macOS compatibility

[mlin]

miniwdl is tested on Intel macOS, with a few specific setup steps:

• Install Docker Desktop for Mac
• Use Docker's menu bar icon to select:
  • Settings > General > Choose file sharing... > osxfs (Legacy) (info: macOS: task input files sporadically fail to mount (zero length) #461)
  • Settings > Advanced > Allow the default Docker socket to be used
• 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.

---

miniwdl is NOT officially supported on Apple Silicon; but may work experimentally, depending on the required task container images. Further discussion #652

---

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)

[illusional]

Hey @mlin, I'm trying out WDL and having troubles using the run functionality on macOS when running an untar workflow. (I thought i'd drop it here in case it relates to macOS). I'm getting the error:

franklinmichael$ miniwdl run simple.wdl -i inp-local.json 
WARNING:wdl-workflow:simple:starting workflow simple (simple.wdl Ln 7 Col 1) in /Users/franklinmichael/Desktop/workflows-for-testing/03-simple/wdl/20190722_073803_simple
WARNING:wdl-worfklow:simple:issue call-untar on untar
ERROR:wdl-task:call-untar:failed to close docker-py client
Traceback (most recent call last):
  File "/anaconda3/lib/python3.7/site-packages/WDL/runtime/task.py", line 296, in _run
    assert exit_info
AssertionError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/anaconda3/lib/python3.7/site-packages/WDL/runtime/task.py", line 306, in _run
    client.close()
  File "/anaconda3/lib/python3.7/site-packages/docker/client.py", line 187, in __getattr__
    raise AttributeError(' '.join(s))
AttributeError: 'DockerClient' object has no attribute 'close' In Docker SDK for Python 2.0, this method is now on the object APIClient. See the low-level API section of the documentation for more details.
ERROR:wdl-task:call-untar:task untar (tools/untar.wdl Ln 3 Col 1) failed: AssertionError
ERROR:wdl-workflow:simple:call-untar failed
ERROR:miniwdl-run:AssertionError, 

I presume this might be related to needing permission to control Docker.

The invoking user must have permission to control Docker.

I've already changed my user-specific temp directory for mixing CWLTool and Docker, and I'm running miniwdl 0.3.0, Docker Desktop community 2.0.5.0, and the Docker python module 2.5.1.

[mlin]

@illusional based on those tracebacks I suspect the installed docker-py package might need updating (pip3 install --upgrade docker or such). Can you see if that makes a difference?

(More broadly, we don't have routine testing on macOS yet, need to plow through the issues above and get the test suite going on Travis)

[illusional]

@mlin Amazing, I didn't realise how out of date my Docker was (due to a Toil dependency). miniwdl run works on my small workflow. Will try on some bigger workflows and let you know how to goes.

I'm not sure what the min version of Docker this would require, but might be worth adding a minimum in setuptools install_requires.

[mlin]

Dang, it seems that Travis' macOS environment doesn't support Docker for Mac, so we're going to have to come up with some other approach for Mac testing.

[illusional]

Hey @mlin, just wanted to report back and say that I ran miniwdl on a germline processing pipeline (3 variant callers, scattering, gathering and small expressions) and my outputs were identical to Cromwell. This is totally awesome!

[mlin]

@illusional thank you for the field report; much appreciated! @mckinsel @bkmartinjr @tjchen

[mlin]

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

[tomkinsc]

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).

[markjschreiber]

What is the expected pyre version for running make test. I have pyre 0.9.8 in the virtual env but when I run make test I see the following which suggests that the --show-parse-errors flag doesn't exist:

# regression test against pyre doing nothing (issue #100)
echo "check_check: str = 42" > WDL/DELETEME_check_check.py
/Applications/Xcode.app/Contents/Developer/usr/bin/make check > /dev/null 2>&1 && exit 1 || exit 0
rm WDL/DELETEME_check_check.py
pyre \
                --search-path stubs \
                --typeshed `python3 -c 'import sys, site, os; print(next(p for p in (os.path.join(dir,"lib/pyre_check/typeshed") for dir in (sys.prefix,site.getuserbase())) if os.path.isdir(p)))'` \
                --show-parse-errors check
Usage: pyre [OPTIONS] COMMAND [ARGS]...
Try 'pyre -h' for help.

Error: No such option: --show-parse-errors (Possible options: --no-show-error-traces, --show-error-traces)
make: *** [check] Error 2

[vsmalladi]

Have the issue that inputs are not found.

This is on macOS Monterey 12.0.1 w/ Docker Desktop 4.2.0 and Docker Engine 20.10.10. Toggled Use gRPC FUSE for file sharing off. Any help would be appreciated?

[aofarrel]

Minor update needed on the original post here. "Use gRPC FUSE for file sharing" is no longer under Docker's experimental features, it's in general.

