High Performance Clusters Usage Guide

New Server TinkerCliffs Quick Guide

1. Login in:

ssh -Y (yourID)@tinkercliffs1.arc.vt.edu or ssh -Y (yourID)@tinkercliffs2.arc.vt.edu

For quick login, edit your local .bash_profile by: emacs ~/.bash_profile Adding this part:

alias tinkercliffs="ssh -Y (yourID)@tinkercliffs1.arc.vt.edu"

Then you can login by just type tinkercliffs locally.

1. After logging in, setup your home directory .bashrc file:

emacs /home/$(whoami)/.bashrc

Add this part to the end:

if [ $SYSNAME == "tinkercliffs" ]

then
source /home/hxin/tinkercliffs/.bashrc

fi

1. For using VASP modules:

For using python2 and ase3.12, source:

source /home/hxin/tinkercliffs/.modules.vasp-arc
source /home/hxin/tinkercliffs/.modules.vasp-grg

For using python3 and ase3.19, source:

source /home/hxin/tinkercliffs/.modules.vasp-arc3
source /home/hxin/tinkercliffs/.modules.vasp-grg3

For using python3 and ase3.19 and vtsttools, source:

source /home/hxin/tinkercliffs/.modules.vasp-vtst3

1. Preparing your .qsub file for submitting jobs:

Using vasp_sub.sh to submit Script.py jobs. Native vasp is still under testing. For options of vasp_sub.sh, use: vasp_sub.sh -h

Tinkercliffs has about 280 nodes in total and 128 cores per node, so for normal usage you can specify how many cores you want to use by -c option, and currently available allocations are DFT_XinLab and AmmoniaCat, you can specify it by -x option. Other options (-j, -n, -q, -s, etc.)are the same as other severs.

Example:

vasp_sub.sh -j test -n 1 -w 1:00:00 -c 32 -q normal_q -x tcfriendly -s Script.py

1. Submitting and checking jobs:

Tinkercliffs uses original slurm system for jobs: Submit your job:

sbatch Script.py.qsub

Cancel your job:

scancel JOBID 

Check your job list (cannot use qstat):

squeue -u $(whoami) or squeue -u yourID

Check all jobs on queue:

squeue

Check available idle nodes:

sinfo -t idle

Check detail info of your specific job:

scontrol show jobid JOBID

Some online references for you : https://ubccr.freshdesk.com/support/solutions/articles/5000688140-submitting-a-slurm-job-script

You can also alias them to your familiar commands in .bashrc file.

1. Modules

Purge all modules:

module purge

For tinkercliffs, all useful system tools and packages are setup by modules, so every time you make some changes to the modules and then you want to go back to the default settings using:

module reset

Check your current modules:

module list 

Check if the server has specific modules:

module spider MODULENAME

Visualize geometries:

You can still use ase gui (or ag) to visualize you structures. Remember to source vasp modules with python3 and ase3.19.

Usage Update

1. Edit your .bashrc

For newriver: emacs -nw ~/.bashrc

source /work/common/hxin_lab/hxin/newriver/.bashrc

For cascades: emacs -nw ~/.bashrc

source /work/common/hxin_lab/hxin/cascades/.bashrc

1. Source VASP

For newriver:

source /work/common/hxin_lab/hxin/newriver/.modules.vasp-arc3 source /work/common/hxin_lab/hxin/newriver/.modules.vasp-grg3 source /work/common/hxin_lab/hxin/newriver/.modules.vasp-vtst3

For cascades:

source /work/common/hxin_lab/hxin/cascades/.modules.vasp-arc3 source /work/common/hxin_lab/hxin/cascades/.modules.vasp-grg3 source /work/common/hxin_lab/hxin/cascades/.modules.vasp-vtst3

1. Source Quantum Espresso

For newriver:

source /work/common/hxin_lab/hxin/newriver/.modules.espresso6.5

For cascades:

source /work/common/hxin_lab/hxin/cascades/.modules.espresso6.5

1. New allocations

DFT_XinLab and hxin_lab

AmmoniaCat is not available anymore.

1. Comments

Tinkercliffs can’t be used since there is no access to /work folder. Only the python 3 version is available. ASE 3.17 and ASE 3.19 can be loaded.

Tianyou Mou

Chemical Engineer and Data Scientist