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

[Xavier Brazzolotto]

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: command_line_PHASER.log
Type: application/octet-stream
Size: 37556 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20230704/9c615ddb/attachment-0001.dms>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: GUI_phaser.log
Type: application/octet-stream
Size: 37648 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20230704/9c615ddb/attachment-0001.a>
-------------- next part --------------


> Le 4 juil. 2023 à 12:54, Luca Jovine <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>> on behalf of Xavier Brazzolotto <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>>
> Cc: PHENIX user mailing list <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>> 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>> 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
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>>> http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb>
>>> Unsubscribe: phenixbb-leave at phenix-online.org <mailto:phenixbb-leave at phenix-online.org>
>> 
>> 
>> -----
>> 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
>> 
> 
> 
> 
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb>
> Unsubscribe: phenixbb-leave at phenix-online.org <mailto:phenixbb-leave at phenix-online.org>
> 
> 
> 
> 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<https://ki.se/medarbetare/integritetsskyddspolicy>.
> 
> 
> 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<https://ki.se/en/staff/data-protection-policy>.