Getting Started
Logging Into the Computing Clusters
Half of the class have been assigned computing accounts on Sherlock and the other half have been assigned accounts on CEES. Follow the instructions for using the one you have been assigned to and follow the tests to make sure everything is set up properly and functional.
Contents
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
- Kerberos (needed for Sherlock only)
- 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 (needed for Sherlock only):
sudo apt-get install krb5-user
Logging onto the Clusters
For the Sherlock cluster, make sure to read through the login instructions here.
For the CEES cluster, read through the login instructions here.
In both cases, login with your SUNetID and password.
Follow the instructions below for your system:
Mac OSX
For Sherlock only, authenticate using Kerberos:
kinit sunetid@stanford.edu
Then,
ssh -K -X sunetid@sherlock.stanford.edu
to log onto Sherlock, where sunetid is your Stanford SUNET ID. kinit does not need to be rerun unless the Kererbos ticket is expired. On Mac OSX you can type klist to check the status of the ticket.
For CEES,
ssh -X sunetid@cees-cluster.stanford.edu
Windows
Open Kerberos and authenticate using your SUNetID and password. Alternatively, ppen a “Command Prompt” (open a new one, if you have just installed Kerberos) and run:
kinit -5 sunetid@stanford.edu
Next, 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”
sunetid@sherlock.stanford.edufor Sherlock orsunetid@cees-cluster.stanford.edufor CEES. - “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 kinit and Xming needed.
Linux
In a terminal (Sherlock only):
kinit sunetid@stanford.edu
Then for Sherlock:
ssh -X sunetid@sherlock.stanford.edu
Open new terminals to run ssh again if you need several terminals on sherlock;
kinit only needs to be run once per boot (or as long as the Kerberos ticket remains valid). Type klist to check the ticket’s status.
For CEES:
ssh -X sunetid@cees-cluster.stanford.edu
First Time Logging in
Sherlock only:
For the first login only, run the following command:
echo $'\nexport PATH=/home/vossj/suncat/bin:$PATH' >>~/.bashrc
echo 'export LD_LIBRARY_PATH=/home/vossj/suncat/lib:/home/vossj/suncat/lib64:$LD_LIBRARY_PATH' >>~/.bashrc
source ~/.bashrc
This will enable you to run SUNCAT specific software on the Sherlock cluster, including the ASE interface to Quantum ESPRESSO.
There are two file partitions, the home and the scratch partition. Go ahead and make a symbolic link to the scratch partition using:
ln -s $SCRATCH scratch
Perform all your calculations from the scratch partition.
CEES only:
If you access the CEES cluster from off-campus or wireless connection at Stanford Residences, you need to connect to Stanford’s VPN service before login to the cluster. The information regarding to Stanford’s VPN can be found here.
For the first login only, run the following command:
echo "setenv PATH /home/vossj/suncat/bin:${PATH}" >> ~/.tcshrc
source ~/.tcshrc
Create a folder in /data/cees/, from where you will create additional folders for performing your calculations. Type the following to create a directory and a symbolic link from the home directory:
mkdir /data/cees/$USER
ln -s /data/cees/$USER
Make sure to perform all your work in this directory.
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