– Home and scratch
Access from VSCHT|
– VPN and X-windows
– File transfer
Access from outside
– File transfer
– X-windows graphics
– Managing files
– Editing text files
– Submit jobs
– List jobs
– Remove jobs
We have three clusters:
User home directory is /home/USER.
On nodes (clients), a user can use scratch disk space in directory
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 -sIt 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)marge.uochb.cas.cz in case you need to restore a file.
(answer yes for adding the computer to your list of trusted hosts)
One option is scp:
to copy file /home/USER/MYFILE/ from cluster to your local ./:Another option is sftp.
scp USER@a324-2.vscht.cz:MYFILE .
to copy your local file file ./MYFILE to /home/USER/MYFILE on the cluster:
scp MYFILE USER@a324-2.vscht.cz:MYFILE
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.
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).
ssh -X USER@403-a324-01.vscht.cz
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:
xhost +a324-2.vscht.czSometimes it may be also needed to set the DISPLAY environment variable.
setenv DISPLAY NAME:0.0 # in csh, tcshwhere NAME is the name of your computer, e.g., mycomp.vscht.cz or 220.127.116.11.
export DISPLAY=NAME:0.0 # in sh, bash
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.
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 vpn.vscht.czNote 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 vpn2.vscht.cz.
As soon as you are connected by VPN to VSCHT, the usage is the same as if you are in the domain (ssh -X USER@as67-1.vscht.cz).
scp REMOTEFILE LOCALUSER@OFFICE_MODE_IP:LOCALFILE(At this moment, cluster is not "Kategorie 2" so that this direction does not work.)
scp LOCALUSER@OFFICE_MODE_IP:LOCALFILE REMOTEFILE
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).
To get a remote shell, you may use the SSH gateway: use any ssh connection to ftpin.vscht.cz 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.
firstname.lastname@example.org's password: sshgw
Zadejte adresu systemu ke kteremu se chcete pripojit
Zadejte jmeno uzivatele, pod kterym se chcete pripojit
Probiha pripojovani... USER@a324-2's password: PASSWORD
One option is to use the ftp server ftpin.vscht.cz, otherwise see above. You need a (temporary) account on ftpin.vscht.cz. From a shell at the cluster, run
telnet ftpinThen you can access USER@ftpin.vscht.cz from both the VSCHT domain and outside by your favorite ftp client.
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)? DAYS_ACTIVE (account active max 7 days)
Zmacknete ENTER pro zalozeni uzivatele nebo ukoncete spojeni. ENTER
Hint: Consider putting your ftpin login data into file .netrc, e.g.
machine ftpin.vscht.cz login USER
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:
|passwd||Change your password|
|man COMMAND||Get the manual page of COMMAND|
|xman||Manual pages browsing tool, requires X11|
|info||Comprehensive manual of GNU software|
|info COMMAND||Info on COMMAND (often more up-to-date than the man-page)|
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.
ls -l DIRECTORY/
|List files with verbose info|
|cat FILE||Print a (short) text file|
|less FILE||View a (long) text file; use arrows, PgUp/PgDn or u/space, quit by q|
|cp -i FILE1 FILE2|
cp FILE(s) DIRECTORY/
|mv -i FILE1 FILE2|
mv FILE(s) DIRECTORY/
|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:
|mc [F4]||Internal editor of the Midnight Commander is invoked by typing [F4]|
|nano FILE||Very simple text editor|
|joe FILE||Reasonably simple but powerful editor of the WordStar/Turbo family|
|emacs FILE||Powerful but complicated editor|
|vi FILE||UNIX classical text editor (incomprehensible for Windows users)|
Another possibility is to edit files locally (on your Windows) and to move them using WinSCP.
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:
sgesec qsub nicescript.sh
qsub -q aq -cwd -b y -pe shm 2 -N MyParJob MyExe MyParm1 MyParm2
qsub -q aq-gpu-gtx690 -l num_gpu=64 MyScript.sh
#$ -q "sq-8-16"
#$ -j y
ln -s fort.11 myin.dat
mv fort.22 myout.dat
chmod +x myscript.sh
qsub -N MYJOB myscript.sh
qsubsec -q "mq-*-*" simul.sh
jsub a.outRun jsub without arguments to get help.
kill -2 ID
# SIGINT, the same as Ctrl-C interactively;
# many applications finish (some) work and close files
kill ID # try harder (signal SIGTERM) kill -9 ID # kill unconditionally (nothing saved)