====== Quick start ======

This document is intended for new users of the service. It gives information on such basics as how to log in, how to run application and where to get help.

**Computation Workflow on the HPC**

A typical Computation workflow will be:
  - Connect to the HPC
  - Transfer your files to the HPC
  - Compile your code and test it
  - Create a job script
  - Submit your job
  - Wait while
      * your job gets into the queue
      * your job gets executed  
      * your job finishes
  - Move your results


====== Connecting to clusters ======
Once your account is created you need to connect to the cluster to change your password.


<note important>**Before starting using the cluster, remember that mesocentre is composed of one cluster and one shared multi-core machine:**
 
  -<color red> mesologin1.univ-fcomte.fr </color>    dedicated for sequential, array tasks, MPI and openMP programs (only with SGE)
  - <color green>mesoshared.univ-fcomte.fr</color>  a single SMP machine dedicated for interactive jobs: matlab, visualization, post-processing, ...

You can show the characteristic of each cluster [[moyens_de_calcul|here]]. 
</note>

Example, connect and change password:

<code bash>
$ ssh user@mesologin1.univ-fcomte.fr

</code>

And then:
<code bash>
$ passwd
</code>


===== Connection mode =====
The easiest way to connect to the cluster is by using SSH protocol. Windows users can use  **PuTTY**.

However you can use [[x2go|X2GO client]], a powerful graphical user interface to run interactive applications like matlab on ''mesoshared.univ-fcomte.fr'' machine. 


<note tip>To transfer data from/to cluster you can use ''scp'', ''sftp'' or other graphical applications (based on ssh) like : **winscp**, **filezella**, ...</note> 

===== User workspace =====

Once connected each user will have a home directory organized as follow :

  * ''HOME'': this is the home directory, total allowed size: **10GB**
  * ''WORK'': Computation and software must be **Started** from here, total allowed size: **1TB**

Read more [[environnement_travail|here]] 
====== Installed software ======

<note>See the list of installed software and how to use them [[logiciels_installes|]]</note>

Several software are installed on the clusters. You can show them by :
<code bash>
$ module avail
</code>
This will show the list of software installed and their version.

the output looks like this :

<code bash>

$ 
------------------------------------------------------------------------------------------- /Softs/lumiere-modules --------------------------------------------------------------------------------------------
bio/bamtools/2.3.0           bio/t-coffee/default         intel/14.0.2(default)        lang/java/1.8                lib/libreadline/6.2          numlib/armadillo/icc/6.300.2 tools/gama/1.6.1
bio/bcftools/1.1             bio/velvet/1.2.09            intel/15.0.3                 lang/ocaml/4.00.0            lib/libxml2/2.8.0            numlib/fftw/gcc/3.3.4        tools/gate/6.2
bio/beagle/1.1.0             castem/2015                  intel/icc/2013_sp1.2.144     lang/perl/5.12.3             lib/libxml2/2.9.1            numlib/fftw/icc/3.3.4        tools/git/2.1.2
bio/bwa/0.7.12               comsol/3.5a                  intel/icc/2015.3.187         lang/pgi64/15.7              lib/libxml2/2.9.2            numlib/gsl/1.15              tools/h5utils/1.12.1
bio/cdhit/4.6.4              comsol/4.0                   intel/ifort/2013_sp1.2.144   lang/pgi64/2015              lib/ncurses/5.9              numlib/openblas/0.2.15       tools/mercurial/2.5.2
bio/emboss/6.6.0             comsol/4.1                   intel/ifort/2015.3.187       lang/python/2.6.5            lib/pteros/2.0               numlib/petsc/3.6.3           tools/mercurial/2.7.2
bio/exabayes-mpi/1.2.1       comsol/4.2  
[root@mesocomte0 ~]# 

</code>

You view the software installed in category, for example for  languages (lang):

<code bash>
$ module avail lang
</code>   


Another way to know if a software is installed or not :

<code bash>
$ module avail softwarename
</code>

For example, let's see if matlab is installed:

