BUG: build failure with Xcode 15 linker #24964

adamjstewart · 2023-10-19T18:31:26Z

Describe the issue:

I'm unable to build numpy 1.26.1 with the new linker added in Xcode 15. However, adding the following allows the build to work:

export LDFLAGS=-Wl,-ld_classic

Reproduce the code example:

Error message:

Run-time dependency scipy-openblas found: NO (tried pkgconfig, framework and cmake)
  WARNING: CMake Toolchain: Failed to determine CMake compilers state
  Run-time dependency openblas found: NO (tried pkgconfig, pkgconfig, pkgconfig and system)

  ../../numpy/meson.build:169:4: ERROR: Problem encountered: No BLAS library detected! Install one, or use the `allow-noblas` build option (note, this may be up to 100x slower for some linear algebra operations).

Runtime information:

Numpy 1.26.1
Python 3.11.6
OpenBLAS 0.3.24

Context for the issue:

Possibly related to scipy/scipy#19357

@rgommers

rgommers · 2023-10-19T19:12:55Z

Thanks @adamjstewart. Could you add the contents of meson-log.txt:

/private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-fpvytybgj754onbg7pdnjyxxrwvdlkec/spack-src/.mesonpy-pg7fuk8j/build/meson-logs/meson-log.txt

I think that that shows why OpenBLAS gets rejected.

adamjstewart · 2023-10-19T22:00:13Z

That's the neat part, this file doesn't exist 😄

andyfaff · 2023-10-19T22:18:36Z

I have scipy_openblas32==0.3.23.293.1 installed and I can build numpy main.

git clean -xdf
pip install scipy_openblas32==0.3.23.293.1
export LDFLAGS=-Wl,-ld_classic
spin build --with-scipy-openblas=32

works for me on Sonoma. If I don't use scipy_openblas32 then numpy picks up the Accelerate library instead. It seems that when you're building via spack it's not picking up Accelerate.

Have you tried setting PKG_CONFIG_PATH to the location of the OpenBLAS pkgconfig file?

adamjstewart · 2023-10-20T09:16:37Z

@andyfaff it works because you're using the old linker. If you don't override LDFLAGS you may be able to reproduce my issue.

Have you tried setting PKG_CONFIG_PATH to the location of the OpenBLAS pkgconfig file?

See the "build env" file. PKG_CONFIG_PATH contains /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/pkgconfig which contains openblas.pc, which contains:

libdir=/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib
libsuffix=
includedir=/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/include
openblas_config= USE_64BITINT= DYNAMIC_ARCH=1 DYNAMIC_OLDER=1 NO_CBLAS= NO_LAPACK= NO_LAPACKE= NO_AFFINITY=1 USE_OPENMP=0 generic MAX_THREADS=10
version=0.3.24
extralib=-lgfortran -lgfortran
Name: openblas
Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version
Version: ${version}
URL: https://github.com/xianyi/OpenBLAS
Libs: -L${libdir} -lopenblas${libsuffix}
Libs.private: ${extralib}
Cflags: -I${includedir}

rgommers · 2023-10-20T09:25:12Z

That's the neat part, this file doesn't exist

Oh yes, this is a continual pain. You can preserve it by adding -Cbuilddir=build to pip install, and then it'll be located at build/meson-logs/meson-log.txt.

It seems that when you're building via spack it's not picking up Accelerate.

Adam's build explicitly uses -Dblas=openblas -Dlapack=openblas, that's why. And that's done to get all packages in the env to build against the exact same BLAS library (which is healthy).

adamjstewart · 2023-10-20T09:36:30Z

Thanks for the tip! Here's the meson log: meson-log.txt

Also:

> otool -L /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas.dylib
/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas.dylib:
	/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas.0.dylib (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	@rpath/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1336.0.0)

rgommers · 2023-10-20T10:05:03Z

Okay, so pkg-config finds openblas just fine, but it's the symbol check for cblas_dgemm that fails with a linker error. Relevant lines from the log:

Determining dependency 'openblas' with pkg-config executable '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/bin/pkg-config'
env[PKG_CONFIG_PATH]: /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/python-3.11.6-ylad4axebkcsdilseqetxyecuhlbsi3f/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/sqlite-3.42.0-s3sr5nn6bwvs5f77zfngincdciajtlnh/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openssl-3.1.3-n7drqo4b5taqelmp5w4s5lreolt65ygt/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxcrypt-4.4.35-isqux3dausvm4dkfmplelfbs4mvmw7po/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libffi-3.4.4-hvu7kno6itjof43awvr6wxrzrspu5hm2/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxml2-2.10.3-4fw6bp73f24u6jmnnx2ucxxmpz5qxscz/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/zlib-ng-2.1.3-udbedjfxmaeoizr4at4b6b6hevpz3s3p/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/xz-5.4.1-n2svr6k5c6cjq72uwfqab6p2iwp6pcfl/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/readline-8.2-vutsa2grq6b6ah4d26sx2nb4cab7juux/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/ncurses-6.4-mpuvfeqtcht6btblblzfjttv6ozqvidd/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/expat-2.5.0-vrnr3zgscr7eontokwoj2tbjqa65jrk6/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/bzip2-1.0.8-gkrn62h4dkkykl2ymhbtscdz4brn5ki7/lib/pkgconfig
-----------
Called: `/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/bin/pkg-config --modversion openblas` -> 0
stdout:
0.3.24
-----------
env[PKG_CONFIG_PATH]: /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/python-3.11.6-ylad4axebkcsdilseqetxyecuhlbsi3f/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/sqlite-3.42.0-s3sr5nn6bwvs5f77zfngincdciajtlnh/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openssl-3.1.3-n7drqo4b5taqelmp5w4s5lreolt65ygt/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxcrypt-4.4.35-isqux3dausvm4dkfmplelfbs4mvmw7po/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libffi-3.4.4-hvu7kno6itjof43awvr6wxrzrspu5hm2/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxml2-2.10.3-4fw6bp73f24u6jmnnx2ucxxmpz5qxscz/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/zlib-ng-2.1.3-udbedjfxmaeoizr4at4b6b6hevpz3s3p/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/xz-5.4.1-n2svr6k5c6cjq72uwfqab6p2iwp6pcfl/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/readline-8.2-vutsa2grq6b6ah4d26sx2nb4cab7juux/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/ncurses-6.4-mpuvfeqtcht6btblblzfjttv6ozqvidd/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/expat-2.5.0-vrnr3zgscr7eontokwoj2tbjqa65jrk6/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/bzip2-1.0.8-gkrn62h4dkkykl2ymhbtscdz4brn5ki7/lib/pkgconfig
-----------
Called: `/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/bin/pkg-config --cflags openblas` -> 0
stdout:
-I/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/include
-----------
env[PKG_CONFIG_PATH]: /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/python-3.11.6-ylad4axebkcsdilseqetxyecuhlbsi3f/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/sqlite-3.42.0-s3sr5nn6bwvs5f77zfngincdciajtlnh/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openssl-3.1.3-n7drqo4b5taqelmp5w4s5lreolt65ygt/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxcrypt-4.4.35-isqux3dausvm4dkfmplelfbs4mvmw7po/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libffi-3.4.4-hvu7kno6itjof43awvr6wxrzrspu5hm2/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxml2-2.10.3-4fw6bp73f24u6jmnnx2ucxxmpz5qxscz/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/zlib-ng-2.1.3-udbedjfxmaeoizr4at4b6b6hevpz3s3p/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/xz-5.4.1-n2svr6k5c6cjq72uwfqab6p2iwp6pcfl/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/readline-8.2-vutsa2grq6b6ah4d26sx2nb4cab7juux/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/ncurses-6.4-mpuvfeqtcht6btblblzfjttv6ozqvidd/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/expat-2.5.0-vrnr3zgscr7eontokwoj2tbjqa65jrk6/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/bzip2-1.0.8-gkrn62h4dkkykl2ymhbtscdz4brn5ki7/lib/pkgconfig
env[PKG_CONFIG_ALLOW_SYSTEM_LIBS]: 1
-----------
Called: `/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/bin/pkg-config --libs openblas` -> 0
stdout:
-L/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib -lopenblas
-----------
env[PKG_CONFIG_PATH]: /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/python-3.11.6-ylad4axebkcsdilseqetxyecuhlbsi3f/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/sqlite-3.42.0-s3sr5nn6bwvs5f77zfngincdciajtlnh/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openssl-3.1.3-n7drqo4b5taqelmp5w4s5lreolt65ygt/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxcrypt-4.4.35-isqux3dausvm4dkfmplelfbs4mvmw7po/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libffi-3.4.4-hvu7kno6itjof43awvr6wxrzrspu5hm2/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxml2-2.10.3-4fw6bp73f24u6jmnnx2ucxxmpz5qxscz/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/zlib-ng-2.1.3-udbedjfxmaeoizr4at4b6b6hevpz3s3p/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/xz-5.4.1-n2svr6k5c6cjq72uwfqab6p2iwp6pcfl/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/readline-8.2-vutsa2grq6b6ah4d26sx2nb4cab7juux/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/ncurses-6.4-mpuvfeqtcht6btblblzfjttv6ozqvidd/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/expat-2.5.0-vrnr3zgscr7eontokwoj2tbjqa65jrk6/lib/pkgconfig:/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/bzip2-1.0.8-gkrn62h4dkkykl2ymhbtscdz4brn5ki7/lib/pkgconfig
-----------
Called: `/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol/bin/pkg-config --libs openblas` -> 0
stdout:
-L/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib -lopenblas
-----------
Running compile:
Working directory:  /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp2wrdpzug
Code:
 
