<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> Hi Nacho<o:p></o:p> <o:p> </o:p> 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.<o:p></o:p> <docker image> is your docker container and <graph flags> are the command flags for the graph.psmp code.<o:p></o:p> You can also try to run <o:p></o:p> docker run --shm-size=1g -ti -v $PWD:/mnt cp2k_prod_psmp graph.psmp <flags and arguments of graph.psmp><o:p></o:p> like for the cp2k code. Maybe, that will work as well.<o:p></o:p> <o:p> </o:p> HTH<o:p></o:p> <o:p> </o:p> Matthias<o:p></o:p> <o:p> </o:p> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> From: cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Nacho Sanz Martinez <naxo.sanzmartinez@gmail.com> Date: Thursday, 16 February 2023 at 18:52 To: cp2k <cp2k@googlegroups.com> Subject: Re: [CP2K:18459] fes.dat generation (docker)<o:p></o:p> </div> <div> Hi Matthias,<o:p></o:p> </div> thanks for the help.<o:p></o:p> <div> <o:p> </o:p> </div> <div> I'm triying to run:<o:p></o:p> </div> <div> docker run --rm -it --mount src=$PWD,target=/mnt,type=bind --entrypoint /opt/cp2k/exe/local/graph.psmp <docker image> <graph flags><o:p></o:p> But i have some questions.<o:p></o:p> i don't have my input files in $PWD, can i modify the command to use /media/disk 3/cp2k directory because it is in this directory where my input files are?<o:p></o:p> i don't understand what's the meaning of <docker image> <graph flags>, can you help me with this?<o:p></o:p> in summary, i have my restar file in one directory (/media/disk3/cp2k), the same directory where i ran my metadynamic using this command:<o:p></o:p> <o:p> </o:p> docker run --shm-size=1g -ti -v "$(pwd)":/mnt cp2k_prod_psmp mpiexec -genv OMP_NUM_THREADS=N -np N cp2k -i filename.inp -o filename.out<o:p></o:p> <o:p> </o:p> but currently i can't get the fes.dat from the METADYN-1.restart<o:p></o:p> <o:p> </o:p> Regards,<o:p></o:p> <o:p> </o:p> Nacho<o:p></o:p> </div> <div> <div> El jueves, 16 de febrero de 2023 a las 18:14:00 UTC+1, Krack Matthias escribió:<o:p></o:p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> Hi Nacho<o:p></o:p> <o:p></o:p> In principle, there should be a graph binary in your docker container. You can try to run<o:p></o:p> <o:p></o:p> docker run --rm -it --mount src=$PWD,target=/mnt,type=bind --entrypoint /opt/cp2k/exe/local/graph.psmp <docker image> <graph flags><o:p></o:p> <o:p></o:p> assuming that the input files are in $PWD of your host environment.<o:p></o:p> <o:p></o:p> Best<o:p></o:p> <o:p></o:p> Matthias<o:p></o:p> </div> </div> <div> <div> <o:p></o:p> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> From: cp...@googlegroups.com <cp...@googlegroups.com> on behalf of Nacho Sanz Martinez <naxo.san...@gmail.com> Date: Thursday, 16 February 2023 at 17:14 To: cp2k <cp...@googlegroups.com> Subject: [CP2K:18457] fes.dat generation (docker)<o:p></o:p> </div> Hi all.<o:p></o:p> <div> we were trying to install cp2k in the workstation but we couldn't, but a colleague could install cp2k in a docker.<o:p></o:p> </div> <div> i can run cp2k with<o:p></o:p> </div> <div> $run docker ....<o:p></o:p> </div> <div> 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.<o:p></o:p> </div> <div> i try to search something similar a graph.() in my docker but it doesn't have it or i can't find it.<o:p></o:p> </div> <div> Can someone give me tips to get this file or how i can install graph-tools in the docker?<o:p></o:p> </div> <div> <o:p></o:p> </div> <div> Regards,<o:p></o:p> </div> <div> <o:p></o:p> </div> <div> Nacho<o:p></o:p> </div> </div> </div> <div> <div> -- You received this message because you are subscribed to the Google Groups "cp2k" group. 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