SGE main commands

A good reference can be found in the links

• https://web.njit.edu/topics/HPC/basement/sge/SGE.html
• https://www.hoffman2.idre.ucla.edu/computing/sge-commands/

Start by one of the below commands (login to the head node):

ssh <username>@lecs2

ssh lecs2 -l <username>

Create a batch job script, which contains the following lines:

#!/bin/tcsh

cd executables

./a.out

 

Send the script to be executed to one of the ‘resources’, you are belong to, using flag -l (=small ‘L’). For example, if you belong to Itay’s group:

qsub -l itaym <script>

This ‘resource’ parameter appears in the ‘complex_values’ field in the output of command:

qconf -sq <queue name>

The number which is returned from this command is the job id that was assigned to the new job:

Your job 6790845 (“<script>”) has been submitted

You can see the status of your executing jobs by executing:

qstat -u <username>

Which lists all the jobs running or being queued for the specified user.

Job status may be mainly one of the following:

qw – queued (waiting for its run)

r – running

Eqw – in error state

Rr – job was reran, due to some failure in one of the nodes.

You can see the status of all the executing jobs by executing:

qstat -u \*

To see the current available queues and their cputime and memory limits, execute:

qstat -f -g c

To see a list of all the queues:

qconf -sql

To see the status of a specific job, you may run:

qstat -j <job number>

e.g.      qstat -j 6790845

The standard output and standard error files will be written by default at the end of the execution to files in your home directory: <script>.o#n and <script>.e#n (where #n is the job number given to your job by the batch queueing system).

To delete a job, use the qdel command:

qdel <job number>

 

SGE file parameters

The script to be ran may have additional commands which are directions to the scheduler, instead of adding parameters to the qsub command line.

The commands for SGE scheduler should have prefix ‘#$’, please see reference in http://bioinformatics.mdc-berlin.de/intro2UnixandSGE/sun_grid_engine_for_beginners/how_to_submit_a_job_using_qsub.html

 

An example to a script:

#!/bin/tcsh

#$ -e $JOB_NAME.ERR            ⇒ error file name

#$ -o $JOB_NAME.OUT            ⇒ error file name

#$ -cwd                                      ⇒ run in current working directory

#$ -l dorothee                            ⇒ use resource dorothee

#$ -N script_name

#$ -M dvory@tauex.tau.ac.il      ⇒ my email address

#$ -m e                                      ⇒ send an email when the script ends

#$ -l hostname=compute-5-0    ⇒ specific node to be used

 

# Below are regular commands

module load python/python-2.7.2

setenv SOME_ENV_VAR 55

cd /home/dvory

perl my_script.pl

 

The script can be ran with the command:

qsub script

 

Interactive session

Interactive sessions (line mode) are enabled using the command:

qsh

 

Running matlab example

There 2 options to run matlab via SGE

1. Command to run interactive job:

qsh -q all.q

bash

matlab

2. Submitting a matlab batch job to queue:

qsub -q all.q my_table_script.sh

While:

myTable.m                         ⇒  This matlab file calculates something

function [] = myTable()

fprintf('=======================================\n');

fprintf('   a          b          c          d          \n');

fprintf('=======================================\n');

while 1

  for j = 1:10

              a = sin(10*j);

              b = a*cos(10*j);

              c = a + b;

              d = a - b;

              fprintf('%+6.5f   %+6.5f   %+6.5f   %+6.5f   \n',a,b,c,d);

  end

end

fprintf('=======================================\n');

 

my_table_script.sh        ⇒ This script executes the matlab program:

#!/bin/tcsh

#$ -N this_is_name

#$ -S /bin/tcsh

#$ -cwd

#$ -e /tmp/a.err

#$ -o /tmp/a.out

module load freesurfer

setenv KEY_MODELLER9v8 a

/usr/local.cc/bin/matlab -nodisplay -nojvm -nosplash -nodesktop myTable.m