Hello and welcome!
This post provides an example of taking an sbatch script that you previously ran on Discovery and converting the script to run on the Explorer cluster.
- Confirm that you have access to running jobs on the Explorer cluster by logging in to Explorer.
2. Check if your Slurm account is set up. If you see a value for the categories “User” and “Def Acct” then your slurm account is setup.
However, if you do not have a Slurm account, you will see the following. In this case, please create a ticket with Research Computing by emailing rchelp@northeastern.edu, and we will assist you in creating your account on the Explorer cluster.
Once you have determined that you have a Slurm account, you can convert your sbatch script. There are three items you want to check:
- sbatch directives
- modules names
- change paths from /work to /projects
Consider the following example sbatch script for the Discovery cluster:
Below is the modified script for the Explorer cluster. We did not need to change the sbatch directives, but did change the modules that are loaded, and the path was changed from /work to /projects.
We no longer needed to load a module, as we have the container run-time engine Apptainer installed on every node.
We have container images in this directory path that you are welcome to access:
If you specify other modules in your sbatch scripts you will need to check that they are present in Explorer and update your sbatch script with the correct version.
You can see the modules available on Explorer with the command “module avail”:
If you need a module that you do see listed please send a request to rchelp@northeastern.edu.
Happy Computing!
Serena has extensive experience with non-model organism genomics, including de novo genome or transcriptome assembly, genome annotation, genome liftover, variant calling, and population genetics. She is eager to help biologists with their computing needs and is skilled in experimental design (GWAS, Population genetics, and quantitative genetics), data analysis, and visualization in RStudio. Serena earned her PhD from UC Davis in Population Biology.
