Thanks for pointing out that link. The graph makes the point I was going to mention, i.e. that you notice a big difference in using up to about 4 processors for typical jobs, but after that point the non-parallelisable parts of the code start to dominate and there's less improvement. This is very useful if you have one MR job to run on a typical modern workstation (2-8 cores), but if you have several separate jobs to run then you're better off submitting them simultaneously, each using a subset of the available cores. Of course, that assumes you have enough memory for several simultaneous separate jobs!
Regards,
Randy Read
On 9 Nov 2011, at 07:21, Ed Pozharski wrote:
> See page 3 of this
>
> http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf
>
>
>
> On Wed, 2011-11-09 at 09:22 +0900, Francois Berenger wrote:
>> Hello,
>>
>> How faster is the OpenMP version of Phaser
>> versus number of cores used?
>>
>> In the past I have been quite badly surprised by
>> the no-acceleration I gained when using OpenMP
>> with some of my programs... :(
>>
>> Regards,
>> F.
>>
>> On 11/09/2011 02:59 AM, Dr G. Bunkoczi wrote:
>>> Hi Ed,
>>>
>>> in the CCP4 distribution, openmp is not enabled by default, and there
>>> seems to be no easy way to enable it (i.e. by setting a flag at the
>>> configure stage).
>>>
>>> On the other hand, you can easily create a separate build for phaser
>>> that is openmp enabled and use phaser from there. To do this, create a
>>> new folder, say "phaser-build", cd into it, and issue the following
>>> commands (this assumes you are using bash):
>>>
>>> $ python $CCP4/lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py
>>> --repository=$CCP4/src/phaser/source phaser
>>> --build-boost-python-extensions=False --enable-openmp-if-possible=True
>>>
>>> $ . ./setpaths.sh ("source ./setpaths.csh" with csh) $ libtbx.scons (if
>>> you have several CPUs, add -jX where X is the number of CPUs you want to
>>> use for compilation)
>>>
>>> This will build phaser that is openmp-enabled. You can also try passing
>>> the --static-exe flag (to configure.py), in which case the executable is
>>> static and can be relocated without any headaches. This works with
>>> certain compilers.
>>>
>>> Let me know if there are any problems!
>>>
>>> BW, Gabor
>>>
>>> On Nov 8 2011, Ed Pozharski wrote:
>>>
>>>> Could anyone point me towards instructions on how to get/build
>>>> parallelized phaser binary on linux? I searched around but so far found
>>>> nothing. The latest updated phaser binary doesn't seem to be
>>>> parallelized.
>>>> Apologies if this has been resolved before - just point at the relevant
>>>> thread, please.
>>>>
>>>>
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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