Computing clusters: Local Guide

  – Home and scratch
  – Quotas
  – Backups
      Access from VSCHT
  – VPN and X-windows
  – Shell
  – File transfer
Access from outside
  – Shell
  – File transfer
  – X-windows graphics
      Getting started
  – Managing files
  – Editing text files
Managing jobs
  – Queues
  – Submit jobs
  – List jobs
  – Remove jobs
            historical decomissioned cluster


We have three clusters:

Home and scratch

User home directory is /home/USER.

On nodes (clients), a user can use scratch disk space in directory /scratch/USER/.
On Selenium (as67-1), scratch disks are periodically cleared. Your files will not be erased if:


User disk space (/home) is limited by quotas. To check your quota status, use command:

quota -s
It is wise to put this command to your .login (if you are using tcsh) or .profile (if you are using bash). The quota value reported can be somehow exceeded up to the limit, but not for more than the grace period of 7 days.


Backups are performed daily at night. All user home directories (/home/*/) are periodically backed up. Four daily backups are kept, and weekly backups (Saturday to Sunday) up to the backup server capacity. Older files are lost.

Only root can access the backup server. Ask jiri.polach(at) in case you need to restore a file.

Access from the VSCHT domain

Shell access

From Linux

(answer yes for adding the computer to your list of trusted hosts)

From Windows

There are several implementations of ssh for Windows. We recommend Putty. Start Putty, enter the host and select SSH as the service (the TCP port should be 22).

File transfer

From Linux

One option is scp:

to copy file /home/USER/MYFILE/ from cluster to your local ./:
scp .

to copy your local file file ./MYFILE to /home/USER/MYFILE on the cluster:

Another option is sftp.

From Windows

One option is WinSCP, which provides a Windows-commander-like or Explorer-like interface to transfering files. Start WinSCP.exe, enter the host, then your name and the password. The TCP port should be 22.

X-windows (X11) graphics

To use graphical applications like gnuplot, xxgdb, etc., on the cluster, you need an X11 server running on your machine.
Note: People are often confused by the client/server model of X11. A client (running on a remote machine, i.e., the cluster [server or node]) asks the server (running, e.g., on your M$ Windoze PC) to display graphics (e.g., to draw a rectangle).

From Linux

Normally an X11 server is running and ssh with option -X provides transparent X forwarding, e.g.:
ssh -X

In case of problems: You may need to add the client computer to the list of allowed hosts on your computer. Thus, on your computer, run:

Sometimes it may be also needed to set the DISPLAY environment variable.

From Windows

The recommended X server is XMing. To establish a connection, you must A running XMing is indicated by a small X in the right side of your task bar.
If anything gets wrong, try set the DISPLAY environment variable in your Putty shell:
setenv DISPLAY NAME:0.0     # in csh, tcsh
export DISPLAY=NAME:0.0     # in sh, bash
where NAME is the name of your computer, e.g., or
Note: An X11 session cannot be started automatically from Windows because rexec and rsh are disabled on the server (for safety reasons).

Access from outside

VPN and X-windows (X11)

The recommended way how to connect to a cluster from home is to establish a VPN session to VSCHT. Then you may connect (incl. X-forwarding) and access remote files directly from your PC. You need to install a VPN client to do this, see computer center info.

From Linux

VPN client

The Computer Center recommends the Cisco client – see instructions there. However, I experienced incompatibility with the Ubuntu/Debian update system (some time ago, may be fixed now).

The openconnect package available via the Synaptic package manager (or similar) works, too. On older systems, the connect script vpnc-script is missing and must be installed separately. To connect to a cluster, first start a VPN session by:

sudo openconnect -s /etc/vpnc/vpnc-script
Note that the VSCHT user must be enetered in the short form (novakj, not josef.novak). In case of problems, check the location of the vpnc-script and/or try the alternative server

As soon as you are connected by VPN to VSCHT, the usage is the same as if you are in the domain (ssh -X

Back connection
You can access your home computer via the OFFICE_MODE_IP from computers in the VSCHT domain; e.g., you can transfer files from a computer (of "Kategorie 2") to home like
(At this moment, cluster is not "Kategorie 2" so that this direction does not work.)

