pipeline:utilities:sp_batch

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pipeline:utilities:sp_batch [2019/04/02 11:24] (current)
lusnig created
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 +~~NOTOC~~
 +
 +===== sp_batch =====
 +Batch Pipeline Execution: Run jobs that wait with the execution on each other.
 +
 +\\
 +===== Usage =====
 +
 +Usage in command line
 +
 +  sp_batch.py ​ submission_command ​ input_run_dir --hold_flag=HOLD_FLAG --first_hold_number=FIRST_HOLD_NUMBER
 +\\
 +===== Typical usage =====
 +
 +sp_batch exists only in non-MPI version.
 +
 +The pipeline directory can be easily added within the GUI.
 +
 +Run sp_batch locally with bash:
 +
 +  sp_batch.py bash input_run_dir
 +
 +Run sp_batch within a SGE/​PBS/​Torque queuing environment:​
 +
 +  sp_batch.py '​qsub'​ input_run_dir --hold_flag='​-hold_jid'​
 +
 +Run sp_batch within a SGE/​PBS/​Torque queuing environment waiting for another job with the id 3456:
 +
 +  sp_batch.py '​qsub'​ input_run_dir --hold_flag='​-hold_jid'​ --first_hold_number=3456
 +
 +\\
 +===== Input =====
 +=== Main Parameters ===
 +  ; submission_command : Submission command : Submission command, e.g., qsub, qsub -V, sbatch, bash (default required string)
 +  ; input_run_dir:​ Pipeline directory : Directory containin the pipeline submission files (default required string)
 +  ; %%--%%hold_flag:​ Hold flag: Hold flag for the submission command, e.g. -hold_jid=, --wait=, --dependency=afterany:;​ Default is None and should be used in combination with a local execution with bash (default none)
 +  ; %%--%%first_hold_number:​ First hold number : Wait number for the first job that is submitted. By default, the first job will not wait for others (default none)
 +
 +\\
 +===== Output =====
 +Content of the commands in the PIPELINE folder.
 +
 +\\
 +===== Description =====
 +
 +\\
 +==== Method ====
 +
 +\\
 +==== Reference ====
 +
 +\\
 +==== Developer Notes ====
 +
 +\\
 +==== Author / Maintainer ====
 +Markus Stabrin
 +
 +\\
 +==== Keywords ====
 +Category 1:: APPLICATIONS
 +
 +\\
 +==== Files ====
 +sparx/​bin/​sp_unblur.py
 +
 +\\
 +==== See also ====
 +
 +\\
 +==== Maturity ====
 +Beta:: Under evaluation and testing. Please let us know if there are any bugs.
 +
 +\\
 +==== Bugs ====
 +There are no known bugs so far.
 +
 +\\
  
  • pipeline/utilities/sp_batch.txt
  • Last modified: 2019/04/02 11:24
  • by lusnig