Yambo via Docker

An alternative to get the Yambo code is to install the Yambo container in your machine and this can be done in few steps:

• Install the docker platform (Linux or Mac). Follow the instruction in the docker website.

It is possible to run Docker by a normal user without the sudo privileges. In order to do that you have to add your username to the group "docker" (suggested on Linux!).

For Linux users:

 sudo groupadd docker
 sudo usermod -aG docker $USER

For Mac users:

 sudo dscl . create /Groups/docker
 sudo dseditgroup -o edit -a $USER -t user docker

Log out and log back in so that your group membership is re-evaluated.

If you you prefer to use sudo please remember to add the "sudo" command before all the commands below.

• Pull the Yambo container:

 docker pull maxcentre/yambo:5.1.0_gcc9

• You are done. To run Yambo into the container:

docker run -ti --user $(id -u):$(id -g) \
   --mount type=bind,source="$(pwd)",target=/tmpdir \
   -e OMP_NUM_THREADS=4  \
   maxcentre/yambo:5.1.0_gcc9 \
   yambo -F yambo.in -J yambo.out

Otherwise (suggested!), copy and paste the code below in a file, i.e called drun.sh:

#!/bin/bash
threads=1
environment="--env-file env.txt"
container="maxcentre/yambo:5.1.0_gcc9"
command_prefix=""

### MAIN ###
while $1 == -* ; do
  case $1 in
    -t | --threads ) threads=$2
                     shift 2
                     ;;
    -c | --container) container=$2
                      shift 2
                      ;;
    -np | --nprocess ) command_prefix="mpirun --use-hwthread-cpus -np $2"
                       shift 2
                       ;;
    --env-file ) environment="--env-file $2"
                 shift 2
                 ;;
    -i | --init ) docker pull ${container}
                  docker run -ti --user $(id -u):$(id -g) \
                    --mount type=bind,source="$(pwd)",target=/scratch \
                    ${container} cat /opt/spack/env.txt > env.txt
                    exit 0
                    ;;
    * ) echo "Error: \"$1\" unrecognized argument."
        exit 1
  esac
done

docker run -ti --user $(id -u):$(id -g) \
  --mount type=bind,source="$(pwd)",target=/scratch \
  -e OMP_NUM_THREADS=${threads} ${environment} \
  ${container} ${command_prefix} $@

then give the file execute privileges:

chmod +x drun.sh

Move (or copy) this file in the directory where you want to use Yambo and use it as prefix of your Yambo calculation.

First you have to initialize the environment needed by the container:

./drun.sh -i

this command will pull the container if not already done and will create a file named env.txt needed by the container to run Yambo.

Now you can run yambo like in this example:

./drun.sh yambo -F yambo.in -J yambo.out

If the yambo container is working correctly you should obtain:

./drun.sh yambo

yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

./drun.sh yambo -h

should provide in output the help for yambo usage.

To delete the container images downloaded you can use this command:

docker image rm <image_name>

To remove all the stopped containers use this command:

docker system prune