Re: [ccp4bb] CCP4i under M1Pro

[Billy Poon]

Hi everyone,

As a workaround for phaser, I compiled an Apple Silicon version of phaser
with Xcode 13.4.1 and statically linked any non-system libraries. In your
Phenix installation, you can replace

/build/phaser/exe/phaser

with the file from the link.

https://drive.google.com/file/d/1fC4EXMulueJEwKmKBpACwlFTpL21pBvZ/view?usp=sharing

The link should allow access for anyone with the link. To get around the
security warnings from macOS, you will need to clear the
extended attributes for the download

xattr -c phaser

and make the file executable

chmod +x phaser

Also, because this file is for Apple Silicon, the minimum macOS version is
11 (Big Sur).

I tested it locally with a Phenix 1.20.1-4487 installation on my M1 Macbook
Pro and the speed is much better than the phaser executable built for Intel.

Also, for Phenix, OpenMP is not currently enabled for our macOS builds, but
we will be enabling it for the next release since the installers will be
using the compiler for building conda packages. Essentially, we will be
building Phenix the same way we are currently building the cctbx conda
packages for different architectures and different Python versions (
https://anaconda.org/conda-forge/cctbx-base).

Let me know if the file does not work. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Fax: (510) 486-5909
Web: https://phenix-online.org


On Wed, Jun 29, 2022 at 8:34 AM Lau Kelvin <
5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote:

> Thanks for everyone’s responses
>
> I just want to add its not limited to Phaser on my end (either implemented
> through CCP4 or Phenix), but also certain refinement programs Phenix.refine
> (even when telling it to use 8 processors, seems like its only using 1)
>
> For Coot1, it is known issue I believe.
>
> For earlier Coot versions, it is fine for me, but I feel it is a bit laggy
> too.
>
>
> --
> Kelvin Lau
> Protein production and structure core facility - PTPSP
> EPFL SV PTECH PTPSP
> AI 2146 (Bâtiment AI)
> Station 19
> CH-1015 Lausanne
> Switzerland
> Email: kelvin@epfl.ch 
> Phone: +41 21 69 34494
>
> On 29 Jun 2022, at 10:48, Charles Ballard - STFC UKRI <
> 78bb5c0443c5-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> That openmp is not functioning is an issue that I will investigate.  It
> should be, so something is wrong.  Mostly I find that Sophos is sitting
> there using 2 cores, and much of my IO.
>
> Charles
>
>
> *From: *CCP4 bulletin board  on behalf of Randy
> John Read 
> *Date: *Tuesday, 28 June 2022 at 20:16
> *To: *ccp4bb 
> *Subject: *Re: [ccp4bb] CCP4i under M1Pro
> We don’t have any computers with Apple silicon in our group yet to test
> Phaser on ourselves. When preparing the Phenix distribution, Billy Poon has
> run tests and when Phaser is compiled for Intel and run through Rosetta 2,
> it’s generally faster than on a recent Intel Mac. However, there have been
> reports from Phenix users of severe slowdowns, and we don’t understand what
> the special circumstances are that cause it to slow down on specific jobs.
>
> The best performance is when it’s compiled natively for the M1 processor,
> and I believe both Phenix and CCP4 are aiming to distribute
> natively-compiled software as soon as technical complications are worked
> out. So hopefully this is just temporary!
>
> I hadn’t realised that the OpenMP wasn’t enabled on CCP4. In Phenix, there
> were issues preventing the use of OpenMP with Python2, but those should go
> away when the Python3 version is ready to deploy.
>
> Best wishes,
>
> Randy Read
>
> > On 28 Jun 2022, at 16:45, Lau Kelvin <
> 5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Hello
> >
> > I have noticed running normal programs like Phaser MR on a MacBook Pro
> (M1Pro) that jobs are extremely slow compared to my older computers.
> >
> > It doesn’t seem to be running over multiple CPUs anymore.
> >
> > Has this also been seen by others?
> >
> > Best
> >
> > Kelvin
> >
> >
> > --
> > Kelvin Lau
> > Protein production and structure core facility - PTPSP
> > EPFL SV PTECH PTPSP
> > AI 2146 (Bâtiment AI)
> > Station 19
> > CH-1015 Lausanne
> > Switzerland
> > Email: kelvin@epfl.ch 
> > Phone: +41 21 69 34494
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 

Re: [ccp4bb] CCP4i under M1Pro

[Lau Kelvin]

Thanks for everyone’s responses

I just want to add its not limited to Phaser on my end (either implemented 
through CCP4 or Phenix), but also certain refinement programs Phenix.refine 
(even when telling it to use 8 processors, seems like its only using 1)

For Coot1, it is known issue I believe.

