Python: SEGFAULT when certain modules are used in a project with Alpine 3.6/Python 3.6

[beaugunderson]

We've recently upgraded several of our containers to Python 3.6.

Some of the containers always segfault immediately after starting Django's runserver command.

In a couple of the containers upgrading our dependencies fixed the issue, but on some of the other containers that didn't have the issue upgrading the dependencies caused it to start happening.

In one example upgrading requests from 2.12.1 to 2.18.1 stopped the SEGFAULTs but adding the latest version of boto3 caused them to start again.

The issue only happens when run under docker.

I have a simple example repo here and would like to offer a bounty of $100 to whoever can either fix the issue or explain it in a way that allows me to fix it. ✨

Edit: we've tested with 3-alpine and 3-alpine3.6; same result.

Also SEGFAULTs on 3.6.2rc2-alpine3.6.

More clues: requests is also implicated in boto3 which includes botocore--which includes a vendored requests 2.7.0.

[xyzz]

Can you check this https://github.com/esnme/ultrajson/issues/254#issuecomment-314862445

[yosifkit]

A couple pointers, don't install python3 or python3-dev from apk if you are using the python docker image. The python in the docker image is installed from source so anything that links to or uses the apk installed python will probably have issues. But this is not the source of the segfault.

Don't remove dependencies in a later RUN line as this won't save any image size. Don't apk update on its own RUN line (use && to chain it to the command using it). Don't apk upgrade in a container; it is best to wait for the base image to update.

Following are the two Dockerfiles that I ran your compose on; both still segfault. The first is using just the python provided in the docker python image (alpine based). The second is using python3 from Alpine Linux (apk). So, my opinion is that this is not a bug in the docker python image, but I would suspect is one of the "package expects glibc but has muslc" as noted on the readme from Docker Hub. Therefore, it is most likely to need a fix in python upstream or muslc. @ncopa, do you think you could help debug where the fix is needed?

FROM python:3.6-alpine3.6

# logging to the console breaks without this
ENV PYTHONUNBUFFERED 1
ENV PYTHONFAULTHANDLER 1

RUN apk add --no-cache \
        bash \
        build-base \
        gettext \
        linux-headers \
        musl-dev \
        postgresql-client \
        postgresql-dev

RUN mkdir -p /app/

WORKDIR /app/

# so we can cache the installed python modules apart from the app files
COPY *.txt /app/

RUN pip3 install --upgrade pip setuptools
RUN pip3 install -r requirements.txt -r dev-requirements.txt

COPY . /app/

FROM alpine:3.6

# logging to the console breaks without this
ENV PYTHONUNBUFFERED 1
ENV PYTHONFAULTHANDLER 1

RUN apk add --no-cache \
        bash \
        build-base \
        gettext \
        linux-headers \
        musl-dev \
        postgresql-client \
        postgresql-dev \
        python3 \
        python3-dev \
# alpine doesn't provide a `python` symlink to `python3`, so create your own
    && ln -s /usr/bin/python3 /usr/local/bin/python

RUN mkdir -p /app/

WORKDIR /app/

# so we can cache the installed python modules apart from the app files
COPY *.txt /app/

RUN pip3 install --upgrade pip setuptools
RUN pip3 install -r requirements.txt -r dev-requirements.txt

COPY . /app/

This Dockerfile, on the other hand, works fine.

# Debian based image
FROM python:3.6

RUN mkdir -p /app/

WORKDIR /app/

# so we can cache the installed python modules apart from the app files
COPY *.txt /app/

RUN pip3 install --upgrade pip setuptools
RUN pip3 install -r requirements.txt -r dev-requirements.txt

COPY . /app/

[beaugunderson]

@yosifkit good catch on not installing python3; I had just removed that locally as well :)

re: the other Docker optimizations, thanks! I have more reading to do I guess :)

[beaugunderson]

@xyzz I implemented your changes here; I still get a segfault: https://github.com/beaugunderson/crash-test/compare/bg-stack-fix

is there a way to test that LD_PRELOAD is working correctly? I don't see any output for the printf I added...

[xyzz]

RUN cd /app/ && gcc -shared -fPIC stack-fix.c -o stack-fix.o

.so, not .o

[beaugunderson]

oof, simple typo! thanks :)

[beaugunderson]

@xyzz that works! where shall I send your $100? :)

[xyzz]

awesome! Please donate it to Doctors Without Borders or a similar charity.

[beaugunderson]

@xyzz done! i assume I'll get some confirmation once it goes through (I did it through work) and am happy to send that along when I get it :)

also: do you happen to know where the best place to escalate this issue might be? it seems like an 'alpine's use of musl' issue, correct?

[xyzz]

I've already poked an alpine developer about it, I think they will patch python to use bigger stack argument in pthread_create.

[beaugunderson]

thanks so much!

---

Sent from my phone.

