Grid5000

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

USAGE POLICY - Very important, after booking nodes (oarsub ...) run the command:

outofchart

This will check that you haven't booked too many resources and therefore get in trouble with grid5000 admin.

1 Login, job submission, deployment of image
2 Compiling and running MPI applications
3 Setting up new deploy image
4 GotoBLAS2
5 Paging and the OOM-Killer
6 Example of experiment setup across several sites
7 Check network speed
8 Choose which network interface to use
9 Installing Gadget-2.0.7
10 Installing Wrekavoc
11 Installing Extrae

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"']

Specifying cluster name to reserve:

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

If the resources are available two nodes from the cluster "Genepi" will be reserved for the specified time.

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

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

http://www.tacc.utexas.edu/tacc-projects/gotoblas2 When compiling gotoblas on a node without direct internet access get this error:

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

Then Extrae

 # apt-get install

Grid5000

Contents

Login, job submission, deployment of image

Compiling and running MPI applications

Setting up new deploy image

GotoBLAS2

Paging and the OOM-Killer

Example of experiment setup across several sites

Check network speed

Choose which network interface to use

Installing Gadget-2.0.7

Installing Wrekavoc

Installing Extrae

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