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docker-gamess

Deployment of the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry code via a Docker container.

Requirements:

Installation:

  1. Open up a terminal window.

  2. Clone/download the docker-gamess repository:

    git clone https://github.com/saromleang/docker-gamess.git docker-gamess

  3. Navigate into the docker-gamess folder:

    cd docker-gamess

  4. Understand available build arguments:

    • Ubuntu release version. Optional. Default 16.04

      --build-arg IMAGE_VERSION=[12.04|14.04|15.10|16.04]

    • Math library choice. Optional. Default none

      --build-arg BLAS=[none|atlas]

    • GAMESS weekly password for souce code download. Required. Available via email after accepting GAMESS license agreement.

      --build-arg WEEKLY_PASSWORD=password

    • Reduce final image size. Optional. Default true

      --build-arg REDUCE_IMAGE_SIZE=[true|false]

  5. Build the image (choose with or without the ATLAS math library):

    without ATLAS math library:

    docker build --no-cache=true -t docker-gamess:public --build-arg IMAGE_VERSION=16.04 --build-arg BLAS=none --build-arg REDUCE_IMAGE_SIZE=true --build-arg WEEKLY_PASSWORD=xxxxxx .

    with ATLAS math library (Warning! Long build time):

    docker build --no-cache=true -t docker-gamess:public --build-arg IMAGE_VERSION=16.04 --build-arg BLAS=atlas --build-arg REDUCE_IMAGE_SIZE=true --build-arg WEEKLY_PASSWORD=xxxxxx .

  6. Verify the image docker-gamess:public is available to run:

    docker images

    You should see:

   REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
   docker-gamess       public              xxxxxxxxxxxx        About an hour ago   XXX MB

Usage:

Overview: We will launch a container to perform a GAMESS calculation. The container will delete itself after the run is completed. Log files and restart files will be retained by mapping a host folder to the container.

  1. Execute the following commanded to perform a GAMESS run on 1 cpu:
docker run --rm -v /path/to/docker-gamess:/home/gamess docker-gamess:public X-0165-thymine-X.inp -p 1

Explaination:

docker run runs a command in a new container

--rm automatically remove the container when it exits

-v /path/to/docker-gamess:/home/gamess binds the volume /path/to/docker-gamess from the host over to /home/gamess on the container

docker-gamess:public image name:image tag

X-0165-thymine-X.inp the input file

-p 1 peform the calculation using 1 GAMESS compute process

Expected output:

[Running input X-0165-thymine-X on 1 core(s)]
   o
  o                  ##        .
    o          ## ## ##       ==
   o        ## ## ## ##      ===
     o  /""""""""""""""""\\\___/ ===
  ~~~ {~~ ~~~~ ~~~ ~~~~ ~~ ~ /  ===- ~~~
       \\\______ o          __/         
         \\\    \\\        __/          
          \\\____\\\______/             


    [Run completed]
   o
  o                  ##        .
    o          ## ## ##       ==
   o        ## ## ## ##      ===
     o  /""""""""""""""""\\\___/ ===
  ~~~ {~~ ~~~~ ~~~ ~~~~ ~~ ~ /  ===- ~~~
       \\\______ o          __/         
         \\\    \\\        __/          
          \\\____\\\______/

The log file: X-0165-thymine-X.log will be located in /path/to/docker-gamess and all restart and scratch files will be located in /path/to/docker-gamess/restart and /path/to/docker-gamess/scratch, respectively.

  1. Remove the .dat file from the previous run:

    rm restart/X-0165-thymine-X.dat

  2. Execute the following command to perform a GAMESS run on 2 cpus using sockets:

docker run --rm -v /path/to/docker-gamess:/home/gamess docker-gamess:public X-0165-thymine-X.inp -p 2
  1. Execute the following command to output the syntax for running GAMESS on Docker:
docker run --rm docker-gamess:public help