Date: Mon, 9 Nov 2009 15:07:55 -0600 (CST) From: Scott Bennett <bennett@cs.niu.edu> To: bf1783@googlemail.com Cc: maho@freebsd.org, freebsd-questions@freebsd.org Subject: Re: math/py-numpy vs. math/atlas-devel Message-ID: <200911092107.nA9L7tHX029304@mp.cs.niu.edu>
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On Mon, 9 Nov 2009 20:26:15 +0000 "b. f." <bf1783@googlemail.com>
wrote:
>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
Okay, but be advised that the ATLAS library takes around six hours
to build on a 3.4 GHz Prescott with little else active on the machine
at the time. (ATLAS should be built on a very quiet machine, so that
its timing tests will be fairly accurate. The build is likely to die
if several runs of a timing test yield a variance greater than what the
build procedure wants.)
>send a full build transcript to me and the math/py-numpy maintainer
>via private email.
Will do, but probably not till tonight sometime.
>
>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
1046:-lgfortran.3 => /usr/local/lib/gcc43/libgfortran.so.3
1056:-lgfortran.3 => /usr/local/lib/gcc44/libgfortran.so.3
1068:-lgfortran.3 => /usr/local/lib/gcc45/libgfortran.so.3
>
>and for static libraries or unregistered shared libraries, locate(1)
>and find(1) are your friends.
>
Well, locate(1) *ought* to be, you're right. However, although it
worked fine on FreeBSD 5, I've never succeeded in getting FreeBSD 6 or 7
to build the locate database properly. It would be nice, but I've already
spent too many hours on too many occasions trying to track down the trouble,
so I just use find(1).
find(1) turns up the following.
/usr/local/lib/gcc43/gcc/i386-portbld-freebsd7.2/4.3.5/libgfortranbegin.la
/usr/local/lib/gcc43/gcc/i386-portbld-freebsd7.2/4.3.5/libgfortranbegin.a
/usr/local/lib/gcc43/libgfortran.so.3
/usr/local/lib/gcc43/libgfortran.so
/usr/local/lib/gcc43/libgfortran.a
/usr/local/lib/gcc44/gcc/i386-portbld-freebsd7.2/4.4.3/libgfortranbegin.la
/usr/local/lib/gcc44/gcc/i386-portbld-freebsd7.2/4.4.3/libgfortranbegin.a
/usr/local/lib/gcc44/libgfortran.so.3
/usr/local/lib/gcc44/libgfortran.so
/usr/local/lib/gcc44/libgfortran.a
/usr/local/lib/gcc45/gcc/i386-portbld-freebsd7.2/4.5.0/libgfortranbegin.la
/usr/local/lib/gcc45/gcc/i386-portbld-freebsd7.2/4.5.0/libgfortranbegin.a
/usr/local/lib/gcc45/libgfortran.so.3
/usr/local/lib/gcc45/libgfortran.so
/usr/local/lib/gcc45/libgfortran.a
I'll get the rest of the stuff off to you later tonight. Thank you
very much for looking at all of this. I wonder if I'm the only person
trying to install science/gnudatalanguage. There have been enough
obstacles to getting that done that I have to wonder how the maintainer
managed to test it.
Scott Bennett, Comm. ASMELG, CFIAG
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