diff --git a/cryosparc_install.sh b/cryosparc_install.sh index 86ed50a..4ba5fa0 100755 --- a/cryosparc_install.sh +++ b/cryosparc_install.sh @@ -1,198 +1,204 @@ #!/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 "${script_path}" && pwd) # absolutized and normalized license_id= install_path="$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 your license id: " license_id read -p "Enter password for the user account to be created [leave empty to not create the initial account]: " password # 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 } if [ "x${license_id}" == "x" ]; then echo "[Error] No license id was provided" >&2 usage exit 2 fi message "[Info] Preparing the install path and dowloading cryosparc_master and cryosparc_worker" # go get the installers mkdir -p $install_path cd $install_path # Download master curl -sL -C - -\# https://get.cryosparc.com/download/master-latest/$license_id -o cryosparc2_master.tar.gz # Download worker curl -sL -C - -\# https://get.cryosparc.com/download/worker-latest/$license_id -o cryosparc2_worker.tar.gz message "[Info] Expanding tarballs" tar -xf cryosparc2_master.tar.gz tar -xf cryosparc2_worker.tar.gz module purge module load gcc cuda/11.0.2 python message "[Info] Installing master" cd ${install_path}/cryosparc_master ./install.sh --license $license_id --hostname $(hostname) --dbpath $db_path --yes set +u #source ~/.bashrc set -u message "[Info] Installing worker" cd ${install_path}/cryosparc_worker ./install.sh --license $license_id --cudapath $CUDA_HOME --yes set +u #source ~/.bashrc set -u message "[Info] Creating worker configs" cryosparc_master_path=${install_path}/cryosparc_master if [ $(grep -c "export PATH" ${cryosparc_master_path}/config.sh) -eq 0 ]; then echo "export PATH=${cryosparc_master_path}/bin:\$PATH" >> ${cryosparc_master_path}/config.sh fi if [ $(grep -c "export CRYOSPARC_HOSTNAME_CHECK" ${cryosparc_master_path}/config.sh) -eq 0 ]; then echo "export CRYOSPARC_HOSTNAME_CHECK=${HOSTNAME}" >> ${cryosparc_master_path}/config.sh fi cryosparc_worker_path=${install_path}/cryosparc_worker if [ $(grep -c "export PATH" ${cryosparc_worker_path}/config.sh) -eq 0 ]; then echo "export PATH=${cryosparc_worker_path}/bin:\$PATH" >> ${cryosparc_worker_path}/config.sh fi cp ${script_path}/cryosparcm.sh ${install_path}/cryosparc_master/bin 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) mail=$(ldapsearch -x -LLL -h scoldap.epfl.ch -b "o=epfl,c=ch" uid=${user_name} mail | grep mail | awk '{ print $2 }') firstname=$(ldapsearch -x -LLL -h scoldap.epfl.ch -b "o=epfl,c=ch" uid=${user_name} givenName | grep givenName | awk '{ print $2 }') lastname=$(ldapsearch -x -LLL -h scoldap.epfl.ch -b "o=epfl,c=ch" uid=${user_name} sn | grep sn | awk '{ print $2 }') if [ "x$password" != "x" ]; then ${install_path}/cryosparc_master/bin/cryosparcm.sh createuser --email "${mail}" --firstname "${firstname}" --lastname "${lastname}" --username "${user_name}" --password "${password}" echo "Initial account \"${user_name} - ${firstname} ${lastname} <${mail}>\" was created with the provided password" fi 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} mkdir -p ${install_path}/site_configs/${_worker_name} && cd ${install_path}/site_configs/${_worker_name} - cat << EOF > cluster_info.json + + max_wall=$(sacctmgr show assoc where account=${_account} format=MaxWall -P | grep -v MaxWall | head -1) + + for i in 90 180 360 720; do + cat << EOF > cluster_info.json { - "name": "${_worker_name}", + "name": "${_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": "null", "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 + 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 --mem {{ ram_gb|int }}GB -#SBATCH --time 48:0:0 +#SBATCH --mem ${mem}GB +#SBATCH --time ${max_wall} #SBATCH -o {{ job_dir_abs }}/slurm.out #SBATCH -e {{ job_dir_abs }}/slurm.err #SBATCH -A ${_account} module load gcc cuda/11.0.2 python -ln -sf \${TMPDIR} /tmp/${USER}/cryosparc2_cache +mkdir -p /tmp/${USER} +ln -sf \${TMPDIR} /tmp/${USER}/cryosparc_cache {{ run_cmd }} EOF - ${install_path}/cryosparc_master/bin/cryosparcm cluster connect + ${install_path}/cryosparc_master/bin/cryosparcm cluster connect + done fi done if [ "x$password" = "x" ]; then echo "" echo "================================================================================" echo "================================================================================" echo " No password was given the initial account cannot be created" echo " Create one using the following command:" echo " ${install_path}/cryosparc_master/bin/cryosparcm.sh createuser --email \"${mail}\" --firstname \"${firstname}\" --lastname \"${lastname}\" --username \"${user_name}\" --password \"\"" echo "================================================================================" echo "================================================================================" echo "" fi ${install_path}/cryosparc_master/bin/cryosparcm.sh stop