Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#31183 closed defect (fixed)

Fix scipy for MacOS 11 (Big Sur)

Reported by: John Palmieri Owned by:
Priority: critical Milestone: sage-9.3
Component: packages: standard Keywords:
Cc: Merged in:
Authors: John Palmieri Reviewers: Zachary Scherr
Report Upstream: N/A Work issues:
Branch: 470ffac (Commits, GitHub, GitLab) Commit:
Dependencies: #31186 Stopgaps:

Status badges

Description

scipy currently fails to build on the latest Mac OS, Big Sur.

Change History (17)

comment:1 Changed 2 years ago by John Palmieri

One option seems to be: if running Big Sur (i.e., if MACOSX_VERSION is "20"), then set MACOSX_DEPLOYMENT_TARGET=11.0 in the spkg-install.in script. See #30651 for some discussion.

comment:2 Changed 2 years ago by John Palmieri

Here is a branch to try out.

comment:3 Changed 2 years ago by John Palmieri

Branch: u/jhpalmieri/scipy-big-sur

comment:4 Changed 2 years ago by John Palmieri

Authors: John Palmieri
Commit: 470ffac111a769b3f2b02631e5174ff6fa483f2b
Dependencies: #31186

New commits:

470ffactrac 31183: build scipy on Mac OS X Big Sur.

comment:5 Changed 2 years ago by Zachary L Scherr

Do you know at what point in the build process the variable MACOSX_VERSION gets set? I just checked out the ticket and ran

./configure
make scipy-clean
make scipy

but it fails because MACOSX_VERSION isn't picked up. I'd like to test the ticket but I'd rather not have to rebuild sage from scratch.

comment:6 Changed 2 years ago by Zachary L Scherr

I just saw your other ticket, I see that on my system MACOSX_VERSION never gets set.

comment:7 Changed 2 years ago by Zachary L Scherr

looks good to me.

comment:8 Changed 2 years ago by John Palmieri

Status: newneeds_review

I'll mark it ready for review. I wish there were an upstream fix, but I couldn't find one.

comment:9 Changed 2 years ago by Zachary L Scherr

Yea, I'm not really sure what is going on with gcc/homebrew. A few days ago when I looked at the formula it seemed that it was applying a patch for MACOSX_DEPLOYMENT_TARGET=11 on intel based Macs, but when I checked again today I see that the patch is only applied on arm based Macs.

It feels like this is a problem homebrew should be able to fix, which in turn would allow scipy to compile without any problems.

comment:10 Changed 2 years ago by Matthias Köppe

Shouldn't the branch of #31186 be merged in?

comment:11 Changed 2 years ago by Zachary L Scherr

Reviewers: Zachary Scherr
Status: needs_reviewpositive_review

comment:12 in reply to:  10 ; Changed 2 years ago by John Palmieri

Replying to mkoeppe:

Shouldn't the branch of #31186 be merged in?

I never know the right way to handle this. What works best for the release manager? Do the patchbots pay attention to the dependencies field? If they touched the same code and so one had to be merged first, it would be clear what to do.

comment:13 in reply to:  12 Changed 2 years ago by Matthias Köppe

Replying to jhpalmieri:

Do the patchbots pay attention to the dependencies field?

No, the patchbots only merge the branch into the current beta. Only Volker's release management scripts read the dependencies field.

It's not important for the present ticket because you have tested it sufficiently on your machines. But in general, for the purpose of portability testing with GH Actions, we need branches that have merged the branches of the dependencies.

comment:14 Changed 2 years ago by Zachary L Scherr

Is it also worthwhile to add Matthias's numpy patch as a dependency?

comment:15 in reply to:  14 Changed 2 years ago by John Palmieri

Replying to gh-zlscherr:

Is it also worthwhile to add Matthias's numpy patch as a dependency?

Good idea, but that branch has already been merged, so I think it would be superfluous.

comment:16 Changed 2 years ago by Volker Braun

Branch: u/jhpalmieri/scipy-big-sur470ffac111a769b3f2b02631e5174ff6fa483f2b
Resolution: fixed
Status: positive_reviewclosed

comment:17 Changed 2 years ago by Zachary L Scherr

Commit: 470ffac111a769b3f2b02631e5174ff6fa483f2b

Just wanted to point out that Homebrew gcc updated today and I think the MACOSX_DEPLOYMENT_TARGET issue for gfortran has been fixed.

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