        #include<stdio.h>
        int main(void) {
            printf("%ld\n", (long)(sizeof(void *)));
            return 0;
        }
-----------
Command line: `/Users/Adam/spack/lib/spack/env/clang/clang++ /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp2wrdpzug/testfile.cpp -o /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp2wrdpzug/output.exe -O0 -fpermissive -Werror=implicit-function-declaration` -> 0
Program stdout:

8

Program stderr:


Running compile:
Working directory:  /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmpw0c2imi9
Code:
 
-----------
Command line: `/Users/Adam/spack/lib/spack/env/clang/clang++ /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmpw0c2imi9/testfile.cpp -o /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmpw0c2imi9/output.obj -c -O0 -fpermissive -Werror=implicit-function-declaration -Werror=unknown-warning-option -Werror=unused-command-line-argument -Werror=ignored-optimization-argument --print-search-dirs` -> 0
stdout:
programs: =/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
libraries: =/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0
-----------
Running compile:
Working directory:  /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp6b7iqv0_
Code:
 #ifdef __cplusplus
               extern "C" {
               #endif
               void dgemm_();
void cblas_dgemm();
int main(int argc, const char *argv[])
{
  dgemm_();
  cblas_dgemm();
  return 0;
}
               #ifdef __cplusplus
               }
               #endif
               
-----------
Command line: `/Users/Adam/spack/lib/spack/env/clang/clang++ /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp6b7iqv0_/testfile.cpp -o /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp6b7iqv0_/output.exe -O0 -fpermissive -Werror=implicit-function-declaration /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas.dylib` -> 1
stderr:
ld: duplicate LC_RPATH '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/gcc-13.2.0-qhn4xdjhn2p7k2fnvllfz2ca6xhwl2yu/lib' in '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas-r0.3.24.dylib'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
-----------
Running compile:
Working directory:  /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp420bxawd
Code:
 int main(void) { return 0; }

-----------
Command line: `/Users/Adam/spack/lib/spack/env/clang/clang++ /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp420bxawd/testfile.cpp -o /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp420bxawd/output.exe -O0 -fpermissive -Werror=implicit-function-declaration -lopenblas -Wl,-undefined,dynamic_lookup` -> 1
stderr:
ld: duplicate LC_RPATH '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/gcc-13.2.0-qhn4xdjhn2p7k2fnvllfz2ca6xhwl2yu/lib' in '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas-r0.3.24.dylib'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
-----------
Running compile:
Working directory:  /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp_r258wx2
Code:
 
        #ifdef __has_include
         #if !__has_include("openblas_config.h")
          #error "Header 'openblas_config.h' could not be found"
         #endif
        #else
         #include <openblas_config.h>
        #endif
-----------
Command line: `/Users/Adam/spack/lib/spack/env/clang/clang++ /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/tmp_r258wx2/testfile.cpp -E -P -P -O0 -fpermissive -Werror=implicit-function-declaration` -> 0
CMake binary for 1 is cached.

