[ccp4bb] Clear Linux
Dear Program devs and enthusiasts, After seeing James' email (on dismal CPU performance), I was searching for various ideas and found the so-called "Clear Linux Project". Seems " function multi-version patch" leads to significant improvements. Though I could install the precompiled binary of CCP4 and phenix without any issues but there are no improvements to runtime as FMV needs 'patching' and compiling. Could DIALS, CCP4 or Phenix programmers see if this is useful/possible? Has anyone tried it? https://clearlinux.org/documentation/clear-linux/tutorials/fmv https://www.phoronix.com/scan.php?page=article=clear-faster-blas=1 Best regards, Karthik Paithankar On 30/11/2018, James Holton < > wrote: > I have a dissenting opinion about computers "moving on a bit". At least > when it comes to most crystallography software. > > Back in the late 20th century I defined some benchmarks for common > crystallographic programs with the aim of deciding which hardware to > buy. By about 2003 the champion of my refmac benchmark > (https://bl831.als.lbl.gov/~jamesh/benchmarks/index.html#refmac) was the > new (at the time) AMD "Opteron" at 1.4 GHz. That ran in 74 seconds. > > Last year, I bought a rather expensive 4-socket Intel Xeon E7-8870 v3 > (turbos to 3.0 GHz), which is the current champion of my XDS benchmark. > The same old refmac benchmark on this new machine, however, runs in 68.6 > seconds. Only a smidge faster than that old Opteron (which I threw away > years ago). To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] images
May be wwPDB should introduce a clause that all structure depositions (upon release) must allow raw images accessible to anyone upon request provided the requester pays (for postage and/or CD/DVD - if applicable). This may be followed until google/NSA will offer free and _reliable_ storage in a neighbouring planet forever. AFAIK, GPL based software agreements work like this. Karthik Bernhard Rupp wrote: Maybe I was misunderstood. There is no doubt in my opinion and that of those that have put effort into image conservation issues years ago that keeping and archiving the images is more than desirable, for precisely the reasons mentioned. Nail my nauseating spell checker for the nausea that may have caused you. Cheers, BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Gerard Bricogne Sent: Wednesday, March 18, 2009 11:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Dear Bernhard, I suppose you meant ad nauseam ;-) . In any case, what is the use of discussions and recommendations that are not followed by action, and only result in making their contributors themselves nauseated to the point of wanting to put this to rest? As Ethan has nicely stated in his reply to Garib's double-check of whether we do need images, this matter should NOT be put to rest: it should be dealt with. As was argued at the end of the paper by Joosten, Womack et al. (Acta Cryst. D65, 176-185), the main advantage of depositing images would be that it would enable and stimulate the further developement and testing of image integration and data processing software, to the same degree that the deposition of structure factors has stimulated progress and testing for structure refinement software. Far from a boring issue only capable of giving headaches to Standards Committee members, this is a vital issue: with each undeposited set of images that contributed in one way or another to the determination or refinement of a deposited structure, there disappears an opportunity to test improvements in methods and software that would be likely to improve that deposited entry (and most others) at a future stage. I think we need to take a long view on this, and abandon the picture of the PDB as a static archive of frozen results: instead, it should be seen as a repository of what is required not only to validate/authenticate the deposited models, but to feed the continued improvement of the methods used - and hence, at the next iteration, the constant revision and improvement of those very models. In what way can this topic be a source of nausea? With best wishes, Gerard. -- On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: As Herb will attest, the need for keeping images and the various reasons for it have been discussed ad nauseum and agreed upon in various imgCIF meetings - I am sure Herb or Andy Howard can provide links to the documents/recommendations, to put this to rest. Best, BR Past ACA Data Standards Committee serf -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay Diederichs Sent: Wednesday, March 18, 2009 10:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images
[ccp4bb] Announcement: TotalCryst school in Grenoble, April 1 -3, 2009
TotalCryst is a universal methodology for crystallographic structure solution and refinements of arbitrary polycrystals and powders. The method determines the molecular arrangement within each grain. It applies to simple inorganic structures as well as to large macromolecules and it attempts to probe grains on all scales from 100 nm to 1 mm. The 3-day School aims at explaining the TotalCryst methods and demonstrating the software packages. There is even an option to work on personal data, provided contact is made to organizers beforehand. Location: ESRF, Grenoble, FRANCE Dates:April 1 -3, 2009 Participants: Students (ECTS points given), users, software developers and beamline scientists are welcome Registration and further information: www.totalcryst.dk or henning.sorensen @ risoe . dk Sponsors: EU 6th Framework program, ESRF, Danish National Research Foundation Regards, -Karthik
Re: [ccp4bb] Crystallographic computing platform recommendations?
Hi 1. Mac vs. Linux (which flavor?) vs. Windows Ubuntu - just works(TM). Gentoo - install only if know vi :-) 2. Graphics cards any NV quadro series. Buy at least one year old card so that linux will have drivers. Intel integrated cards also work well and have good drivers (Coot/ono shows good performance if you have 1.5GB system RAM). 3. Displays Budget dependent. 4. Processors - multiple processors, multiple cores? Speed? I would suggest a quad core Xeon or Opteron (with Debian - you need rock solid) that will be a workhorse (where I put images also) to do refinement jobs that users can ssh -X into. make sure the directories in the remote machine are available for exports via NFS/autofs. For local workstations (use ubuntu to get the bling) any AMD/Intel Core2 series would be OK (that way my office would be quiet and cool). Even I can hibernate to save power. Regards, Karthik About half of what I do involves ~1.0 A X-ray structures - data processing, rebuilding in Coot, refinement, and so forth - so my current desktop (Optiplex GX745, Radeon X1300) machine drags on graphics sometimes. I don't seem to need stereo these days, for what it's worth. Anybody have suggestions or specs they'd like to share? Thanks in anticipation of your advice. Regards, Anna Gardberg My workstations and data servers: 1. Linux (Fedora Core 8, currently, as this distro is well supported in xtallography circles--I'm tempted to try Ubuntu next upgrade cycle) 2. If stereo is not an issue, any 8000 or 9000 series GeForce NVidia card is fine. I avoid ATI because of flaky Linux drivers. The 9600GT Nvidia is a bargain, but an 8600 is OK, too. 3. I use a 24 Samsung LCD display. You need CRTs only if doing stereo, but then you would need a really expensive Quadro card with stereo outputs. 4. Quad cores are so cheap right now, there is no reason not to go this route. I built my workstations from really cheap Intel DG35EC boards with Intel Q9300 processors. 250Gbyte drive for the OS and programs, and a 400 Gbyte drive for data, all SATA-300. I loaded up with a memory card reader, SATA DVD-writer, and packaged it all up in a tiny cubical micro-ATX box. You can build the whole workstation for under $1500, including the LCD monitor. My data and backup servers are installed on junk machines salvaged from offices and labs. Anything with a Pentium 4 is fast enough to be a data or backup server. The nice thing about building your own computer is when it comes time for an upgrade, you can save many of the parts (case, power supply, DVD writer, etc.) and just upgrade the motherboard, CPU, and maybe the hard drives.
