Date: Mon, 9 Nov 2009 20:26:15 +0000 From: "b. f." <bf1783@googlemail.com> To: Scott Bennett <bennett@cs.niu.edu> Cc: maho@freebsd.org, freebsd-questions@freebsd.org Subject: Re: math/py-numpy vs. math/atlas-devel Message-ID: <d873d5be0911091226x206ea98cxb3c65c456183d10c@mail.gmail.com> In-Reply-To: <200911091037.nA9Abq9b021278@mp.cs.niu.edu> References: <200911091037.nA9Abq9b021278@mp.cs.niu.edu>
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On 11/9/09, Scott Bennett <bennett@cs.niu.edu> wrote:
> On Sun, 08 Nov 2009 23:59:29 -0800 Doug Barton <dougb@FreeBSD.org>
> wrote:
...
> Anyway, the math/py-numpy port now proceeds to build without bothering
> with math/atlas. It quickly goes astray when it doesn't recognize that any
> of gfortran4[345] has been installed--I guess there no longer is a FORTRAN
> compiler included in the base system--and instead tries to use lang/g95,
> which has also been installed. Of course, this won't work because the ATLAS
> library needs to have been compiled with the same compiler as the programs
> that use it.
>
> ===> Configuring for py26-numpy-1.3.0_2,1
> Running from numpy source directory.
> [39mF2PY Version 2 [0m
> [39mblas_opt_info: [0m
> [39mblas_mkl_info: [0m
> [39m libraries mkl,vml,guide not found in /usr/lib [0m
> [39m libraries mkl,vml,guide not found in /usr/local/lib [0m
> [39m libraries mkl,vml,guide not found in
> /usr/local/lib/gcc44/gcc/i386-portbld-freebsd7.2/4.4.3/../../../ [0m
> [39m NOT AVAILABLE [0m
> [39m [0m
> [39matlas_blas_threads_info: [0m
> [39mSetting PTATLAS=ATLAS [0m
> [39mSetting PTATLAS=ATLAS [0m
> [39mSetting PTATLAS=ATLAS [0m
> [39m FOUND: [0m
> [39m libraries = ['alapack_r', 'f77blas_r', 'cblas_r', 'atlas_r'] [0m
> [39m library_dirs = ['/usr/local/lib'] [0m
> [39m language = c [0m
> [39m include_dirs = ['/usr/local/include'] [0m
> [39m [0m
> /usr/ports/math/py-numpy/work/numpy-1.3.0/numpy/distutils/command/config.py:361:
> DeprecationWarning:
> +++++++++++++++++++++++++++++++++++++++++++++++++
> Usage of get_output is deprecated: please do not
> use it anymore, and avoid configuration checks
> involving running executable on the target machine.
> +++++++++++++++++++++++++++++++++++++++++++++++++
>
> DeprecationWarning)
> [39mcustomize GnuFCompiler [0m
> [32mFound executable /usr/local/bin/gfortran44 [0m
> [31mgnu: no Fortran 90 compiler found [0m
> [31mgnu: no Fortran 90 compiler found [0m
> [39mcustomize Gnu95FCompiler [0m
> [39mcustomize Gnu95FCompiler [0m
> [39mcustomize Gnu95FCompiler using config [0m
> compiling '_configtest.c':
>
