<div dir="ltr">Gaeme<div><br></div><div>We were evacuated yesterday ~2pm but the lab is reopened now and the servers are coming on line.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Aug 2, 2017 at 10:29 PM, <span dir="ltr"><<a href="mailto:Graeme.Winter@diamond.ac.uk" target="_blank">Graeme.Winter@diamond.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Rob<br>
<br>
For data processing we are very interested in classic threading because our calculations include the word “if” - we have looked at pushing some of the calculations which do not include if (i.e. summed area tables) and there we get clobbered by the need to push the data of GPU memory also…<br>
<br>
Re: Python3<br>
<br>
Well there is a question. ISTR people have looked (with some success, apparently) at building cctbx with cmake, which could be an alternative to using SCons? Ergo not a p3 blocker (other blockers may exist, ymmv etc)<br>
<br>
Cheers Graeme<br>
<br>
PS - any ideas how long the server outage is likely to last? Appreciate fires are a pretty good reason to take out kit. Not a problem in the UK ATM, flooding more likely :-\<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
<br>
<br>
<br>
> On 2 Aug 2017, at 22:13, Dr. Robert Oeffner <<a href="mailto:rdo20@cam.ac.uk">rdo20@cam.ac.uk</a>> wrote:<br>
><br>
> If efficient threading is desired I would have thought that these days GPUs are all the rage and that it would be worth looking into openCL and CUDA implementations for doing this.<br>
><br>
> On an unrelated note are there any thoughts on moving CCTBX to Python3? One issue, which may not be insurmountable is that SCons does not yet support Python3.<br>
><br>
> Rob<br>
><br>
><br>
><br>
> -----Original Message----- From: <a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.ac.uk</a><br>
> Sent: Tuesday, August 1, 2017 10:16 PM<br>
> To: <a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
> Subject: Re: [cctbxbb] Should we enable boost threads in bootstrap?<br>
><br>
> Lee,<br>
><br>
> End game for us is moving to “proper” threading i.e. lots of threads / cores working on one problem in one address space - be it regular 20 core xeon or 64 core KNL<br>
><br>
> Boost threads came up in conversation today as a C++11 like threading model, so I wondered if it would be a stepping stone...<br>
><br>
> Don’t have this book, maybe should get it….<br>
><br>
> Cheers Graeme<br>
><br>
><br>
><br>
> On 1 Aug 2017, at 18:14, Lee O'Riordan <<a href="mailto:loriordan@lbl.gov">loriordan@lbl.gov</a><mailto:<a href="mailto:loriordan@lbl.gov">lori<wbr>ordan@lbl.gov</a>>> wrote:<br>
><br>
> Graeme, Nigel,<br>
><br>
> I would be a little bit worried about Boost threads when it comes to our KNL port of cctbx. In this instance the use of OpenMP or Intel TBB (at least accordingly to Intel docs) would be optimal over boost threads (or pthreads, etc.)[see Intel Xeon Phi High Performance Programming, KNL edition P155 --- no ebook, sorry]. That being said, there is no way to know unless we try it out first, but it isn't something we can test right now.<br>
><br>
> As for Threads vs MP, this again falls into our KNL port, where threads would be better suited (and become a necessity for optimal performance) when running on high-core count devices. If the OpenMP functionality exists, then maybe this would be a more portable way of taking advantage of all cores/hyperthreads.<br>
><br>
> In this instance I think turning boost threads on for a build-by-build basis would be better, rather than as a default? Though if I am wrong, feel free to correct me.<br>
><br>
> Best,<br>
> Lee.<br>
><br>
> On Tue, Aug 1, 2017 at 9:36 AM, Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov">nwmoriarty@lbl.gov</a><mailto:<a href="mailto:nwmoriarty@lbl.gov">nwm<wbr>oriarty@lbl.gov</a>>> wrote:<br>
> Graeme<br>
><br>
> The short answer is "Why?" but that may start a very long discussion. There are a number of multiprocessing modules in easy_mp that seem to cover all the bases. Are there situations where threading is "better" to multiprocessing?<br>
><br>
> Articles on multiprocessing in cctbx.<br>
><br>
> <a href="https://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6" rel="noreferrer" target="_blank">https://www.phenix-online.org/<wbr>newsletter/CCN_2017_01.pdf#<wbr>page=6</a><br>
><br>
> <a href="https://www.phenix-online.org/newsletter/CCN_2013_07.pdf" rel="noreferrer" target="_blank">https://www.phenix-online.org/<wbr>newsletter/CCN_2013_07.pdf</a><br>
><br>
> <a href="https://www.phenix-online.org/newsletter/CCN_2013_01.pdf" rel="noreferrer" target="_blank">https://www.phenix-online.org/<wbr>newsletter/CCN_2013_01.pdf</a><br>
><br>
><br>
> Cheers<br>
><br>
> Nigel<br>
><br>
> ---<br>
> Nigel W. Moriarty<br>
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging<br>
> Lawrence Berkeley National Laboratory<br>
> Berkeley, CA 94720-8235<br>
> Phone : <a href="tel:510-486-5709" value="+15104865709">510-486-5709</a><tel:(510)%20486-5709> Email : NWMoriarty@LBL.gov<mailto:<a href="mailto:NWMoriarty@LBL.gov">NWMo<wbr>riarty@LBL.gov</a>><br>
> Fax : <a href="tel:510-486-5909" value="+15104865909">510-486-5909</a><tel:(510)%20486-5909> Web : <a href="http://CCI.LBL.gov" rel="noreferrer" target="_blank">CCI.LBL.gov</a><<a href="http://cci.lbl.gov/" rel="noreferrer" target="_blank">http://cci.lbl.<wbr>gov/</a>><br>
><br>
> On Tue, Aug 1, 2017 at 7:54 AM, <<a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.ac.uk</a><<wbr>mailto:<a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.<wbr>ac.uk</a>>> wrote:<br>
> Afternoon all,<br>
><br>
> Should we do this? Any opinions? Could be useful for threads in a semi-portable way...<br>
><br>
> Thanks & cheerio Graeme<br>
><br>
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