gantry.md

gantry | ˈɡantrē |

Introduction

Run Singularity containers a bit easier! Allows users the ablility to:

• List all currently available singularity images.
• Run single or multiple commands through a singularity container.
• Launch singularity jobs to interactive nodes or CHPC compute nodes via sbatch.

Usage

To use gantry you must run the following on the CHPC

$> ml ucgd_modules
$> gantry.py
usage:

    ~~~ Run Singularity containers a bit easier! ~~~

Description:

Allows users the ablility to:

* List all currently available singularity images.
* Run single or multiple commands through a singularity container.
* Launch singularity jobs to interactive nodes or CHPC compute nodes via sbatch.

Note:

* Jobs launched to CHPC compute nodes are not monitored.

optional arguments:
  -h, --help            show this help message and exit
  -l, --list            List all currently available container img files.
  -i IMG, --img IMG     Use the following img.
  -c COMMAND, --command COMMAND
                        Command to pass to selected img file. Must be enclose in quotes!
  -cf COMMAND_FILE, --command_file COMMAND_FILE
                        File containing commands to run.
  --path PATH           Path to singularity images directory.
  --sbatch              Submit jobs to the UCGD processing nodes.
  -nl, --no_launch      Will create sbatch scripts, but not launch them to the UCGD nodes
  -j JOBNAME, --jobname JOBNAME
                        Jobname to use when launching on sbatch.
  -a ACCOUNT, --account ACCOUNT
                        sbatch account to submit job to.
  -p PARTITION, --partition PARTITION
                        partition to submit job to.
  -as ADDITIONAL_STEPS, --additional_steps ADDITIONAL_STEPS
                        add additional steps or commands to sbatch script.

Option Examples

Option	Explanation	Example
-l, --list	List all available .img files and exit	gantry.py -l
-i, --img	Use the following images	gantry.py -i bedtools.img
-c, --command	Execute a command within a container (Must be enclose in quotes)	gantry.py -i bcftools.img -c "bcftools view"
-cf, --command_file	Single file containing all commands to run	gantry.py -i bcftools.img -cf bcftools_cmd.txt
-p, --path	Path to the directory containing one or more .img files. Defaults to: $APPS/el7/UCGD-Containers/img	gantry.py -i bcftools.img -cf bcftools_cmd.txt -p /my/containers/location/
--sbatch	Will create and launch commands on UCGD nodes	gantry.py -i bcftools.img -cf bcftools_cmd.txt --sbatch
-nl, --no_launch	Will create but not launch sbatch scripts	gantry.py -i bcftools.img -cf bcftools_cmd.txt --sbatch -nl`
-j, --jobname	Run on compute nodes under given name. Default: gantry	gantry.py -i bcftools.img -cf bcftools_cmd.txt --sbatch -j bcftools-run
-a, --account	Run on compute nodes using this account. Default: ucgd-rw	gantry.py -i bcftools.img -cf bcftools_cmd.txt --sbatch (run on default)
-p, --partition	Run on compute nodes using this partition. Default: ucgd-rw	gantry.py -i bcftools.img -cf bcftools_cmd.txt --sbatch (run on default)
-as, --additional_steps	Add additional commands to sbatch script (Must be enclose in quotes)	gantry.py -i bcftools.img -cf bcftools_cmd.txt --sbatch -as "module load vt"