Difference between revisions of "Grid5000"

Latest revision as of 20:16, 22 July 2013

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

outofchart

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"']

oarsub -r 'YYYY-MM-dd HH:mm:ss' -l nodes=2,walltime=1 -p "cluster='Genepi'"

• 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

List available images

kaenv3 -l

Then book node and launch:

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

default password: grid5000

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 iperf bc gsl-bin libgsl0-dev

Possibly also install (for using extrae):

apt-get install libxml2-dev binutils-dev libunwind7-dev

Compiled for sources by us:

• gsl-1.14 (download: ftp://ftp.gnu.org/gnu/gsl/)  Now with squeeze it is in repository.

./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 --with-pm=mpd
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

Change root password.

rm sources from root dir.

Edit the "message of the day"

vi /etc/motd.tail

echo 90 > /proc/sys/vm/overcommit_ratio
echo 2 > /proc/sys/vm/overcommit_memory
date >> release

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

GotoBLAS2

wget http://www.netlib.org/lapack/lapack-3.1.1.tgz
--2011-05-19 03:11:03--  http://www.netlib.org/lapack/lapack-3.1.1.tgz
Resolving www.netlib.org... 160.36.58.108
Connecting to www.netlib.org|160.36.58.108|:80... failed: Connection timed out.
Retrying.

--2011-05-19 03:14:13--  (try: 2)  http://www.netlib.org/lapack/lapack-3.1.1.tgz
Connecting to www.netlib.org|160.36.58.108|:80... failed: Connection timed out.
Retrying.
...

Fix by downloading http://www.netlib.org/lapack/lapack-3.1.1.tgz to the GotoBLAS2 source directory and editing this line in the Makefile

184c184
< 	-wget http://www.netlib.org/lapack/lapack-3.1.1.tgz
---
> #	-wget http://www.netlib.org/lapack/lapack-3.1.1.tgz

GotoBLAS needs to be compiled individualy for each unique machine - ie each cluster. Add the following to .bashrc

export CLUSTER=`hostname |sed 's/\([a-z]*\).*/\1/'`
LD_LIBRARY_PATH=$HOME/lib/$CLUSTER:$HOME/lib:/usr/local/lib:$LD_LIBRARY_PATH
export LIBRARY_PATH=$HOME/lib/$CLUSTER:$HOME/lib:/usr/local/lib:$LIBRARY_PATH

Run the following script once on each cluster:

#! /bin/bash
echo "Compiling gotoblas for cluster: $CLUSTER"
cd $HOME/src
if [ ! -d "$CLUSTER" ]; then
        mkdir $CLUSTER
fi
cd $CLUSTER
tar -xzf ../Goto*.tar.gz
cd Goto*
make &> m.log


if [ ! -d "$HOME/lib/$CLUSTER" ]; then
        mkdir $HOME/lib/$CLUSTER
fi

cp libgoto2.so $HOME/lib/$CLUSTER

echo results
ls -d $HOME/src/$CLUSTER
ls $HOME/src/$CLUSTER

ls -d $HOME/lib/$CLUSTER
ls $HOME/lib/$CLUSTER

note: for newer processors this may fail. If it is a NEHALEM processor try:

make clean
make TARGET=NEHALEM

Paging and the OOM-Killer

When doing exhaustion of available memory experiments, problems can occur with over-commit. See HCL cluster#Paging_and_the_OOM-Killer for more detail.

Example of experiment setup across several sites

Sources of all files mentioned below is available at: Grid5000:sources.

Pick one head node as the main head node (I use grenoble, but any will do). Setup sources

cd dave/fupermod-1.1.0
make clean
./configure --with-cblas=goto --prefix=/usr/local/

Reserve 2 nodes from all clusters on a 3 cluster site:

oarsub -r "2011-07-25 11:01:01" -t deploy  -l cluster=3/nodes=2,walltime=11:59:00

Automate with:

for a in 2 3 4; do for i in `cat sites.$a`; do echo $a $i; ssh $i oarsub -r "2011-07-25 11:01:01" -t deploy -l cluster=$a/nodes=2,walltime=11:59:00; done; done

Then on each site, where xxx is site name:

kadeploy3 -a $HOME/grid5000/lenny-dave.env  -f $OAR_NODE_FILE --output-ok-nodes deployed.xxx

Gather deployed files to a head node:

for i in `cat ~/sites `; do echo $i; scp $i:deployed* . ; done
cat deployed.* > deployed.all

Copy cluster specific libs to each deployed node /usr/local/lib dir with script

copy_local_libs.sh deployed.all

Copy source files to root dir of each deployed node. Then make install each (node ssh -f does this in parallel)

for i in `cat ~/deployed.all`; do echo $i; rsync -aP ~/dave/fupermod-1.1.0 root@$i: ; done
for i in `cat ~/deployed.all`; do echo $i; ssh -f root@$i "cd fupermod-1.1.0 ; make all install" ; done

ssh to the first node

ssh `head -n1 deployed.all`
n=$(cat deployed.all |wc -l)
mpdboot --totalnum=$n --file=$HOME/deployed.all
mpdtrace

cd dave/data/
mpirun -n $n /usr/local/bin/partitioner -l /usr/local/lib/libmxm_col.so -a0 -D10000 -o N=100

Cleanup after:

for i in `cat ~/sites `; do echo $i; ssh $i rm deployed.* ; done

Check network speed

apt-get install iperf

Choose which network interface to use

mpirun --mca btl self,openib ...

or

mpirun --mca btl self,tcp ...

Installing Gadget-2.0.7

 # apt-get install hdf5-openmpi-dev sfftw-dev
$ tar -xzvf gadget2.tar.gz
$ cd Gadget-2.0.7/Gadget2
$ make CFLAGS="-DH5_USE_16_API
$ make clean; make

Installing Wrekavoc

Download from http://wrekavoc.gforge.inria.fr/

 # apt-get install libxml2-dev pkg-config
# tar -xzvf wrekavoc-1.1.tar.gz 
# cd wrekavoc-1.1/
# ./configure 
# make
# ./src/burn 50

Installing Extrae

(on grid5000 wheezy big)

First install Dyninst

 # apt-get install libelf-dev libdwarf-dev 
# tar -xzvf DyninstAPI-8.1.2.tgz 
# cd DyninstAPI-8.1.2
# ./configure --with-libdwarf-static
# make
# make install

Then Extrae

 # apt-get install
 # ./configure  --with-mpi=/usr --with-mpi-libs=/usr/lib --with-papi=/usr/local --with-unwind=/usr --with-dyninst=/usr/local --with-dwarf=/usr