Difference between revisions of "Singularity with grid engine"

From wiki
Jump to: navigation, search
Line 7: Line 7:
  
  
now a requestable resource with "-l singularity" to make sure you get a node with singularity on
+
now a request-able resource with "-l singularity" to make sure you get a node with singularity on
  
  
 
Example:
 
Example:
 
  qsub -l singularity -b y singularity run /full_path_to/ubuntu.sif ./test_script.sh
 
  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
+
  replace: ubuntu.sif with whatever image you are trying to run
  
 +
Lets go through that command in more depth:
 +
qsub -l singularity -b y singularity run
  
example2:
+
this is a special command so singularity will run on a specific server
 +
  /full_path_to/ubuntu.sif
 +
this is the image you download for the software you are interested in
 +
 
 +
  ./test_script.sh
 +
this needs to contain the commands you want to run
 +
 
 +
 
 +
example 2:
 
  qsub -pe multi 8 -l singularity -b y singularity run /full_path/funannotate_latest.sif /full_path/fun_singularity.sh
 
  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 shell must have the current working directory full path in it as cd /ful_path/   
  the #!cwd command will not work!
+
  putting #!cwd command in your shell scripts will not work!
 +
cd /ful_path/
 +
-pe multi 8    this asks for 8 cores, just as normal.
  
  
Line 27: Line 39:
  
 
On the complex_values line remove NONE if present, and add "singularity=TRUE"
 
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.
 

Revision as of 10:40, 24 May 2019

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 request-able 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

Lets go through that command in more depth:

qsub -l singularity -b y singularity run

this is a special command so singularity will run on a specific server

 /full_path_to/ubuntu.sif 

this is the image you download for the software you are interested in

 ./test_script.sh
this needs to contain the commands you want to run


example 2:

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 current working directory full path in it as cd /ful_path/

putting #!cwd command in your shell scripts will not work!
cd /ful_path/
-pe multi 8     this asks for 8 cores, just as normal. 


To add another node with singularity on:


qconf -me <nodename>

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