Re: [ccp4bb] phaser openmp
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 RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] phaser openmp
Le Tue, 8 Nov 2011 16:25:22 -0800, Nat Echols nathaniel.ech...@gmail.com a écrit : On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger beren...@riken.jp wrote: In the past I have been quite badly surprised by the no-acceleration I gained when using OpenMP with some of my programs... :( You need big parallel jobs and avoid synchronisations, barriers or this kind of things. Using data reduction is much more efficient. It's working very well for structure factors calculations for exemple. Amdahl's law is cruel: http://en.wikipedia.org/wiki/Amdahl's_law You can have much less than 5% of serial code. I have more problems with L2 misse cache events and memory bandwidth. A quad cores means 4 times the bandwidth necessary for a single process... If your code is already a bit greedy, the scale up is not good. Pascal
Re: [ccp4bb] phaser openmp
On 11/09/2011 07:21 PM, Pascal wrote: Le Tue, 8 Nov 2011 16:25:22 -0800, Nat Echolsnathaniel.ech...@gmail.com a écrit : On Tue, Nov 8, 2011 at 4:22 PM, Francois Berengerberen...@riken.jp wrote: In the past I have been quite badly surprised by the no-acceleration I gained when using OpenMP with some of my programs... :( You need big parallel jobs and avoid synchronisations, barriers or this kind of things. Using data reduction is much more efficient. It's working very well for structure factors calculations for exemple. Amdahl's law is cruel: http://en.wikipedia.org/wiki/Amdahl's_law You can have much less than 5% of serial code. I have more problems with L2 misse cache events and memory bandwidth. A quad cores means 4 times the bandwidth necessary for a single process... If your code is already a bit greedy, the scale up is not good. I never went down to this level of optimization. Are you using valgrind to detect cache miss events? After gprof, usually I am done with optimization. I would prefer to change my algorithm and would be afraid of introducing optimizations that are architecture-dependent into my software. Regards, F.
[ccp4bb] [gsheldr: Re: [ccp4bb] phaser openmp]
-- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 ---BeginMessage--- In my experience, writing efficient multithreaded code is much harder than writing efficient single-thread code, and some algorithms scale up much better than others. It is important to avoid cache misses, but because each CPU has its own cache, on rare occasions it is possible to scale up by more than the number of CPUs, because by dividing up the memory the number of cache misses can be reduced. In the case of the multi-CPU version of SHELXD (part of the current beta-test, available on email request) I was able - with some effort - to keep the effects of Amdahl's law within limits (on a 32 CPU machine it is about 29 times faster than with one CPU). George On Wed, Nov 09, 2011 at 11:21:11AM +0100, Pascal wrote: Le Tue, 8 Nov 2011 16:25:22 -0800, Nat Echols nathaniel.ech...@gmail.com a écrit : On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger beren...@riken.jp wrote: In the past I have been quite badly surprised by the no-acceleration I gained when using OpenMP with some of my programs... :( You need big parallel jobs and avoid synchronisations, barriers or this kind of things. Using data reduction is much more efficient. It's working very well for structure factors calculations for exemple. Amdahl's law is cruel: http://en.wikipedia.org/wiki/Amdahl's_law You can have much less than 5% of serial code. I have more problems with L2 misse cache events and memory bandwidth. A quad cores means 4 times the bandwidth necessary for a single process... If your code is already a bit greedy, the scale up is not good. Pascal -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 ---End Message---
[ccp4bb] Refmac 5.6 and Twin operator
Hi All, Is it possible to define twin operator and twin fraction in the latest version of Refmac (i.e., in version 5.6.0117) ? I tried to define these two keywords in Buccaneer but it fails with an error message Refmac_5.6.0117: Problem in some of the instructions. Please help me to fix this. Many thanks, -Kiran
Re: [ccp4bb] RFI on access to digital data
On Tue, 8 Nov 2011, Gerard DVD Kleywegt wrote: Relevant to the discussion about archiving image data: http://federalregister.gov/a/2011-28621 Interesting that it quotes MIAME (minimum information about a microarray experiment) as an example of community-driven standardisation. When MIAME was being formulated, it drew in part, and learned from, the history of the PDB. It is also a field where (I am told) the raw data really are useless without metadata about the experiment. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
[ccp4bb] small molecule crystal data collection
Dear All, I have a small molecule single crystal. I want to solve its structure by x-ray diffraction. Could you please teach me how to collect the diffraction data? I have some experience with protein crystals. But it's the first time for small molecule. I don't how to set the parameters, like oscillating angle. And are there any key points I should pay special attention to? Thanks in advance! Pengfei
Re: [ccp4bb] RFI on access to digital data
I also found this interesting: http://www.datadryad.org/ Ashley. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Keller [pkel...@globalphasing.com] Sent: Wednesday, November 09, 2011 8:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] RFI on access to digital data On Tue, 8 Nov 2011, Gerard DVD Kleywegt wrote: Relevant to the discussion about archiving image data: http://federalregister.gov/a/2011-28621 Interesting that it quotes MIAME (minimum information about a microarray experiment) as an example of community-driven standardisation. When MIAME was being formulated, it drew in part, and learned from, the history of the PDB. It is also a field where (I am told) the raw data really are useless without metadata about the experiment. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
[ccp4bb] 回复:[ccp4bb] small molecule crystal data collection
Thank everyone for trying to help me! I am going to synchrotron. As Bernie said, I will try to use the closest distance, and 5-10deg. Thanks again! Pengfei On 11/9/11 5:13 PM, Santarsiero, Bernard D. b...@uic.edu wrote: You can collect 5-10deg images, and go ahead and collect 360deg. I usually use 1-3 seconds exposures, depending on the diffraction. The detector is set as close as possible, to get data to 0.8-0.9A resolution. For a MAR CCD 300mm detector, that's around 90-100mm, with the wavelength set at 0.8A, or around 15.5KeV in energy. You can process it with HKL2000 or XDS easily. Bernie On 11/9/11 7:36 PM, Xiaopeng Hu huxp...@mail.sysu.edu.cn wrote: X-ray machine designed for protein usually is not good for small molecule. Just go find a chemistry department/school, they can do it for you in one day. On 11/9/11 5:15 PM, Kris Tesh kris.t...@att.net wrote: Pengfei, The first thing to consider is what system you have and is it capable of collecting data to high enough resolution. So, what data collection system is available? Kris Kris F. Tesh, Ph. D. Department of Biology and Biochemistry University of Houston On Wed, November 9, 2011 3:28 pm, Pengfei Fang wrote: Dear All, I have a small molecule single crystal. I want to solve its structure by x-ray diffraction. Could you please teach me how to collect the diffraction data? I have some experience with protein crystals. But it's the first time for small molecule. I don't how to set the parameters, like oscillating angle. And are there any key points I should pay special attention to? Thanks in advance! Pengfei -- Bernard D. Santarsiero Research Professor Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds
