[buster-discuss] problem with buster (release 20240710) on MacM4 / Sequoia 15.2

[Laurent Maveyraud]

Hi Clemens,

just to follow up about this crossec problem on M4 chips when running 
buster...

Using "AutomaticFormfactorCorrectionAnalyse=no", as you suggested, did 
the trick with buster. However, I now try to use pipedream....

Without any specific instructions, I observe the same behavior of buster 
: it stalls at the crossec step.

When I add  -abcommands "AutomaticFormfactorCorrectionAnalyse=no"  on 
the pipedream command, it does not seem to have any effect : buster 
stalls at the crossec step... It looks like buster does not inherit the 
command from the pipedream command line.

What's strange, though, is that I can kill the crossec process, and then 
buster proceeds normally until it tries to run crossec on the next big 
cycle...

I hope it can help to identify the source of the problem...

kind regards,

Laurent

Le 13/01/2025 à 10:44, Clemens Vonrhein a écrit :
> Hi Laurent,
>
> On Wed, Jan 08, 2025 at 09:26:31AM +0100, Laurent Maveyraud via buster-discuss wrote:
>> I just upgraded my MacBookPro to the latest M4 chip, and have problems while
>> running buster (snapshot 20240710) with CCP4 9.
>>
>> It seems that it get stuck at crossec step at the first cycle : crossec
>> keeps running (I stopped it after 15 minutes....).
> That suggests a problem with the CCP4 "crossec" program. Can you try
> running e.g.
>
>    crossec <<e
>    ATOM S
>    NWAV 1 1.0
>    e
>
> This should be VERY fast and return you something like
>
>    ...
>     $TABLE:Wave length v F' and F"-  S    :
>     $GRAPHS:Lambda v F' and F" S    :A:2,3,4: $$
>     Atom_type Lambda  F'  F" $$
>     Lambda  F'  F" $$
>
>    S           1.0000     0.1886     0.2439
>    ...
>
>> Are there any known problems with M4 / Sequoia ?
> Not from our (Global Phasing software) side (yet) - but we have only
> access to a M1 system running 15.1 (where the above command works
> fine).
>
> You can switch off the check about formfactors (which is the part that
> runs CROSSEC) via the
>
>    AutomaticFormfactorCorrectionAnalyse=no
>
> parameter (until there is a better understanding where the problem
> comes from).
>
> Does that help here?
>
> Cheers
>
> Clemens
>
>> have a nice day,
>>
>> laurent
>>
>> this is the command I used :
>>
>> refine -p ./refine_02/refine-coot-0.pdb -Gelly ./refine_02/occ.gelly -l
>> ../../my.restraints.cif -m ./scale_01/staraniso_alldata-unique.mtz -WAT 3 -d
>> refine_03 -nthreads 6 > refine_03.log &
>>
>> here are the last lines of the logfile :
>>
>>   ################################ BIG cycle 1
>> #################################
>>
>>
>>   ESC[1mNOTEESC[m : (controllable) refinement parameters = XYZ B OCC
>>
>>   running BUSTER (187.01405 - 1.48565 A) in refine_03/01-BUSTER/Cycle-1
>> [extra library /tmp/maveyrau-BUSTER/maveyrau-1736324017-refine__22844.elib]:
>>
>>   ESC[1mNOTEESC[m : created file for BABSLV by removing 165 atom(s)
-- 
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  Laurent Maveyraud


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Doctoral School Biology - Health - Biotechnologies

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