<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Randy<div><br></div><div>Many thanks for your feedback and explanations.</div><div>I’ll check the nightly or wait until the next stable. I’ve seen an RC1 recently, meaning the next stable should come soon.</div><div><br></div><div>Best,</div><div>Xavier</div><div><div><div><br><blockquote type="cite"><div>Le 4 juil. 2023 à 17:37, Randy John Read <rjr27@cam.ac.uk> a écrit :</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Hi,</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Thanks for sending the log files!</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">The jobs turn out not actually to be identical. The GUI automatically chose to use the intensity data (which is what we prefer for use in Phaser) whereas your job run from a script is using amplitude data. The issue I alluded to earlier occurs only for intensity data, because the analysis of those data involves applying different equations, which use a special function (tgamma from the Boost library). For some reason I don’t understand, when the Intel version of the tgamma algorithm is computed using the Rosetta functionality to run it on an ARM processor, it’s much much slower than other calculations.</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Just last week (right after I finally got an M2 MacBook Pro), we tracked this down and replaced the calls to Boost tgamma with alternative code, and that problem should exist any more. You can use it already in Phenix by getting a recent nightly build, and I’ve asked the CCP4 people to compile a new version of Phaser and release it as an update to CCP4 as well.</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Best wishes,</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Randy</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">On 4 Jul 2023, at 12:05, Xavier Brazzolotto <<a href="mailto:xbrazzolotto@gmail.com">xbrazzolotto@gmail.com</a>> wrote:<br><br>For information<br><br>Apple M2 running Ventura 13.4.1 with 64 Go memory<br>Phenix 1.20.1-4487 (Intel one).<br><br>I’ve run MR of the same dataset (2.15A - I422) with the same model both with the command line and through the GUI.<br><br>Command line (phenix.phaser) : 48 secs.<br>GUI (Phaser-MR simple one component interface): 18 mins !<br><br>In copy the two log files if this helps<br><br><br><br><blockquote type="cite">Le 4 juil. 2023 à 12:54, Luca Jovine <<a href="mailto:luca.jovine@ki.se">luca.jovine@ki.se</a>> a écrit :<br><br>Hi Xavier and Randy, I'm also experiencing the same on a M2 Mac!<br>-Luca<br><br>-----Original Message-----<br>From: <<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a><span class="Apple-converted-space"> </span><<a href="mailto:phenixbb-bounces@phenix-online.org">mailto:phenixbb-bounces@phenix-online.org</a>>> on behalf of Xavier Brazzolotto <<a href="mailto:xbrazzolotto@gmail.com">xbrazzolotto@gmail.com</a><span class="Apple-converted-space"> </span><<a href="mailto:xbrazzolotto@gmail.com">mailto:xbrazzolotto@gmail.com</a>>><br>Date: Tuesday, 4 July 2023 at 12:38<br>To: Randy John Read <<a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a><span class="Apple-converted-space"> </span><<a href="mailto:rjr27@cam.ac.uk">mailto:rjr27@cam.ac.uk</a>>><br>Cc: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><span class="Apple-converted-space"> </span><<a href="mailto:phenixbb@phenix-online.org">mailto:phenixbb@phenix-online.org</a>>><br>Subject: Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR<br><br><br>Hi Randy,<br><br><br>Indeed I’m running Phenix on a brand new M2 Mac.<br>I will benchmark the two processes (GUI vs command line) and post them here.<br><br><br><blockquote type="cite">Le 4 juil. 2023 à 12:32, Randy John Read <<a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a><span class="Apple-converted-space"> </span><<a href="mailto:rjr27@cam.ac.uk">mailto:rjr27@cam.ac.uk</a>>> a écrit :<br><br>Hi Xavier,<br><br>We haven’t noticed that, or at least any effect is small enough not to stand out. There shouldn’t be a lot of overhead in communicating with the GUI (i.e. updating the terse log output and the graphs) but if there is we should look into it and see if we can do something about it.<br><br>Could you tell me how much longer (say, in percentage terms) a job takes when you run it through the GUI compared to running the same job outside the GUI on the same computer? Also, it’s possible the architecture matters so could you say which type of computer and operating system you’re using? If it’s a Mac, is it one with an Intel processor or an ARM (M1 or M2) processor? (By the way, we finally managed to track down and fix an issue that cause Phaser to run really slowly on an M1 or M2 Mac when using the version compiled for Intel, once I got my hands on a new Mac.)<br><br>Best wishes,<br><br>Randy<br><br><blockquote type="cite">On 4 Jul 2023, at 10:44, Xavier Brazzolotto <<a href="mailto:xbrazzolotto@gmail.com">xbrazzolotto@gmail.com</a><span class="Apple-converted-space"> </span><<a href="mailto:xbrazzolotto@gmail.com">mailto:xbrazzolotto@gmail.com</a>>> wrote:<br><br>Dear Phenix users<br><br>I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser).<br><br>Did you also observe such behavior?<br><br>Best<br>Xavier<br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><span class="Apple-converted-space"> </span><<a href="mailto:phenixbb@phenix-online.org">mailto:phenixbb@phenix-online.org</a>><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><span class="Apple-converted-space"> </span><<a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>><br>Unsubscribe:<span class="Apple-converted-space"> </span><a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a><span class="Apple-converted-space"> </span><<a href="mailto:phenixbb-leave@phenix-online.org">mailto:phenixbb-leave@phenix-online.org</a>><br></blockquote><br><br>-----<br>Randy J. Read<br>Department of Haematology, University of Cambridge<br>Cambridge Institute for Medical Research Tel: +44 1223 336500<br>The Keith Peters Building<br>Hills Road E-mail:<span class="Apple-converted-space"> </span><a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a><span class="Apple-converted-space"> </span><<a href="mailto:rjr27@cam.ac.uk">mailto:rjr27@cam.ac.uk</a>><br>Cambridge CB2 0XY, U.K.<span class="Apple-converted-space"> </span><a href="http://www-structmed.cimr.cam.ac.uk/">www-structmed.cimr.cam.ac.uk</a><br><br></blockquote><br><br><br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><span class="Apple-converted-space"> </span><<a href="mailto:phenixbb@phenix-online.org">mailto:phenixbb@phenix-online.org</a>><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><span class="Apple-converted-space"> </span><<a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>><br>Unsubscribe:<span class="Apple-converted-space"> </span><a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a><span class="Apple-converted-space"> </span><<a href="mailto:phenixbb-leave@phenix-online.org">mailto:phenixbb-leave@phenix-online.org</a>><br><br><br><br>När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<<a href="https://ki.se/medarbetare/integritetsskyddspolicy">https://ki.se/medarbetare/integritetsskyddspolicy</a>>.<br><br><br>Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<<a href="https://ki.se/en/staff/data-protection-policy">https://ki.se/en/staff/data-protection-policy</a>>.<br></blockquote><br><command_line_PHASER.log><GUI_phaser.log><br></blockquote><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">-----</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Randy J. Read</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Department of Haematology, University of Cambridge</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Cambridge Institute for Medical Research Tel: +44 1223 336500</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">The Keith Peters Building</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Hills Road E-mail:<span class="Apple-converted-space"> </span></span><a href="mailto:rjr27@cam.ac.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">rjr27@cam.ac.uk</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;">Cambridge CB2 0XY, U.K. </span><a href="http://www-structmed.cimr.cam.ac.uk/" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">www-structmed.cimr.cam.ac.uk</a></div></blockquote></div><br></div></div></body></html>