変なつまり方をしたのでメモ

まとめ

dockerのpython:3.9をベースイメージに環境を作ろうとしていたが、動かなくて困っていた
pystan 3.0 は gcc ≥ 9.0 が必要であるにも関わらず、python:3.9のイメージに入っているgccはver.8系だったのが原因と思われる
ubuntu:20.04をベースにしたら治った

症状

ドキュメントのQuick Startにあるコードを実行しようとしていたが、次のようなエラーが起こっていた

Building... This may take some time.
Messages from stanc:
Warning:
  The parameter mu has no priors.
Warning:
  The parameter tau has no priors.
Error handling request
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/aiohttp/web_protocol.py", line 422, in _handle_request
    resp = await self._request_handler(request)
  File "/usr/local/lib/python3.9/site-packages/aiohttp/web_app.py", line 499, in _handle
    resp = await handler(request)
  File "/usr/local/lib/python3.9/site-packages/httpstan/views.py", line 253, in handle_show_params
    services_module = httpstan.models.import_services_extension_module(model_name)
  File "/usr/local/lib/python3.9/site-packages/httpstan/models.py", line 90, in import_services_extension_module
    module: ModuleType = importlib.util.module_from_spec(spec)  # type: ignore
  File "<frozen importlib._bootstrap>", line 565, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 1108, in create_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
ImportError: /root/.cache/httpstan/4.4.2/models/dnt4r2yw/stan_services_model_dnt4r2yw.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZNSt19basic_ostringstreamIcSt11char_traitsIcESaIcEEC1Ev
Traceback (most recent call last):
  File "/src/getting-started.py", line 27, in <module>
    posterior = stan.build(schools_code, data=schools_data, random_seed=1)
  File "/usr/local/lib/python3.9/site-packages/stan/model.py", line 450, in build
    return asyncio.run(go())
  File "/usr/local/lib/python3.9/asyncio/runners.py", line 44, in run
    return loop.run_until_complete(main)
  File "/usr/local/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
    return future.result()
  File "/usr/local/lib/python3.9/site-packages/stan/model.py", line 439, in go
    raise RuntimeError(resp.json()["message"])
  File "/usr/local/lib/python3.9/site-packages/stan/common.py", line 24, in json
    return simdjson.loads(self.content)
  File "/usr/local/lib/python3.9/site-packages/simdjson/__init__.py", line 61, in loads
    return parser.parse(s, True)
ValueError: The JSON document has an improper structure: missing or superfluous commas, braces, missing keys, etc.

原因

おそらく、python:3.9のイメージに入っているgccが古すぎた

# gcc --version
gcc (Debian 8.3.0-6) 8.3.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

apt-get updateして新しいgccを入れようとしても「これが最新」と言われてしまい、このイメージでなんとかしようとするのは手間がかかりそうだった

対処

もっと新しいgccが入ったものを使うことにした

例えばubuntu 20.04はgcc 9.3.0がデフォルトで入っているのでこれを使うことにした

# gcc --version
gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.