> /* This file is generated from numpy/distutils/system_info.py */
> void ATL_buildinfo(void);
> int main(void) {
> ATL_buildinfo();
> return 0;
> }
> [39mC compiler: gcc44 -DNDEBUG -O2 -fno-strict-aliasing -pipe
> -march=prescott -D__wchar_t=wchar_t -DTHREAD_STACK_SIZE=0x100000 -O2
> -fno-strict-aliasing -pipe -march=prescott -Wl,-rpath=/usr/local/lib/gcc44
> -fPIC
> [0m
> [39mcompile options: '-c' [0m
> [39mgcc44: _configtest.c [0m
> [39mgcc44 _configtest.o -L/usr/local/lib -lalapack_r -lf77blas_r -lcblas_r
> -latlas_r -o _configtest [0m
> /usr/bin/ld: _configtest: hidden symbol `__powisf2' in
> /usr/local/lib/gcc44/gcc/i386-portbld-freebsd7.2/4.4.3/libgcc.a(_powisf2.o)
> is referenced by DSO
> collect2: ld returned 1 exit status
> /usr/bin/ld: _configtest: hidden symbol `__powisf2' in
> /usr/local/lib/gcc44/gcc/i386-portbld-freebsd7.2/4.4.3/libgcc.a(_powisf2.o)
> is referenced by DSO
> collect2: ld returned 1 exit status
> [39mfailure. [0m
> [39mremoving: _configtest.c _configtest.o [0m
> [39mStatus: 255 [0m
> [39mOutput: [0m
> [39m FOUND: [0m
> [39m libraries = ['alapack_r', 'f77blas_r', 'cblas_r', 'atlas_r'] [0m
> [39m library_dirs = ['/usr/local/lib'] [0m
> [39m language = c [0m
> [39m define_macros = [('NO_ATLAS_INFO', 2)] [0m
> [39m include_dirs = ['/usr/local/include'] [0m
> [39m [0m
> [39mlapack_opt_info: [0m
> [39mlapack_mkl_info: [0m
> [39mmkl_info: [0m
> [39m libraries mkl,vml,guide not found in /usr/lib [0m
> [39m libraries mkl,vml,guide not found in /usr/local/lib [0m
> [39m libraries mkl,vml,guide not found in
> /usr/local/lib/gcc44/gcc/i386-portbld-freebsd7.2/4.4.3/../../../ [0m
> [39m NOT AVAILABLE [0m
> [39m [0m
> [39m NOT AVAILABLE [0m
> [39m [0m
> [39matlas_threads_info: [0m
> [39mSetting PTATLAS=ATLAS [0m
> [39m libraries lapack_atlas not found in /usr/local/lib [0m
> [39mnumpy.distutils.system_info.atlas_threads_info [0m
> [39mSetting PTATLAS=ATLAS [0m
> /usr/ports/math/py-numpy/work/numpy-1.3.0/numpy/distutils/system_info.py:999:
> UserWarning:
> *********************************************************************
> Lapack library (from ATLAS) is probably incomplete:
> size of /usr/local/lib/libalapack_r.so is 3832k (expected >4000k)
>
> Follow the instructions in the KNOWN PROBLEMS section of the file
> numpy/INSTALL.txt.
> *********************************************************************
>
> warnings.warn(message)
>
>
> The above sequence gets more or less repeated several more times, and
> after much compiling, running of python26, and other activities, the
> process runs aground as follows.
