When trying to install openFOAM inside a docker container, How do I set the workDir to a location in my mac user directory - linux

Question

I'm using the following script to install openFOAM in a docker container:
#!/bin/sh
#------------------------------------------------------------------------------
# ========= |
# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
# \\ / O peration |
# \\ / A nd | Copyright (C) 2017-2020 OpenFOAM Foundation
# \\/ M anipulation |
#-------------------------------------------------------------------------------
# License
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
# for more details.
#
# You should have received a copy of the GNU General Public License
# along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
#
# Script
# openfoam8-macos
#
# Description
# Run script for an OpenFOAM 8 Docker image at:
# https://hub.docker.com/r/openfoam
#
#------------------------------------------------------------------------------
Script=${0##*/}
VER=8
usage () {
exec 1>&2
while [ "$#" -ge 1 ]; do echo "$1"; shift; done
cat <<USAGE
Usage: ${0##*/} [OPTIONS]
options:
-d | -dir host directory mounted (defaults to current directory)
-x | -xhost use custom X authority and give container host network
-h | -help help
-p | -paraview include ParaView in the Docker image
Launches the OpenFOAM ${VER} Docker image.
- Requires installation of docker-engine.
- Runs a "containerized" bash shell environment where the user can run OpenFOAM
and, optionally, ParaView (see below).
- The container mounts the user's file system so that case files are stored
permanently. The container mounts the current directory by default, but the
user can also specify a particular directory using the "-d" option.
- Mounting the user's HOME directory is disallowed.
- The '-xhost' option is useful when accessing the host via 'ssh -X'.
This option should only be used when strictly necessary, as it relies on the
option '--net=host' when launching the container in Docker, which will
give to the container full access to the Docker host network stack and
potentially the host's system services that rely on network communication,
making it potentially insecure.
ParaView:
Graphical applications from the Docker container require installation of the
Xquartz X server to display on the host machine. While applications such as
Gedit, Emacs and GnuPlot will run effectively using Xquartz, more intensive
OpenGL applications, in particular ParaView, can be prohibitively slow.
Therefore, the default Docker image does not contain ParaView and users can
instead install ParaView directly from the vendor and use the built-in reader
module for OpenFOAM: http://www.paraview.org/download
However, if the user wishes to include ParaView with the official OpenFOAM
reader module in their Docker container, they can do so with the "-p" option.
Example:
To store data in ${HOME}/OpenFOAM/${USER}-${VER}, the user can launch
${Script} either by:
cd ${HOME}/OpenFOAM/${USER}-${VER} && ${Script}
or
${Script} -d ${HOME}/OpenFOAM/${USER}-${VER}
Further Information:
http://openfoam.org/download/8-macos
Note:
The container user name appears as "openfoam" but it is just an alias.
USAGE
exit 1
}
DOCKER_IMAGE='openfoam/openfoam8-graphical-apps'
MOUNT_DIR=$(pwd)
CUSTOM_XAUTH=""
DOCKER_OPTIONS=""
while [ "$#" -gt 0 ]
do
case "$1" in
-d | -dir)
[ "$#" -ge 2 ] || usage "'$1' option requires an argument"
MOUNT_DIR=$2
shift 2
;;
-x | -xhost)
CUSTOM_XAUTH=yes
shift
;;
-h | -help)
usage
;;
-p | -paraview)
DOCKER_IMAGE='openfoam/openfoam8-paraview56'
shift
;;
*)
usage "Invalid option '$1'"
;;
esac
done
[ -d "$MOUNT_DIR" ] || usage "No directory exists: $MOUNT_DIR"
MOUNT_DIR=$(cd "$MOUNT_DIR" && pwd -P)
[ "$MOUNT_DIR" = "$(cd "$HOME" && pwd -P)" ] && \
usage "Mount directory cannot be the user's home directory" \
"Make a subdirectory and run from there, e.g." \
" mkdir -p ${HOME}/OpenFOAM/$(whoami)-${VER}" \
" ${Script} -d ${HOME}/OpenFOAM/$(whoami)-${VER}"
if [ -n "$CUSTOM_XAUTH" ]
then
XAUTH_PATH="${MOUNT_DIR}/.docker.xauth.$$"
touch "${XAUTH_PATH}"
# Generate a custom X-authority file that allows any hostname
xauth nlist "$DISPLAY" | sed -e 's/^..../ffff/' | \
xauth -f "$XAUTH_PATH" nmerge -
DOCKER_OPTIONS="-e XAUTHORITY=$XAUTH_PATH
-v $XAUTH_PATH:$XAUTH_PATH
--net=host"
fi
USER_ID=$(id -u 2> /dev/null)
[ -n "$USER_ID" ] || usage "Cannot determine current user ID"
GROUP_ID=$(id -g)
HOME_DIR='/home/openfoam'
echo "Launching $0"
echo "User: \"$(id -un)\" (ID $USER_ID, group ID $GROUP_ID)"
IFACES=$(ifconfig | grep ^en | cut -d: -f1)
[ "$IFACES" ] || \
usage "Cannot find a network interface for DISPLAY with ifconfig" \
"Please report an issue at http://bugs.openfoam.org" \
" providing the output of the command: ifconfig"
for I in $IFACES
do
IP=$(ifconfig "$I" | grep inet | awk '$1=="inet" {print $2}')
[ "$IP" ] && break
done
[ "$IP" ] || \
usage "Cannot find a network IP for DISPLAY with ifconfig" \
"Please report an issue at http://bugs.openfoam.org" \
" providing the output of the command: ifconfig"
xhost + "$IP"
docker run -it \
--rm \
-e DISPLAY=$IP:0 \
-u $USER_ID:$GROUP_ID \
-v /tmp/.X11-unix:/tmp/.X11-unix \
-v $MOUNT_DIR:$HOME_DIR \
$DOCKER_OPTIONS \
$DOCKER_IMAGE
[ -n "$CUSTOM_XAUTH" -a -e "${XAUTH_PATH}" ] && rm "${XAUTH_PATH}"
This creates a user 'ofuser'. Why? Once I run the above script and then
xhost +local:of_v2006
docker start of_v2006
docker attach of_v2006
I end up in docker with:
[ofuser#3032b6018d82 woo]$ whoami
ofuser
I follow instructions to do a simulation and it creates files that are supposed to be available from the mac os itself, i.e. outside the docker container, but they seem to be in locations like /home/ofuser/...../ofuser/run/..., which don't seem to exist outside the container. Part of output:
[ofuser#5b3db0ac969b woo]$ mkdir $FOAM_RUN
mkdir: cannot create directory '/home/ofuser/OpenFOAM/ofuser-v2006/run': No such file or directory
So, how do I make the user 'foam' or 'woo' instead of ofuser. How did that user come to be? How an I set the workDir to be something like /Users/woo/Containers/foam? Do I have to have that /tmp/.X11-unix stuff in the setup? The display doesn't connect to my XQuartz display I've set up, etc.

Answer 1

I have the same setup running and yes it is possible. Took some time for me to get it running as well but I think I can clarify a few things.
First about the question regarding the directory. This can be set up in the dockerfile. The default dockerfile provided was not sufficient for me as well.
See the extract below:
"Mounts": [
...
{
"Type": "bind",
"Source": "/home/*****/OpenFOAM/run",
"Destination": "/home/openfoam",
"Mode": "Z",
"RW": true,
"Propagation": "rprivate"
},
......
This binds the "Source" - on your machine - with the "Destination" directory inside the container. The crucial option here for me was the "Z" flag which was not present in the default docker file.
The X11 setup also depends on the rights set by the "Z" flag in the dockerfile and can / should be set there. I am not completely sure about your actual setup but this works fine for me.
"Mounts": [
...
{
"Type": "bind",
"Source": "/tmp/.X11-unix",
"Destination": "/tmp/.X11-unix",
"Mode": "Z",
"RW": true,
"Propagation": "rprivate"
},
......
Regarding the new added user I still not get the reason behind it myself but I can tell you I had to use a second user and its working fine.
Normally you only use this user to log in into the container and nothing else. Under Linux execute these steps and verify the new user is in the docker usergroup
$ sudo groupadd docker
$ sudo usermod -aG docker <user>
$ sudo groups <user>