<code bash>
$ module avail matlab
----------------------------------------------------------------------------------------
matlab/r2010b matlab/r2011b matlab/r2012a matlab/r2012b
</code>

Say we need to use matlab, we first need to load **matlab/r2012b** in our environment, this is done by: 

<code bash>
$ module load matlab/r2012b
</code>
and then launch matlab:
<code bash>
$ matlab 
</code>

to unload module 

<code bash>

$ module rm softwareName

</code>








====== Submitting Jobs with SGE======

Jobs are submitted to the compute nodes via the Sun Grid Engine (SGE) batch submission system. Basic SGE batch scripts should conform to the following template: 

<code bash>

#!/bin/bash


#$ -M toto@univ-xxx.fr   # Email address for job notification

#$ -m abe		 # Send mail when job begins, ends and aborts

#$ -pe put_here_pe 12    # Specify parallel environment and legal core size

#$ -q put_here_queue     # Specify queue

#$ -N job_name	         # Specify job name


module load xyz	         # Required modules

./foo			 # run Application
</code>

===== Submitting a Job =====


<code bash>
qsub jobscript.sge

</code>

Where ''jobscript.sh'' is the script that you have prepared.\\

These files will be stored in the directory you submitted the jobs from if you use the -cwd option, and in your home directory otherwise. The names are constructed from the name of the job script, ''.o'' for output or ''.e'' for errors, and the job number. So the command above might create files such as 'jobscript.sh.o12345' and 'jobscript.sh.e12345' where ''12345'' is the number that is assigned to your job when you submit it.
<note important>
JOB must bhe launched from WORK directory. 
</note>

===== Cancelling a Job =====
To cancel a job, use the command:

<code bash>
qdel 12345
</code>

where 12345 is the job number assigned to your job.

===== Job status =====


To query the status of your submitted jobs, use the command:

''qstat'' or for further information

===== SGE example SCRIPT =====

==== Sequential script ====


<code bash>
#!/bin/bash


#$ -N test_sge
#$ -o $JOB_NAME.$JOB_ID.out
#$ -e $JOB_NAME.$JOB_ID.err
#$ -q all.q

     
./my program myParam1 myParam2


</code>

==== Array tasks  script ====

<note tip>When you want to run a number of mostly identical jobs with the only difference being input parameters or data sets you should submit an Array Job</note>


<code bash>
#!/bin/bash 

#$ -N test_sge
#$ -o $JOB_NAME.$JOB_ID.out
#$ -e $JOB_NAME.$JOB_ID.err
#$ -q all.q
#$ -t 1-32     ## 32 tasks 
./appli input$SGE_TASK_ID output$SGE_TASK_ID

</code>
==== OpenMP  script ====

<note tip>To use **OpenMP**, you need to specify that you wish to use that Parallel Environment (-pe openmp) , and declare the number of slots</note>

<code bash>
#!/bin/bash 

#$ -N test_sge

#$ -o $JOB_NAME.$JOB_ID.out
#$ -e $JOB_NAME.$JOB_ID.err
#$ -q all.q
#$ -pe openmp 8  ## we request 8 cores
 
export OMP_NUM_THREAD=$NSLOTS
 
## lancement de l'application 
 
./appli input
</code>
==== MPI script ====
<note tip>
To use MPI, you need to specify that you wish to use that Parallel Environment (-pe mpi), and declare the number of slots</note>


<code bash>
#!/bin/bash 

#$ -N test_sge
#$ -o $JOB_NAME.$JOB_ID.out
#$ -e $JOB_NAME.$JOB_ID.err
#$ -q parallel.q
#$ -pe mpi 64

### load MPI to use
module load mpi/openmpi/icc/1.7.5
 
## lancement de l'application
mpirun -np $NSLOTS ./appli_mpi  myparams

</code>
===== More about SGE =====
For further information about SGE visit this [[sge|link]]  
====== Getting Help ======


More information is available in this site (in french) or the [[faq|FAQ section]] or you may wish to contact admins: svpmeso@univ-fcomte.fr