diff --git a/.cluster_script.sh.swp b/.cluster_script.sh.swp deleted file mode 100644 index 3f14acb..0000000 Binary files a/.cluster_script.sh.swp and /dev/null differ diff --git a/cluster_info.json b/cluster_info.json deleted file mode 100644 index 9423084..0000000 --- a/cluster_info.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "name" : "merlin5", - "worker_bin_path" : "/gpfs/data/ozerov_d/cryosparc/cryosparc2_worker/bin/cryosparcw", - "cache_path" : "/ssd-scratch/", - "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", - "transfer_cmd_tpl" : "cp {{ src_path }} {{ dest_path }}" -} diff --git a/cluster_script.sh b/cluster_script.sh deleted file mode 100644 index 4358cd9..0000000 --- a/cluster_script.sh +++ /dev/null @@ -1,52 +0,0 @@ -#!/usr/bin/env bash -#### cryoSPARC cluster submission script template for SLURM -## Available variables: -## {{ run_cmd }} - the complete command string to run the job -## {{ num_cpu }} - the number of CPUs needed -## {{ num_gpu }} - the number of GPUs needed. -## Note: the code will use this many GPUs starting from dev id 0 -## the cluster scheduler or this script have the responsibility -## of setting CUDA_VISIBLE_DEVICES so that the job code ends up -## using the correct cluster-allocated GPUs. -## {{ ram_gb }} - the amount of RAM needed in GB -## {{ job_dir_abs }} - absolute path to the job directory -## {{ project_dir_abs }} - absolute path to the project dir -## {{ job_log_path_abs }} - absolute path to the log file for the job -## {{ worker_bin_path }} - absolute path to the cryosparc worker command -## {{ run_args }} - arguments to be passed to cryosparcw run -## {{ project_uid }} - uid of the project -## {{ job_uid }} - uid of the job -## -## What follows is a simple SLURM script: - -#SBATCH --job-name cryosparc_{{ project_uid }}_{{ job_uid }} -#SBATCH -n {{ num_cpu }} -##SBATCH --gres=gpu:{{ num_gpu }} -#SBATCH -p gpu -##SBATCH --mem={{ (ram_gb*1000)|int }}MB -#SBATCH --mem=64000MB -#SBATCH -o {{ job_dir_abs }}/job.out -#SBATCH -e {{ job_dir_abs }}/job.err -#SBATCH --nodes=1 -#SBATCH --exclusive -#SBATCH --exclude=merlin-g-02 - -available_devs="" -for devidx in $(seq 0 15); -do - if [[ -z $(nvidia-smi -i $devidx --query-compute-apps=pid --format=csv,noheader) ]] ; then - if [[ -z "$available_devs" ]] ; then - available_devs=$devidx - else - available_devs=$available_devs,$devidx - fi - fi -done -export CUDA_VISIBLE_DEVICES=$available_devs - -hostname -echo "CUDA_VISIBLE_DEVICES : ${CUDA_VISIBLE_DEVICES}" -echo "{{ run_cmd }}" - -{{ run_cmd }} -