Csvkit on HPC

Csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load csvkit
[user@cn3144 ~]$ cd /data/$USER/dir
[user@cn3144 ~]$ curl -L -O https://github.com/onyxfish/csvkit/raw/master/examples/realdata/ne_1033_data.xlsx
[user@cn3144 ~]$ in2csv /data/$USER/dir/ne_1033_data.xlsx

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. batch.sh). For example:

set -e
module load csvkit
in2csv exampleInfile

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; in2csv infile
cd dir2; in2csv infile
cd dir3; in2csv infile

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module csvkit
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module Loads the module for each subjob in the swarm