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 <pems...@mrc-lmb.cam.ac.uk>
*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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