Using MeSU - Revision history

Emillour at 15:04, 9 July 2024

2024-07-09T15:04:57Z

Emillour at 07:49, 9 July 2024

2024-07-09T07:49:26Z

Mlefevre: /* Compiling the WRF on MeSU */

2023-12-13T13:45:20Z

‎Compiling the WRF on MeSU

Mlefevre: Changed the arch in the job script

2023-12-13T13:45:10Z

Changed the arch in the job script

Mlefevre: Creation of the page about the usage the MeSU computer

2023-12-13T13:43:48Z

Creation of the page about the usage the MeSU computer

New page

This page provides some information for those who use the Sorbonne Université clusters MeSU

== How to access the cluster ==
You need first to open an account (this is of course reserved to people in labs connected to Sorbonne Université) then proceed to this page: https://sacado.sorbonne-universite.fr/mesu/index.php/accounts-and-access/

Once you have an account you can ssh to the cluster :
<syntaxhighlight lang="bash">
ssh username@mesu.dsi.upmc.fr
</syntaxhighlight>

For people not on linux : https://sacado.sorbonne-universite.fr/mesu/index.php/usage/howtos/how-to-connect-to-mesu/

== OS and disk space ==
As the welcome message will remind you:
<pre>
__ __ ____ _ _
| \/ | ___/ ___|| | | |
| |\/| |/ _ \___ \| | | |
| | | | __/___) | |_| |
|_| |_|\___|____/ \___/

⢎⡑ ⢀⡀ ⡀⣀ ⣇⡀ ⢀⡀ ⣀⡀ ⣀⡀ ⢀⡀ ⡇⢸ ⣀⡀ ⠄ ⡀⢀ ⢀⡀ ⡀⣀ ⢀⣀ ⠄ ⣰⡀ ⢠⡂
⠢⠜ ⠣⠜ ⠏ ⠧⠜ ⠣⠜ ⠇⠸ ⠇⠸ ⠣⠭ ⠣⠜ ⠇⠸ ⠇ ⠱⠃ ⠣⠭ ⠏ ⠭⠕ ⠇ ⠘⠤ ⠣⠭

https://sacado.sorbonne-universite.fr/mesu
mesu@sorbonne-universite.fr

beta: 144x 24 Intel Haswell CPUs, 128 GB RAM
gamma: 2x 12 Intel Haswell CPUs, 2 NVidia K5200, 256 GB RAM
</pre>
This is Ubuntu Linux and the "HOME" is quite limited in size. Most work should be done on the '''/scratchbeta''' disks.

It is up to you to tailor your environment. By default it is quite bare; it is up to you to load the modules you'll need to have access to specific software or compilers or libraries (and versions thereof).
To know what modules are available:
<syntaxhighlight lang="bash">
module avail
</syntaxhighlight>
To load a given module, here the Panoply software:
<syntaxhighlight lang="bash">
module load panoply
</syntaxhighlight>

The list of available software is available at https://sacado.sorbonne-universite.fr/mesu/index.php/usage/available-software/

== Compiling the PCMs on MeSU ==

To do

== Compiling the WRF on MeSU ==

To do

Environment:
<syntaxhighlight lang="bash">
module load intel/intel-compilers-18.2/18.2
module load intel/intel-mpi/2018.2
module load intel/intel-cmkl-18.0/18.0
export NETCDF="/home/lefevrema/NETCDF/netcdf-4.0.1"
export NETCDF_INCDIR="/home/lefevrema/NETCDF/netcdf-4.0.1/include/"
export NETCDF_LIBDIR="/home/lefevrema/NETCDF/netcdf-4.0.1/lib/"
export WHERE_MPI="/opt/dev/intel/2018_Update2/impi/2018.2.199/bin64"
</syntaxhighlight>

== Submit your job ==
MeSU Supercomputer uses a queuing system to match users jobs with available computing resources.

Users submit their programs to the job scheduler (PBS), which maintains a queue of jobs and distributes them on the compute nodes according to the servers status, scheduling policies and jobs parameters (number of compute nodes / cores, estimated execution time, required memory, etc.).

The interface with PBS is done via a text file – the PBS script – created by the user, which will define your job requirements and execution steps. This file is mainly comprised of two sections :
* the header in which you specify the job requirements (execution time, number of CPU cores to use, memory requirements…) in the form of PBS directives
* the body in which you will write the commands to load specific software, define environment variables, and run your job.

More information https://sacado.sorbonne-universite.fr/mesu/index.php/usage/howtos/job-submission/

Here is an example of job script to run using 24 cpus:
<syntaxhighlight lang="bash">
#!/bin/bash
#PBS -q beta
#PBS -l select=1:ncpus=24
#PBS -l place=free:exclhost
#PBS -l walltime=23:59:00
#PBS -N RUN_GCM
#PBS -j oe

# Load your environment
source ../trunk/LMDZ.COMMON/arch/arch-ifort_MESOIPSL.env

# Go to job directory
cd $PBS_O_WORKDIR
cd ./RUN_DIR

#Magic trick
ulimit -s unlimited

mpirun gcm.e > gcm.out 2>&1
</syntaxhighlight>

Submitting your job to the PBS scheduler is easy once you have authored the corresponding PBS script file, using the qsub command:

<syntaxhighlight lang="bash">
qsub ./myScript
</syntaxhighlight>

[[Category:FAQ]]

@@ Line 47: / Line 47: @@
 To do
-== Compiling the WRF on MeSU ==
+== Compiling WRF on MeSU ==
 To do

@@ Line 1: / Line 1: @@
 This page provides some information for those who use the Sorbonne Université clusters MeSU : https://sacado.sorbonne-universite.fr/plateforme-mesu/
 == How to access the cluster ==
 You need first to open an account (this is of course reserved to people in labs connected to Sorbonne Université) then proceed to this page: https://sacado.sorbonne-universite.fr/account-creation/ where you can download the registration form to fill and upload.
-Once you have an account you can ssh to the cluster :
+Once you have an account you can ssh to the MCMeSU cluster :
 <syntaxhighlight lang="bash">
-ssh username@mesu.dsi.upmc.fr
+ssh username@login.mesu.sorbonne-universite.fr
 </syntaxhighlight>
-For people not on linux : https://sacado.sorbonne-universite.fr/mesu/index.php/usage/howtos/how-to-connect-to-mesu/
+Link to Online MCMeSU documentation : https://sacado.sorbonne-universite.fr/documentation-mcmesu/
-== OS and disk space ==
+== OS and disk space (old MeSU) ==
 As the welcome message will remind you:
 <pre>
@@ Line 43: / Line 45: @@
 The list of available software is available at https://sacado.sorbonne-universite.fr/mesu/index.php/usage/available-software/
-== Compiling the PCMs on MeSU ==
+== Compiling the PCMs on MeSU (old MeSU) ==
 To do
-== Compiling WRF on MeSU ==
+== Compiling WRF on MeSU (old MeSU) ==
 To do
@@ Line 62: / Line 64: @@
 </syntaxhighlight>
-== Submit your job ==
+== Submit your job (old MeSU) ==
 MeSU Supercomputer uses a queuing system to match users jobs with available computing resources.

@@ Line 84: / Line 84: @@
 # Load your environment
-source ../trunk/LMDZ.COMMON/arch/arch-ifort_MESOIPSL.env
+source ../trunk/LMDZ.COMMON/arch/arch-X64_MESU.env
 # Go to job directory