Common mistakes to avoid

job submission (qsub) options positioning

When submitting a job with qsub, it’s important to list any options before the name of the job script. For instance, use qsub -l h_data=4G,h_rt=4:00:00 job_script.sh to allocate 4GB of data and a 4-hour runtime. If you place options after the script name, like qsub job_script.sh -l gpu,V100, the job won’t recognize them, which in this case means it won’t be sent to the V100 GPU node. Always remember: options first, then script name, such as qsub -l gpu,V100 job_script.sh.

Microsoft Windows end-of-line characters in job scripts

When transferring job script files from a Microsoft Windows system to the Hoffman2 Cluster, you may encounter issues with incompatible end-of-line characters. To resolve this, you can adjust your Windows text editor settings to use the Linux-compatible \n as the end-of-line character. Alternatively, after uploading the file to Hoffman2, you can convert the end-of-line characters by executing the dos2unix command, like this:

$ dos2unix job_script.sh

This will ensure your script runs correctly on the cluster.