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#author("2023-08-27T12:42:36+00:00","default:sysosa","sysosa") #author("2025-10-24T16:58:43+00:00","default:sysosa","sysosa") slurmでcryoSPARCを運用する場合. &color(darkorange){cluster_info.json};と&color(darkorchid){cluster_script.sh};は下記コマンドで取得できます. #code(nonumber){{ cryosparcm cluster example slurm }} cluster_info.json内にある「qstat_code_cmd_tpl」のコマンド行が微妙でエラーになります どうもパイプ(|)がダメらしくて下記に変更します ***&color(darkorange){cluster_info.json}; [#lae79ece] 中身はこんな感じ #code(nonumber){{ "qstat_code_cmd_tpl": "squeue -j {{ cluster_job_id } } --format=%T | sed -n 2p", ↓ "qstat_code_cmd_tpl": "squeue --noheader -j {{ cluster_job_id } } --format=%T", }} &size(10){Pukiwikiの表記のため一部表記を変えてます}; #code(nonumber){{ { "name" : "node01", "worker_bin_path" : "/home/cryosparc/cryosparc_worker/bin/cryosparcw", "cache_path" : "/scratch/cryosparc", "send_cmd_tpl" : "{{ command } }", "name" : "slurmcluster", "worker_bin_path" : "/path/to/cryosparc_worker/bin/cryosparcw", "cache_path" : "/path/to/local/SSD/on/cluster/nodes", "send_cmd_tpl" : "ssh loginnode {{ command } }", "qsub_cmd_tpl" : "sbatch {{ script_path_abs } }", "qstat_cmd_tpl" : "squeue -j {{ cluster_job_id } }", "qstat_code_cmd_tpl": "squeue --noheader -j {{ cluster_job_id } } --format=%T", "qstat_code_cmd_tpl": "squeue -j {{ cluster_job_id } } --format=%T | sed -n 2p", "qdel_cmd_tpl" : "scancel {{ cluster_job_id } }", "qinfo_cmd_tpl" : "sinfo", "transfer_cmd_tpl" : "cp {{ src_path } } {{ dest_path } }" "qinfo_cmd_tpl" : "sinfo" } }} &size(10){***Pukiwikiの表記のため一部表記を変えてます***}; ただ、、「qstat_code_cmd_tpl」のコマンド行が微妙でエラーになる場合がある. そのため #code(nonumber){{ "qstat_code_cmd_tpl": "squeue -j {{ cluster_job_id } } --format=%T | sed -n 2p", ↓ "qstat_code_cmd_tpl": "squeue --noheader -j {{ cluster_job_id } } --format=%T", }} とした方がいいかも. あとcluster_script.shはデフォのままかな &size(10){Pukiwikiの表記のため一部表記を変えてます}; cluster_info.json内にある「qstat_code_cmd_tpl」のコマンド行が微妙でエラーになります どうもパイプ(|)がダメらしくて下記に変更します ***&color(darkorchid){cluster_script.sh}; [#uc13e0c9] 中身はこんな感じ #code(nonumber){{ #!/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. ## {{ num_gpu } } - the number of GPUs needed. ## Note: The code will use this many GPUs starting from dev id 0. ## The cluster scheduler has the responsibility ## of setting CUDA_VISIBLE_DEVICES or otherwise enuring that the ## job uses 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 ## {{ job_creator } } - name of the user that created the job (may contain spaces) ## {{ cryosparc_username } } - cryosparc username of the user that created the job (usually an email) ## ## 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 --partition=gpu #SBATCH --mem={{ (ram_gb*1000)|int } }MB #SBATCH --output={{ job_log_path_abs } } #SBATCH --error={{ job_log_path_abs } } #SBATCH --mem={{ (ram_gb*1000)|int } }M #SBATCH --output={{ job_dir_abs } }/slurm.out #SBATCH --error={{ job_dir_abs } }/slurm.err 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 {{ run_cmd } } }} &size(10){***Pukiwikiの表記のため一部表記を変えてます***};
