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PGFem3D Docker Deployment Image

Requirements

Quick Start

Clone this repository and enter it

user@host~$ git clone https://github.com/C-SWARM/pgfem-3d-docker.git
user@host~$ cd pgfem-3d-docker

If you are building on a Linux machine running the 4.19 Linux Kernel, you may see an error:

error creating new backup file '/var/lib/dpkg/status-old': Invalid cross-device link

Running the following before building should solve:

echo N | sudo tee /sys/module/overlay/parameters/metacopy

Next, build the docker container. Be sure the docker daemon is running, most likely dockerd.

user@host~/pgfem-3d-docker $ docker build -t "cswarm:pgfem3d" .

Docker will pull the required base image and begin building the PGFem3D software. This may take a considerable amount of time depending on your hardware. 10m to 20m is common.

Software is installed to the /opt prefix within the container image.

Once the build is complete, you may launch PGFem3d from within your docker container. For example:

user@host~$ docker images -a      # to list images
user@host~$ docker run "cswarm:pgfem3d" /opt/pgfem-3d/bin/PGFem3D -SS

Interactive

In order to build, run, and visualize output from an interactive shell in your container:

  • For X forwarding from the docker container, Mac OS X users must first follow XQuartz instructions at the end of this document.
user@host~$ docker run --net=host -e DISPLAY --volume="$HOME/.Xauthority:/home/cswarm/.Xauthority:rw" -ti "cswarm:pgfem3d" /bin/bash
cswarm@container~$ cd pgfem-3d
cswarm@container~$ make check

Running examples

To run the example from the interactive shell inside the container:

cswarm@container~$ cd pgfem-3d-examples 
cswarm@container~$ ./local_makeset.pl clean -np 4  # to generate input (for 4-core job)
cswarm@container~$ ./run.sh 4                      # to run the example (for 4-core job)

To visualize the resulting output launch paraview.

cswarm@container~$ paraview &

On Linux systems, if you see an error similar to the following:

X Error: BadAccess (attempt to access private resource denied) 10

run the following before the above paraview command:

cswarm@container~$ export QT_X11_NO_MITSHM=1

Once the paraview GUI is open:

  1. File -> Load State -> select the file "parview_displacement_z.pvsm" (or "parview_displacement_y.pvsm") and click OK
  2. Once the paraview state is loaded, point to: out -> box_4CPU -> VTK -> box_..pvtu
  3. Click onto the "Play" button to see the effect of thermal expansion

In order to retain changes made within the container, from a second terminal on the host (not the terminal inside the container).

user@host~$ docker ps                       # to find the CONTAINER_ID to commit changes
user@host~$ docker commit CONTAINER_ID cswarm:pgfem3d # to commit the changes to cswarm:pgfem3d

Preparing XQuartz On Mac OS X for visualizatoin (use a terminal on the host)

  • XQuartz can be installed from https://www.xquartz.org/.
  • You may need to log out and log back in after a new XQuartz install.
  • The homebrew install is untested.
  • Ensure that X11 Preferences -> Security -> enable "Allow connection from network clients" is clicked in the preference pane.
user@host~$ open -a XQuartz
user@host~$ defaults write org.macosforge.xquartz.X11 enable_iglx -bool true # without iglx, paraview gets frozen
user@host~$ xhost + $(hostname)
user@host~$ export DISPLAY=$(hostname):0

Technical Assistance

For any technical assistance, please contact:

  1. Ezra Kissel [email protected]
  2. Kamal K Saha [email protected]
  3. Luke D'Alessandro [email protected]