[gmx-developers] /gromacs/bin.SSE2/gmx: not found

[Mark Abraham]

Hi,

The container image got rebuilt automatically recently after some updates
to the bioexcel gromacs-docker repo, and I saw it hasn't got the
SIMD-specific builds in it that the container expects to find. But I
haven't yet found out why.

Mark

On Mon, 13 Apr 2020 at 22:53, <fernando at hypernetlabs.io> wrote:

> Erik, happy to be the guinea pig! Just have to get other time-sensitive
> work out of the way and will look into this. I am no Gromacs/Docker expert
> (but I learn fast!) so it may take me a little longer than other guinea
> pigs in this listserv.
>
>
>
> Will provide status update when there is one!
>
>
>
> *From:* gromacs.org_gmx-developers-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> *On Behalf Of *Erik
> Lindahl
> *Sent:* Monday, April 13, 2020 1:57 PM
> *To:* gmx-developers at gromacs.org
> *Cc:* Discussion list for GROMACS development <
> gromacs.org_gmx-developers at maillist.sys.kth.se>
> *Subject:* Re: [gmx-developers] /gromacs/bin.SSE2/gmx: not found
>
>
>
> Hi Fernando,
>
>
>
> I have to confess that Windows isn't a normal target for us, but at least
> in theory that shouldn't matter for Docker :-)
>
>
>
> Background: GROMACS has some very heavy CPU-specific optimization, so
> normally we use separate builds for SSE2, SSE4.1, AVX, AVX2, AVX512, etc.
> To make this work well with Docker, but also make sure you get the fastest
> possible binary, the Dockerfile actually builds all of these targets and
> installs them in separate directories, and then we check your CPU
> architecture at runtime, select the right CPU target, and execute the
> command in that subdirectory.
>
>
>
> 1) Can you check (in the container) what the contents of the directory
> /gromacs/bin.SSE2/ is?  (and any other bin.XXX directories under /gromacs)?
>
>
>
> 2) As far as I know, SSE2 should be one of the default builds, simply
> because it's the oldest possible platform we can imagine. However, it's
> pretty rare for a machine to actually be that old, so maybe our detection
> misses something on your windows machine. Do you know what CPU model you
> have?  If you can execute a shell in the container, doing "lscpu" might
> help us diagnose it!
>
>
>
> Getting things to work well in Docker under Windows would be great, so if
> you don't mind being a guinea-pig we'll make sure to help you get it
> working :-)
>
>
>
> Cheers,
>
>
>
> Erik
>
>
>
>
>
>
>
> On Mon, Apr 13, 2020 at 8:34 PM <fernando at hypernetlabs.io> wrote:
>
> Good day all.
>
> Using Docker Desktop and my Windows command prompt, I first successfully
> built the https://hub.docker.com/r/gromacs/gromacs image.
>
>
>
> Successfully built d96a903309fa
>
> Successfully tagged test5:latest
>
>
>
> Then I used the following command “docker run --publish 8000:8080 --name
> ctest5 test5” to run a container from that image ‘test5’.
>
> And the CLI printed the following “/gromacs/bin/gmx: 12: /gromacs/bin/gmx:
> /gromacs/bin.SSE2/gmx: not found”
>
>
>
> Anyone has experienced the same that could provide some advice? Many
> thanks!
>
> Fernando
>
> +18147778447
>
>
>
> --
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>
>
>
> --
>
> Erik Lindahl <erik.lindahl at dbb.su.se>
>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
> University
>
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
> --
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