VMD-L Mailing List

From: Matthew Kenney (matthew.kenney_at_cellsignal.com)
Date: Fri Jul 06 2018 - 15:50:59 CDT

Hi everyone,

I am attempting to use a version of vmd containerized with docker, pulled
from the nvidia gpu cloud's container repository, however, I cannot get vmd
to run graphically from within the container. I can only see the vmd
command line. While vmd works perfectly well within the container if I use
tcl scripting, I am completely unable to run vmd through the graphical
interface. It would be hugely appreciated if anyone can provide me some
advice on solving this problem.

Click here <https://www.nvidia.com/en-us/gpu-cloud/> for more information
on the nvidia gpu cloud repo I am using. The docker image name, and the
command to run the image per nvidia's instructions are as follows (note
that nvidia-docker is a GPU accelerated version of docker, and this image
cannot be pulled unless you have an nvidia gpu card installed on your
machine and have signed up for free online to use the nvidia gpu cloud):

Image Name: nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17

Command to pull image:
docker pull nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17

Command to get to container's bash:
nvidia-docker run -it --rm -v $(pwd):/workspace
nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17 /bin/bash

Command to run vmd directly without going through bash:
nvidia-docker run -it --rm -v $(pwd):/workspace
nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17 /opt/vmd/bin/vmd -dispdev
openglpbuffer

These commands, however, do not suffice to launch the vmd container in
graphical mode, since there is no way for the container to access the
native display. To circumvent this issue, I instead launched the container
using the following commands to enable X-forwarding (enables the container
to see the host's display):

*First:*
XSOCK=/tmp/.X11-unix
XAUTH=/tmp/.docker.xauth
touch $XAUTH
xauth nlist $DISPLAY | sed -e 's/^..../ffff/' | xauth -f $XAUTH nmerge -
xhost +local:docker

*Then:*
 nvidia-docker run -it --rm -v $(pwd):/workspace \
-v /tmp/.X11-unix:/tmp/.X11-unix -v /tmp/.docker.xauth:/tmp/.docker.xauth \
-v $(pwd):/work -e XAUTHORITY=/tmp/.docker.xauth -e DISPLAY=:$DISPLAY \
nvcr.io/hpc/vmd:cuda9-ubuntu1604-egl-1.9.4a17 /bin/bash

After completing these steps, I was able to download a few GUI applications
from within the container, and ran them perfectly with no issue, thus
proving that the container was 100% capable of running GUI applications on
my screen. Downloading geany from within the container and running it
resulted in a perfectly normal, gui-based application showing up on my
display.

However, vmd STILL will not show up graphically (only the terminal style
vmd shows up). This indicates to me that somehow, the vmd installed in the
container is lacking some component to enable the graphical interface. Any
ideas about what could be causing this issue, or how to fix it would be
incredibly helpful. Thanks in advance!

Best,
Matt 

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