Computer Manual

Before you access to ebi, you need to be familiar with LINUX, namely terminal and command lines. If you are a WINDOWS user, CYGWIN will be useful to learn LINUX on your WINDOWS PC.

In the following,


means you are on your PC, and


means you are on ebi.

How to login

 (local)$ ssh (username)@ebi
 (type your password)


 (local)$ ssh -Y (username)@ebi
 (type your password)

How to logout

 (ebi)$ exit

How to check your directory size

 (ebi)$ du -sh /home/(username)

Transfer local data to ebi

 (local)$ scp (local data) (username)@ebi:.
 (type your password)


 (local)$ sftp (username)@ebi
 (type your password)
 (ebi)$ put (local data)

If you are a WINDOWS user, WinSCP is available.

Transfer data on ebi to local

 (local)$ sftp (username)@ebi
 (type your password)
 (ebi)$ get (data on ebi)

.If you are a WINDOWS user, WinSCP is available.

File System

  • User data
    /home/(username)Home directory (4.3TB)
    /home1/(username)For large data (16.9TB)
    /home2/(username)For large data (3.3TB)
    /home3/(username)For large data (19.5TB)

Compiler and Library

Job Scheduling

Job scheduler used in ebi is Sun Grid Engine (SGE). For more information to use SGE, see the following web site.

(Note) When you want to run a program using our cluster machines, you have to obey the following instruction. Do not run a bare program on ebi.

How to submit your job

First, you need to prepare a script file as follows.

 #$ -S /bin/sh
 #$ -N name
 #$ -cwd
 #$ -q tako1.q
 #$ -pe openmp 8

Save the script file as '' (for example).
Then, type the following command.

 (ebi)$ qsub

That's all. To check your running job, type the following command.

 (ebi)$ qstat

You will find the status of your job running or waiting.

For more information, read here

  • Explanations on the above example.
    -S /bin/shset shell to /bin/sh
    -N nameset job name as nane
    -cwdset the working directory to current directory
    -q tako1.qset que to tako1.q
    -pe openmp 8set parallel environment to openmp with 8 cores
    -v OMP_NUM_THREADS=8set environmental variable OMP_NUM_THREADS=8
  • Available ques
    tako_all.qdeadline job (user limited)
    ika1_all.qdeadline job (user limited)
  • Number of cores

The following commands are minimum to use SGE.

  • qsub : submit your job
  • qstat : show the status of jobs
  • qhost : show the status of clusters For more information, type
     (ebi)$ (command name) --help

LINKS for more information