cryoSPARC/sbatch をテンプレートにして作成
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開始行:
slurmでcryoSPARCを運用する場合.
&color(darkorange){cluster_info.json};と&color(darkorchid...
#code(nonumber){{
cryosparcm cluster example slurm
}}
***&color(darkorange){cluster_info.json}; [#lae79ece]
中身はこんな感じ
#code(nonumber){{
{
"name" : "slurmcluster",
"worker_bin_path" : "/path/to/cryosparc_worker/bin/cr...
"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 -j {{ cluster_job_id } ...
"qdel_cmd_tpl" : "scancel {{ cluster_job_id } }",
"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...
#code(nonumber){{
"qstat_code_cmd_tpl": "squeue -j {{ cluster_job_id } } --...
↓
"qstat_code_cmd_tpl": "squeue --noheader -j {{ cluster_jo...
}}
とした方がいいかも.
cluster_info.json内にある「qstat_code_cmd_tpl」のコマンド...
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 strin...
## {{ num_cpu } } - the number of CPUs needed
## {{ num_gpu } } - the number of GPUs needed.
## Note: The code will use thi...
## The cluster scheduler...
## of setting CUDA_VISIB...
## job uses the correct ...
## {{ ram_gb } } - the amount of RAM needed i...
## {{ job_dir_abs } } - absolute path to the job d...
## {{ project_dir_abs } } - absolute path to the proje...
## {{ job_log_path_abs } } - absolute path to the log f...
## {{ worker_bin_path } } - absolute path to the cryos...
## {{ run_args } } - arguments to be passed to ...
## {{ project_uid } } - uid of the project
## {{ job_uid } } - uid of the job
## {{ job_creator } } - name of the user that crea...
## {{ cryosparc_username } } - cryosparc username of the ...
##
## What follows is a simple SLURM script:
#SBATCH --job-name cryosparc_{{ project_uid } }_{{ job_ui...
#SBATCH -n {{ num_cpu } }
#SBATCH --gres=gpu:{{ num_gpu } }
#SBATCH --partition=gpu
#SBATCH --mem={{ (ram_gb*1000)|int } }M
#SBATCH --output={{ job_dir_abs } }/slurm.out
#SBATCH --error={{ job_dir_abs } }/slurm.err
{{ run_cmd } }
}}
&size(10){***Pukiwikiの表記のため一部表記を変えてます***};
終了行:
slurmでcryoSPARCを運用する場合.
&color(darkorange){cluster_info.json};と&color(darkorchid...
#code(nonumber){{
cryosparcm cluster example slurm
}}
***&color(darkorange){cluster_info.json}; [#lae79ece]
中身はこんな感じ
#code(nonumber){{
{
"name" : "slurmcluster",
"worker_bin_path" : "/path/to/cryosparc_worker/bin/cr...
"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 -j {{ cluster_job_id } ...
"qdel_cmd_tpl" : "scancel {{ cluster_job_id } }",
"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...
#code(nonumber){{
"qstat_code_cmd_tpl": "squeue -j {{ cluster_job_id } } --...
↓
"qstat_code_cmd_tpl": "squeue --noheader -j {{ cluster_jo...
}}
とした方がいいかも.
cluster_info.json内にある「qstat_code_cmd_tpl」のコマンド...
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 strin...
## {{ num_cpu } } - the number of CPUs needed
## {{ num_gpu } } - the number of GPUs needed.
## Note: The code will use thi...
## The cluster scheduler...
## of setting CUDA_VISIB...
## job uses the correct ...
## {{ ram_gb } } - the amount of RAM needed i...
## {{ job_dir_abs } } - absolute path to the job d...
## {{ project_dir_abs } } - absolute path to the proje...
## {{ job_log_path_abs } } - absolute path to the log f...
## {{ worker_bin_path } } - absolute path to the cryos...
## {{ run_args } } - arguments to be passed to ...
## {{ project_uid } } - uid of the project
## {{ job_uid } } - uid of the job
## {{ job_creator } } - name of the user that crea...
## {{ cryosparc_username } } - cryosparc username of the ...
##
## What follows is a simple SLURM script:
#SBATCH --job-name cryosparc_{{ project_uid } }_{{ job_ui...
#SBATCH -n {{ num_cpu } }
#SBATCH --gres=gpu:{{ num_gpu } }
#SBATCH --partition=gpu
#SBATCH --mem={{ (ram_gb*1000)|int } }M
#SBATCH --output={{ job_dir_abs } }/slurm.out
#SBATCH --error={{ job_dir_abs } }/slurm.err
{{ run_cmd } }
}}
&size(10){***Pukiwikiの表記のため一部表記を変えてます***};
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