Discrepancy between Phenix GUI and command line for MR

older
General interest, education article

Xavier Brazzolotto

4 Jul 2023 4 Jul '23

9:44 a.m.

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

Show replies by date

Randy John Read

4 Jul 4 Jul

10:32 a.m.

New subject: Discrepancy between Phenix GUI and command line for MR

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 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] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [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] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

Xavier Brazzolotto

10:37 a.m.

New subject: 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 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 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] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [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] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

Luca Jovine

10:54 a.m.

New subject: Discrepancy between Phenix GUI and command line for MR

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.

Xavier Brazzolotto

11:05 a.m.

New subject: 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.

Randy John Read

3:37 p.m.

New subject: 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 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 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.

Xavier Brazzolotto

3:46 p.m.

New subject: Discrepancy between Phenix GUI and command line for MR

Hi Randy Many thanks for your feedback and explanations. I’ll check the nightly or wait until the next stable. I’ve seen an RC1 recently, meaning the next stable should come soon. Best, Xavier

...

Le 4 juil. 2023 à 17:37, Randy John Read a écrit :

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 mailto:[email protected]> 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 mailto:[email protected]> a écrit :

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

-----Original Message----- From: mailto:[email protected] mailto:[email protected]> on behalf of Xavier Brazzolotto mailto:[email protected] mailto:[email protected]> Date: Tuesday, 4 July 2023 at 12:38 To: Randy John Read mailto:[email protected] mailto:[email protected]> Cc: PHENIX user mailing list mailto:[email protected] 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] 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] 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] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[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] mailto:[email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/

_______________________________________________ phenixbb mailing list [email protected] mailto:[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] 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.

----- 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 http://www-structmed.cimr.cam.ac.uk/

Luca Jovine

8:02 p.m.

New subject: Discrepancy between Phenix GUI and command line for MR

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 mailto:[email protected]> Date: Tuesday, 4 July 2023 at 17:37 To: Xavier Brazzolotto mailto:[email protected]> Cc: PHENIX user mailing list mailto:[email protected]>, Luca Jovine mailto:[email protected]> 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 mailto:[email protected]> 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 mailto:[email protected]> a écrit :

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

-----Original Message----- From: mailto:[email protected] mailto:[email protected]>> on behalf of Xavier Brazzolotto mailto:[email protected] mailto:[email protected]>> Date: Tuesday, 4 July 2023 at 12:38 To: Randy John Read mailto:[email protected] mailto:[email protected]>> Cc: PHENIX user mailing list mailto:[email protected] 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] 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] 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] mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb; Unsubscribe: [email protected] mailto:[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] mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb; Unsubscribe: [email protected] mailto:[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 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 herehttps://ki.se/en/staff/data-protection-policy https://ki.se/en/staff/data-protection-policy>.

----- 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

Randy John Read

9:17 p.m.

New subject: Discrepancy between Phenix GUI and command line for MR

Fantastic! Sorry it took so long to get my hands on an ARM-based Mac since the first reports of problems! ---- Randy J. Read

...

On 4 Jul 2023, at 21:02, Luca Jovine wrote:

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 mailto:[email protected]> Date: Tuesday, 4 July 2023 at 17:37 To: Xavier Brazzolotto mailto:[email protected]> Cc: PHENIX user mailing list mailto:[email protected]>, Luca Jovine mailto:[email protected]> 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 mailto:[email protected]> 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 mailto:[email protected]> a écrit :

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

-----Original Message----- From: mailto:[email protected] mailto:[email protected]>> on behalf of Xavier Brazzolotto mailto:[email protected] mailto:[email protected]>> Date: Tuesday, 4 July 2023 at 12:38 To: Randy John Read mailto:[email protected] mailto:[email protected]>> Cc: PHENIX user mailing list mailto:[email protected] 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.

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Le 4 juil. 2023 à 12:32, Randy John Read mailto:[email protected] 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

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On 4 Jul 2023, at 10:44, Xavier Brazzolotto mailto:[email protected] 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] mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb; Unsubscribe: [email protected] mailto:[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] mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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

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

Xavier Brazzolotto

5 Jul 5 Jul

5:41 a.m.

New subject: Phenix 1.21rc1-5015 Refinement issue on Apple M2

Dear Phenix users, Following the slow Molecular Replacement issue in the last stable version 1.20.1-4487 on Apple M2, I’ve tried the last Nightly (1.21rc-5015). Under the GUI, the MR went OK (as fast as before), but when I try to launch a Refinement (Rigid Body) after the MR, Phenix goes into an error : "Multiple equally suitable arrays of observed xray data found. » If I launch the previous version (1.20.1-4487) I am still able to launch the rigid body refinement from the MR results without any issues. I includes the log file if this helps. Cheers Xavier

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Le 4 juil. 2023 à 23:17, Randy John Read a écrit :

Fantastic! Sorry it took so long to get my hands on an ARM-based Mac since the first reports of problems!

---- Randy J. Read

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On 4 Jul 2023, at 21:02, Luca Jovine wrote:

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 mailto:[email protected]> Date: Tuesday, 4 July 2023 at 17:37 To: Xavier Brazzolotto mailto:[email protected]> Cc: PHENIX user mailing list mailto:[email protected]>, Luca Jovine mailto:[email protected]> 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

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On 4 Jul 2023, at 12:05, Xavier Brazzolotto mailto:[email protected]> 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

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Le 4 juil. 2023 à 12:54, Luca Jovine mailto:[email protected]> a écrit :

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

-----Original Message----- From: mailto:[email protected] mailto:[email protected]>> on behalf of Xavier Brazzolotto mailto:[email protected] mailto:[email protected]>> Date: Tuesday, 4 July 2023 at 12:38 To: Randy John Read mailto:[email protected] mailto:[email protected]>> Cc: PHENIX user mailing list mailto:[email protected] 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] 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] 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] mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb; Unsubscribe: [email protected] mailto:[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] mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb http://phenix-online.org/mailman/listinfo/phenixbb; Unsubscribe: [email protected] mailto:[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 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 herehttps://ki.se/en/staff/data-protection-policy https://ki.se/en/staff/data-protection-policy>.

----- 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

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Luca Jovine
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Discrepancy between Phenix GUI and command line for MR

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