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:

1. Connect to the HPC
2. Transfer your files to the HPC
3. Compile your code and test it
4. Create a job script
5. Submit your job
6. Wait while
   • your job gets into the queue
   • your job gets executed
   • your job finishes
7. Move your results

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

Example, connect and change password:

$ ssh user@mesologin1.univ-fcomte.fr

And then:

$ passwd

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

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

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 here

Several software are installed on the clusters. You can show them by :

$ module avail

This will show the list of software installed and their version.

the output looks like this :

$ 
------------------------------------------------------------------------------------------- /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 ~]#

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

$ module avail lang

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

$ module avail softwarename

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

$ module avail matlab
----------------------------------------------------------------------------------------
matlab/r2010b matlab/r2011b matlab/r2012a matlab/r2012b

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

$ module load matlab/r2012b

and then launch matlab:

$ matlab 

to unload module

$ module rm softwareName

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:

#!/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

qsub jobscript.sge

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.

To cancel a job, use the command:

qdel 12345

where 12345 is the job number assigned to your job.

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

qstat or for further information

#!/bin/bash
 
 
#$ -N test_sge
#$ -o $JOB_NAME.$JOB_ID.out
#$ -e $JOB_NAME.$JOB_ID.err
#$ -q all.q
 
 
./my program myParam1 myParam2

#!/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

#!/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

#!/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

For further information about SGE visit this link

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