Grid5000

https://www.grid5000.fr/mediawiki/index.php/Grid5000:Home

Login, job submission, deployment of image

• Select sites and clusters for experiments, using information on the Grid5000 network and the Status page
• Access is provided via access nodes access.SITE.grid5000.fr marked here as accessible from everywhere via ssh with keyboard-interactive authentication method. As soon as you are on one of the sites, you can directly ssh frontend node of any other site:

access_$ ssh frontend.SITE2

• There is no access to Internet from computing nodes (external IPs should be registered on proxy), therefore, download/update your stuff at the access nodes. Several revision control clients are available.
• Each site has a separate NFS, therefore, to run an application on several sites at once, you need to copy it scp, sftp, rsync between access or frontend nodes.
• Jobs are run from the frondend nodes, using a PBS-like system OAR. Basic commands:
  • oarstat - queue status
  • oarsub - job submission
  • oardel - job removal

Interactive job on deployed images:

fontend_$ oarsub -I -t deploy -l [/cluster=N/]nodes=N,walltime=HH[:MM[:SS]] [-p 'PROPERTY="VALUE"']

Batch job on installed images:

fontend_$ oarsub BATCH_FILE -t allow_classic_ssh -l [/cluster=N/]nodes=N,walltime=HH[:MM[:SS]] [-p 'PROPERTY="VALUE"']

• The image to deploy can be created and loaded with help of a Systemimager-like system Kadeploy. Creating: described here

Loading:

fontend_$ kadeploy3 -a PATH_TO_PRIVATE_IMAGE_DESC -f $OAR_FILE_NODES

A Linux distribution lenny-x64-nfs-2.1 with mc, subversion, autotools, doxygen, MPICH2, GSL, Boost, R, gnuplot, graphviz, X11, evince is available at Orsay /home/nancy/alastovetsky/grid5000.

Compiling and running MPI applications

• Compilation should be done on one of the reserved nodes (e.g. ssh `head -n 1 $OAR_NODEFILE`)
• Running MPI applications is described here
  • mpirun/mpiexec should be run from one of the reserved nodes (e.g. ssh `head -n 1 $OAR_NODEFILE`)

Setting up new deploy image

... launch image ...

Edit /etc/apt/sources.list

deb http://ftp.fr.debian.org/debian/ sid main contrib non-free

Upgrade image

apt-get update

Got the error:

W: GPG error: http://ftp.fr.debian.org sid Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY AED4B06F473041FA

Fixed with

apt-get install debian-archive-keyring
apt-get update
apt-get upgrade

Install packages

apt-get install linux-headers-2.6.38-2-all autoconf automake ctags gsl-bin libgsl0-dev vim mc colorgcc libboost-serialization-dev libboost-graph-dev openmpi-bin openmpi-dev libtool gdb valgrind libatlas-dev screen 

apt-get install mpich2 libmpich2-dev