尝试在 docker 容器内安装 openFOAM 时，如何将 workDir 设置到我的 mac 用户目录中的某个位置
When trying to install openFOAM inside a docker container, How do I set the workDir to a location in my mac user directory
我正在使用以下脚本在 docker 容器中安装 openFOAM：
#!/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 ""; 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 [ "$#" -gt 0 ]
do
case "" in
-d | -dir)
[ "$#" -ge 2 ] || usage "'' option requires an argument"
MOUNT_DIR=
shift 2
;;
-x | -xhost)
CUSTOM_XAUTH=yes
shift
;;
-h | -help)
usage
;;
-p | -paraview)
DOCKER_IMAGE='openfoam/openfoam8-paraview56'
shift
;;
*)
usage "Invalid option ''"
;;
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 [=12=]"
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 '=="inet" {print }')
[ "$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}"
这将创建一个用户 'ofuser'。为什么？一旦我 运行 上面的脚本然后
xhost +local:of_v2006
docker start of_v2006
docker attach of_v2006
我最终在 docker 中获得：
[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
那么，如何让用户 'foam' 或 'woo' 而不是用户。那个用户是怎么来的？我如何将 workDir 设置为 /Users/woo/Containers/foam 之类的东西？我是否必须在设置中包含 /tmp/.X11-unix 内容？显示器无法连接到我设置的 XQuartz 显示器等
我有相同的设置 运行 是的，这是可能的。我也花了一些时间才弄明白 运行，但我想我可以澄清一些事情。
首先关于目录的问题。这可以在 docker 文件中设置。提供的默认 docker 文件对我来说也不够用。
请参阅以下摘录：
"Mounts": [
...
{
"Type": "bind",
"Source": "/home/*****/OpenFOAM/run",
"Destination": "/home/openfoam",
"Mode": "Z",
"RW": true,
"Propagation": "rprivate"
},
......
这会将您计算机上的 “源” 与容器内的 “目标” 目录绑定。对我来说，这里的关键选项是默认 docker 文件中不存在的“Z”标志。
X11 设置还取决于 docker 文件中“Z”标志设置的权限，可以/应该在那里设置。我不完全确定你的实际设置，但这对我来说很好。
"Mounts": [
...
{
"Type": "bind",
"Source": "/tmp/.X11-unix",
"Destination": "/tmp/.X11-unix",
"Mode": "Z",
"RW": true,
"Propagation": "rprivate"
},
......
关于新添加的用户，我自己仍然不明白背后的原因，但我可以告诉你我不得不使用第二个用户并且它工作正常。
通常，您仅使用此用户登录容器，仅此而已。在 Linux 下执行这些步骤并验证新用户在 docker 用户组
中
$ sudo groupadd docker
$ sudo usermod -aG docker <user>
$ sudo groups <user>
我正在使用以下脚本在 docker 容器中安装 openFOAM：
#!/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 ""; 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 "" in
-d | -dir)
[ "$#" -ge 2 ] || usage "'' option requires an argument"
MOUNT_DIR=
shift 2
;;
-x | -xhost)
CUSTOM_XAUTH=yes
shift
;;
-h | -help)
usage
;;
-p | -paraview)
DOCKER_IMAGE='openfoam/openfoam8-paraview56'
shift
;;
*)
usage "Invalid option ''"
;;
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=$(id -g)
HOME_DIR='/home/openfoam'
echo "Launching [=12=]"
echo "User: \"$(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 "$I" | grep inet | awk '=="inet" {print }')
[ "$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}"
这将创建一个用户 'ofuser'。为什么？一旦我 运行 上面的脚本然后
xhost +local:of_v2006
docker start of_v2006
docker attach of_v2006
我最终在 docker 中获得：
[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 $FOAM_RUN
mkdir: cannot create directory '/home/ofuser/OpenFOAM/ofuser-v2006/run': No such file or directory
那么，如何让用户 'foam' 或 'woo' 而不是用户。那个用户是怎么来的？我如何将 workDir 设置为 /Users/woo/Containers/foam 之类的东西？我是否必须在设置中包含 /tmp/.X11-unix 内容？显示器无法连接到我设置的 XQuartz 显示器等
我有相同的设置 运行 是的，这是可能的。我也花了一些时间才弄明白 运行，但我想我可以澄清一些事情。
首先关于目录的问题。这可以在 docker 文件中设置。提供的默认 docker 文件对我来说也不够用。 请参阅以下摘录：
"Mounts": [
...
{
"Type": "bind",
"Source": "/home/*****/OpenFOAM/run",
"Destination": "/home/openfoam",
"Mode": "Z",
"RW": true,
"Propagation": "rprivate"
},
......
这会将您计算机上的 “源” 与容器内的 “目标” 目录绑定。对我来说，这里的关键选项是默认 docker 文件中不存在的“Z”标志。
X11 设置还取决于 docker 文件中“Z”标志设置的权限，可以/应该在那里设置。我不完全确定你的实际设置，但这对我来说很好。
"Mounts": [
...
{
"Type": "bind",
"Source": "/tmp/.X11-unix",
"Destination": "/tmp/.X11-unix",
"Mode": "Z",
"RW": true,
"Propagation": "rprivate"
},
......
关于新添加的用户，我自己仍然不明白背后的原因，但我可以告诉你我不得不使用第二个用户并且它工作正常。 通常，您仅使用此用户登录容器，仅此而已。在 Linux 下执行这些步骤并验证新用户在 docker 用户组
中$ sudo groupadd docker
$ sudo usermod -aG docker <user>
$ sudo groups <user>