On Wed, 28 Oct 2020, 14:33 Zachary Scherr, <zsc...@gmail.com> wrote: > Hopefully somebody with more experience can weigh in, but for the record I > have pari installed via homebrew and there the configure is only with > --with-gmp and --with-readline and that works with building sage. It's > plausible that the -mt=pthread is what's causing the issues. >
Hombrew does not provide Pari packages. Unless you install them manually (these are just data files) it will not be used by Sage. If you install Pari with -mt=pthread into /usr/local, with its packages, it will be accepted by Sage, causing this problem. Patches to fix this are welcome. Ideally it can be a short C program to link against libpari, which would fail with the error message reported on this thread. > On Wednesday, October 28, 2020 at 10:12:35 AM UTC-4 modp...@gmail.com > wrote: > >> Yes, I have manually installed Pari 2.11.4 after configuring it with: >> Confgure --mt=pthread --tune >> >> On Wednesday, October 28, 2020 at 3:04:01 PM UTC+1 zsc...@gmail.com >> wrote: >> >>> Just wanted to make a couple of comments. First off, brew installs llvm >>> as keg-only meaning that sage shouldn't even be able to find it unless you >>> manually added something like: >>> >>> export PATH="/usr/local/opt/llvm/bin:$PATH" >>> export LDFLAGS="-L/usr/local/opt/llvm/lib" >>> export CPPFLAGS="-I/usr/local/opt/llvm/include" >>> >>> to your profile. But even after I tried that myself, I failed to >>> reproduce your error on my own Mac machine. This makes me think that you >>> might want to have a look at the version of Pari you installed on your >>> computer. I noticed that ./configure finds a copy of Pari in /usr/local on >>> your computer. You can see that the specific error it references mentions: >>> >>> ld: illegal thread local variable reference to regular symbol >>> _PARI_SIGINT_block for architecture x86_64 >>> >>> If removing llvm and make distclean doesn't solve your problem then you >>> may want to look into where you got your Pari. It seems plausible that >>> Pari might have been built in some funky way and that is what's causing >>> your issue. >>> On Wednesday, October 28, 2020 at 7:27:27 AM UTC-4 dim...@gmail.com >>> wrote: >>> >>>> try >>>> make distclean >>>> >>>> and the build >>>> >>>> On Wed, 28 Oct 2020, 09:57 modp...@gmail.com, <modp...@gmail.com> >>>> wrote: >>>> >>>>> >>>>> I tried uninstalling LLVM and building it again, but it fails again >>>>> for cysignals. >>>>> But the problem now seems that it still sets -I and -L flags with >>>>> non-existent LLVM directories. >>>>> On Tuesday, October 27, 2020 at 5:10:58 PM UTC+1 Matthias Koeppe wrote: >>>>> >>>>>> From config.log: >>>>>> >>>>>> configure:5906: gcc -v >&5 >>>>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr >>>>>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 >>>>>> Apple clang version 12.0.0 (clang-1200.0.32.21) >>>>>> Target: x86_64-apple-darwin19.6.0 >>>>>> Thread model: posix >>>>>> InstalledDir: >>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>>>>> configure:5917: $? = 0 >>>>>> ... >>>>>> >>>>>> configure:6029: gcc -o conftest -I/usr/local/opt/llvm/include >>>>>> -L/usr/local/opt/llvm/lib conftest.c >&5 >>>>>> >>>>>> >>>>>> This looks like an unsupported configuration - injecting these -L and >>>>>> -I flags via environment variables, but continuing to use Apple's gcc. >>>>>> If you are trying to compile with homebrew's llvm, you should >>>>>> probably configure by setting CC and CXX as well. But this is also >>>>>> untested >>>>>> - I have created https://trac.sagemath.org/ticket/30835#ticket for >>>>>> testing such a configuration. >>>>>> >>>>>> >>>>>> On Tuesday, October 27, 2020 at 3:46:10 AM UTC-7, Dima Pasechnik >>>>>> wrote: >>>>>> >>>>>>> I'd have tried removing llvm and trying again. Perhaps this is a >>>>>>> conflict between Homebrew packages. >>>>>>> >>>>>>> On Tue, Oct 27, 2020 at 8:42 AM modp...@gmail.com <modp...