Determining dependency 'OpenBLAS' with CMake executable '/Users/Adam/spack/var/spack/environments/system/.spack-env/view/bin/cmake'
CMake Toolchain: Calling CMake once to generate the compiler state
Calling CMake (['/Users/Adam/spack/var/spack/environments/system/.spack-env/view/bin/cmake']) in /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/__CMake_compiler_info__ with:
  - "--trace-expand"
  - "--trace-format=json-v1"
  - "--no-warn-unused-cli"
  - "--trace-redirect=cmake_trace.txt"
  - "-G"
  - "Ninja"
  - "-DCMAKE_TOOLCHAIN_FILE=/private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/__CMake_compiler_info__/CMakeMesonTempToolchainFile.cmake"
  - "."
  - "-DCMAKE_PREFIX_PATH=/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/py-pyproject-metadata-0.7.1-t3nphl5nbf5uli3tet2qhwbvymhc2lsu;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/py-cython-3.0.0-aka24ggjwhr3fm25acotma3xgweecyvm;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/py-wheel-0.37.1-kaul57dgtdjcg2kwgvyd3tkyqnbpqegl;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/py-pip-23.1.2-ysprj2hfy6tbxh2vqvkr2vl2r5cmiviy;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/python-3.11.6-ylad4axebkcsdilseqetxyecuhlbsi3f;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/gettext-0.21.1-5h3562itimi7rrfpc5ks6r6sivmhg3be;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/ninja-1.11.1-6vrybrmj5cqfbehsop6ts6fqz62jo4ni;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/sqlite-3.42.0-s3sr5nn6bwvs5f77zfngincdciajtlnh;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openssl-3.1.3-n7drqo4b5taqelmp5w4s5lreolt65ygt;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxcrypt-4.4.35-isqux3dausvm4dkfmplelfbs4mvmw7po;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libffi-3.4.4-hvu7kno6itjof43awvr6wxrzrspu5hm2;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/tar-1.34-fgos7l7uuyvrpopbjtr57iwvf3l5hfbz;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxml2-2.10.3-4fw6bp73f24u6jmnnx2ucxxmpz5qxscz;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/zlib-ng-2.1.3-udbedjfxmaeoizr4at4b6b6hevpz3s3p;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/xz-5.4.1-n2svr6k5c6cjq72uwfqab6p2iwp6pcfl;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/gdbm-1.23-tlvs2i3rs5gxg3uad5sqkgdj6o5iswrp;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/readline-8.2-vutsa2grq6b6ah4d26sx2nb4cab7juux;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/ncurses-6.4-mpuvfeqtcht6btblblzfjttv6ozqvidd;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/expat-2.5.0-vrnr3zgscr7eontokwoj2tbjqa65jrk6;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/bzip2-1.0.8-gkrn62h4dkkykl2ymhbtscdz4brn5ki7;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libiconv-1.17-3tm2ez733pxbo2itak6g23rfzmv6ej6m"
WARNING: CMake Toolchain: Failed to determine CMake compilers state
Try CMake generator: auto
Calling CMake (['/Users/Adam/spack/var/spack/environments/system/.spack-env/view/bin/cmake']) in /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/cmake_OpenBLAS with:
  - "-DNAME=OpenBLAS"
  - "-DARCHS="
  - "-DVERSION="
  - "-DCOMPS="
  - "-DSTATIC=False"
  - "--trace-expand"
  - "--trace-format=json-v1"
  - "--no-warn-unused-cli"
  - "--trace-redirect=cmake_trace.txt"
  - "-DCMAKE_TOOLCHAIN_FILE=/private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/cmake_OpenBLAS/CMakeMesonToolchainFile.cmake"
  - "."
