Usando los contenedores de Singularity en HTCondor

December 20, 2016

Usando los contenedores de Singularity en HTCondor

Introducción

Singularity ha sido diseñado al rededor de la idea de brindar mobilidad y reproducibilidad de experimientos computacionales a los programas, ademas, permite a los usuarios tener un control pleno del sistema operativo.

Instalando Singularity

Singularity needs to be installer in a modern linux distribution, it’s installed as follows

VERSION=2.2
wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
tar xvf singularity-$VERSION.tar.gz
cd singularity-$VERSION
./configure --prefix=/usr/local
make
sudo make install

Then, check that everything is alright

singularity -v

Configuring HTCondor

It can be used along with HTCondor by adding some entries to the HTCondor configuration file:

sudo nano /etc/condor/config.d/condor_config.local

# Tell HTCondor where is the singularity executable
SINGULARITY = /usr/local/bin/singularity

SINGULARITY_JOB = (TARGET.DESIRED_OS isnt MY.OpSysAndVer) && ((TARGET.DESIRED_OS is "CentOS6") || (TARGET.DESIRED_OS is "CentOS7"))
SINGULARITY_IMAGE_EXPR = (TARGET.DESIRED_OS is "CentOS6") ? "/tmp/Centos7.img" : "/tmp/Centos7.img"
# Maps $_CONDOR_SCRATCH_DIR on the host to /srv inside the image.
SINGULARITY_TARGET_DIR = /srv
# Writable scratch directories inside the image.  Auto-deleted after the job exits.
MOUNT_UNDER_SCRATCH = /tmp, /var/tmp

Then restart HTCondor sudo service condor restart and check if the machine has singularity enable.

condor_status -const HasSingularity

Testing your configuration

Lets first create a singularity container from Docker Centos image

sudo singularity create --size 2048 /tmp/Centos7.img
sudo singularity import /tmp/Centos7.img docker://centos:latest
sudo singularity exec --writable /tmp/Centos7.img  echo "Hello World"  > /tmp/hola

An then, create a HTCondor submit file

nano /tmp/sing.submit

executable = /bin/hostname
universe = vanilla
+SingularityImage = "/tmp/Centos7.img"
+DESIRED_OS="CentOS6"
output = example1.$(cluster).$(process).out
error =  example1.$(cluster).$(process).err
log =    example1.$(cluster).$(process).log
queue 1

Then execute and wait

condor_submit /tmp/sing.submit

You can find more information here