cryoSPARC/qsub

[cryosparc@cryosparc ~]$ cryosparcm cluster example
Writing example cluster_info.json and cluster_script.sh to current dir
Unknown cluster type. Supported templates are:
  pbs
  slurm
  gridengine
Any cluster scheduler is supported, but you may have to write your own custom submission script.
[cryosparc@cryosparc ~]$

[cryosparc@cryosparc ~]$ cryosparcm cluster example pbs
Writing example cluster_info.json and cluster_script.sh to current dir
[cryosparc@cryosparc ~]$

[cryosparc@cryosparc ~]$ cat cluster_info.json
{
    "name" : "pbscluster",
    "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" : "qsub {{ script_path_abs } }",
    "qstat_cmd_tpl" : "qstat -as {{ cluster_job_id } }",
    "qdel_cmd_tpl" : "qdel {{ cluster_job_id } }",
    "qinfo_cmd_tpl" : "qstat -q"
}
[cryosparc@cryosparc ~]$

[cryosparc@cryosparc ~]$ cat cluster_script.sh
#!/usr/bin/env bash
#### cryoSPARC cluster submission script template for PBS
## 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 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 PBS script:
 
#PBS -N cryosparc_{{ project_uid } }_{{ job_uid } }
#PBS -l select=1:ncpus={{ num_cpu } }:ngpus={{ num_gpu } }:mem={{ (ram_gb*1000)|int } }mb:gputype=P100
#PBS -o {{ job_log_path_abs } }
#PBS -e {{ job_log_path_abs } }
 
{{ run_cmd } }
 
[cryosparc@cryosparc ~]$

[cryosparc@cryosparc ~]$ cryosparcm cluster connect
 :
Successfully added cluster lane pbscluster
 
(確認は下記コマンドで)
[cryosparc@cryosparc ~]$ cryosparcm cli "get_scheduler_lanes()"
 
(削除はcluster_info.jsonのnameを使います)
[cryosparc@cryosparc ~]$ cryosparcm cluster remove pbscluster
(あるいは)
[cryosparc@cryosparc ~]$ cryosparcm cli "remove_scheduler_lane('pbscluster')"

ExecStart=/home/cryosparc/cryosparc_master/bin/cryosparcm start
  ↓
ExecStart=/bin/bash -l /home/cryosparc/cryosparc_master/bin/cryosparcm start

cryosparcm patch

cryosparcm patch --download
あるいは
cryosparcm patch --download --force

cd cryosparc_worker/
cp ../cryosparc_master/cryosparc_worker_patch.tar.gz .
bin/cryosparcw patch

#!/usr/bin/env bash
#PBS -N cryosparc_{{ project_uid } }_{{ job_uid } }
#PBS -l select=1:ncpus={{ num_cpu } }:ngpus={{ num_gpu } }:mem={{ (ram_gb|float * (ram_gb_multiplier|default(1))|float)|int } }G
#PBS -o {{ job_log_path_abs } }
#PBS -e {{ job_log_path_abs } }
 
{{ run_cmd } }