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Re: OpenBLAS and performance
From: |
Dave Love |
Subject: |
Re: OpenBLAS and performance |
Date: |
Wed, 20 Dec 2017 11:50:23 +0000 |
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/24.5 (gnu/linux) |
Pjotr Prins <address@hidden> writes:
> The last weeks I have been toying with OpenBlas and tweaking it boosts
> performance magnificently over the standard install we do now.
How so? I haven't measured it from Guix, but I have with Fedora
packages, and OB is basically equivalent to MKL in the normal
configuration for AVX < 512.
> A configuration for Haswell looks like:
>
>
> https://gitlab.com/genenetwork/guix-bioinformatics/blob/master/gn/packages/gemma.scm#L64
Why make it Haswell-specific? The cpuid dispatch is the main reason to
use OB over at least BLIS currently.
> It will benefit python-numpy and R users greatly to use
> multi-threading (particularly). How do we make a flavour that supports
> this.
[I assume/hope it's not intended to default to multithreading.]
Fedora sensibly builds separately-named libraries for different flavours
<https://apps.fedoraproject.org/packages/openblas/sources/>, but I'd
argue also for threaded versions being available with the generic soname
in librray sub-directories. There's some discussion and measurements
(apologies if I've referenced it before) at
<https://loveshack.fedorapeople.org/blas-subversion.html> -- not that
measurements sway people who insist on Microsoft R ☹. Fedora should
sort out support for optimal BLAS/LAPACK, but those sort of dynamic
loading tricks are important in HPC systems for various reasons, and
seem rather at odds with the Guix approach. I should write something
about that sometime.
If you do provide some sort of threaded version for Python, then as far
as I remember it must use pthreads, not OpenMP, though you want the
OpenMP version for other purposes, and I hadn't realized there wasn't
one currently. That's covered in some combination of the OB and Debian
issue trackers. I don't know if the same applies to R in general.
> Or are channels going to solve this for us?
>
> Btw the latest stable release worked fine too:
>
>
> https://gitlab.com/genenetwork/guix-bioinformatics/commit/474524a5a0d57744c1727442b33d8f2889eb0397
>
> Pj.
Beware that 0.2.20 has one or two significant problems that I don't
remember, but could check.
- OpenBLAS and performance, Pjotr Prins, 2017/12/19
- Re: OpenBLAS and performance, Ludovic Courtès, 2017/12/19
- Re: OpenBLAS and performance,
Dave Love <=
- Re: OpenBLAS and performance, Dave Love, 2017/12/20
- Re: OpenBLAS and performance, Pjotr Prins, 2017/12/20
- Re: OpenBLAS and performance, Ricardo Wurmus, 2017/12/20
- Re: OpenBLAS and performance, Pjotr Prins, 2017/12/20
- Re: OpenBLAS and performance, Ludovic Courtès, 2017/12/21
- Re: OpenBLAS and performance, Dave Love, 2017/12/22
- Re: OpenBLAS and performance, Ricardo Wurmus, 2017/12/22
- Re: OpenBLAS and performance, Pjotr Prins, 2017/12/20
- Re: OpenBLAS and performance, Ricardo Wurmus, 2017/12/20
- Re: OpenBLAS and performance, Pjotr Prins, 2017/12/21