Miscellaneous - jubayer98/UKD_DOCS Wiki

Interactive Job

Interactive Job is an important task to do while working in HPC. If you want to do some kind of operation like generating reports (executing snakemake rule), executing different file formats (encryption), etc. for handling large files then you have to use the Interactive Job command.

qsub -I -A ngsukdkohi -l select=1:ncpus=1:mem=10GB -l walltime=02:00:00

The following command ensures that you allocated a specific memory and runtime for performing your job. Where your allocated memory is mem=10GB and runtime is walltime=02:00:00 (which means two hours). After two hours your job will be killed by HPC automatically whether it is finished or not. So before running the Interactive Job, always try to use a sufficient amount of memory and runtime to perform your task.

Load Module

Load Module is another important thing to do before executing any operation like executing reports/encryption, etc. Because sometimes, it seems that, after initiating the Interactive Job, your environment will behave like the default mode of the HPC environment. And you will get errors to perform operations because some of the modules will not load if you start the Interactive Job. And you will get some class missing and module missing errors. To ignore this issue after initiating the Interactive Job, you have to Load Module for the specific tasks of operation. You will get all the available modules to load. To get all the available module lists to type the following command first:

module avail

Then you will see a bunch of module lists and select your preferred module to work with. Suppose to execute a snakemake rule like generating yield reports or qualimap reports, you have to load the following module after initiating the Interactive Job.

module load Snakemake/5.10.0