View source for Singularity with grid engine

JW may 2019


Followed guide here: https://blogs.univa.com/2019/01/using-univa-grid-engine-with-singularity/

Pete installed singularity on phylo


now a requestable resource with "-l singularity" to make sure you get a node with singularity on


Example:
 qsub -l singularity -b y singularity run /full_path_to/ubuntu.sif ./test_script.sh
 replace:ubuntu.sif with whatever image you are trying to run


example2:
 qsub -pe multi 8 -l singularity -b y singularity run /full_path/funannotate_latest.sif /full_path/fun_singularity.sh
 The shell must have the curent working directory full path in it as cd /ful_path/   
 the #!cwd command will not work!


To add another node with singularity on:


qconf -me <nodename>

On the complex_values line remove NONE if present, and add "singularity=TRUE"




-b is a normal qsub command

       -b y[es]|n[o]
              Available for qsub, qrsh only. Qalter does not allow changing this option. This  option  cannot
              be embedded in the script file itself.

              Gives  the  user  the  possibility  to indicate explicitly whether command should be treated as
              binary or script. If the argument of -b is ’y’, then command  may be a binary or  script.   The
              command  might not be accessible from the submission host.  Nothing except the path of the com-
              mand will be transferred from the submission host to the execution host. Path aliasing will  be
              applied to the path of command before it is executed.

              If the argument of -b is ’n’ then command needs to be a script, and it will be handled as such.
              The script file has to be accessible by the submission host. It will be transferred to the exe-
              cution host. qsub/qrsh will search directive prefixes within scripts.

              qsub will implicitly use -b n, whereas qrsh will apply the -b y option if nothing else is spec-
              ified.

              The value specified with this option or the corresponding value specified in qmon will only  be
              passed  to defined JSV instances if the value is yes.  The name of the parameter will be b. The
              value will be y also when the long form yes was specified during submission.  (See -jsv  option
              below or find more information concerning JSV in jsv(1).)

              Please  note  that  submission of command as a script (-b n) can have a significant performance
              impact, especially for short running jobs and big job scripts.  Script submission adds a number
              of operations to the submission process: The job script needs to be
              - parsed at client side (for special comments)
              - transferred from submit client to qmaster
              - spooled in qmaster
              - transferred to execd at job execution
              - spooled in execd
              - removed from spooling both in execd and qmaster once the job is done
              If job scripts are available on the execution nodes, e.g. via NFS, binary submission can be the
              better choice.