For earlier Coot versions, it is fine for me, but I feel it is a bit laggy too.


--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin@epfl.ch<mailto:kelvin@epfl.ch>
Phone: +41 21 69 34494

On 29 Jun 2022, at 10:48, Charles Ballard - STFC UKRI 
<78bb5c0443c5-dmarc-requ...@jiscmail.ac.uk<mailto:78bb5c0443c5-dmarc-requ...@jiscmail.ac.uk>>
 wrote:

That openmp is not functioning is an issue that I will investigate.  It should 
be, so something is wrong.  Mostly I find that Sophos is sitting there using 2 
cores, and much of my IO.

Charles

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Randy John Read mailto:rj...@cam.ac.uk>>
Date: Tuesday, 28 June 2022 at 20:16
To: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] CCP4i under M1Pro
We don’t have any computers with Apple silicon in our group yet to test Phaser 
on ourselves. When preparing the Phenix distribution, Billy Poon has run tests 
and when Phaser is compiled for Intel and run through Rosetta 2, it’s generally 
faster than on a recent Intel Mac. However, there have been reports from Phenix 
users of severe slowdowns, and we don’t understand what the special 
circumstances are that cause it to slow down on specific jobs.

The best performance is when it’s compiled natively for the M1 processor, and I 
believe both Phenix and CCP4 are aiming to distribute natively-compiled 
software as soon as technical complications are worked out. So hopefully this 
is just temporary!

I hadn’t realised that the OpenMP wasn’t enabled on CCP4. In Phenix, there were 
issues preventing the use of OpenMP with Python2, but those should go away when 
the Python3 version is ready to deploy.

Best wishes,

Randy Read

> On 28 Jun 2022, at 16:45, Lau Kelvin 
> <5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk<mailto:5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk>>
>  wrote:
>
> Hello
>
> I have noticed running normal programs like Phaser MR on a MacBook Pro 
> (M1Pro) that jobs are extremely slow compared to my older computers.
>
> It doesn’t seem to be running over multiple CPUs anymore.
>
> Has this also been seen by others?
>
> Best
>
> Kelvin
>
>
> --
> Kelvin Lau
> Protein production and structure core facility - PTPSP
> EPFL SV PTECH PTPSP
> AI 2146 (Bâtiment AI)
> Station 19
> CH-1015 Lausanne
> Switzerland
> Email: kelvin@epfl.ch<mailto:kelvin@epfl.ch>
> Phone: +41 21 69 34494
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk<mailto:rj...@cam.ac.uk>
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk<http://www-structmed.cimr.cam.ac.uk>




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Re: [ccp4bb] CCP4i under M1Pro

[Charles Ballard - STFC UKRI]

That openmp is not functioning is an issue that I will investigate.  It should 
be, so something is wrong.  Mostly I find that Sophos is sitting there using 2 
cores, and much of my IO.

Charles

From: CCP4 bulletin board  on behalf of Randy John Read 

Date: Tuesday, 28 June 2022 at 20:16
To: ccp4bb 
Subject: Re: [ccp4bb] CCP4i under M1Pro
We don’t have any computers with Apple silicon in our group yet to test Phaser 
on ourselves. When preparing the Phenix distribution, Billy Poon has run tests 
and when Phaser is compiled for Intel and run through Rosetta 2, it’s generally 
faster than on a recent Intel Mac. However, there have been reports from Phenix 
users of severe slowdowns, and we don’t understand what the special 
circumstances are that cause it to slow down on specific jobs.

The best performance is when it’s compiled natively for the M1 processor, and I 
believe both Phenix and CCP4 are aiming to distribute natively-compiled 
software as soon as technical complications are worked out. So hopefully this 
is just temporary!

I hadn’t realised that the OpenMP wasn’t enabled on CCP4. In Phenix, there were 
issues preventing the use of OpenMP with Python2, but those should go away when 
the Python3 version is ready to deploy.

