fes.dat generation (docker)

[Nacho Sanz Martinez]

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

[Krack Matthias]

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

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[Nacho Sanz Martinez]

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

[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

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[Nacho Sanz Martinez]

Hi Matthias, 

thanks you so much,

you are right, i can get my fes.dat running your code.

Regards,

Nacho