Useful hints:







The most common problem with X programs is wrongly set DISPLAY variable.

Check your IP address (ifconfig for Linux, and ipconfig for Windows)

For bash:

export DISPLAY=computer_name:0         (instead of computer name you can us IP address)

For csh or tcsh:

setenv DISPLAY computer_name:0


How to install USB devices - memory stick, external USB disk, etc.

Insert memory stick and than check under which partition is located (usually /dev/sda1): fdisk -l /dev/sda
If you have already another SCSI device than it will be the following SCSI device sdb, sdc...
It is the best idea to format it with FAT32 than you can use it under Windows and Linux
Edit /etc/fstab and add following line:

/dev/sda1   /mnt/usb     vfat    default,users     0 0

Create mount point /mnt/usb (or whatever name you prefer). Than mount memory stick:
mount /mnt/usb
Check with df if your memory stick was properly mounted.

Before removing memory stick: umout /mnt/usb     because if device is not unmounted you can loose your data.

More detailed guied for working with USB devices

Looking for big or old files and deleting them

If you want to decrease disk usage you can localize big files and delete them if not needed:

find /your_directory -size +10000k -exec ls -la {} \;           (Finds all files bigger than 10 MB and displays them)

find /your_directory -size +10000k -exec rm -f {} \;           (Finds all files bigger than 10MB and deletes them)

find /your_directory -atime +30 -exec rm -f {} \;                 (Finds all files not accessed during 30 days and deletes them)

After -exec statement you can put other commands like: gzip, ls or rm


Setting system variables

For bash:

export TMP=/scratch/$USER        (sets TMP variable as /scratch/your_user_name)

For csh or tcsh:

setenv TMP /scratch/$USER


Queuing system - submitting jobs and monitoring free resources

To submit jobs on the cluster type:

qsub /apps/bin/run_script job_name         This command will submit program run_script with the job job_name

You can copy one of the scripts located in /apps/bin and modify it for your needs; remember to change path for your script

To submit job to specific node use

qsub -q node12.q /apps/bin/run_script job_name       this command will submit job to node12

Killing submitted jobs

To kill the submitted job first type: qstat |sort
to obtain ID of the job and than type:
qdel ID_of_the_job

To monitor running jobs on the cluster type:

qstat          display running jobs on the cluster (use qstat |sort to sort jobs with the submission time)

qstat -f |more         display status for all nodes. Average load shows usage of specific node

qacct -o -d 14          queue accounting. Display usage of the cluster for all users in last 14 days

qacct -g -d 7            Display usage of the cluster for all groups in last 7 days


 Automatic jobs - your own cron jobs

You can create your own automatic jobs which will execute periodically

Use crontab -e command and set the timing when your job should execute:

00 8 * * * *  your_shell_script        executes your_shell script daily at 8:00 AM


What is Quota and disk usage monitoring

Disk quota limits the user disk space usage. For standard user we set it up to: 1.3GB soft limit and 1.5 GB hard limit. When you exceed soft limit you have one week to clean up your files.
You will be automatically notify with the e-mail that you are exceeded the quota limits.

You won't be allowed to use more space than hard limit. If you have specific needs those limit can be increased by reasonable number.

To check your quota type: quota           It displays your quota limit and your disk usage

To decrease your disk usage you can locate your big files and compress them with gzip command


How to find rpm's and solve problems with your program errors:

To find specific rpm try to locate it on the web (use google and search for your rpm and put system name too) or use one of the sites below:

If you have a problem with your program I suggest to check the web first (probably somebody had the same problem before).
Use google and search for your error message (it usually give you solution to your problem).



Creating authorized keys for ssh - no more password typing

You can create your public key and use it to authorize yourself with all the nodes. Follow this procedure:

ssh-keygen -t rsa           Do not put any phrase

Than copy public key (usually to authorized_keys:

cat > authorized_keys

First time you ssh to the node you need to answer yes to add this node to authorized clients.

To make it automatic for all nodes use for instance Runall date or dsh -a date and answer yes for all nodes

find and slocate commands

To locate files you can use one of the following commands:

locate file

slocate file

find / -name name*

ssh, sftp, scp - secure protocols

ssh, sftp, scp are replacement of non secure protocols like: telnet, ftp. They are using crypted session (port 22) and data are transmitted in crypted form between two computers.


ssh and sftp are very similar to telnet and ftp protocols

ssh username@computer_name

sftp username@computer_name

scp file_name           This command will transfer file file_name to with specified directory

scp -r directory_name        Corresponding syntax for directory transfer