Opened 13 years ago
Closed 10 years ago
#7831 closed defect (duplicate)
numpy-1.5.0 fixes for FreeBSD
Reported by: | Peter Jeremy | Owned by: | Peter Jeremy |
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Priority: | major | Milestone: | sage-duplicate/invalid/wontfix |
Component: | porting: BSD | Keywords: | |
Cc: | Merged in: | ||
Authors: | Reviewers: | Stephen Montgomery-Smith | |
Report Upstream: | None of the above - read trac for reasoning. | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
- By default, numpy references threaded atlas libraries, as well as a custom variant on the lapack library, on FreeBSD. The reasoning behind this is unclear - there is nothing in the numpy documentation to indicate whether a threaded or non-threaded atlas is needed and the publicly available SVN logs do not mention this code. A query to the numpy mailing list elicited a response that either threaded or non-threaded atlas can be used and suggesting that the special-casing for FreeBSD may be obsolete. By default, atlas is built non-threaded and r-2.6.1.p23 assumes a non-threaded atlas and fails when only the threaded libraries are installed. Based on this, the special casing for FreeBSD was removed from numpy - it now uses the same libraries irrespective of the host OS. This part of the patch could potentially be integrated upstream but this has not been done yet.
- A patch to spkg-install is required to ensure that the <math.h> in $SAGE_LOCAL/include is used in place of the system <math.h>, otherwise the additional maths functions provided by cephes are not prototyped, leading to lots of "implicit declaration" warnings whilst compiling (eg) numpy/core/src/npymath/npy_math_complex.c.src
Attachments (1)
Change History (17)
comment:1 Changed 13 years ago by
Status: | new → needs_review |
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comment:2 Changed 13 years ago by
Reviewers: | → Mike Hansen |
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Status: | needs_review → positive_review |
comment:3 Changed 13 years ago by
Reviewers: | Mike Hansen → Mike Hansen, Minh Van Nguyen |
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Status: | positive_review → needs_work |
Updated spkg at
http://sage.math.washington.edu/home/mvngu/spkg/standard/numpy/numpy-1.3.0.p3.spkg
which incorporates the patch 7831.numpy.patch. This spkg needs review by anyone other than me.
comment:4 Changed 13 years ago by
Status: | needs_work → needs_review |
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comment:5 Changed 12 years ago by
Status: | needs_review → positive_review |
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Looks fine. The the changes based on the newest spkg are at
http://sage.math.washington.edu/home/mhansen/numpy-1.3.0.p4.spkg
comment:6 Changed 12 years ago by
There is another ticket updating numpy as well: #8010. These two conflicting spkg's need to be resolved.
comment:7 Changed 12 years ago by
Status: | positive_review → needs_work |
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comment:8 Changed 12 years ago by
Since #8010 has been closed, it would be helpful to know whether the changes here are still needed (which I can't test, unfortunately).
comment:9 Changed 12 years ago by
Can someone verify whether this is fixed by other changes to the numpy package in 4.6.1alpha0?
comment:10 Changed 12 years ago by
Description: | modified (diff) |
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Summary: | numpy-1.3.0.p2 fixes for FreeBSD → numpy-1.5.0 fixes for FreeBSD |
The init.py changes don't appear to be needed any longer but the remaining fixes are still required.
Changed 12 years ago by
Attachment: | 7831.numpy.patch added |
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comment:11 Changed 12 years ago by
Note that numpy 1.5.1 is on the way to Sage - #10792. It would be great to get this incorporated with that.
comment:12 Changed 11 years ago by
Apparently Stephen Montgomery-Smith has had some success with this recently as a "port".
comment:13 Changed 10 years ago by
Status: | needs_work → needs_info |
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More success at this thread. Checking whether it was with a system version or Sage version.
comment:14 Changed 10 years ago by
Authors: | Peter Jeremy |
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Milestone: | sage-5.1 → sage-duplicate/invalid/wontfix |
Reviewers: | Mike Hansen, Minh Van Nguyen |
Status: | needs_info → needs_review |
Just noting here that although this was the Sage version, Numpy upstream still has the special FreeBSD code, here as of June 2012, so the patch definitely hasn't been applied. My sense is that probably the R upgrades over the years is what made this obsolete.
So I'm putting this to positive review as it builds (and so does R) and passes the overwhelming majority of tests on FreeBSD 8 and 9, but leaving this info here in case in certain unusual cases this ends up being a problem after all.
comment:15 Changed 10 years ago by
Reviewers: | → Stephen Montgomery-Smith |
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Status: | needs_review → positive_review |
comment:16 Changed 10 years ago by
Resolution: | → duplicate |
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Status: | positive_review → closed |
These changes look good to me. Could you look over the ones at #7321? I'll handle making an spkg with all of these rolled together.
Thanks!