Singularity Support

Singularity (https://sylabs.io/singularity/) is a container runtime system popular in scientific and HPC communities. HTCondor can run jobs inside Singularity containers either in a transparent way, where the job does not know that it is being contained, or, the HTCondor administrator can configure the HTCondor startd so that a job can opt into running inside a container. This allows the operating system that the job sees to be different than the one on the host system, and provides more isolation between processes running in one job and another.

The decision to run a job inside Singularity ultimately resides on the worker node, although it can delegate that to the job.

By default, jobs will not be run in Singularity.

For Singularity to work, the administrator must install Singularity on the worker node. The HTCondor startd will detect this installation at startup. When it detects a useable installation, it will advertise two attributes in the slot ad:

HasSingularity = true
SingularityVersion = "singularity version 3.7.0-1.el7"

HTCondor will run a job under Singularity when the startd configuration knob SINGULARITY_JOB evaluates to true. This is evaluated in the context of the slot ad and the job ad. If it evaluates to false or undefined, the job will run as normal, without singularity.

When SINGULARITY_JOB evaluates to true, a second HTCondor knob is required to name the singularity image that must be run, SINGULARITY_IMAGE_EXPR. This also is evluated in the context of the machine and the job ad, and must evaluate to a string. This image name is passed to the singularity exec command, and can be any valid value for a singularity image name. So, it may be a path to file on a local file system that contains an singularity image, in any format that singularity supports. It may be a string that begins with docker://, and refer to an image located on docker hub, or other repository. It can begin with http://, and refer to an image to be fetched from an HTTP server. In this case, singularity will fetch the image into the job’s scratch directory, convert it to a .sif file and run it from there. Note this may require the job to request more disk space that it otherwise would need. It can be a relative path, in which case it refers to a file in the scratch directory, so that the image can be transfered by HTCondor’s file transfer mechanism.

Here’s the simplest possible configuration file. It will force all jobs on this machine to run under Singularity, and to use an image that it located in the filesystem in the path /cvfms/cernvm-prod.cern.ch/cvm3:

# Forces _all_ jobs to run inside singularity.
SINGULARITY_JOB = true

# Forces all jobs to use the CernVM-based image.
SINGULARITY_IMAGE_EXPR = "/cvmfs/cernvm-prod.cern.ch/cvm3"

Another common configuration is to allow the job to select whether to run under Singularity, and if so, which image to use. This looks like:

SINGULARITY_JOB = !isUndefined(TARGET.SingularityImage)
SINGULARITY_IMAGE_EXPR = TARGET.SingularityImage

Then, users would add the following to their submit file (note the quoting):

+SingularityImage = "/cvmfs/cernvm-prod.cern.ch/cvm3"

or maybe

+SingularityImage = "docker://ubuntu:20"

By default, singularity will bind mount the scratch directory that contains transfered input files, working files, and other per-job information into the container, and make this the initial working directory of the job. Thus, file transfer for singularity jobs works just like with vanilla universe jobs. Any new files the job writes to this directory will be copied back to the submit node, just like any other sandbox, subject to transfer_output_files, as in vanilla universe.

Assuming singularity is configured on the startd as described above, A complete submit file that uses singularity might look like

executable = /usr/bin/sleep
arguments = 30
+SingularityImage = "docker://ubuntu"

Requirements = HasSingularity

Request_Disk = 1024
Request_Memory = 1024
Request_cpus = 1

should_transfer_files = yes
tranfer_input_files = some_input
when_to_transfer_output = on_exit

log = log
output = out.$(PROCESS)
error = err.$(PROCESS)

queue 1

HTCondor can also transfer the whole singularity image, just like any other input file, and use that as the container image. Given a singularity image file in the file named “image” in the submit directory, the submit file would look like:

executable = /usr/bin/sleep
arguments = 30
+SingularityImage = "image"

Requirements = HasSingularity

Request_Disk = 1024
Request_Memory = 1024
Request_cpus = 1

should_transfer_files = yes
tranfer_input_files = image
when_to_transfer_output = on_exit

log = log
output = out.$(PROCESS)
error = err.$(PROCESS)

queue 1

The administrator can optionally specify additional directories to be bind mounted into the container. For example, if there is some common shared input data located on a machine, or on a shared filesystem, this directory can be bind-mounted and be visible inside the container. This is controlled by the configuration parameter SINGULARITY_BIND_EXPR. This is an expression, which is evaluated in the context of the machine and job ads, and which should evaluated to a string which contains a space separated list of directories to mount.

