At a glance my guess would be that the user needs to place a double dash
(/--/) after/rstudio_4.2.sif/ or that the command to be executed needs
to be double-quoted. Otherwise singularity might be trying to parse the
rstudio flags as its own.
WTERMSIG 53 <https://man7.org/linux/man-pages/man2/wait.2.html> mostly
just indicates that the rstudio process was killed with the SIGRTMAX-11
signal (not sure why exactly as I don't believe SLURM makes use of this
signal).
On 11/10/2023 1:25 PM, Robert Kudyba wrote:
The user is launching a Singularity container for RStudio and the
final option for --rsession-path does not exist.
scontrol show job 420719
JobId=420719 JobName=r2.sbatch
UserId=ouruser(552199) GroupId=user(500) MCS_label=N/A
Priority=1428 Nice=0 Account=ouracct QOS=xxx
JobState=FAILED Reason=RaisedSignal:53(Real-time_signal_19)
Dependency=(null)
Fromslurmctld.log:
[2023-11-10T11:40:20.569] _slurm_rpc_submit_batch_job: JobId=420719
InitPrio=1428 usec=272
[2023-11-10T11:40:20.973] sched: Allocate JobId=420719
NodeList=node001 #CPUs=2 Partition=xxx
[2023-11-10T11:40:21.143] _job_complete: JobId=420719 WTERMSIG 53
[2023-11-10T11:40:21.144] _job_complete: JobId=420719 done
I think I may know the reason but wanted to see if this error meant
something else.Here is the snippet in the sbatch file:
singularity exec --cleanenv rstudio_4.2.sif \
/usr/lib/rstudio-server/bin/rserver --www-port ${PORT} \
--auth-none=0 \
--auth-pam-helper-path=pam-helper \
--auth-stay-signed-in-days=30 \
--auth-timeout-minutes=0 \
--rsession-path=/path/to/4.2/rsession.sh
Thanks.
