Singularity Condor

Interactive Singularity Jobs and condor_ssh_to_job

Starting with HTCondor 8.8, condor_ssh_to_job and hence also interactive jobs use an sshd running directly on the execute node with user privileges. Since 8.8.10, most issue have been ironed out, and connecting into the job happens using condor_nsenter , which is an nsenter -like tool to "enter" container namespaces in a generic way. This tool is spawned by the starter in parallel to sshd .

There are a few remaining issues related to X11 forwarding which can be worked around, and which are partially dependent on the utilised setup. These are discussed on this page in addition to a short discussion of the handling of locale environment variables.

X11 forwarding

X11 forwarding in general works by running xauth as a child of the sshd process on the execute node. sshd mostly prunes the environment before, setting a new DISPLAY variable to a forwarded X11 port. It then runs xauth which by default uses the user's home directory to store the X11 authorization information.

Two issues arise:

  • Since condor_nsenter does not run as a child of the sshd , but as a child of the starter , it can not pass on the DISPLAY environment variable to the user session.
  • In many cases, when containers are used, the actual users may not have a home directory on the execute node, or might not have it mounted inside the container. However, we cannot override the location to store the .Xauthority file with the environment variable XAUTHORITY since sshd prunes that.

Another related issue is that the TERM environment variable is not inherited from the condor_ssh_to_job command, which may lead to strange behaviour of special key escape sequences (e.g. HOME or END keys).

A possible workaround

To solve all these issues at once, we can make use of the fact that sshd is spawned and configured by HTCondor via the condor_ssh_to_job_sshd_config_template . The location of this template can be set via the knob SSH_TO_JOB_SSHD_CONFIG_TEMPLATE . We can patch the file shipped with HTCondor and add the line: XAuthLocation /usr/local/bin/condor_xauth_wrapper Subsequently, we can create the wrapper script (make sure it is executable) with the following content:
#!/bin/bash

# Walk up the process tree until we find the second sshd which rewrites cmdline to "sshd: user@tty".
# The first sshd is our parent process which does not log itself.
SSHD_PID=$$
SSHD_CNT=0
while true; do
  IFS= read -r -d '' CMDLINE </proc/${SSHD_PID}/cmdline || [[ $cmdline ]]
  #echo "Checking ID ${SSHD_PID}, cmdline ${CMDLINE^^}"
  SSHD_MATCHER="^SSHD: "
  if [[ ${CMDLINE^^} =~ ${SSHD_MATCHER} ]]; then
    # We found the sshd!
    SSHD_CNT=$(( SSHD_CNT + 1))
    if [ ${SSHD_CNT} -gt 1 ]; then
      break;
    fi
  fi
  SSHD_PID=$(ps -o ppid= -p ${SSHD_PID} | awk '{print $1}')
  if [ ${SSHD_PID} -eq 1 ]; then
    # We arrived at the INIT process, something very wrong... Let's stop and alert the user.
    echo "Error: Could not determine sshd process, X11 forwarding will not work!"
    echo "       Please let your admins know you got this error!"
    exit 0
  fi
done
#echo "SSHD PID is ${SSHD_PID}."

# Find sshd.log, checking through fds.
FOUND_SSHD_LOG=0
for FD in $(ls -1 /proc/${SSHD_PID}/fd/); do
  FILE=$(readlink -f /proc/${SSHD_PID}/fd/$FD)
  #echo "Checking FD $FD, file is $FILE"
  SSHD_LOG_MATCHER="sshd\.log$"
  if [[ "${FILE}" =~ ${SSHD_LOG_MATCHER} ]]; then
    #echo "Found ${FILE}!"
    FOUND_SSHD_LOG=1
    SSH_TO_JOB_DIR=$(dirname ${FILE})
    JOB_WORKING_DIR=$(dirname ${SSH_TO_JOB_DIR})
    break;
  fi
done

if [ ${FOUND_SSHD_LOG} -eq 0 ]; then
  # We could not identify sshd.log, let's stop and alert the user.
  echo "Error: Could not determine sshd process' (PID: ${SSHD_PID}) log, X11 forwarding will not work!"
  echo "       Please let your admins know you got this error!"
  exit 0
fi

# Finally, if we arrive here, all is well.

# This does NOT work, since env.sh is sourced as forced command, too early.
#echo "export DISPLAY=${DISPLAY}" >> ${SSH_TO_JOB_DIR}/env.sh

# Ugly hack needed with HTCondor 8.8.10 which does not yet pass through DISPLAY or TERM.
echo "export DISPLAY=${DISPLAY}" > ${JOB_WORKING_DIR}/.display
echo "export TERM=${TERM}" >> ${JOB_WORKING_DIR}/.display

export XAUTHORITY=${JOB_WORKING_DIR}/.Xauthority
/usr/bin/xauth "$@" </dev/stdin

Please note that this script is pretty verbose, and handles very unlikely errors not observed in practice (yet). Most of the code is just there to find out which directory is used as the execute directory for the job, then place the DISPLAY environment variable and the TERM environment variable inside a file .display in there, and finally adjust the environment variable XAUTHORITY to place the .Xauthority file there.

This script works combined with two environment hack inside the container:

  • The container needs to use the execute directory as HOME directory. You can for example do that by setting SINGULARITY_HOME in the STARTER_JOB_ENVIRONMENT knob, which you may likely touch anyways to set SINGULARITY_NOHOME=true if you run without the users' home directories on the execute node.
  • The container needs to source .display from the HOME directory on start (and may also clean up by deleting it). Example code for the latter task could be, assuming your in-container HOME directory is /jwd : if [ -r /jwd/.display ]; then source /jwd/.display rm -f /jwd/.display fi A good place could be a file in /etc/profile inside the container(s) you use.

An alternative workaround

Note that if your sshd is recent enough and understands SetEnv (should be the case starting from versions >=7.8), you could additionally patch /usr/libexec/condor/condor_ssh_to_job_sshd_setup , for example, you could add:
echo "SetEnv JOB_WORKING_DIR=${base_dir}" >> ${sshd_config}

directly after the sshd_config is generated from the template. You can then simplify the /usr/local/bin/condor_xauth_wrapper script to the much less error-prone code:
#!/bin/bash

# Ugly hack needed with HTCondor 8.8.10 which does not yet pass through DISPLAY or TERM.
echo "export DISPLAY=${DISPLAY}" > ${JOB_WORKING_DIR}/.display
echo "export TERM=${TERM}" >> ${JOB_WORKING_DIR}/.display

export XAUTHORITY=${JOB_WORKING_DIR}/.Xauthority

/usr/bin/xauth "$@" </dev/stdin

Note that we can not SetEnv the variable XAUTHORITY directly with SetEnv , it is overwritten by sshd after setting the defined environment variables.

Locale settings

You may note that the locale environment variables ( LANGUAGE , LANG ,...) are not "adopted" in the interactive job or when using condor_ssh_to_job to attach to a running job, similar as is the case with DISPLAY and TERM . This may cause issues such as UTF-8 not working if the default locale inside your job is not set, e.g. because you are using a container without a default locale, which usually means the C locale is assumed.

While forwarding such variables is convenient in regular ssh? usage, it would change the behaviour of the payload of the interactive job versus a batch job. This is especially true e.g. for =LC_NUMERIC which affects the way some libraries parse numbers. To overcome this kind of issue, the best approach seems to be to set a default locale inside the used container, which is then consistently used both for batch and interactive jobs.