[CP2K-user] [CP2K:18465] fes.dat generation (docker)

[Nacho Sanz Martinez]

Hi Matthias, 

thanks you so much,

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

Regards,

Nacho





El viernes, 17 de febrero de 2023 a las 9:24:19 UTC+1, Krack Matthias 
escribió:

> 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 $PWD:/mnt cp2k_prod_psmp graph.psmp 
> <flags and arguments of graph.psmp>
>
> like for the cp2k code. Maybe, that will work as well.
>
>  
>
> HTH
>
>  
>
> Matthias
>
>  
>
> *From: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of 
> Nacho Sanz Martinez <naxo.san... at gmail.com>
> *Date: *Thursday, 16 February 2023 at 18:52
> *To: *cp2k <cp... at googlegroups.com>
> *Subject: *Re: [CP2K:18459] fes.dat generation (docker)
>
> Hi Matthias,
>
> thanks for the help.
>
>  
>
> I'm triying to run:
>
> docker run --rm -it --mount src=$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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