Re: [scipion-users] scipion-installer - how do i change compiler optimization flags?

[David M. <dma...@cn...>]

Thank you very much Wolfgang,

We are including this information to our documentation.


Thanks for reporting and enhancing Scipion/Xmipp.

Do not hesitate if any other issue is found.


Cheers,


<http://ucm.es/>

*_____Dr. David Maluenda Niubó*
dma...@ub... - (+34) 619 029 310
CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

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On Thu, Nov 19, 2020 at 12:06 PM Lugmayr, Wolfgang <w.l...@uk...> wrote:

> dear all,
>
> just for documentation of the scipion 3.0.6 official release.
>
> i changed in xmipp.conf the line:
> CXXFLAGS= -mtune=native -march=native -std=c++11 -O3
> to
> CXXFLAGS= -mfma -mavx2 -m3dnow -fomit-frame-pointer -std=c++11 -O3
> and rebuild xmipp.
> now the exes run fine on intel and amd epyc processors.
>
> the flags come from recommended for gcc:
> https://prace-ri.eu/wp-content/uploads/Best-Practice-Guide_AMD.pdf
>
> cheers and thanks for the help,
> wolfgang
>
>
> ------------------------------
> *From: *"Carlos Oscar Sorzano" <co...@cn...>
> *To: *"Pablo Conesa" <pc...@cn...>, "David" <dst...@cn...>,
> dma...@cn..., "w lugmayr" <w.l...@uk...>, "Mailing list for
> Scipion users" <sci...@li...>
> *Sent: *Thursday, 29 October, 2020 16:11:16
> *Subject: *Re: Fwd: [scipion-users] scipion-installer - how do i change
> compiler optimization flags?
>
> Dear Wolfgang,
>
> in the compilation of Xmipp, you can set the environment variable CXXFLAGS
> before calling the xmipp script. From the Scipion installation I am not
> sure how to pass it to the xmipp script. It may be that setting it in the
> shell before calling scipion suffices. But I have never tried.
>
> Kind regards, Carlos Oscar
> El 29/10/2020 a las 11:13, Pablo Conesa escribió:
>
> ?
>
>
> -------- Forwarded Message --------
> Subject: [scipion-users] scipion-installer - how do i change compiler
> optimization flags?
> Date: Wed, 28 Oct 2020 14:19:29 +0100 (CET)
> From: Lugmayr, Wolfgang <w.l...@uk...> <w.l...@uk...>
> Reply-To: Mailing list for Scipion users
> <sci...@li...>
> <sci...@li...>
> To: Mailing list for Scipion users <sci...@li...>
> <sci...@li...>
>
>
> hi,
>
> i installed and compiled scipion 3.0.5-devel on a system with intel cpus.
>
> when i run now scipion on new nodes with "AMD EPYC 7402" processors the
> executable fails with:
> $ scipion3 last Scipion v3.0.5 () devel
> sh: line 1: 45875 Illegal instruction python -m scipion last
>
> so i do not want to have 2 versions of scipion3 but maybe compile it with
> intel and amd compatibility flags.
> how do i set these flags?
>
> cheers,
> wolfgang
>
> --
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Deutsches Elektronen-Synchrotron (DESY)
> Notkestrasse 85 Gebäude 15
> 22607 Hamburg, Germany
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> Email: wol...@cs...http://www.cssb-hamburg.de/
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