So, to always bind mount a directory named /nfs into the image, and administrator could set

SINGULARITY_BIND_EXPR = "/nfs"

Or, if a trusted user is allowed to bind mount anything on the host, an expression could be

SINGULARITY_BIND_EXPR = (Owner == "TrustedUser") ? SomeExpressionFromJob : ""

If the source directory for the bind mount is missing on the host machine, HTCondor will skip that mount and run the job without it. If the image is an exploded file directory, and the target directory is missing inside the image, and the configuration parameter SINGULRITY_IGNORE_MISSING_BIND_TARGET is set to true (the default is false), then this mount attempt will also be skipped. Otherwise, the job will return an error when run.

In general, HTCondor will try to set as many Singularity command line options as possible from settings in the machine ad and job ad, as make sense. For example, if the slot the job runs in is provisioned with GPUs, perhaps in response to a request_GPUs line in the submit file, the Singularity flag -nv will be passed to Singularity, which should make the appropriate nvidia devices visible inside the container. If the submit file requests environment variables to be set for the job, HTCondor passes those through Singularity into the job.

Before the condor_starter runs a job with singularity, it first runs singularity test on that image. If no test is defined inside the image, it runs /bin/sh /bin/true. If the test returns non-zero, for example if the image is missing, or malformed, the job is put on hold. This is controlled by the condor knob SINGULARITY_RUN_TEST_BEFORE_JOB, which defaults to true.

If an administrator wants to pass additional arguments to the singularity exec command that HTCondor does not currently support, the parameter SINGULARITY_EXTRA_ARGUMENTS allows arbitraty additional parameters to be passed to the singularity exec command. Note that this can be a classad expression, evaluated in the context of the job ad and the machine, so the admin could set different options for different kinds of jobs. For example, to pass the -w argument, to make the image writeable, an administrator could set

SINGULARITY_EXTRA_ARGUMENTS = "-w"

There are some rarely-used settings that some administrators may need to set. By default, HTCondor looks for the Singularity runtime in /usr/bin/singularity, but this can be overridden with the SINGULARITY parameter:

SINGULARITY = /opt/singularity/bin/singularity

By default, the initial working directory of the job will be the scratch directory, just like a vanilla universe job. This directory probably doesn’t exist in the image’s filesystem. Usually, Singularity will be able to create this directory in the image, but unprivileged versions of singularity with certain image types may not be able to do so. If this is the case, the current directory on the inside of the container can be set via a knob. This will still map to the scratch directory outside the container.

# Maps $_CONDOR_SCRATCH_DIR on the host to /srv inside the image.
SINGULARITY_TARGET_DIR = /srv

When the HTCondor starter runs a job under Singularity, it always prints to the log the exact command line used. This can be helpful for debugging or for the curious. An example command line printed to the StarterLog might look like the following:

About to exec /usr/bin/singularity exec -S /tmp -S /var/tmp --pwd /execute/dir_462373 -B /execute/dir_462373 --no-home -C /images/debian /execute/dir_462373/condor_exec.exe 3

In this example, no GPUs have been requested, so there is no -nv option. MOUNT_UNDER_SCRATCH is set to the default of /tmp,/var/tmp, so condor translates those into -S (scratch directory) requests in the command line. The --pwd is set to the scratch directory, -B bind mounts the scratch directory with the same name on the inside of the container, and the -C option is set to contain all namespaces. Then the image is named, and the executable, which in this case has been transfered by HTCondor into the scratch directory, and the job’s argument (3). Not visible in the log are any environment variables that HTCondor is setting for the job.