  - "-DCMAKE_PREFIX_PATH=/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/py-pyproject-metadata-0.7.1-t3nphl5nbf5uli3tet2qhwbvymhc2lsu;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/py-cython-3.0.0-aka24ggjwhr3fm25acotma3xgweecyvm;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/py-wheel-0.37.1-kaul57dgtdjcg2kwgvyd3tkyqnbpqegl;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/py-pip-23.1.2-ysprj2hfy6tbxh2vqvkr2vl2r5cmiviy;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/python-3.11.6-ylad4axebkcsdilseqetxyecuhlbsi3f;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/gettext-0.21.1-5h3562itimi7rrfpc5ks6r6sivmhg3be;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/ninja-1.11.1-6vrybrmj5cqfbehsop6ts6fqz62jo4ni;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/sqlite-3.42.0-s3sr5nn6bwvs5f77zfngincdciajtlnh;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openssl-3.1.3-n7drqo4b5taqelmp5w4s5lreolt65ygt;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxcrypt-4.4.35-isqux3dausvm4dkfmplelfbs4mvmw7po;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libffi-3.4.4-hvu7kno6itjof43awvr6wxrzrspu5hm2;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/tar-1.34-fgos7l7uuyvrpopbjtr57iwvf3l5hfbz;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libxml2-2.10.3-4fw6bp73f24u6jmnnx2ucxxmpz5qxscz;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/zlib-ng-2.1.3-udbedjfxmaeoizr4at4b6b6hevpz3s3p;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/xz-5.4.1-n2svr6k5c6cjq72uwfqab6p2iwp6pcfl;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/gdbm-1.23-tlvs2i3rs5gxg3uad5sqkgdj6o5iswrp;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/readline-8.2-vutsa2grq6b6ah4d26sx2nb4cab7juux;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/ncurses-6.4-mpuvfeqtcht6btblblzfjttv6ozqvidd;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/pkgconf-1.9.5-qqypctpzhh2ovbi42iin6qdtgnqyn6ol;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/expat-2.5.0-vrnr3zgscr7eontokwoj2tbjqa65jrk6;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/bzip2-1.0.8-gkrn62h4dkkykl2ymhbtscdz4brn5ki7;/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/libiconv-1.17-3tm2ez733pxbo2itak6g23rfzmv6ej6m"
CMake trace warning: add_executable() non imported executables are not supported
CMake TRACE: /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/cmake_OpenBLAS/CMakeFiles/CMakeScratch/TryCompile-nqxvDZ/CMakeLists.txt:18 add_executable(['cmTC_568ee', '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/cmake-3.27.6-6g357lfiwm2qllfg7v4u36cy6t2zohxl/share/cmake-3.27/Modules/CMakeCCompilerABI.c'])
CMake trace warning: target_link_options() TARGET cmTC_568ee not found
CMake TRACE: /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/cmake_OpenBLAS/CMakeFiles/CMakeScratch/TryCompile-nqxvDZ/CMakeLists.txt:21 target_link_libraries(['cmTC_568ee', ''])
CMake trace warning: add_executable() non imported executables are not supported
CMake TRACE: /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/cmake_OpenBLAS/CMakeFiles/CMakeScratch/TryCompile-kOKmuq/CMakeLists.txt:18 add_executable(['cmTC_2fc17', '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/cmake-3.27.6-6g357lfiwm2qllfg7v4u36cy6t2zohxl/share/cmake-3.27/Modules/CMakeCXXCompilerABI.cpp'])
CMake trace warning: target_link_options() TARGET cmTC_2fc17 not found
CMake TRACE: /private/var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/Adam/spack-stage/spack-stage-py-numpy-1.26.1-42rdd3ko5lefvbteif7fj5xbwfqdrzf4/spack-src/build/meson-private/cmake_OpenBLAS/CMakeFiles/CMakeScratch/TryCompile-kOKmuq/CMakeLists.txt:21 target_link_libraries(['cmTC_2fc17', ''])
Dependency lookup for openblas with method 'cmake' failed: Dependency OpenBLAS not found: CMake: invalid module cblas for OpenBLAS.
Try to explicitly specify one or more targets with the "modules" property.
Valid targets are:
[]
Run-time dependency openblas found: NO (tried pkgconfig, pkgconfig, pkgconfig and system)

