Bug 273240 - biology/star: Drop hardcoded avx2 argument
Summary: biology/star: Drop hardcoded avx2 argument
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Only Me
Assignee: Jason W. Bacon
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2023-08-20 06:14 UTC by Daniel Engberg
Modified: 2023-08-21 22:10 UTC (History)
1 user (show)

See Also:
bugzilla: maintainer-feedback? (jwb)

Attachments
Patch for star (587 bytes, patch)
2023-08-20 06:14 UTC, Daniel Engberg 		no flags Details | Diff
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Description Daniel Engberg freebsd_committer freebsd_triage 2023-08-20 06:14:25 UTC 
Created attachment 244221 [details]
Patch for star

This breaks on all platforms, rely on CPUTYPE from the framework instead
Comment 1 Daniel Engberg freebsd_committer freebsd_triage 2023-08-20 06:17:41 UTC 
The build info is also borked (git hash is incorrect for example)

Comment out BUILD_DATE, BUILD_PLACE and GIT_BRANCH_COMMIT_DIFF and define something sane instead.

See https://cgit.freebsd.org/ports/tree/net/libwebsockets/Makefile#n18 for example
Comment 2 commit-hook freebsd_committer freebsd_triage 2023-08-21 14:35:09 UTC 
A commit in branch main references this bug:

URL: https://cgit.FreeBSD.org/ports/commit/?id=0e8f22496e314bf6c0f863722217eb8bebef9cf2

commit 0e8f22496e314bf6c0f863722217eb8bebef9cf2
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-08-21 14:33:20 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-08-21 14:33:20 +0000

    biology/star: Fix SIMD issue on non-amd64

    Also remove some extraneous build flags from upstream Makefile

    PR:             273240
    Reported by:    dizzy

 biology/star/Makefile             |  9 ++-------
 biology/star/files/patch-Makefile | 12 +++++++-----
 2 files changed, 9 insertions(+), 12 deletions(-)
Comment 3 Jason W. Bacon freebsd_committer freebsd_triage 2023-08-21 14:36:43 UTC 
(In reply to Daniel Engberg from comment #0)

ALL platforms?  The port was poudriere-tested on amd64 12.4 and 13.2.

I normally test on aarch64 as well, but apparently it slipped my mind this time.

Thanks for the heads-up.
Comment 4 Jason W. Bacon freebsd_committer freebsd_triage 2023-08-21 14:41:48 UTC 
(In reply to Daniel Engberg from comment #1)

Borked it may be, but the date/time format needs to match what upstream provides, since users might be parsing the output in order to document methods in their publications.  I'm not concerned about the git has as it is not included in the output.

Binary provided by upstream:

# ./STAR-linux 

STAR version=2.7.11a
STAR compilation time,server,dir=2023-08-15T11:38:34-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source

FreeBSD port:

# STAR

STAR version=2.7.11a
STAR compilation time,server,dir=2023-08-21T09:30:32-05:00 :/usr/ports/biology/star/work/STAR-2.7.11a/source
Comment 5 Daniel Engberg freebsd_committer freebsd_triage 2023-08-21 15:47:07 UTC 
(In reply to Jason W. Bacon from comment #3)
Since it builds I'm going to assume it also runs which means it'll likely break on any platform that don't support avx instructions on AMD64.

Thanks for looking into the git stuff
Comment 6 Jason W. Bacon freebsd_committer freebsd_triage 2023-08-21 18:13:15 UTC 
(In reply to Daniel Engberg from comment #5)

Seems to work fine on my ROCK64.
Comment 7 Daniel Engberg freebsd_committer freebsd_triage 2023-08-21 22:10:18 UTC 
(In reply to Jason W. Bacon from comment #6)
As expected :-)

Commmit 0e8f22496e314bf6c0f863722217eb8bebef9cf2 fixed it on all platforms including AMD64, in case I wasn't clear "all platforms" was valid before this commit landed.