[ExM Users] LSF Job Launcher?

[Timothy Stitt (TGAC)]

Thanks Justin. Will give that a go and let you know if I get something to work.

---

Timothy Stitt PhD / Head of Scientific Computing

The Genome Analysis Centre (TGAC)

http://www.tgac.ac.uk/


p: +44 1603 450378

e: timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>

From: Justin M Wozniak <wozniak at mcs.anl.gov<mailto:wozniak at mcs.anl.gov>>
Date: Monday, 16 March 2015 21:27
To: Timothy Stitt <timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>>, "exm-user at lists.mcs.anl.gov<mailto:exm-user at lists.mcs.anl.gov>" <exm-user at lists.mcs.anl.gov<mailto:exm-user at lists.mcs.anl.gov>>
Subject: Re: [ExM Users] LSF Job Launcher?

Hi
    No, and I don't have access to any LSF systems.
    The way to get started is to check the information here: http://swift-lang.org/Swift-T/turbine-sites.html#_turbine_as_mpi_program
Turbine runs as an MPI program.
    Then, take a look at some other scheduler script that you have used before.  In PBS, the turbine-pbs-run.zsh script is in control.  It substitutes variables into a template named turbine.pbs.m4, creating turbine.pbs, and qsubs that. In turbine.pbs.m4, the key line is:

${TURBINE_LAUNCHER} ${TCLSH} ${PROGRAM} ${ARGS}

which will run as something like:

mpiexec /path/to/tclsh myprogram.tic args...

Everything else is just setting up environment variables, most of which are optional.  The key Turbine settings are set by this command (line 54):

source ${TURBINE_HOME}/scripts/turbine-config.sh

You should be able to construct an ad hoc solution with those two key lines.

Alternatively, you could copy turbine/scripts/submit/pbs to turbine/scripts/submit/lsf and edit the shell scripts until it works.  Then you could send us a patch!

    Justin

On 03/16/2015 04:08 PM, Timothy Stitt (TGAC) wrote:
Hi all,

Has anyone developed a Turbine job launcher script for the LSF batch system? If so, could you kindly pass on some assistance on how to set it up with my local LSF cluster.

Thanks in advance,

Tim.

---

Timothy Stitt PhD / Head of Scientific Computing

The Genome Analysis Centre (TGAC)

http://www.tgac.ac.uk/


p: +44 1603 450378

e: timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>



_______________________________________________
ExM-user mailing list
ExM-user at lists.mcs.anl.gov<mailto:ExM-user at lists.mcs.anl.gov>https://lists.mcs.anl.gov/mailman/listinfo/exm-user



--
Justin M Wozniak
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/exm-user/attachments/20150316/2a86a9b1/attachment-0001.html>