If that does work with the classic linker, then I guess it's a linker problem indeed. The check works fine for me with the XCode 15 clang/clang++/ld. So I guess it depends also on how OpenBLAS is built.

The check is:

 #ifdef __cplusplus
               extern "C" {
               #endif
               void dgemm_();
void cblas_dgemm();
int main(int argc, const char *argv[])
{
  dgemm_();
  cblas_dgemm();
  return 0;
}
               #ifdef __cplusplus
               }
               #endif

Maybe that standalone test helps? It should build with clang++ and the right link/include paths, something like:

clang++ testfile.cpp -o testfile -I/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/include -L/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib -lopenblas

Did you build gfortran and openblas from scratch with the new XCode compilers inside your Spack env? I guess that's where the difference comes from; the conda-forge ones built on an older macOS version seem fine.

adamjstewart · 2023-10-20T10:05:56Z

Yes, Spack-installed gfortran and openblas from source.

adamjstewart · 2023-10-20T10:07:52Z

Yes, that testfile.cpp example fails for me:

> clang++ testfile.cpp -o testfile -I/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/include -L/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib -lopenblas -v

Apple clang version 15.0.0 (clang-1500.0.40.1)
Target: arm64-apple-darwin23.0.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple arm64-apple-macosx14.0.0 -Wundef-prefix=TARGET_OS_ -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -Werror=implicit-function-declaration -emit-obj -mrelax-all --mrelax-relocations -disable-free -clear-ast-before-backend -disable-llvm-verifier -discard-value-names -main-file-name testfile.cpp -mrelocation-model pic -pic-level 2 -mframe-pointer=non-leaf -fno-strict-return -ffp-contract=on -fno-rounding-math -funwind-tables=1 -fobjc-msgsend-selector-stubs -target-sdk-version=14.0 -fvisibility-inlines-hidden-static-local-var -target-cpu apple-m1 -target-feature +v8.5a -target-feature +crc -target-feature +lse -target-feature +rdm -target-feature +crypto -target-feature +dotprod -target-feature +fp-armv8 -target-feature +neon -target-feature +fp16fml -target-feature +ras -target-feature +rcpc -target-feature +zcm -target-feature +zcz -target-feature +fullfp16 -target-feature +sm4 -target-feature +sha3 -target-feature +sha2 -target-feature +aes -target-abi darwinpcs -mllvm -treat-scalable-fixed-error-as-warning -debugger-tuning=lldb -target-linker-version 1015.6 -v -fcoverage-compilation-dir=/Users/Adam/Downloads -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/include -I/usr/local/include -internal-isystem /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1 -internal-isystem /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/local/include -internal-isystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include -internal-externc-isystem /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include -internal-externc-isystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include -Wno-reorder-init-list -Wno-implicit-int-float-conversion -Wno-c99-designator -Wno-final-dtor-non-final-class -Wno-extra-semi-stmt -Wno-misleading-indentation -Wno-quoted-include-in-framework-header -Wno-implicit-fallthrough -Wno-enum-enum-conversion -Wno-enum-float-conversion -Wno-elaborated-enum-base -Wno-reserved-identifier -Wno-gnu-folding-constant -fdeprecated-macro -fdebug-compilation-dir=/Users/Adam/Downloads -ferror-limit 19 -stack-protector 1 -fstack-check -mdarwin-stkchk-strong-link -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fgnuc-version=4.2.1 -fno-cxx-modules -fcxx-exceptions -fexceptions -fmax-type-align=16 -fcommon -fcolor-diagnostics -clang-vendor-feature=+disableNonDependentMemberExprInCurrentInstantiation -fno-odr-hash-protocols -clang-vendor-feature=+enableAggressiveVLAFolding -clang-vendor-feature=+revert09abecef7bbf -clang-vendor-feature=+thisNoAlignAttr -clang-vendor-feature=+thisNoNullAttr -mllvm -disable-aligned-alloc-awareness=1 -D__GCC_HAVE_DWARF2_CFI_ASM=1 -o /var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/testfile-bf393f.o -x c++ testfile.cpp
clang -cc1 version 15.0.0 (clang-1500.0.40.1) default target arm64-apple-darwin23.0.0
ignoring nonexistent directory "/usr/local/include"
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/local/include"
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/include
 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include
 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks (framework directory)
End of search list.
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -lto_library /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/libLTO.dylib -no_deduplicate -dynamic -arch arm64 -platform_version macos 14.0.0 14.0 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -o testfile -L/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib -L/usr/local/lib /var/folders/jv/cgkfvslj6nq1l7cw0c8c_8gm0000gn/T/testfile-bf393f.o -lopenblas -lc++ -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/lib/darwin/libclang_rt.osx.a
ld: duplicate LC_RPATH '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/gcc-13.2.0-qhn4xdjhn2p7k2fnvllfz2ca6xhwl2yu/lib' in '/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas-r0.3.24.dylib'
clang: error: linker command failed with exit code 1 (use -v to see invocation)