>
>
> [39mcreating build/temp.freebsd-7.2-STABLE-i386-2.6/numpy/fft [0m
> [39mcompile options: '-Inumpy/core/include
> -Ibuild/src.freebsd-7.2-STABLE-i386-2.6/numpy/core/include/numpy
> -Inumpy/core/src -Inumpy/core/include -I/usr/local/include/python2.6 -c' [0m
> [39mgcc44: numpy/fft/fftpack_litemodule.c [0m
> [39mgcc44: numpy/fft/fftpack.c [0m
> [39mcc -shared -pthread -O2 -fno-strict-aliasing -pipe -march=prescott
> -Wl,-rpath=/usr/local/lib/gcc44
> build/temp.freebsd-7.2-STABLE-i386-2.6/numpy/fft/fftpack_litemodule.o
> build/temp.freebsd-7.2-STABLE-i386-2.6/numpy/fft/fftpack.o
> -Lbuild/temp.freebsd-7.2-STABLE-i386-2.6 -o
> build/lib.freebsd-7.2-STABLE-i386-2.6/numpy/fft/fftpack_lite.so [0m
> [39mbuilding 'numpy.linalg.lapack_lite' extension [0m
> [39mcompiling C sources [0m
> [39mC compiler: gcc44 -DNDEBUG -O2 -fno-strict-aliasing -pipe
> -march=prescott -D__wchar_t=wchar_t -DTHREAD_STACK_SIZE=0x100000 -O2
> -fno-strict-aliasing -pipe -march=prescott -Wl,-rpath=/usr/local/lib/gcc44
> -fPIC
> [0m
> [39mcreating build/temp.freebsd-7.2-STABLE-i386-2.6/numpy/linalg [0m
> [39mcompile options: '-DATLAS_INFO="\"3.9.11\"" -I/usr/local/include
> -Inumpy/core/include
> -Ibuild/src.freebsd-7.2-STABLE-i386-2.6/numpy/core/include/numpy
> -Inumpy/core/src -Inumpy/core/include -I/usr/local/include/python2.6 -c' [0m
> [39mgcc44: numpy/linalg/lapack_litemodule.c [0m
> [39mgcc44: numpy/linalg/python_xerbla.c [0m
> [39mcc -shared -pthread -O2 -fno-strict-aliasing -pipe -march=prescott
> -Wl,-rpath=/usr/local/lib/gcc44
> build/temp.freebsd-7.2-STABLE-i386-2.6/numpy/linalg/lapack_litemodule.o
> build/temp.freebsd-7.2-STABLE-i386-2.6/numpy/linalg/python_xerbla.o
> -L/usr/local/lib -Lbuild/temp.freebsd-7.2-STABLE-i386-2.6 -lalapack_r
> -lalapack_r -lf77blas_r -lcblas_r -latlas_r -lgfortran -lm -lpthread -o
> build/lib.freebsd-7.2-STABLE-i386-2.6/numpy/linalg/lapack_lite.so [0m
> /usr/bin/ld: cannot find -lgfortran
> /usr/bin/ld: cannot find -lgfortran
> error: Command "cc -shared -pthread -O2 -fno-strict-aliasing -pipe
> -march=prescott -Wl,-rpath=/usr/local/lib/gcc44
> build/temp.freebsd-7.2-STABLE-i386-2.6/numpy/linalg/lapack_litemodule.o
> build/temp.freebsd-7.2-STABLE-i386-2.6/numpy/linalg/python_xerbla.o
> -L/usr/local/lib -Lbuild/temp.freebsd-7.2-STABLE-i386-2.6 -lalapack_r
> -lalapack_r -lf77blas_r -lcblas_r -latlas_r -lgfortran -lm -lpthread -o
> build/lib.freebsd-7.2-STABLE-i386-2.6/numpy/linalg/lapack_lite.so" failed
> with exit status 1
> *** Error code 1
>
> Stop in /usr/ports/math/py-numpy.
>
> ===>>> make failed for math/py-numpy
> ===>>> Aborting update
>
> I looked in /usr/local/lib and didn't spot libraries by name for
> gfortran[345], so I assume they have either been renamed or included in
> with the corresponding gcc libraries. What is the best way to proceed?
> Will simply deleting the instances of "-lgfortran" do the job? Or do I
> need to specify the library explicitly?
>
The port is broken WITH_ATLAS=yes on your system: it reverts to using
the base system C compiler, cc, when it should be using gcc44. You
trimmed off some relevant parts, so it is difficult to tell at a
glance whether this is because something is wrong with your system, or
with the port itself, although the port has a history of problems
with this non-default option. If I have some time later, I may play
with it, but at the moment, I don't have atlas installed. You should
send a full build transcript to me and the math/py-numpy maintainer
via private email.
The libraries in question should be in /usr/local/lib/gcc44. When
searching for registered shared libraries, it is easier to do
something like:
ldconfig -vr | grep -ie fortran
and for static libraries or unregistered shared libraries, locate(1)
and find(1) are your friends.
b.
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