installing cryoSPARC2 on Farnam

install_cryosparc2.sh

#!/bin/bash
## cryosparc install
# where to install cryosparc2 and its sample database
install_path=$HOME/project/software/cryosparc2
# the license ID you got from Structura
license_id=
# your email
my_email=$(cat ~/.forward)
# partition to submit your cryosparc jobs to
# not sure you can change at runtime
partition=gpu

# don't edit below here
###########################
my_name="$USER"
db_path=${install_path}/cryosparc_database
# a temp password
cryosparc_passwd=Password123
module load CUDA/9.0.176
worker_path=${install_path}/cryosparc2_worker
ssd_path=/tmp/${USER}/cryosparc_cache

mkdir -p $install_path
cd $install_path
curl -sL https://get.cryosparc.com/download/master-latest/$license_id > cryosparc2_master.tar.gz
curl -sL https://get.cryosparc.com/download/worker-latest/$license_id > cryosparc2_worker.tar.gz

tar -xf cryosparc2_master.tar.gz
tar -xf cryosparc2_worker.tar.gz

cd ${install_path}/cryosparc2_master
./install.sh --license $license_id --hostname $(hostname) --dbpath $db_path --yes
source ~/.bashrc

cd ${install_path}/cryosparc2_worker
./install.sh --license $license_id --cudapath $CUDA_HOME --yes
source ~/.bashrc

# Farnam cluster setup
mkdir -p ${install_path}/site_configs && cd ${install_path}/site_configs
cat << EOF > cluster_info.json
{
    "name" : "farnam",
    "worker_bin_path" : "${install_path}/cryosparc2_worker/bin/cryosparcw",
    "cache_path" : "/tmp/{{ cryosparc_username }}/cryosparc_cache",
    "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
#!/usr/bin/env bash
#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }}
#SBATCH -c {{ num_cpu }}
#SBATCH --gres=gpu:{{ num_gpu }}
#SBATCH -p ${partition}
#SBATCH --mem={{ (ram_gb*1024)|int }}             
#SBATCH -o {{ job_dir_abs }}
#SBATCH -e {{ job_dir_abs }}

module load CUDA/9.0.176
mkdir -p /tmp/${USER}/cryosparc_cache
{{ run_cmd }}
EOF


cryosparcm start
cryosparcm createuser --email $my_email --password $cryosparc_passwd --name $my_name
cryosparcm cluster connect
cryosparcm stop