Difference between revisions of "HTCondor Jobs In Containers"

Revision as of 19:00, 18 January 2017

This page explains two methods of running LHC jobs in SL6 containers using HTCondor with SL7 worker nodes.

Docker

The SL7 or Centos7 worker nodes should have:CVMFS, HTCondor, Docker engine, CA certs and fetch-crl installed. See https://docs.docker.com/engine/installation/linux/rhel/ for information on how to install Docker engine.

Usually autofs is used with CVMFS but this will not work with Docker - you will likely get errors of the form:

ls: cannot open directory /cvmfs/cms.cern.ch: Too many levels of symbolic links

Each CVMFS repository must be mounted manually, e.g.

mount -t cvmfs grid.cern.ch /cvmfs/grid.cern.ch
mount -t cvmfs grid.cern.ch /cvmfs/cms.cern.ch

In a production environment /etc/fstab should be used instead of course. For example

atlas         /cvmfs/atlas.cern.ch   cvmfs   defaults   0 0
cms           /cvmfs/cms.cern.ch   cvmfs   defaults   0 0
grid          /cvmfs/grid.cern.ch   cvmfs   defaults   0 0

Add the condor user to the Docker group so that HTCondor has permission to run containers:

usermod -G docker condor

Some additional HTCondor configuration required in order to automatically bind mount CVMFS and /etc/grid-security into all Docker containers run by HTCondor:

DOCKER_MOUNT_VOLUMES=CVMFS, GRID_SECURITY, PASSWD, GROUP
DOCKER_VOLUMES=CVMFS, GRID_SECURITY
DOCKER_VOLUME_DIR_CVMFS=/cvmfs:/cvmfs:ro
DOCKER_VOLUME_DIR_GRID_SECURITY=/etc/grid-security:/etc/grid-security:ro
DOCKER_VOLUME_DIR_PASSWD=/etc/passwd:/etc/passwd:ro
DOCKER_VOLUME_DIR_GROUP=/etc/group:/etc/group:ro

Here we also bind mount /etc/passwd and /etc/group into the containers so that pool accounts are available. The pool accounts must be configured on the host (in order for HTCondor to run a job as a particular user the user must exist on the host!)

With HTCondor 8.5.8 and above it's possible to specify what directories to mount in containers using an expression. For example, with this configuration:

DOCKER_VOLUME_DIR_GRID_SECURITY=/etc/grid-security:/etc/grid-security:ro
DOCKER_VOLUME_DIR_PASSWD=/etc/passwd:/etc/passwd:ro
DOCKER_VOLUME_DIR_GROUP=/etc/group:/etc/group:ro
DOCKER_VOLUME_DIR_CVMFS_GRID=/cvmfs/grid.cern.ch:/cvmfs/grid.cern.ch:ro
DOCKER_VOLUME_DIR_CVMFS_CMS=/cvmfs/cms.cern.ch:/cvmfs/cms.cern.ch:ro
DOCKER_VOLUME_DIR_CVMFS_ATLAS=/cvmfs/atlas.cern.ch:/cvmfs/atlas.cern.ch:ro
DOCKER_MOUNT_VOLUMES=GRID_SECURITY, PASSWD, GROUP, CVMFS_GRID, CVMFS_CMS, CVMFS_ATLAS
DOCKER_VOLUME_DIR_CVMFS_CMS_MOUNT_IF=regexp("cms",Owner)
DOCKER_VOLUME_DIR_CVMFS_ATLAS_MOUNT_IF=regexp("atl",Owner)

the CMS CVMFS repository would only be available to jobs which are running with a username containing "cms" and the ATLAS CVMFS repository would only be available to jobs which are running with a username containing "atl". Other volumes, such as the grid CVMFS repository, are made available to all jobs.

If you want to force all jobs to run in Docker containers by default, this can be done easily by some configuration like the following:

WantDocker = True
DockerImage = "alahiff/grid-worker-node:1"
SUBMIT_EXPRS = $(SUBMIT_EXPRS), WantDocker, DockerImage

where the image name should be changed as appropriate.

Singularity

Follow the instructions http://singularity.lbl.gov/install-linux in order to build the Singularity RPM which should be installed on your worker nodes.

HTCondor 8.5.8 or above must be used. Example HTCondor configuration which will run all jobs in a SL6 CernVM container using Singularity with CVMFS mounted inside the containers:

SINGULARITY = /usr/bin/singularity
SINGULARITY_JOB = true
SINGULARITY_IMAGE_EXPR = "/cvmfs/cernvm-prod.cern.ch/cvm3"
SINGULARITY_TARGET_DIR = /srv
SINGULARITY_BIND_EXPR = "/cvmfs"
MOUNT_UNDER_SCRATCH = /tmp, /var/tmp

Note that by default /etc/grid-security/certificates is a symbolic link to /cvmfs/grid.cern.ch/etc/grid-security/certificates so in theory you don't need to install CA certs and run fetch-crl on the worker nodes and bind mount /etc/grid-security/certificates from the host into the containers.