This project is maintained by CCML-UCONN
For the first login only, run the following command:
mkdir -p /scratch/$USER
ln -s /scratch/$USER $HOME/scratch
chgrp -R hpc-ccml /scratch/$USER
chmod g+s /scratch/$USER
chmod -R 750 /scratch/$USER
cp /home/liz18025/Group/share/bash/bashrc_copy ~/.bashrc
source ~/.bashrc
This will enable you to run specific software on the HCP-Storrs cluster, including the ASE interface to VASP and Quantum ESPRESSO.
There are two file systems, home and scratch. The above lines created your directory under the scratch partition and a symbolic link(shortcut) under your home directory pointing to your scratch directory. The rest of the lines set the group id to hpc-ccml and makes the directory only readable and executable to all group members.
Once you are logged into the terminal, run:
ase-gui
and make sure a graphical interface appears. Next, run Python in interactive mode by typing:
python
and make sure the following commands work:
import ase
import numpy
###Job Management### Most of our jobs require dedication of multiple nodes. Therefore jobs cannot be executed on the front node(the node everyone interfaces when logged onto the cluster). The HPC cluster use a job management system to process the resource requirements and its distribution to working/slave nodes. Some more useful information about the batch system on HPC-Storrs can be found here
You can find several different job submission scripts in the following directory:
$GRPDIR/share/example/scripts/batch/
Pick the one meets your need most and edit the corresponding fields.
These instructions are specific to the HPC-Storrs cluster.
sbatch <script_file>
Submit the job defined by the script file to the queue.
sq
Check the status of your jobs. You will get something like the following:
JOBID PARTITION QOS NAME USER ST TIME NODES CPUS NODELIST(REASON)
1775578 general general vasp.sub ******* PD 0:00 5 120 (Resources)
Shows more useful details about the job, including the working directory of the script.
squeue -u $USER -o '%.7i %.9P %.8j %.8u %.2t %.10M %.6D %R %Z'
You will get something like the following:
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) WORK_DIR
1775578 general vasp.sub ******* PD 0:00 5 (Resources) /gpfs/scratchfs1/*******/projects/seed/PdO/lsf-npo/101/high-co-cov/h2_ads/neb/0t/step2/neb
To delete your job. You can get the job ID from sq and use scancel to delete it.
scancel <job_ID>