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

Erik Lindahl erik.lindahl at gmail.com
Mon Apr 13 20:56:57 CEST 2020

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 :-)



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
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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