sge

Avoid generating empty STDOUT and STDERR files with Sun Grid Engine (SGE) and array jobs

I am running array jobs with Sun Grid Engine (SGE). My carefully scripted array job workers generate no stdout and no stderr when they function properly. Unfortunately, SGE insists on creating an empty stdout and stderr file for each run. Sun's manual states: STDOUT and STDERR of array job tasks will be written into ...

How to specify the equivalent of ppn (on PBS) in SGE queuing system ?

Hello All, Is there a way to specify the ppn ( or equivalent ) in SGE ? i don't want to use all cpus in one node so i will be able to have more memory per core. ( In PBS you would do -l nodes=16:ppn=2 for exemple) Thanks. ...

Getting the exit code from a process submitted with qsub on Sun Grid Engine

I would like to submit jobs via qsub on Sun Grid Engine (now: Oracle Grid Engine?). I do not wish to use the -sync yes option or qrsh, because I want my controlling program to be single-threaded and able to launch many jobs at a time. These options would block my controlling program's thread. However, I would like to receive the exit ...

Spreading a job over different nodes of a cluster in sun grid engine (SGE)

Hey, I'm tryin get sun gridending (sge) to run the separate processes of an MPI job over all of the nodes of my cluster. What is happening is that each node has 12 processors, so SGE is assigning 12 of my 60 processes to 5 separate nodes. I'd like it to assign 2 processes to each of the 30 nodes available, because with 12 processes (d...

How can I control the Perl version used when submitting grid jobs?

I'm working with SGE (Sun Grid Engine) to submit jobs to a grid. I also use perlbrew to manage my installed Perl versions. I wrote some short sh scripts that I use to run a perl script which requires a specific Perl version (5.12.2), which look something like this: #!/bin/bash #$-S /bin/bash source /home/dave/.bash_profile /home/dave/p...