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. >>>>> >>>>> >> >>>>> >> -- >>>>> >> 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/7ba7ef07-8460-4180-8670-397e1fb6df93n%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/CA%2B01voNTGybhpxULUXSuBxFFc2fAXkwyer%3DQ0pSAPpP3Am8uDQ%40mail.gmail.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/e0f2c485-cb29-4db3-85bc-3c2632835c90n%40googlegroups.com >>>> <https://groups.google.com/d/msgid/sage-devel/e0f2c485-cb29-4db3-85bc-3c2632835c90n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- > 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+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/37a70675-95bb-419d-ab3c-4baa10eb632an%40googlegroups.com > <https://groups.google.com/d/msgid/sage-devel/37a70675-95bb-419d-ab3c-4baa10eb632an%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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