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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superseded by phaser).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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Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
