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One question about this suggestion for composite SA-omit maps: has anyone
ever seen any benefit from doing this? I'm sceptical, though I admit I've
seldom tried it
Phil
--On 16 October 2006 14:41:14 -0600 Olve Peersen
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I agree with Kay that for most refinement things, CPUs are getting fast
enough that single processor jobs do it reasonably well. However, the
one place I've thought it would be very nice to build in MP support is
on CNS's composite SA-omit maps - the routine where CNS systematically
deletes bit of your structure, carries out simulated annealing, makes
(mini) maps from the portion that was omitted, and then in the end
merges all these mini-maps together to make a SA-omit map of your entire
molecule.
I typically like to run these after the last round of refinement of a
structure just to have a permanent copy of the omit map, but they often
take a week or more to run because for the ~20x20x20 grid of simulated
anneal jobs that must be done.
It would be great is someone could find a way to MP enable this process
(in CNS?), even if it means just clever scripting to split the XYZ space
up into 2 or 4 regions, running each region as a separate CNS job, and
then fusing the resulting maps together.
Is there anything like this in the works for Phenix?
- Olve
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Olve Peersen
Associate Professor
Dept. of Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Ft. Collins, CO 80523-1870
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970.491-0433 Office (MRB 279)
970.491-0271 Lab (MRB 149)
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On Oct 16, 2006, at 2:14 PM, Kay Diederichs wrote:
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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(beast is superseded by phaser).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
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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
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