*Computer Manual [#xc5cb59c]
#contents

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.
-[[Beginners： Learn LINUX:http://linuxreviews.org/beginner/]]
-[[CYGWIN:http://www.cygwin.com/]]
-[[LINUX Commands:http://onlamp.com/linux/cmd/]]

In the following,
  (local)$
means you are on ''your PC'', and
  (ebi)$
means you are on ''ebi''.

**How to login [#td145fbc]
  (local)$ ssh (username)@ebi
  (type your password)
  (ebi)$
or
  (local)$ ssh -Y (username)@ebi
  (type your password)
  (ebi)$

**How to logout [#c928c3d4]
  (ebi)$ exit

**How to check your directory size [#e59a8914]
  (ebi)$ du -sh /home/(username)

**Transfer local data to ebi [#d1146de9]
  (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.
-[[WinSCP:http://winscp.net/eng/docs/start]]

**Transfer data on ebi to local [#s54773aa]
  (local)$ sftp (username)@ebi
  (type your password)
  (ebi)$ get (data on ebi)

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

**File System [#af169ef3]
-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 [#t7949fb2]
-Intel C, C++, Fortran compilers
--[[Intel Documentation Library:http://software.intel.com/en-us/articles/intel-software-technical-documentation/]]
--[[User Guide for C++:http://software.intel.com/sites/products/documentation/hpc/composerxe/en-us/2011Update/cpp/lin/index.htm]]
--[[User Guide for Fortran:http://software.intel.com/sites/products/documentation/hpc/composerxe/en-us/2011Update/fortran/lin/index.htm]]
-Intel Math Kernel Library
--[[Math Kernel Library Documentation:http://software.intel.com/en-us/articles/intel-math-kernel-library-documentation/]]

*Job Scheduling [#ubab04b7]
Job scheduler used in ''ebi'' is ''Sun Grid Engine (SGE)''.
For more information to use SGE, see the following web site.
-[[Sun Grid Engine:http://wikis.sun.com/display/gridengine62u2/Home]]

''(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 [#vbef6132]
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:http://wikis.sun.com/display/gridengine62u2/Submitting+Jobs]]

-Explanations on the above example.
|-S /bin/sh| set shell to /bin/sh|
|-N name| set job name as nane|
|-cwd| set the working directory to current directory|
|-q tako1.q| set que to tako1.q|
|-pe openmp 8| set parallel environment to openmp with 8 cores|
|-v OMP_NUM_THREADS=8| set environmental variable OMP_NUM_THREADS=8|

-Available ques
|tako1.q | tako01-05|
|tako2.q | tako06-09,0a|
|tako3.q | tako10-15|
|ika_s.q | ika00-05|
|ika_p.q | ika06-09,0a|
|ika1.q | ika10-19,1a-1m|
|uni1.q | uni01-06|
|tako_all.q | deadline job (user limited)|
|ika1_all.q | deadline job (user limited)|

-Number of cores
|ika|4|
|tako|8|
|uni|12|


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