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 cuurent 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.