They actually don't solve the same problem. Specifically OpenMP only supports parallel threads on a single machine whereas MPI supports parallel processes over a cluster of machines. OpenMP is simpler because the problem is simpler.
In the src directory of an fsl distribution you'll find directories for each project, eg, $FSLDIR/src/flirt, and within a Makefile. Put your flags in there. There's plenty of instructions on our web site: www.fmrib.ox.ac.uk/fsl
Regards,
Dave
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-----Original Message-----
From: Julio Duarte <[log in to unmask]>
Date: Mon, 22 Mar 2010 18:11:25
To: <[log in to unmask]>
Subject: Re: [FSL] OpenMP
Actually, I have worked with OpenMP in the past and it is way simpler to
use than say MPI and I have it installed on the cluster. On the other hand,
I'm extending, for our own research purposes flirt, so I know exactly how
to parallelize it and it fits the OpenMp model (my extended version).
However, what I do not know is what changes to make on the make files or
scripts you use to make install for instance.
Could you give me pointers assuming that I know how to use OpenMP, I have
OpenMP and I just need to compile it?
Julio
On Mar 22 2010, Dave Flitney wrote:
>Julio,
>
> OpenMP isn't free. You can't simply recompile and have your code
> parallelised. You would need to recode the sources to manually add the
> parallel instructions. This is a very difficult process requiring
> intimate knowledge of the program sources and how to make them
> multi-thread safe.
>
> When we originally looked at parallel support we quickly realised that
> our programming team (mostly PhD students working on their thesis
> projects) would never have the time or inclinatin to acquire the skill
> set to do this. Fortunately one can run multiple instances of much of our
> code on subsets of the data so we chose to take the pragmatic approach of
> parallelising by scripting independent sub jobs. We achieve this by
> running the program via a queing systen such as SGE.
>
>Sadly though, flirt simply doesn't fit into this model, sorry.
>
>Hope that helps,
>Dave
>
>------Original Message------
>From: Julio Duarte
>Sender: FSL - FMRIB's Software Library
>To: [log in to unmask]
>ReplyTo: FSL - FMRIB's Software Library
>Subject: [FSL] OpenMP
>Sent: 22 Mar 2010 16:21
>
>Hi,
>
>I'd like to use OpenMP to speed up some code in FSL. What changes should I
>made to compile using openMP (for which I have support) for instance flirt.
>It probably means just to add -lgomp -fopenmp flags on some make files, but
>I do not exactly where.
>
>thanks
>
>Julio
>
>
>
>Sent using BlackBerry® from Orange
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