Difference between revisions of "Grid5000"

Revision as of 18:35, 3 May 2011

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

USAGE POLICY

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

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

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

fontend_$ kadeploy3 -a PATH_TO_PRIVATE_IMAGE_DESC -f $OAR_FILE_NODES

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

oarsub -I -t deploy -l nodes=1,walltime=12
kadeploy3 -e lenny-x64-nfs -f $OAR_FILE_NODES -k
ssh root@`head -n 1 $OAR_NODEFILE`

edit /etc/apt/sources.list

apt-get update
apt-get upgrade

apt-get install libtool autoconf automake mc colorgcc ctags libboost-serialization-dev libboost-graph-dev libatlas-base-dev gfortran vim gdb valgrind screen subversion

Compiled for sources by us:

• gsl-1.14 (download: ftp://ftp.gnu.org/gnu/gsl/)

./configure && make && make install

• mpich2 (download: http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads)

./configure --enable-shared --enable-sharedlibs=gcc
make && make install

Mpich2 installed to:

Installing MPE2 include files to /usr/local/include
Installing MPE2 libraries to /usr/local/lib
Installing MPE2 utility programs to /usr/local/bin
Installing MPE2 configuration files to /usr/local/etc
Installing MPE2 system utility programs to /usr/local/sbin
Installing MPE2 man to /usr/local/share/man
Installing MPE2 html to /usr/local/share/doc/
Installed MPE2 in /usr/local

• hwloc (and lstopo) (download: http://www.open-mpi.org/software/hwloc/v1.2/)

compile from sources. To get xml support install libxml2-dev and pkg-config

apt-get install libxml2-dev pkg-config
tar -xzvf hwloc-1.1.1.tar.gz
cd hwloc-1.1.1
./configure && make && make install

Cleanup

apt-get clean
rm /etc/udev/rules.d/*-persistent-net.rules

Make image

ssh root@node tgz-g5k > $HOME/grid5000/imagename.tgz

make appropriate .env file.

kaenv3 -p lenny-x64-nfs -u deploy > lenny-x64-custom-2.3.env