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Re: Octave: Question on running parallel package on linux HPC cluster

From: Olaf Till
Subject: Re: Octave: Question on running parallel package on linux HPC cluster
Date: Mon, 14 Sep 2015 16:05:39 +0200
User-agent: Mutt/1.5.23 (2014-03-12)

On Sun, Sep 13, 2015 at 11:18:43PM -0700, Tung Nguyen wrote:
> Hello everyone,
> I'm trying to get octave running on our Red Hat Linux cluster in parallel
> mode. I'm looking at the wiki page but couldn't find any example
> I'm wondering if anyone has any simple example that can help me to get
> started? The cluster uses the Torque/Maui scheduling system. Basically,
> I'll use qsub to submit computing job and will get 2 nodes which has 8
> processors each. Their names will be stored in $PBS_NODEFILE variable e.g.
> compute-1-12
> compute-1-12
> compute-1-12
> compute-1-12
> compute-1-12
> compute-1-12
> compute-1-12
> compute-1-12
> ...
> Then I'd like to do parallel evaluation (16 separated CPUs) for an
> objective_function.m file using arx matrix (10 x 16) using feval
> *result = feval(objective_function, arx); *

I had already replied to this question of Tung off-list, but I repeat
the reply here since he asked me to do so:

I'm not familiar with qsub (gridengine?), but it has a different
concept and you don't need the parallel package for it.

If you use the parallel package instead of gridengine, you have to
start the server contained in the parallel package at each server
machine. The server is started with the function 'pserver', so you
should read its documentation with 'help pserver' in Octave. If your
server machines (or their ports used by the parallel package) are not
made secure in another way, you should use the function
'parallel_generate_srp_data' before starting the servers and you
should use TLS (this is detailed in the documentation of this function
and of functions 'pserver' and 'pconnect'). But I have heard that
Redhat does not contain the necessary parts of the used TLS library
(SRP extension of libgnutls). After starting the servers, you can use
the function 'pconnect' (read its documentation) to connect to the
server machines. After this, you can possibly use the function
'netcellfun' (read its documentation) for your application. This
function should be able to use all available processors at all
available machines.

The page at is not written by
me and I wasn't even aware of it. It is not up to date. The official
documentation is at


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