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/Clusters/

Getting Started

  1. Logging Into the Computing Clusters
  2. Basic UNIX
  3. Python

Logging Into the Computing Clusters

Once you account on Stampede has been activated. Follow the instructions and tests to make sure everything is set up properly and functional.

Contents

  1. Installation
  2. Logging On
  3. First Time Logging On
  4. Making Sure Everything Works

Installation

Mac OSX

Download and install:

To prevent X11 from timing out, open the terminal and type:

mkdir -p ~/.ssh
echo $'\nHost *\n ForwardX11Timeout 1000000\n' >>~/.ssh/config

Windows

Download and install:

  • PuTTY
  • Xming (Note: disable automatic installation of PuTTY with Xming. The above installer is a newer version)

Linux (Debian-based, e.g. Ubuntu)

From the terminal

Logging onto the Clusters

For the Stampede cluster, make sure to read through the User Guide here.

login with your Stampede username (most probably start with tgxxxxxx, check your account here)and password (you will aslo be asked for Mulit-factor Authorization).

Follow the instructions below for your system:

Mac OSX

Open "Applications-> Utilities -> Terminal" or "Command+Space" to search Terminal using "spotlight search" In a terminal:

ssh -X username@stampede.tacc.utexas.edu

Windows

Launch Xming. You will always need to have this open in order to forward graphical windows from the external clusters.

Start PuTTY, and:

  • “Session” → “Host Name” username@stampede.tacc.utexas.edu for Stampede
  • “Connection” → “SSH” → “X11” check “Enable X11 forwarding”
  • Back in “Session”, you can save these settings for next time.

You can start putty several times, if you need several terminal windows; only one instance of Xming needed.

Linux

In a terminal:

ssh -X username@stampede.tacc.utexas.edu

First Time Logging in

For the first login only, run the following command:

cp /home1/03672/tg829713/vojgroup/bash_script/bashrc_copy ~/.bashrc 
source ~/.bashrc

This will enable you to run specific software on the Stampede cluster, including the ASE interface to Quantum ESPRESSO.

There are two file partitions, the home and the work partition. Go ahead and make a symbolic link to the work partition using:

ln -s $WORK work

Change the permission of files:

cd
cd work
mkdir CBE544
chmod g+X $WORK
chgrp -R G-818582 CBE544
chmod g+s CBE544
chmod g+rX CBE544

Perform all your calculations from the work/CBE544

For example, Create a folder hw5 under CBE544 and perform all calculations of HW5 in hw5. If you have already started you jobs somewhere else, you can copy the entire folder to CBE544 once you have done all calculations (e.g. cp -r folderpath ~/work/CBE544/hw5). However, you need to complete this step before sending us the report of HW5, and please include the path of CBE544 folder in your report or email. You can obtain the path by

cdw
cd CBE544
pwd

Making Sure Everything Works

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