Hi Isuru, Thank you so much. I missed your message yesterday, but I also asked on their forum and they made the same suggestion and said it would be fixed in 3.11. I still asked the homebrew people to add a TARGET to their builds so hopefully that will get straightened out as well.
On Monday, October 12, 2020 at 11:04:41 PM UTC-4 isu...@gmail.com wrote: > Hi Zachary, > > You might be hitting https://github.com/xianyi/OpenBLAS/issues/2728 which > is fixed in https://github.com/xianyi/OpenBLAS/pull/2729 but not in > 0.3.10. > > Isuru > > On Mon, Oct 12, 2020 at 10:01 PM Zachary Scherr <zsc...@gmail.com> wrote: > >> Hi Isuru, >> >> I've been trying to fix homebrew's openblas, and I'm running into an >> issue that I was hoping you might know something about. If I build >> openBLAS with TARGET=HASWELL then I don't have any issues with numpy. >> However, if I build it with TARGET=NEHALEM, which is what they want for >> homebrew, then I still run into the same numpy error. I see that >> Conda-forge uses TARGET=PRESCOTT, but if I try that I also run into the >> same numpy problem. Do you have any insight into why this might be the >> case? >> >> Thanks, >> Zach >> >> On Monday, October 12, 2020 at 4:14:28 PM UTC-4 Zachary Scherr wrote: >> >>> Ah, thank you. I'll post the issue and see if I can get homebrew to >>> resolve it! >>> >>> On Monday, October 12, 2020 at 2:29:10 PM UTC-4 isu...@gmail.com wrote: >>> >>>> You don't need different TARGETs. `DYNAMIC_ARCH=1` means that it will >>>> detect at runtime what the CPU is and will use the kernel matching the CPU >>>> at runtime. `TARGET` gives the oldest CPU that this code will run on so >>>> that the common code is compiled to target this. >>>> >>>> Isuru >>>> >>>> On Mon, Oct 12, 2020 at 1:24 PM Zachary Scherr <zsc...@gmail.com> >>>> wrote: >>>> >>>>> I posted about it on their discussion page, but I'm not sure there >>>>> will be anything they can do. They build their libraries on several >>>>> different versions of MacOS, but I'm not sure they build with several >>>>> different TARGETS. I can try to pursue this, but the easy fix for now is >>>>> that if people want to install openblas via homebrew they should install >>>>> from source. >>>>> >>>>> On Monday, October 12, 2020 at 2:09:28 PM UTC-4 dim...@gmail.com >>>>> wrote: >>>>> >>>>>> On Mon, Oct 12, 2020 at 6:17 PM Isuru Fernando <isu...@gmail.com> >>>>>> wrote: >>>>>> > >>>>>> > I looked at the openblas formula in homebrew and they are not >>>>>> passing the TARGET option. When using DYNAMIC_ARCH=1, a target should be >>>>>> specified. >>>>>> >>>>>> care to open an issue with them on >>>>>> https://github.com/Homebrew/homebrew-core ? >>>>>> >>>>>> > >>>>>> > Isuru >>>>>> > >>>>>> > On Mon, Oct 12, 2020 at 11:34 AM Zachary Scherr <zsc...@gmail.com> >>>>>> wrote: >>>>>> >> >>>>>> >> In case anyone is curious, I've tracked the problem down to >>>>>> homebrew's openBLAS and so it has nothing to do with sage. If I build >>>>>> numpy >>>>>> from source through homebrew then I get exactly the same error using my >>>>>> system python3. I'm wondering if maybe this has something to do with the >>>>>> fact that openBLAS is bottled with a different processor type than the >>>>>> one >>>>>> that is on my system. In any case I'll ask over there and see if I can >>>>>> get >>>>>> some help. >>>>>> >> >>>>>> >> On Sunday, October 11, 2020 at 10:17:43 PM UTC-4 Zachary Scherr >>>>>> wrote: >>>>>> >>> >>>>>> >>> Hi Dima, >>>>>> >>> >>>>>> >>> My system-wide numpy is installed via pip. I was just remarking >>>>>> that I didn't build my system-wide numpy from source so it's not a fair >>>>>> comparison. It's possible that the issues aren't sage related but are >>>>>> related to building sage's numpy against some homebrew libraries. >>>>>> >>> >>>>>> >>> On Sunday, October 11, 2020 at 8:11:13 PM UTC-4 dim...@gmail.com >>>>>> wrote: >>>>>> >>>> >>>>>> >>>> On Mon, Oct 12, 2020 at 1:00 AM Zachary Scherr <zsc...