macOS compatibility
See original GitHub issueminiwdl is tested on macOS Catalina x86-64, with a few specific setup steps:
- Install Docker Desktop for Mac
- Use Docker’s menu bar icon to switch off this setting: Preferences > Experimental Features > Use gRPC FUSE for file sharing (info: https://github.com/chanzuckerberg/miniwdl/issues/461)
- Install Python using
brew install python3
or Miniconda3 (the OS/Xcode edition has difficulties with CA certificates) - Either
pip3 install miniwdl
(if not using conda) orconda install -c conda-forge miniwdl
- In the terminal session,
export TMPDIR=/tmp
to let containers mount shared temporary directories (info) -
miniwdl run_self_test
Then, proceed through the Getting Started tutorial if so desired.
To set up for miniwdl development:
conda create miniwdl-dev pip jq coreutils
conda activate miniwdl-dev
pip3 install -r requirements.dev.txt
make qtest
(make sure which stat
refers to coreutils’ version)
Issue Analytics
- State:
- Created 4 years ago
- Comments:12 (3 by maintainers)
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I encountered the task-input-is-empty issue repeatedly (deterministically?) tonight when trying to run a wdl workflow on macOS. That gave me a chance to turn some knobs. A temporary solution—for me at least— is to disable the
Use gRPC FUSE for file sharing
toggle in the preferences of the macOS docker VM host (screenshots of the working state attached, along with my docker versions). This is on macOS Catalina 10.15.6 w/ Docker Desktop 2.5.0.0 and Docker Engine 19.03.13. I didn’t want to delve further into FUSE debugging this evening, but wanted to mention this here in case it is something to go on. If the issues on docker/for-mac are any indication, this may be more of a docker problem than a miniwdl problem.Edit: The problem is still present after updating to Docker Desktop 2.5.0.1 if
Use gRPC FUSE for file sharing
is enabled (disabling it still resolves the issue).I’ve been seeing flakiness with Docker for Mac’s volume mounting. Sporadically (maybe less than 1% of container starts) the WDL input files appear to be empty (mount point exists, but zero length) inside the container, with no errors reported by Docker. This is quite concerning because zero-length inputs might be valid for some tasks (e.g., line count) so there’s no obvious way to know to retry them.
The way Docker for Mac mounts host volumes into containers (in a VM) is pretty complicated.
cc @lynnlangit