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macOS compatibility

See original GitHub issue

miniwdl 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) or conda 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)

Top GitHub Comments

3reactions

tomkinsccommented, Nov 25, 2020

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).

Screen Shot 2020-11-24 at 9 44 50 PM Screen Shot 2020-11-24 at 9 47 55 PM

1reaction

mlincommented, Nov 13, 2020

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

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