rgommers · 2023-10-20T10:12:48Z

Can you add -v to the above so we see what the linker fails with, and also post the output of

objdump -t /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas.0.dylib

so we can see the symbols are actually present?

adamjstewart · 2023-10-20T10:17:19Z

> otool -vL /Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas.dylib
/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas.dylib:
	/Users/Adam/spack/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/openblas-0.3.24-lsn4jcy34p62ysj7qq2ghlsawu6sco6a/lib/libopenblas.0.dylib (compatibility version 0.0.0, current version 0.0.0)
	time stamp 1 Thu Jan  1 01:00:01 1970
	@rpath/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	time stamp 2 Thu Jan  1 01:00:02 1970
	@rpath/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	time stamp 2 Thu Jan  1 01:00:02 1970
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1336.0.0)
	time stamp 2 Thu Jan  1 01:00:02 1970

Other request: objects.txt

rgommers · 2023-10-20T10:27:32Z

That looks the same as what I see on my machine:

g     F __TEXT,__text _cblas_dgemm
g     F __TEXT,__text _dgemm_

I think this is a good place to stop, since I don't think there's much of a downside in adding the linker flag to use the classic linker, and revisiting once the new linker is a bit more mature.

Closes numpygh-24964

jfuruness · 2023-10-28T15:42:32Z

I've also had this issue on an ubuntu machine when installing numpy using pypy. I found a fix elsewhere, I no longer remember where, of pip install numpy --config-settings=setup-args="-Dallow-noblas=true", which fixes the issue for me

Closes numpygh-24964

adamjstewart added the 00 - Bug label Oct 19, 2023

rgommers added a commit to rgommers/numpy that referenced this issue Oct 20, 2023

BLD: use classic linker on macOS, the new one in XCode 15 has issues

78f013b

Closes numpygh-24964

rgommers added a commit to rgommers/numpy that referenced this issue Oct 20, 2023

BLD: use classic linker on macOS, the new one in XCode 15 has issues

636111f

Closes numpygh-24964

rgommers mentioned this issue Oct 20, 2023

BLD: use classic linker on macOS, the new one in XCode 15 has issues #24967

Merged

charris closed this as completed in #24967 Oct 21, 2023

charris pushed a commit to charris/numpy that referenced this issue Oct 21, 2023

BLD: use classic linker on macOS, the new one in XCode 15 has issues

e5b1ce1

Closes numpygh-24964

charris mentioned this issue Oct 21, 2023

BLD: use classic linker on macOS, the new one in XCode 15 has issues #24977

Merged

charris pushed a commit to charris/numpy that referenced this issue Nov 11, 2023

BLD: use classic linker on macOS, the new one in XCode 15 has issues

98ebeac

Closes numpygh-24964

adamjstewart mentioned this issue Apr 9, 2025

Installation issue: py-numpy ^openblas %apple-clang@17 spack/spack#49983

Closed

4 tasks

mathomp4 mentioned this issue Apr 9, 2025

Issues with XCode 16.3 GEOS-ESM/ESMA_cmake#438

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