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,

 (local)$

means you are on your PC, and

 (ebi)$

means you are on ebi.

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How to login †

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

or

 (local)$ ssh -Y (username)@ebi
 (type your password)
 (ebi)$
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How to logout †

 (ebi)$ exit
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How to check your directory size †

 (ebi)$ du -sh /home/(username)
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Transfer local data to ebi †

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

or

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

If you are a WINDOWS user, WinSCP is available.

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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.

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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)
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Compiler and Library †

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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.

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How to submit your job †

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

 #!/bin/sh
 #$ -S /bin/sh
 #$ -N name
 #$ -cwd
 #$ -q tako1.q
 #$ -pe openmp 8
 #$ -v OMP_NUM_THREADS=8
  ./a.out

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

 (ebi)$ qsub run.sh

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
    tako1.qtako01-05
    tako2.qtako06-09,0a
    tako3.qtako10-15
    ika_s.qika00-05
    ika_p.qika06-09,0a
    ika1.qika10-19,1a-1m
    uni1.quni01-06
    tako_all.qdeadline job (user limited)
    ika1_all.qdeadline job (user limited)
  • Number of cores
    ika4
    tako8
    uni12

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
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LINKS for more information †