From: Peter Amstutz Date: Wed, 8 Sep 2021 20:09:00 +0000 (-0400) Subject: 18024: Add a note about snap packages X-Git-Tag: 2.3.0~76^2 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/97c90a6cd2650b0799ef99ead3570d513164c805 18024: Add a note about snap packages Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- diff --git a/doc/_includes/_install_compute_docker.liquid b/doc/_includes/_install_compute_docker.liquid index e3814b23c5..a6f2515abb 100644 --- a/doc/_includes/_install_compute_docker.liquid +++ b/doc/_includes/_install_compute_docker.liquid @@ -51,3 +51,11 @@ For information about how to set configuration options for the Docker daemon, se h3. Changing ulimits Docker containers inherit ulimits from the Docker daemon. However, the ulimits for a single Unix daemon may not accommodate a long-running Crunch job. You may want to increase default limits for compute containers by passing @--default-ulimit@ options to the Docker daemon. For example, to allow containers to open 10,000 files, set @--default-ulimit nofile=10000:10000@. + +h2. Troubleshooting + +h3. Workflows fail with @ValidationException: Not found: '/var/lib/cwl/workflow.json#main'@ + +A possible configuration error is having Docker installed as a @snap@ package rather than a @deb@ package. This is a problem because @snap@ packages are partially containerized and may have a different view of the filesystem than @crunch-run@. This will produce confusing problems, for example, directory bind mounts sent to Docker that are empty (instead of containing the intended files) and resulting in unexpected "file not found" errors. + +To check for this situation, run @snap list@ and look for @docker@. If found, run @snap remove docker@ and follow the instructions to above to "install Docker Engine":#install_docker .