From Windows

See the VC page.

As soon as you are connected by VPN to VSCHT, the usage is the same as if you are in the domain (Putty and XMing).

Shell access

To get a remote shell, you may use the SSH gateway: use any ssh connection to and log in as sshgw (mnemonics: SSH GateWay) with passwd=sshgw. Then, type the name of the target computer (as67-1; newer ones are likely not supported), your user ID, and password. X11 forwarding is not supported (unless you create a tunnel); for connecting incl. graphics, see above.

From Linux

ssh's password:

Zadejte adresu systemu ke kteremu se chcete pripojit
Zadejte jmeno uzivatele, pod kterym se chcete pripojit
Probiha pripojovani... USER@a324-2's password: PASSWORD

From Windows

Use Putty as above with and user=sshgw, password=sshgw. Then see above.

File transfer from outside

One option is to use the ftp server, otherwise see above. You need a (temporary) account on From a shell at the cluster, run

telnet ftpin
Password: ftpman
Zadejte nove uzivatelske jmeno: USER (=new user name)
Zadejte uzivatelske heslo:PASSWORD
Zadejte uzivatelske heslo znovu(kontrola):PASSWORD (once more to check)
Kolik dni chcete ponechat ucet aktivni(maximum 7)?[1] DAYS_ACTIVE (account active max 7 days)
Zmacknete ENTER pro zalozeni uzivatele nebo ukoncete spojeni. ENTER
Then you can access from both the VSCHT domain and outside by your favorite ftp client.

Hint: Consider putting your ftpin login data into file .netrc, e.g.

machine login USER
password PASSWORD
macdef init

Getting started

A user is normally logged to the server where (s)he can manage and edit files, compile and debug programs, submit jobs to be run on the client nodes, and analyse the results (incl. X11 graphics). No lengthy calculations are allowed directly on the server!

If necessary (e.g., lengthy interactive debugging), you may also use ssh to connect directly to machines inside the cluster. It is not allowed to jump the queue of submitted jobs in this way! The most important commands to survive are:

passwdChange your password
man COMMANDGet the manual page of COMMAND
xmanManual pages browsing tool, requires X11
infoComprehensive manual of GNU software
info COMMANDInfo on COMMAND (often more up-to-date than the man-page)

Managing files

Your shell is tcsh or bash. (To figure out which one, execute command ps.) To get help, use

man tcsh     or     man bash

It's pretty long, isn't it? A few basic commands, common for both shells, are listed below.

List files
ls -l
List files with verbose info
cat FILEPrint a (short) text file
less FILEView a (long) text file; use arrows, PgUp/PgDn or u/space, quit by q
cp -i FILE1 FILE2
Copy files
mv -i FILE1 FILE2
Rename or move files
rm -i FILE(s)Remove files

(Option -i in the above commands ensures confirmation if a file is about to be overwritten or erased; based on your environment, you may have aliased the above commands so that -i does not have to be used.)

Another possibility is to replace this shell by the Midnight Commander, a clone of the popular Norton/Windows/Total Commander. It is started by:


Editing text files

mc [F4]Internal editor of the Midnight Commander is invoked by typing [F4]
nano FILEVery simple text editor
joe FILEReasonably simple but powerful editor of the WordStar/Turbo family
emacs FILEPowerful but complicated editor
vi FILEUNIX classical text editor (incomprehensible for Windows users)

Another possibility is to edit files locally (on your Windows) and to move them using WinSCP.

Managing jobs

A user batch job (binary executable or a script) is submitted on a server to a queue. As soon as there are resources available, the job is started on a client.


On Selenium (as67-1), there are two instances of queues:

On 403-a324-01, there are only high-priority queues (max 45 cores/user):

Submit jobs


List jobs

Remove jobs