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

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 a écrit :

Hi Xavier and Randy, I'm also experiencing the same on a M2 Mac! -Luca

-----Original Message----- From: mailto:[email protected]> on behalf of Xavier Brazzolotto mailto:[email protected]> Date: Tuesday, 4 July 2023 at 12:38 To: Randy John Read mailto:[email protected]> Cc: PHENIX user mailing list mailto:[email protected]> 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 mailto:[email protected]> 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 mailto:[email protected]> 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 [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

----- 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: [email protected] mailto:[email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

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 personuppgifterhttps://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 herehttps://ki.se/en/staff/data-protection-policy.