I believe this is the result of a Docker bug https://github.com/docker/docker/issues/7792 - (tl;dr a change in go resulted in the volume map being randomized). This bug and supporting Docker volume handling pre, during, and post bug is going to be complicated and I need to work out if that is even possible. So there are some workarounds:
- Move your job working directory and files_path outside of galaxy_root.
(or)
- Mount everything beneath GALAXY_ROOT read-write instead of mixing read-only and read-write. Basically add the following to your job destination:
<param id="docker_volumes">$galaxy_root:rw,$tool_directory:rw,$working_directory:rw,$default_file_path:rw</param>
This is second option is less secure of course - but no less secure than not running things inside of the docker container. For strong security inside of Docker I recommend using Pulsar.
Hope this helps, -John
On Fri, Nov 14, 2014 at 12:55 AM, Weiyan Shen shenwiyn@gmail.com wrote:
Dear all , I am following the guide on https://github.com/apetkau/galaxy-hackathon-2014/tree/master/smalt%E2%80%8D to test the smalt docker integration tutorial.
The SMALT within docker on my local Galaxy sometimes works well as follow:
502 7789 0.0 0.0 271680 6236 ? Sl 21:42 0:00 /usr/bin/docker run -e GALAXY_SLOTS=1 -v /data/Docker/galaxy-dist:/data/Docker/galaxy-dist:ro -v /data/Docker/galaxy-dist/tools/docker:/data/Docker/galaxy-dist/tools/docker:ro -v /data/Docker/galaxy-dist/database/job_working_directory/000/82:/data/Docker/galaxy-dist/database/job_working_directory/000/82:rw -v /data/Docker/galaxy-dist/database/files:/data/Docker/galaxy-dist/database/files:rw -v /data/Docker/galaxy-dist/database/files:/data/Docker/galaxy-dist/database/files:rw -w /data/Docker/galaxy-dist/database/job_working_directory/000/82 --net none smalt-galaxy:shenweiyan /data/Docker/galaxy-dist/database/job_working_directory/000/82/container.sh
But sometimes it failed with the error:
setup mount namespace bind mounts Creating new bind-mount target, mkdir /var/lib/docker/devicemapper/mnt/405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b/rootfs/data/Docker/galaxy-dist/database/files:: read-only file system2014/11/14 21:28:13 Error response from daemon: Cannot start container 405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b: setup mount namespace bind mounts Creating new bind-mount target, mkdir /var/lib/docker/devicemapper/mnt/405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b/rootfs/data/Docker/galaxy-dist/database/files:: read-only file system
It seems that docker running with sudoer unsteadily.Any idear how do I fix it?
Kind regards, weiyan
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