Re: [Psn-general] Grid Engine Deployment

[Darin P. <Dar...@co...>]

Pontus,

Pontus Pihlgren wrote:
> tor 2007-09-27 klockan 10:40 -0400 skrev Darin Perusich:
>> Is there any documentation available for deploying PsN in a Sun Grid 
>> Engine environment, or any grid environment for that matter? In our 
>> environment NONMEM is not available for local execution so understanding 
>> when PsN needs to run NONMEM and how it submits jobs for execution is vital.
> 
> No, there is little documentation as it is a fairly new feature. At
> least SGE support, platform LSF support has been around a little longer.
> I'm not sure what you mean by "local execution", do you mean that it is
> not installed on the execution hosts?

NONMEM, perl, and g77 are available on the execution hosts, but not on 
the submitting hosts. My users perform all of the NONMEM control steam 
and dataset creation on designated submit/login hosts and submit their 
jobs to Grid Engine which then dispatches said jobs to our NONMEM 
execution hosts. NONMEM is not available on these submit/login hosts, 
only our execution hosts. It isn't clear to me which commands require 
the execution of NONMEM from reading the documentation, bare in mind 
that I'm not a PK/PD scientist so I'm not familiar with all the terminology.

>> Additional does PsN rely on nmfe for job execution? We do not use nmfe 
>> but rather a script which is loosely modeled after it. I can go into 
>> detail on what our execution script does if necessary.
> 
> No, PsN implements its own Perl module for executing NONMEM. The module
> is loosely based on the nmfe6 script. This module can be used as a
> script and is as such submitted to the grid system.

Which modules is this and what does it do?

Our script creates a temporary scratch directory in the current working 
directory of and named after the control stream and compiles and runs 
NONMEM from within this scratch directory. This affords our scientist 
the ability to run as many jobs from within a single working directory 
with out having to be concerned with temporary files that NONMEM creates 
clobbering each other.

Say you have 20 NONMEM runs,  run1.ctl - run20.ctl and they reside in 
/some/directory/with/many_nm_jobs. When run1.ctl is submitted and 
executed the directory /some/directory/with/many_nm_jobs/run1.ctl.dir/ 
is created and the job is executed within and contains the FCON, FDATA, 
INTER, FSUBS*, PRDERR, FILE*, nonmem, etc files. If you submitted all 20 
jobs to the grid then you'd have 20 separate 
/some/directory/with/many_nm_jobs/run*.ctl.dir/ directories.

> Deploying PsN in an SGE environment the requires three things:
> 
> * Making PsN available on the submitting hosts and execution hosts.
> 
> * Making NONMEM and a Fortran compiler available on the execution hosts.
> 
> * Adding the path to NONMEM in the PsN configuration file. And selecting
> the compiler used. Queue and resource selection can be entered as well.

I've added the path for NM5, NM6, the compiler and compiler options. How 
would I specify the queue, resources, etc, that you've mentioned? I see 
that common_options.pm defines run_on_sge, sge_resource:s, and 
sge_queue:s, how are these used?

Regards,

-- 
Darin Perusich
Unix Systems Administrator
Cognigen Corporation
395 Youngs Rd.
Williamsville, NY 14221
Phone: 716-633-3463
Email: dar...@co...