Fix segfault / memory corruption in OpenBLAS

[embray]

There is a bug in OpenBLAS already fixed upstream which I am encountering on Cygwin, though it could also affect Linux (in fact the original bug report was for Linux).

For Sage, this bug is causing a segfault on Cygwin when running

./sage -t --long src/sage/manifolds/differentiable/vectorfield.py

but it could happen arbitrarily anywhere that uses OpenBLAS and that happens to use threads (even without using OpenBLAS threads).

I have already confirmed that the upstream fix resolves the issue for me.

Upstream: Fixed upstream, but not in a stable release.

Component: packages: standard

Keywords: openblas

Author: Erik Bray

Branch: 4aa19b0

Reviewer: François Bissey

Issue created by migration from https://trac.sagemath.org/ticket/27565

[embray]

Commit: 9db4320

[embray]

Branch: u/embray/ticket-27565

[embray]

Author: Erik Bray

[kiwifb]

comment:2

There is no changes to openblas on this branch. Did you forget to commit?

[embray]

comment:3

Strange. It looks like I did.

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

3d0a86b

Trac #27565: Add patch from upstream to fix segfaults.

[sagetrac-git]

Changed commit from 9db4320 to 3d0a86b

[embray]

comment:5

There it is. I was working on this on the train last week so who knows what could've interrupted me.

[kiwifb]

comment:6

Including a a patch merged upstream. I think it is safe.

[kiwifb]

Reviewer: François Bissey

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. This was a forced push. New commits:

e5873dc

Trac #27565: Add patch from upstream to fix segfaults.

[sagetrac-git]

Changed commit from 3d0a86b to e5873dc

[embray]

comment:8

Rebased on 8.8.beta0 (not strictly necessary, but I wanted to anyways so that I could test the rest of 8.8.beta0 on Cygwin).

[embray]

Changed commit from e5873dc to none

[embray]

Changed branch from u/embray/ticket-27565 to 4aa19b0

[embray]

comment:10

The branch on this didn't get updated for some reason.