[CP2K-user] [CP2K:18461] fes.dat generation (docker)

[Krack Matthias]

Hi Nacho

You should be able to run the docker container from any host system path, e.g. where your data files are located, so just cd there.
<docker image> is your docker container and <graph flags> are the command flags for the graph.psmp code.
You can also try to run
docker run --shm-size=1g -ti -v $PWD:/mnt cp2k_prod_psmp graph.psmp <flags and arguments of graph.psmp>
like for the cp2k code. Maybe, that will work as well.

HTH

Matthias

From: cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Nacho Sanz Martinez <naxo.sanzmartinez at gmail.com>
Date: Thursday, 16 February 2023 at 18:52
To: cp2k <cp2k at googlegroups.com>
Subject: Re: [CP2K:18459] fes.dat generation (docker)
Hi Matthias,
thanks for the help.

I'm triying to run:

docker run --rm -it --mount src=$PWD,target=/mnt,type=bind --entrypoint /opt/cp2k/exe/local/graph.psmp <docker image> <graph flags>

 But i have some questions.

i don't have my input files in $PWD, can i modify the command to use /media/disk 3/cp2k directory because it is in this directory where my input files are?

i don't understand what's the meaning of <docker image> <graph flags>, can you help me with this?

in summary, i have my restar file in one directory (/media/disk3/cp2k), the same directory where i ran my metadynamic using this command:



docker run --shm-size=1g -ti -v "$(pwd)":/mnt cp2k_prod_psmp mpiexec -genv OMP_NUM_THREADS=N -np N cp2k -i filename.inp -o filename.out



but currently i can't get the fes.dat from the METADYN-1.restart



Regards,



Nacho
El jueves, 16 de febrero de 2023 a las 18:14:00 UTC+1, Krack Matthias escribió:
Hi Nacho

In principle, there should be a graph binary in your docker container. You can try to run

docker run --rm -it --mount src=$PWD,target=/mnt,type=bind --entrypoint /opt/cp2k/exe/local/graph.psmp <docker image> <graph flags>

assuming that the input files are in $PWD of your host environment.

Best

Matthias

From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of Nacho Sanz Martinez <naxo.san... at gmail.com>
Date: Thursday, 16 February 2023 at 17:14
To: cp2k <cp... at googlegroups.com>
Subject: [CP2K:18457] fes.dat generation (docker)
Hi all.
we were trying to install cp2k in the workstation but we couldn't, but a colleague could install cp2k in a docker.
i can run cp2k with
$run docker ....
in fact, i've a metadynamic finished (with this METADYN_1.restart ), but i have a problem, i can't get the fes.dat to see the energy.
i try to search something similar a graph.() in my docker but it doesn't have it or i can't find it.
Can someone give me tips to get this file or how i can install graph-tools in the docker?

Regards,

Nacho
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