On Jul 12, 2017, at 15:49, xyzz [e-mail] wrote:

I've already poked an alpine developer about it, I think they will patch python to use bigger stack argument in pthread_create.

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[beaugunderson]

I'll close this issue since I don't think there's anything to be done here :)

I'll also add this link to a previous discussion of increasing the stack size in musl just to provide another concrete example.

[beaugunderson]

finally verifying that I made that donation ✨

[jozo]

I have solved SEGFAULT issue by adding this code to my python script:

import threading; threading.stack_size(2*1024*1024)

It looks to me that this code does the same job as xyzz's solution but in python. I found this solution on https://github.com/esnme/ultrajson/issues/254

[beaugunderson]

@fadawar this fix improves the SEGFAULT behavior for my containers but doesn't fix it entirely... I go from an immediate SEGFAULT on launch to a few SEGFAULTs a day; not sure why there's a difference! but I have to go back to the old fix

[frol]

Interesting, I have been using Python 3 in Alpine Docker image (frolvlad/alpine-python3) for over 2 years and bumped into this issue only today. I didn't make any significant changes lately, but I got Docker image rebuilt and it might have fetched a newer version of python3 or musl from Alpine repository.

Here is the reproduction:

$ docker run -it --rm --publish 5000:5000 frolvlad/flask-restplus-server-example:alpine-stack-issue

When I query curl http://127.0.0.1:5000/api/v1/swagger.json, Python just segfaults:

python3.6[4701]: segfault at 7f74b665aff8 ip 00007f74b61b611b sp 00007f74b665b000 error 6 in libpython3.6m.so.1.0[7f74b6127000+3e8000]

Setting a bigger stack size suggested by @fadawar solves the issue (or at least masks the problem for now).

I have tested the behaviour on a few different hosts because I thought that it might have been related to the kernel (all resulted in the same segfault):

• Host: Arch Linux with Linux kernel 4.13.9 (latest)
  Docker version: 17.10

• Host: Arch Linux with Linux kernel 4.9.59 (LTS)
  Docker version: 17.10

• Host: Ubuntu 16.04 with Linux kernel 4.4.0-96
  Docker version: 17.05

• Host: Ubuntu 14.04 with Linux kernel 4.4.0-59
  Docker version: 17.05

Interestingly, if I rebase on frolvlad/alpine-python2 (Python 2.7 package from Alpine repositories) everything works just fine.

The project which I reproduce this issue on is public, so you can play with it: https://github.com/frol/flask-restplus-server-example (I have added the hotfix threading.stack_size(2*1024*1024) into the master, so refer to the alpine-stack-issue tag)

[mimischi]

Wow, would never have thought to end up here.

I've been hunting a bug in my Django code for almost a week and finally just nailed it down to python:alpine3.6. For me it was extremely weird, because accessing two specific URLs (which just show forms using crispy-forms) led to a crash of the Django container. No information, just a crash.

Thanks @fadawar for the snippet. That makes my code work again.

So what is the status with this bug now -- will we need to wait for a fix in musl?

[sobolevn]

The same here. I have a segfault when running from rest_framework import routers.
Link to the Dockerfile: https://github.com/wemake-services/wemake-django-template/blob/master/%7B%7Bcookiecutter.project_name%7D%7D/docker/django/Dockerfile

Right now I am using --noreload option for runserver, since it only affects my development containers.

[ncopa]

Does it make any difference if you add ENV JSON_MAX_STACK_BUFFER_SIZE=1024 before running pip?

[IlianIliev]

@ncopa I tried it, but it still crashes for me.

[sobolevn]

@ncopa no luck either.

[IlianIliev]

@sobolevn It works fine with alpine 3.7 so if you can, just upgrade switch to it.

[davidwindell]

@IlianIliev does that mean the LD_PRELOAD hack isn't needed at all with Alpine 3.7?

[IlianIliev]

@davidwindell exactly. I just updated to Alpine 3.7, installed python 3 and it was working like a charm.

[JayH5]

With the latest python images for Alpine this problem should hopefully be fixed across all Python and Alpine Linux versions.

[davidwindell]

@JayH5 is this also fixed on python not just python3?

[JayH5]

@davidwindell yup, Python 2.7 as well. See #211.

[fr0der1c]

I'm using python:3.7-alpine3.8 and I still got the segmentation fault problem. Is this a regression?

[ncopa]

I'm using python:3.7-alpine3.8 and I still got the segmentation fault problem. Is this a regression?

@fr0der1c Please open a new issue. I don't think it is same problem.

````
$ cat test-stacksize.py
import threading
import sys

def fun(i):
try:
fun(i+1)
except:
sys.exit(0)

t = threading.Thread(target=fun, args=[1])
t.start()
$ docker run --rm python:3.7-alpine3.8 < test-stacksize.py
$
````

No segfault here...