@gmail.com> >>>>>> wrote: >>>>>> >>>> > >>>>>> >>>> > That also crashes with: 86622 segmentation fault ./sage >>>>>> --python >>>>>> >>>> > >>>>>> >>>> > I tested this both with building sage against homebrew python >>>>>> 3.8.6 and against sage's default python 3.8.5 and the same error >>>>>> occurred >>>>>> in both cases. I don't have this problem using my system-wide numpy so >>>>>> it's >>>>>> possible that because sage numpy is built from source that maybe one of >>>>>> my >>>>>> homebrew libraries is causing issues. I found >>>>>> https://github.com/numpy/numpy/issues/11551 which could be relevant >>>>>> and might indicate that it's not a sage problem. >>>>>> >>>> >>>>>> >>>> If you are talking about Homebrew's numpy, it should be more or >>>>>> less >>>>>> >>>> identical with Sage's numpy (assuming you use Homebrew's >>>>>> openblas in >>>>>> >>>> Sage) >>>>>> >>>> cf. >>>>>> https://github.com/Homebrew/homebrew-core/blob/master/Formula/numpy.rb >>>>>> >>>> >>>>>> >>>> > >>>>>> >>>> > I should also add that if I lower the dimension of x to 100000 >>>>>> then it works without problem. >>>>>> >>>> > >>>>>> >>>> > On Sunday, October 11, 2020 at 3:26:11 PM UTC-4 >>>>>> dim...@gmail.com wrote: >>>>>> >>>> >> >>>>>> >>>> >> On Sun, Oct 11, 2020 at 8:14 PM Zachary Scherr < >>>>>> zsc...@gmail.com> wrote: >>>>>> >>>> >> > >>>>>> >>>> >> > Hi All, >>>>>> >>>> >> > >>>>>> >>>> >> > I was doing some bug hunting and noticed that scipy's >>>>>> pytests crashed pretty early. I tracked down exactly what was causing >>>>>> the >>>>>> problem and noticed it can be reproduced by the following sequence of >>>>>> commands: >>>>>> >>>> >> > >>>>>> >>>> >> > sage: import numpy as np >>>>>> >>>> >> > sage: x = np.random.randn(1000000,2) >>>>>> >>>> >> > sage: y = np.random.randn(2,2) >>>>>> >>>> >> > sage: x.dot(y) >>>>>> >>>> >> >>>>>> >>>> >> please test this in "plain" Sage python, i.e. does >>>>>> >>>> >> >>>>>> >>>> >> ./sage --python >>>>>> >>>> >> >>>>>> >>>> >> >>> import numpy as np >>>>>> >>>> >> >>> x = np.random.randn(1000000,2) >>>>>> >>>> >> >>> y = np.random.randn(2,2) >>>>>> >>>> >> >>> x.dot(y) >>>>>> >>>> >> >>>>>> >>>> >> reproduce the crash? >>>>>> >>>> >> >>>>>> >>>> >> >>>>>> >>>> >> >>>>>> >>>> >> > >>>>>> >>>> >> > produces: >>>>>> >>>> >> > >>>>>> >>>> >> > >>>>>> ------------------------------------------------------------------------ >>>>>> >>>> >> > 0 signals.cpython-38-darwin.so 0x00000001088bc62a >>>>>> print_backtrace + 58 >>>>>> >>>> >> > 1 signals.cpython-38-darwin.so 0x00000001088c0277 sigdie + >>>>>> 39 >>>>>> >>>> >> > 2 signals.cpython-38-darwin.so 0x00000001088c0212 >>>>>> sigdie_for_sig + 290 >>>>>> >>>> >> > 3 libsystem_platform.dylib 0x00007fff6c88e5fd _sigtramp + >>>>>> 29 >>>>>> >>>> >> > >>>>>> ------------------------------------------------------------------------ >>>>>> >>>> >> > Unhandled SIGBUS: A bus error occurred. >>>>>> >>>> >> > This probably occurred because a *compiled* module has a >>>>>> bug >>>>>> >>>> >> > in it and is not properly wrapped with sig_on(), sig_off(). >>>>>> >>>> >> > Python will now terminate. >>>>>> >>>> >> > >>>>>> ------------------------------------------------------------------------ >>>>>> >>>> >> > /Users/zscherr/sage/src/bin/sage-python: line 2: 78812 Bus >>>>>> error: 10 sage -python "$@" >>>>>> >>>> >> > >>>>>> >>>> >> > I haven't tested on any other platforms, but for what it's >>>>>> worth I have Catalina 10.15.7 with Xcode 12. >>>>>> >>>> >> > >>>>>> >>>> >> > Thanks, >>>>>> >>>> >> > Zach >>>>>> >>>> >> > >>>>>> >>>> >> > -- >>>>>> >>>> >> > You received this message because you are subscribed to the >>>>>> Google Groups "sage-devel" group. >>>>>> >>>> >> > To unsubscribe from this group and stop receiving emails >>>>>> from it, send an email to sage-devel+...@googlegroups.com. >>>>>> >>>> >> > To view this discussion on the web visit >>>>>> https://groups.google.com/d/msgid/sage-devel/28f58136-d3c7-40b7-9a46-36fc347acc2en%40googlegroups.com. >>>>>> >>>>>> >>>>>> >>>> > >>>>>> >>>> > -- >>>>>> >>>> > You received this message because you are subscribed to the >>>>>> Google Groups "sage-devel" group. >>>>>> >>>> > To unsubscribe from this group and stop receiving emails from >>>>>> it, send an email to sage-devel+...@googlegroups.com. >>>>>> >>>> > To view this discussion on the web visit >>>>>> https://groups.google.com/d/msgid/sage-devel/a67ca4b5-526b-40d7-a476-520d49890207n%40googlegroups.com. >>>>>> >>>>>> >>>>>> >> >>>>>> >> -- >>>>>> 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