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*** CCP4 home page http://www.ccp4.ac.uk ***
The CCP4 distribution has a couple of MPI examples (beast_MPI by Ronan,
and fsearch_MPI by Quan Hao) but it is a lot more complicated to code,
and probably not worth the effort.
We have talked about parallelising Phaser with OpenMP, but that hasn't
reached the top of the priority list yet.
As others have said, script-level parallelisation is more likely to
be more fruitful these days, where you use the cluster to try different
things at the same time ("task farming", "parameter searching", call it
what you will).
Cheers
Martyn
On Mon, 2006-10-16 at 22:14 +0200, Kay Diederichs wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> Hi Jonathan,
>
> the answer depends on what you mean with "parallel" -
>
> a) two or more jobs running at the same time? Of course this benefits
> from a cluster provided it has transparent load-balancing (like what
> Mosix2 provides, see http://www.mosix.org, or what "single system image,
> SSI" stands for), or the jobs are submitted through a batch queuing
> system. The standard CCP4 supports this.
> b) there are very few crystallographic programs that use OpenMP (or the
> much more complicated MPI) to make a single program use more than one
> CPU. I actually don't know of any current program in CCP4 (beast is
> superseded by phaser). Phaser and Refmac5 would be worthwhile candidates
> for parallelization with OpenMP, but in both cases to my knowledge
> parallelization is not high on the priority list.
> c) outside CCP4: I use the parallel versions of SHELXL and XDS. XDS can
> even run on several nodes in a cluster to reduce a single dataset.
>
> Thinking about this some more: on one hand the dual-core (and soon
> quad-core) CPUs appear ideally suited for OpenMP parallelization. On the
> other hand a single CPU provides so much speed nowadays that it is not
> important any more to parallelize. So I guess there is a tendency to
> provide a workstation with several CPUs to each crystallographer in a
> lab which allows her to run several calculations at the same time,
> without bothering with real parallelization. Clusters do not offer much
> advantage over workstations in a LAN.
>
> just my 2 cents,
>
> Kay
>
> [EMAIL PROTECTED] schrieb:
> > *** For details on how to be removed from this list visit the ***
> > *** CCP4 home page http://www.ccp4.ac.uk ***
> >
> >
> > Hello everyone,
> >
> > I am trying figure out if it is possible to run CCP4 on a cluster, but I
> > keep
> > finding contradicting answers, from previous posts on this board suggesting
> > there are just no parallel crystallography programs, to Ronan's CCP4 page
> > discussing parallel programing, and even a colleague's claims of having run
> > a
> > parallel version of CCP4 on a Linux cluster called "Synapse" at the
> > University
> > of Oxford.
> >
> > Could someone please settle this issue?
> >
> > Best regards,
> >
> > J. Valencia
> >
> > ----------------------------------------------------------------
> > Este mensaje fue enviado desde el servidor Webmail del Instituto de
> > Biotecnologia.
>
>
