Dear All
Thank you for the detailed response. I will implement the suggested fixes and
report back on a later date.
Kind regards,
Otsile
-Original Message-
From: CCP4 bulletin board On Behalf Of Bernhard Lohkamp
Sent: Wednesday, May 15, 2024 9:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and
RX6600XT GPU hardware PC
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On 15/05/2024 19:03, Paul Emsley wrote:
>
> On 13/05/2024 17:38, Otsile Mojanaga wrote:
>>
>> *From:*Otsile Mojanaga
>> *Sent:* Monday, May 13, 2024 3:29 PM
>> *To:* Paul Emsley
>> *Subject:* RE: [ccp4bb] Request for help in optimizing Coot for AMD
>> 5950x CPU and RX6600XT GPU hardware PC
>>
>> Dear Paul/All
>>
>> Thank you for the response. I am on Windows 11 and I tried looking
>> around Coot to see where I could input the commands you have
>> suggested but I cannot find anything . I also cannot seem to type the
>> commands into the 'Command prompt' that opens alongside Coot. I also
>> tried inputting the commands in the 'Coot Python scripting' within
>> Coot but this did not work. Please advise on when you can input these
>> commands.
>>
>>
>>
>>
>>
>>
>> On 13/05/2024 13:03, Otsile Mojanaga wrote:
>>
>> Dear All
>>
>> I have been using coot as part of my normal workflow but since
>> last week I have been having issues with Coot after I built my own
>> PC which contains the following Hardware:
>>
>> CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads
>>
>> RAM - 64 GB
>>
>> GPU - AMD Radeon RX 6600 XT - Primary/Discrete
>>
>> GPU VRAM - 8176 MB - GDDR6 2000 MHz
>>
>> Despite the improvement in hardware, Coot is now having issues
>> refining molecules when using the 'real space refine' tool and
>> other related tools. When trying to refine, the program becomes
>> stuttering and slow such that it becomes unfeasible to use the
>> program in a reasonable amount of time. My current work around is
>> to run Coot through CCP4 cloud but this greatly slows down my
>> workflow. >From what I can see Coot is not be optimised for the
>> AMD CPU.
>>
>> You don't mention the operating system.
>>
>> Maybe you have too many threads for Coot? Try setting the
>> COOT_N_THREADS to various values (starting, say, with 2) and see what
>> happens.
>>
>> But maybe it's a graphics (driver) issue and not a CPU/threads issue.
>> glxgears is the classic test for that.
>>
>> Paul.
>>
>
> What I mean here is that COOT_N_THREADS is an environment variable. It
> needs to be set in the environment from which Coot is launched -
> before Coot is launched, just to be clear.
>
> From a quick googling, I see that environment variables are a thing
> under windows, but it is not clear to me how they could actually be
> used in the context of Coot.
>
> Paul.
>
You can add the environment variable in the coot startup script, i.e.
edit wincoot.bat and insert the following line (*) before coot-bin.exe is
called:
set COOT_N_THREADS=2
Having said this, for me this doesnt make any difference but more importantly I
dont think this is the issue. Your issue is almost certainly the graphics card
drivers. Please make sure you install the appropriate drivers directly from the
AMD rather than relying on the ones provided by Windows. I am confident this
will resolve your issue.
That is unless some old issue with AMD cards shows up again then you may have
to manually control threading in the Control panel of the graphics card.
HTH,
B
(*) there is another way in Windows to restrict the number of threads used (in
the example to 2). To do so, insert the following BEFORE coot-bin.exe in the
wincoot.bat file (i.e. in the same line):
start /affinity 2
>
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