Opened 6 years ago
Closed 6 years ago
#20524 closed defect (invalid)
numpy fails to compile with SAGE_ATLAS_LIB
Reported by: | vbraun | Owned by: | |
---|---|---|---|
Priority: | blocker | Milestone: | sage-duplicate/invalid/wontfix |
Component: | packages: standard | Keywords: | |
Cc: | fbissey | Merged in: | |
Authors: | Reviewers: | ||
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
If I'm building numpy with my own atlas install it fails. The cblas, atlas libraries are symlinked to SAGE_LOCAL/lib and the correct pkg-config output is present:
$ pkg-config --libs cblas -L/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib -lcblas -latlas
Yet numpy fails with
$ ./sage -p numpy This looks like the first time you are running Sage. Updating various hardcoded paths... (Please wait at most a few minutes.) DO NOT INTERRUPT THIS. Done updating paths. Found local metadata for numpy-1.11.0 Using cached file /mnt/disk/home/buildslave-sage/slave/sage_git/build/upstream/numpy-1.11.0.tar.gz numpy-1.11.0 ==================================================== Setting up build directory for numpy-1.11.0 Finished set up **************************************************** Host system: Linux volker-desktop 4.4.7-300.fc23.x86_64 #1 SMP Wed Apr 13 02:52:52 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=/usr/bin/gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/5.3.1/lto-wrapper Target: x86_64-redhat-linux Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,objc,obj-c++,fortran,ada,go,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --disable-libgcj --with-isl --enable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux Thread model: posix gcc version 5.3.1 20160406 (Red Hat 5.3.1-6) (GCC) **************************************************** Running from numpy source directory. Note: if you need reliable uninstall behavior, then install with pip instead of using `setup.py install`: - `pip install .` (from a git repo or downloaded source release) - `pip install numpy` (last Numpy release on PyPi) blas_opt_info: blas_mkl_info: Disabled blas_mkl_info: (MKL is None) Disabled blas_mkl_info: (MKL is None) libraries mkl,vml,guide not found in [] NOT AVAILABLE openblas_info: Disabled openblas_info: (OPENBLAS is None) libraries openblas not found in [] NOT AVAILABLE atlas_3_10_blas_threads_info: Disabled atlas_3_10_blas_threads_info: (PTATLAS is None) libraries tatlas not found in [] NOT AVAILABLE atlas_3_10_blas_info: Disabled atlas_3_10_blas_info: (ATLAS is None) libraries satlas not found in [] NOT AVAILABLE atlas_blas_threads_info: Disabled atlas_blas_threads_info: (PTATLAS is None) libraries ptf77blas,ptcblas,atlas not found in [] NOT AVAILABLE atlas_blas_info: Disabled atlas_blas_info: (ATLAS is None) libraries f77blas,cblas,atlas not found in [] NOT AVAILABLE /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/var/tmp/sage/build/numpy-1.11.0/src/numpy/distutils/system_info.py:1640: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: C compiler: cc creating /tmp/tmpKqg0LI/tmp creating /tmp/tmpKqg0LI/tmp/tmpKqg0LI compile options: '-I/usr/local/include -I/usr/include -I/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/include -c' cc: /tmp/tmpKqg0LI/source.c cc /tmp/tmpKqg0LI/tmp/tmpKqg0LI/source.o -L/mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib -lcblas -o /tmp/tmpKqg0LI/a.out /usr/bin/ld: warning: libatlas.so.3, needed by /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib/libcblas.so, not found (try using -rpath or -rpath-link) /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib/libcblas.so: undefined reference to `ATL_sasum' /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib/libcblas.so: undefined reference to `ATL_dsyr2' [...]
For some reason numpy forgot -latlas
...
Change History (3)
comment:1 Changed 6 years ago by
comment:2 Changed 6 years ago by
[ALL] library_dirs = /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib include_dirs = /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/include [blas] library_dirs = /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib blas_libs = atlas, f77blas, cblas [lapack] library_dirs = /mnt/disk/home/buildslave-sage/slave/sage_git/build/local/lib lapack_libs = lapack, f77blas, cblas, atlas
comment:3 Changed 6 years ago by
- Milestone changed from sage-7.2 to sage-duplicate/invalid/wontfix
- Resolution set to invalid
- Status changed from new to closed
False alert, was due to #20487 not applying the numpy patches...
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What does the generated
site.cfg
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