cpus-per-task={{ num_cpu }} +#SBATCH --gres=gpu:{{ num_gpu }} #SBATCH --mem ${mem}GB #SBATCH --time 3-00:00:00 #SBATCH -o {{ job_dir_abs }}/slurm.out #SBATCH -e {{ job_dir_abs }}/slurm.err #SBATCH -A ${_account} #SBATCH --reservation $reservation_name module load gcc cuda/11.0.2 python mkdir -p /tmp/${USER} ln -sf \${TMPDIR} /tmp/${USER}/cryosparc_cache {{ run_cmd }} EOF ${install_path}/cryosparc_master/bin/cryosparcm cluster connect done fi done