@gmail.com> >>>>>>> wrote: >>>>>>> >>>>>> Please find config.log and cysignals-1.10.2.log attached. I already >>>>>>>> run "source .homebrew-build-env" before configuring. >>>>>>>> And yes I also have llvm installed through Homebrew. >>>>>>>> >>>>>>>> On Monday, October 26, 2020 at 3:23:38 PM UTC+1 dim...@gmail.com >>>>>>>> wrote: >>>>>>>> >>>>>>>>> also note that you apparently have something in >>>>>>>>> -L/usr/local/opt/llvm/lib (installed from Homebrew ?) which might >>>>>>>>> lead >>>>>>>>> to surprises. >>>>>>>>> Do you have some LDFLAGS set? >>>>>>>>> It would help if you also post logs/pkgs/cysignals-1.10.2.log >>>>>>>>> >>>>>>>>> On Mon, Oct 26, 2020 at 2:15 PM Dima Pasechnik <dim...@gmail.com> >>>>>>>>> wrote: >>>>>>>>> > >>>>>>>>> > also, if you have Homebrew, you should run >>>>>>>>> > >>>>>>>>> > source .homebrew-build-env >>>>>>>>> > >>>>>>>>> > before >>>>>>>>> > >>>>>>>>> > ./configure >>>>>>>>> > >>>>>>>>> > On Mon, Oct 26, 2020 at 1:50 PM Dima Pasechnik <dim...@gmail.com> >>>>>>>>> wrote: >>>>>>>>> >> >>>>>>>>> >> please post the top-level config.log here >>>>>>>>> >> >>>>>>>>> >> On Mon, 26 Oct 2020, 13:45 modp...@gmail.com, < >>>>>>>>> modp...@gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> I'm building Sage 9.2 from source on macOS Catalina 10.15.7, >>>>>>>>> however, it fails >>>>>>>>> >>> when trying to install cysignals. More precisely, it throws >>>>>>>>> the following error: >>>>>>>>> >>> >>>>>>>>> >>> gcc -bundle -undefined dynamic_lookup -isysroot >>>>>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk >>>>>>>>> -L/Users/myUser/app/sage-9.2/local/lib >>>>>>>>> -Wl,-rpath,/Users/myUser/app/sage-9.2/local/lib >>>>>>>>> -L/usr/local/opt/llvm/lib >>>>>>>>> -I/usr/local/opt/llvm/include -Wp,-U_FORTIFY_SOURCE >>>>>>>>> build/temp.macosx-10.15-x86_64-3.8/build/src/cysignals/signals.o >>>>>>>>> -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib >>>>>>>>> -L/usr/local/opt/sqlite/lib -o >>>>>>>>> build/lib.macosx-10.15-x86_64-3.8/cysignals/ >>>>>>>>> signals.cpython-38-darwin.so -lpari -pthread >>>>>>>>> >>> ld: illegal thread local variable reference to regular symbol >>>>>>>>> _PARI_SIGINT_block for architecture x86_64 >>>>>>>>> >>> clang: error: linker command failed with exit code 1 (use -v >>>>>>>>> to see invocation) >>>>>>>>> >>> error: command 'gcc' failed with exit status 1 >>>>>>>>> >>> Building wheel for cysignals (setup.py): finished with status >>>>>>>>> 'error' >>>>>>>>> >>> ERROR: Failed building wheel for cysignals >>>>>>>>> >>> >>>>>>>>> >>> This is my compiler version: >>>>>>>>> >>> >>>>>>>>> >>> Configured with: >>>>>>>>> --prefix=/Applications/Xcode.app/Contents/Developer/usr >>>>>>>>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 >>>>>>>>> >>>>>>>>> >>> Apple clang version 12.0.0 (clang-1200.0.32.21) >>>>>>>>> >>> Target: x86_64-apple-darwin19.6.0 >>>>>>>>> >>> Thread model: posix >>>>>>>>> >>> InstalledDir: >>>>>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>>>>>>>> >>>>>>>>> >>> >>>>>>>>> >>> Any idea what the problem might be, and how to solve it? >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> 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/38ff74b7-a4bf-4118-8519-9f57736ba532n%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-...@googlegroups.com. >>>>>>> >>>>>>> >>>>>>>> To view this discussion on the web visit >>>>>>>> https://groups.google.com/d/msgid/sage-devel/c76466bf-9141-4761-83ef-e97b7d28d691n%40googlegroups.com >>>>>>>> <https://groups.google.com/d/msgid/sage-devel/c76466bf-9141-4761-83ef-e97b7d28d691n%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+...@googlegroups.com. >>>>> >>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/sage-devel/e5318380-9c73-4a85-93de-3583b3be4f6cn%40googlegroups.com >>>>> <https://groups.google.com/d/msgid/sage-devel/e5318380-9c73-4a85-93de-3583b3be4f6cn%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/bce36b24-7c6f-42db-875d-a0b07c86927fn%40googlegroups.com > <https://groups.google.com/d/msgid/sage-devel/bce36b24-7c6f-42db-875d-a0b07c86927fn%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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