asub stands for "array submission". It greatly simplifies batch job submission on LSF (or Grid Engine with limited support). Briefly, it reads mutually independent command lines from stdin or from a shell script and creates a job array with each job for one or multiple command lines in the input.

A job array is an array of LSF/Grid Engine jobs that are submitted together and have the same JobID. It has two major advantages. Firstly, job array is convenient for a batch jobs having similar input/output. You can kill/stop/resume/modify the whole array or some jobs in the array easily by specifying, for example, JobID or JobID[10-100]. You can also specify how many jobs in the array should be run at the same time with bmod -J%10 JodID. Secondly, Tim Cutts from the Sanger Institute used to show that job arrays put less stress on the LSF scheduler. This makes array jobs submitted much faster and also reduces the burden on the entire LSF system.

Submitting array jobs is harder. You have to learn the mechanism of job arrays and frequently need to write a bsub script that takes an array job index as the input. asub simplifies this procedure. You can easily submit a job array if you have your independent command lines kept in a file/stream (see examples below).

In addition to array submission, asub also simplifies resource requirement. You can submit a multi-threaded job without -R'span[hosts=1]', or set a memory limit without -R'rusage[mem=4096]' (and you don't need to remember 4096 is the per-task limit, not the total limit). asub can also optionally group multiple command lines into one job. This feature could be helpful if each individual command line runs too fast.

asub is easily my mostly used Perl script in nearly ten years.

For now, asub only has limited support of Grid Engine. I used to have a better version for SGE, but have lost it. Contribution welcomed!

asub has two modes: submission mode and laucher mode. Endusers only need to care about the submission mode. In this mode, asub writes the input command lines into JobID.sh and generates an on-the-fly bsub script that calls asub -k ${LSB_JOBINDEX} JobID.sh to execute command lines. Here -k <lineno> puts asub in the launcher mode. Without -g, it runs the <lineno>-th command line in JobID.sh.

• Compress large FASTQ files:

  ls *.fq | xargs -i echo gzip {} | asub -j run-gzip

  The i-th job in the job array compresses the i-th file.

• Compress large FASTQ files with parallel jobs:

  ls *.fq | xargs -i echo gzip {} | asub -g2 -q mcore

  The i-th job compresses the 2i-1 and 2i files in parallele. The example is only useful under particular settings (e.g. at HMS). Usually we would not want to do this.

• Compress small FASTQ files by serial batching:

  ls *.fq | xargs -i echo gzip {} | asub -Gg2

  The i-th job compresses the 2i-1 and 2i files in turn. This can be used to group short processes such that the whole job takes reasonable amount of time. Too many short jobs hurt LSF performance.