[mschatz]

FYI - There is a currently a very weird bug in Docker desktop 4.12.0 (docker engine 20.10.17) on Apple M1 where if you try to disable "Use gRPC FUSE for file sharing" via the GUI it will turn itself back on when you try to activate it. Docker is aware of the problem and are working on a fix. In the meantime there is a workaround available: docker/for-mac#6467

Mike

[eholdmore]

Hi @mlin and others, thanks for all the hard work here. I just wanted to add that miniwdl run_self_test fails on macOS Venture 13.1 with M1 for me. Here are the steps I followed:

1. Install Docker Desktop and ensure Docker is running with docker ps
2. Set file sharing to osxfs (Legacy) as suggested by macOS: task input files sporadically fail to mount (zero length) #461 (comment)
3. Install Miniconda3
4. Install miniwdl using conda install -c conda-forge miniwdl
5. export TMPDIR=/tmp
6. Finally, miniwdl run_self_test

System Details
macOS: Ventura 13.2
Chip: M1
Docker: 4.16.2
Python: 3.10.8
MiniWDL: 0.10.0

Output
~ % miniwdl run_self_test
test.wdl
workflow hello_caller
scatter name
call hello
if
task hello

• Suggestion: install shellcheck (www.shellcheck.net) to check task commands. (--no-shellcheck suppresses this message)
  2023-01-31 13:40:45.024 miniwdl-run read configuration defaults :: filename: "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/runtime/config_templates/default.cfg"
  2023-01-31 13:40:45.024 miniwdl-run searching for configuration files :: filenames: ["/Users/ericah/.config/miniwdl.cfg", "/etc/xdg/miniwdl.cfg"]
  2023-01-31 13:40:45.024 miniwdl-run no configuration file found
  2023-01-31 13:40:45.024 miniwdl-run applying configuration overrides :: logging: {"json": "false"}
  2023-01-31 13:40:45.025 miniwdl-run configuration :: download_awscli: {"host_credentials": "false", "docker": "amazon/aws-cli@sha256:98ec84db99a707708f8bfb9a09ce48cccf827a5ed682917f7bd1b2d4be5c4751"}, call_cache: {"put": "false", "dir": "/Users/ericah/.cache/miniwdl", "get": "false"}, logging: {"json": "false"}, download_cache: {"get": "false", "disable_patterns": "[".php", ".aspx"]", "put": "false", "ignore_query": "false", "enable_patterns": "[""]", "dir": "/tmp/miniwdl_download_cache"}, download_aria2c: {"docker": "hobbsau/aria2@sha256:9d4646b1576e88e4061f509b25b8c0c6e1a5fface4ac37d9ecab67de5f7d9a4b"}, task_runtime: {"as_user": "false", "memory_max": "0", "defaults": "{\n"docker": "ubuntu:20.04"\n}", "cpu_max": "0", "memory_limit_multiplier": "0.0"}, docker_swarm: {"auto_init": "true"}, file_io: {"root": "/", "delete_work": "false", "copy_input_files": "false", "output_hardlinks": "false"}, plugins: {"enable_patterns": "[""]", "disable_patterns": "["miniwdl_task_omnibus_example:*"]"}, download_gsutil: {"docker": "google/cloud-sdk@sha256:64ddc4e5d3f7fdc5a198c8acf1c361702994462dbe79e7de5a6bde6e62e60e6b"}, scheduler: {"call_concurrency": "0", "container_backend": "docker_swarm"}
  Traceback (most recent call last):
  File "/Users/ericah/miniconda3/bin/miniwdl", line 10, in
  sys.exit(main())
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 78, in main
  run_self_test(**vars(args))
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 1209, in run_self_test
  raise exn
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 1191, in run_self_test
  outputs = main(argv)["outputs"]
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 76, in main
  runner(**vars(args))
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 625, in runner
  target, input_env, input_json = runner_input(
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 887, in runner_input
  v = runner_input_value(s_value, decl.type, downloadable, root)
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 1034, in runner_input_value
  s_value = validate_input_path(os.path.expanduser(s_value), directory, downloadable, root)
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 1069, in validate_input_path
  if downloadable and downloadable(path, directory):
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/CLI.py", line 632, in
  downloadable=lambda fn, is_dir: runtime.download.able(cfg, fn, directory=is_dir),
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/runtime/download.py", line 68, in able
  return bool(uri and _downloader(cfg, uri, directory=directory) is not None)
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/runtime/download.py", line 56, in _downloader
  _load(cfg)
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/runtime/download.py", line 45, in _load
  for plugin_name, plugin_fn in config.load_plugins(cfg, "file_download"):
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/runtime/config.py", line 355, in load_plugins
  yield from (
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/runtime/config.py", line 355, in
  yield from (
  File "/Users/ericah/miniconda3/lib/python3.10/site-packages/WDL/runtime/config.py", line 346, in load_all_plugins
  importlib_metadata.entry_points().get(f"miniwdl.plugin.{group}", [])
  AttributeError: 'EntryPoints' object has no attribute 'get'
• Hint: ensure Docker is installed & running; and on macOS override the environment variable TMPDIR=/tmp/