HTCondor Jobs In Containers

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This page describes the setup at RAL for running jobs in Centos 6 containers on SL7 worker nodes.

Worker nodes

The SL7 worker nodes are configured to be as close as possible to our original SL6 workernodes. Exceptions:

  • No grid middleware installed
  • No HEP_OSlibs_SL6 RPM and dependencies or equivalent RPMs
  • glexec, lcas and lcmaps configuration files only (no RPMs are required)

We are currently using Docker 17.03.0-ce. We found that the only reliable choice for the storage driver is OverlayFS, which seems to be the default now for RHEL7-based systems. The file /etc/docker/daemon.json contains:

{
    "storage-driver": "overlay",
    "graph": "/pool/docker"
}

The partition /pool is an XFS filesystem which is formatted including the option -n ftype=1. This is essential. Without this there will be lots of kernel errors.

We are using CVMFS 2.3.2. In order to ensure that CVMFS mounts survive autofs restarts, the file /etc/systemd/system/autofs.service.d/fuse.conf should be created:

[Service]
KillMode=process

HTCondor 8.6.3 or above is recommended. Add the following to sudoers to enable HTCondor to use the Docker CLI as root:

User_Alias      CONDORUSER = condor
Cmnd_Alias      DOCKERCMD = /usr/bin/docker
CONDORUSER      ALL = NOPASSWD: DOCKERCMD

and add the following line to the HTCondor configuration:

DOCKER = sudo /usr/bin/docker

The alternative method of giving HTCondor permission to run containers, i.e. adding the condor user to the docker group, is problematic with Docker 1.13.1 and above (Docker commands will try to read a config file from /root and not have permission to do so).

Our full HTCondor configuration relating to Docker is as follows:

DOCKER = sudo /usr/bin/docker
DOCKER_DROP_ALL_CAPABILITIES=regexp("pilot",x509UserProxyFirstFQAN) =?= False
DOCKER_MOUNT_VOLUMES=GRID_SECURITY, MJF, GRIDENV, GLEXEC, LCMAPS, LCAS, PASSWD, GROUP, CVMFS, CGROUPS, ATLAS_RECOVERY, ETC_ATLAS, ETC_CMS, ETC_ARC
DOCKER_VOLUME_DIR_ATLAS_RECOVERY=/pool/atlas/recovery:/pool/atlas/recovery
DOCKER_VOLUME_DIR_ATLAS_RECOVERY_MOUNT_IF=regexp("atl",Owner)
DOCKER_VOLUME_DIR_CGROUPS=/sys/fs/cgroup:/sys/fs/cgroup:ro
DOCKER_VOLUME_DIR_CGROUPS_MOUNT_IF=regexp("atl",Owner)
DOCKER_VOLUME_DIR_CVMFS=/cvmfs:/cvmfs:shared
DOCKER_VOLUME_DIR_ETC_ARC=/etc/arc:/etc/arc:ro
DOCKER_VOLUME_DIR_ETC_ATLAS=/etc/atlas:/etc/atlas:ro
DOCKER_VOLUME_DIR_ETC_ATLAS_MOUNT_IF=regexp("atl",Owner)
DOCKER_VOLUME_DIR_ETC_CMS=/etc/cms:/etc/cms:ro
DOCKER_VOLUME_DIR_ETC_CMS_MOUNT_IF=regexp("cms",Owner)
DOCKER_VOLUME_DIR_GLEXEC=/etc/glexec.conf:/etc/glexec.conf:ro
DOCKER_VOLUME_DIR_GRIDENV=/etc/profile.d/grid-env.sh:/etc/profile.d/grid-env.sh:ro
DOCKER_VOLUME_DIR_GRID_SECURITY=/etc/grid-security:/etc/grid-security:ro
DOCKER_VOLUME_DIR_GROUP=/etc/group:/etc/group:ro
DOCKER_VOLUME_DIR_LCAS=/etc/lcas:/etc/lcas:ro
DOCKER_VOLUME_DIR_LCMAPS=/etc/lcmaps:/etc/lcmaps:ro
DOCKER_VOLUME_DIR_MJF=/etc/machinefeatures:/etc/machinefeatures:ro
DOCKER_VOLUME_DIR_PASSWD=/etc/passwd:/etc/passwd:ro

Some comments on this:

  • by default HTCondor drops all Linux capabilities in the containers it runs. This prevents glexec from working, so we unfortunately have to keep all standard capabilities for jobs using the pilot role.
  • Directories such as /cvmfs, /etc/grid-security, /etc/machinefeatures, /etc/lcas, /etc/lcmaps are bind mounted into the containers for all jobs
  • The glexec config file is bind mounted into the containers
  • For ATLAS jobs only, /sys/fs/cgroup and the job recovery directory are bind mounted into the containers
  • /etc/passwd and /etc/groups are bind mounted into containers so that the pool accounts are available

CEs

We need to ensure that jobs are submitted using the Docker universe with the appropriate image specified rather than the default Vanilla universe. Assuming HTCondor 8.6.x is running on the CEs, a schedd job transform can be used:

JOB_TRANSFORM_NAMES = DefaultDocker
JOB_TRANSFORM_DefaultDocker @=end
[
   Requirements = JobUniverse == 5 && DockerImage =?= undefined && Owner =!= "nagios";
   set_WantDocker = true;
   eval_set_DockerImage = "alahiff/grid-workernode-c6:20170627.1";
   set_Requirements = ( TARGET.HasDocker ) && ( TARGET.Disk >= RequestDisk ) && ( TARGET.Memory >= RequestMemory ) && ( TARGET.Cpus >= RequestCpus ) && ( TARGET.HasFileTransfer );
   copy_TransferInput = "OriginalTransferInput";
   eval_set_TransferInput = strcat(OriginalTransferInput, ",", Cmd);
]
@end

Image

The Dockerfile for the image in use is here: https://github.com/alahiff/grid-workernode/blob/master/centos6/Dockerfile. The contents of the image are based on the standard SL6 worker nodes at RAL.