Best wishes,

Randy Read

> On 28 Jun 2022, at 16:45, Lau Kelvin 
> <5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hello
>
> I have noticed running normal programs like Phaser MR on a MacBook Pro 
> (M1Pro) that jobs are extremely slow compared to my older computers.
>
> It doesn’t seem to be running over multiple CPUs anymore.
>
> Has this also been seen by others?
>
> Best
>
> Kelvin
>
>
> --
> Kelvin Lau
> Protein production and structure core facility - PTPSP
> EPFL SV PTECH PTPSP
> AI 2146 (Bâtiment AI)
> Station 19
> CH-1015 Lausanne
> Switzerland
> Email: kelvin@epfl.ch
> Phone: +41 21 69 34494
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




To unsubscribe from the CCP4BB list, click the following link:
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This email and any attachments are intended solely for the use of the named 
recipients. If you are not the intended recipient you must not use, disclose, 
copy or distribute this email or any of its attachments and should notify the 
sender immediately and delete this email from your system. UK Research and 
Innovation (UKRI) has taken every reasonable precaution to minimise risk of 
this email or any attachments containing viruses or malware but the recipient 
should carry out its own virus and malware checks before opening the 
attachments. UKRI does not accept any liability for any losses or damages which 
the recipient may sustain due to presence of any viruses.




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Re: [ccp4bb] CCP4i under M1Pro

[Randy John Read]

We don’t have any computers with Apple silicon in our group yet to test Phaser 
on ourselves. When preparing the Phenix distribution, Billy Poon has run tests 
and when Phaser is compiled for Intel and run through Rosetta 2, it’s generally 
faster than on a recent Intel Mac. However, there have been reports from Phenix 
users of severe slowdowns, and we don’t understand what the special 
circumstances are that cause it to slow down on specific jobs.

The best performance is when it’s compiled natively for the M1 processor, and I 
believe both Phenix and CCP4 are aiming to distribute natively-compiled 
software as soon as technical complications are worked out. So hopefully this 
is just temporary!

I hadn’t realised that the OpenMP wasn’t enabled on CCP4. In Phenix, there were 
issues preventing the use of OpenMP with Python2, but those should go away when 
the Python3 version is ready to deploy.

Best wishes,

Randy Read

> On 28 Jun 2022, at 16:45, Lau Kelvin 
> <5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hello
> 
> I have noticed running normal programs like Phaser MR on a MacBook Pro 
> (M1Pro) that jobs are extremely slow compared to my older computers.
> 
> It doesn’t seem to be running over multiple CPUs anymore.
> 
> Has this also been seen by others?
> 
> Best
> 
> Kelvin
> 
> 
> -- 
> Kelvin Lau
> Protein production and structure core facility - PTPSP
> EPFL SV PTECH PTPSP 
> AI 2146 (Bâtiment AI) 
> Station 19 
> CH-1015 Lausanne
> Switzerland
> Email: kelvin@epfl.ch
> Phone: +41 21 69 34494
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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Re: [ccp4bb] CCP4i under M1Pro

[Alex Aleshin]

>Has this also been seen by others?

Same is here, thank you for razing this question.

Coot also has problems, like a very slow recentering of a view during scrolling 
along a protein chain.

Alex

From: CCP4 bulletin board  on behalf of Lau Kelvin 
<5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk>
Reply-To: Lau Kelvin 
Date: Tuesday, June 28, 2022 at 8:46 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] CCP4i under M1Pro

[EXTERNAL EMAIL: This message may not be safe, use caution, and please be 
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You don't often get email from 5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk. 
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Hello

I have noticed running normal programs like Phaser MR on a MacBook Pro (M1Pro) 
that jobs are extremely slow compared to my older computers.

It doesn’t seem to be running over multiple CPUs anymore.

Has this also been seen by others?

Best

Kelvin


--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin@epfl.ch<mailto:kelvin@epfl.ch>
Phone: +41 21 69 34494




To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] CCP4i under M1Pro

[Subramanian, Ramaswamy]

Hi  Kelvin,

I have the same problem.

Cheers!

Rams
subra...@purdue.edu



On Jun 28, 2022, at 11:45 AM, Lau Kelvin 
<5aaf8435dbef-dmarc-requ...@jiscmail.ac.uk>
 wrote:

 External Email: Use caution with attachments, links, or sharing data 

Hello

I have noticed running normal programs like Phaser MR on a MacBook Pro (M1Pro) 
that jobs are extremely slow compared to my older computers.

It doesn’t seem to be running over multiple CPUs anymore.

Has this also been seen by others?

Best

Kelvin


--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin@epfl.ch
Phone: +41 21 69 34494




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1




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[ccp4bb] CCP4i under M1Pro

[Lau Kelvin]

Hello

I have noticed running normal programs like Phaser MR on a MacBook Pro (M1Pro) 
that jobs are extremely slow compared to my older computers.

It doesn’t seem to be running over multiple CPUs anymore.

Has this also been seen by others?

Best

Kelvin


--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin@epfl.ch
Phone: +41 21 69 34494




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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