[phenixbb] Discrepancy between Phenix GUI and command line for MR

[Luca Jovine]

Thank you for the info Randy,

I confirm that in the last available nightly build (1.21rc1-5015) the issue is clearly fixed, resulting in a >70-fold speed increase compared to Phaser-MR from 1.21rc1-5008. For two sample jobs using intensity data on a M2 MacBook Pro:

1.21rc1-5008:
------------------
Job 1: CPU Time: 0 days 0 hrs 37 mins 23.01 secs (   2243.01 secs)
Job 2: CPU Time: 0 days 0 hrs 31 mins 10.79 secs (   1870.79 secs)

1.21rc1-5015:
-------------------
Job 1: CPU Time: 0 days 0 hrs 0 mins 31.13 secs (     31.13 secs)
Job 2: CPU Time: 0 days 0 hrs 0 mins 25.44 secs (     25.44 secs)

...thanks for the fix!!

Luca

-----Original Message-----
From: Randy John Read <rjr27 at cam.ac.uk <mailto:rjr27 at cam.ac.uk>>
Date: Tuesday, 4 July 2023 at 17:37
To: Xavier Brazzolotto <xbrazzolotto at gmail.com <mailto:xbrazzolotto at gmail.com>>
Cc: PHENIX user mailing list <phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>>, Luca Jovine <luca.jovine at ki.se <mailto:luca.jovine at ki.se>>
Subject: Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR


Hi,


Thanks for sending the log files!


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.


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.


Best wishes,


Randy


> On 4 Jul 2023, at 12:05, Xavier Brazzolotto <xbrazzolotto at gmail.com <mailto:xbrazzolotto at gmail.com>> wrote:
>
> For information
>
> Apple M2 running Ventura 13.4.1 with 64 Go memory
> Phenix 1.20.1-4487 (Intel one).
>
> I’ve run MR of the same dataset (2.15A - I422) with the same model both with the command line and through the GUI.
>
> Command line (phenix.phaser) : 48 secs.
> GUI (Phaser-MR simple one component interface): 18 mins !
>
> In copy the two log files if this helps
>
>
>
> > Le 4 juil. 2023 à 12:54, Luca Jovine <luca.jovine at ki.se <mailto:luca.jovine at ki.se>> a écrit :
> >
> > Hi Xavier and Randy, I'm also experiencing the same on a M2 Mac!
> > -Luca
> >
> > -----Original Message-----
> > From: <phenixbb-bounces at phenix-online.org <mailto:phenixbb-bounces at phenix-online.org> <mailto:phenixbb-bounces at phenix-online.org <mailto:phenixbb-bounces at phenix-online.org>>> on behalf of Xavier Brazzolotto <xbrazzolotto at gmail.com <mailto:xbrazzolotto at gmail.com> <mailto:xbrazzolotto at gmail.com <mailto:xbrazzolotto at gmail.com>>>
> > Date: Tuesday, 4 July 2023 at 12:38
> > To: Randy John Read <rjr27 at cam.ac.uk <mailto:rjr27 at cam.ac.uk> <mailto:rjr27 at cam.ac.uk <mailto:rjr27 at cam.ac.uk>>>
> > Cc: PHENIX user mailing list <phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org> <mailto:phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>>>
> > Subject: Re: [phenixbb] Discrepancy between Phenix GUI and command line for MR
> >
> >
> > Hi Randy,
> >
> >
> > Indeed I’m running Phenix on a brand new M2 Mac.
> > I will benchmark the two processes (GUI vs command line) and post them here.
> >
> >
> >> Le 4 juil. 2023 à 12:32, Randy John Read <rjr27 at cam.ac.uk <mailto:rjr27 at cam.ac.uk> <mailto:rjr27 at cam.ac.uk <mailto:rjr27 at cam.ac.uk>>> a écrit :
> >>
> >> Hi Xavier,
> >>
> >> 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.
> >>
> >> 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.)
> >>
> >> Best wishes,
> >>
> >> Randy
> >>
> >>> On 4 Jul 2023, at 10:44, Xavier Brazzolotto <xbrazzolotto at gmail.com <mailto:xbrazzolotto at gmail.com> <mailto:xbrazzolotto at gmail.com <mailto:xbrazzolotto at gmail.com>>> wrote:
> >>>
> >>> Dear Phenix users
> >>>
> >>> I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser).
> >>>
> >>> Did you also observe such behavior?
> >>>
> >>> Best
> >>> Xavier
> >>> _______________________________________________
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> >>
> >>
> >> -----
> >> Randy J. Read
> >> Department of Haematology, University of Cambridge
> >> Cambridge Institute for Medical Research Tel: +44 1223 336500
> >> The Keith Peters Building
> >> Hills Road E-mail: rjr27 at cam.ac.uk <mailto:rjr27 at cam.ac.uk> <mailto:rjr27 at cam.ac.uk <mailto:rjr27 at cam.ac.uk>>
> >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
> >>
> >
> >
> >
> >
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> >
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>
> <command_line_PHASER.log><GUI_phaser.log>


-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building
Hills Road E-mail: rjr27 at cam.ac.uk <mailto:rjr27 at cam.ac.uk>
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk