Wrong lapack version detection (32/64bits)
Hi, I'm trying to update numpy by compiling the up to date svn: I get this error : gcc: numpy/linalg/lapack_litemodule.c gcc -pthread -shared build/temp.linux-i686-2.4/numpy/linalg/lapack_litemodule.o -lmkl_lapack32 -lmkl_lapack64 -lmkl -lvml -lguide -lpthread -o build/lib.linux-i686-2.4/numpy/linalg/lapack_lite.so /usr/bin/ld: cannot find -lmkl_lapack64 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lmkl_lapack64 collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-i686-2.4/numpy/linalg/lapack_litemodule.o -lmkl_lapack32 -lmkl_lapack64 -lmkl -lvml -lguide -lpthread -o build/lib.linux-i686-2.4/numpy/linalg/lapack_lite.so" failed with exit status 1 There must be something wrong in the distutils/makefile because I'm on a debian sid *i386* so why should I link against mkl_lapack64 ?? Of course, I do not have lapack64 installed on this i386 machine. I have try to simply fix that in the config file of numpy replacing lapack64 by lapack32 everywhere but it fails (and it is not an acceptable fix). Can anyone reproduce that?? Xavier -- ############################################ Xavier Gnata CRAL - Observatoire de Lyon 9, avenue Charles André 69561 Saint Genis Laval cedex Phone: +33 4 78 86 85 28 Fax: +33 4 78 86 83 86 E-mail: gnata@obs.univ-lyon1.fr ############################################
Xavier Gnata wrote:
Hi,
I'm trying to update numpy by compiling the up to date svn:
I get this error : gcc: numpy/linalg/lapack_litemodule.c gcc -pthread -shared build/temp.linux-i686-2.4/numpy/linalg/lapack_litemodule.o -lmkl_lapack32 -lmkl_lapack64 -lmkl -lvml -lguide -lpthread -o build/lib.linux-i686-2.4/numpy/linalg/lapack_lite.so /usr/bin/ld: cannot find -lmkl_lapack64 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lmkl_lapack64 collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-i686-2.4/numpy/linalg/lapack_litemodule.o -lmkl_lapack32 -lmkl_lapack64 -lmkl -lvml -lguide -lpthread -o build/lib.linux-i686-2.4/numpy/linalg/lapack_lite.so" failed with exit status 1
There must be something wrong in the distutils/makefile because I'm on a debian sid *i386* so why should I link against mkl_lapack64 ?? Of course, I do not have lapack64 installed on this i386 machine. I have try to simply fix that in the config file of numpy replacing lapack64 by lapack32 everywhere but it fails (and it is not an acceptable fix).
Can anyone reproduce that??
Xavier
Trying to modify /numpy/distutils/system_info.py this way (only for test purpose...): # lapack_libs = self.get_libs('lapack_libs',['mkl_lapack32','mkl_lapack64']) lapack_libs = self.get_libs('lapack_libs',['mkl_lapack32']) I'm able to compile numpy but import numpy fails: ImportError: /usr/lib/python2.4/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: zgesdd_ Looks like the procedure to detect the lapack version is fully buggy (or maybe the lapack debian pacakges??) It used to work ;) Xavier -- ############################################ Xavier Gnata CRAL - Observatoire de Lyon 9, avenue Charles André 69561 Saint Genis Laval cedex Phone: +33 4 78 86 85 28 Fax: +33 4 78 86 83 86 E-mail: gnata@obs.univ-lyon1.fr ############################################
Xavier Gnata wrote:
Xavier Gnata wrote:
Hi,
I'm trying to update numpy by compiling the up to date svn:
I get this error : gcc: numpy/linalg/lapack_litemodule.c gcc -pthread -shared build/temp.linux-i686-2.4/numpy/linalg/lapack_litemodule.o -lmkl_lapack32 -lmkl_lapack64 -lmkl -lvml -lguide -lpthread -o build/lib.linux-i686-2.4/numpy/linalg/lapack_lite.so /usr/bin/ld: cannot find -lmkl_lapack64 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lmkl_lapack64 collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-i686-2.4/numpy/linalg/lapack_litemodule.o -lmkl_lapack32 -lmkl_lapack64 -lmkl -lvml -lguide -lpthread -o build/lib.linux-i686-2.4/numpy/linalg/lapack_lite.so" failed with exit status 1
There must be something wrong in the distutils/makefile because I'm on a debian sid *i386* so why should I link against mkl_lapack64 ?? Of course, I do not have lapack64 installed on this i386 machine. I have try to simply fix that in the config file of numpy replacing lapack64 by lapack32 everywhere but it fails (and it is not an acceptable fix).
Can anyone reproduce that??
Xavier
Trying to modify /numpy/distutils/system_info.py this way (only for test purpose...):
# lapack_libs = self.get_libs('lapack_libs',['mkl_lapack32','mkl_lapack64']) lapack_libs = self.get_libs('lapack_libs',['mkl_lapack32'])
I'm able to compile numpy but import numpy fails:
svn numpy and scipy work perfectly on Ubuntu, and there are no noticeable differences between sid and Ubuntu to make a difference a priori. Do you have the mkl installed at all on your computer ? If not, and without any modification to the site.cfg of numpy, I don't see why numpy would try to detect the mkl. Maybe some really recent (eg a few days) changes in the trunk ? I build quite regularly the lastest numpy (several times / week) on Ubuntu without problems.
ImportError: /usr/lib/python2.4/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: zgesdd_
Looks like the procedure to detect the lapack version is fully buggy (or maybe the lapack debian pacakges??)
Quite the contrary: debian LAPACK packages were the only ones working properly for a long time. David
Hi,
I'm trying to update numpy by compiling the up to date svn:
I get this error : gcc: numpy/linalg/lapack_litemodule.c gcc -pthread -shared build/temp.linux-i686-2.4/numpy/linalg/lapack_litemodule.o -lmkl_lapack32 -lmkl_lapack64 -lmkl -lvml -lguide -lpthread -o build/lib.linux-i686-2.4/numpy/linalg/lapack_lite.so /usr/bin/ld: cannot find -lmkl_lapack64 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lmkl_lapack64 collect2: ld returned 1 exit status error: Command "gcc -pthread -shared build/temp.linux-i686-2.4/numpy/linalg/lapack_litemodule.o -lmkl_lapack32 -lmkl_lapack64 -lmkl -lvml -lguide -lpthread -o build/lib.linux-i686-2.4/numpy/linalg/lapack_lite.so" failed with exit status 1
There must be something wrong in the distutils/makefile because I'm on a debian sid *i386* so why should I link against mkl_lapack64 ?? Of course, I do not have lapack64 installed on this i386 machine. I have try to simply fix that in the config file of numpy replacing lapack64 by lapack32 everywhere but it fails (and it is not an acceptable fix).
Can anyone reproduce that??
Xavier
Trying to modify /numpy/distutils/system_info.py this way (only for test purpose...):
# lapack_libs = self.get_libs('lapack_libs',['mkl_lapack32','mkl_lapack64']) lapack_libs = self.get_libs('lapack_libs',['mkl_lapack32'])
I'm able to compile numpy but import numpy fails:
svn numpy and scipy work perfectly on Ubuntu, and there are no noticeable differences between sid and Ubuntu to make a difference a priori.
Do you have the mkl installed at all on your computer ?
Ok I have mkl installed on my machine (it has by installed by a well know closed sources software....) /usr/lib/libmkl.so: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), not stripped /usr/lib/libmkl_lapack32.so: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), not stripped I just cannont remove them (because I will break another part of my system) but anyway, numpy detects them in a wrong way : I have no 64 version of mkl on this i386 machine :)) I have try to remove them and numpy compiles/works again but it is not a solution. I also have debian lapack package installed /usr/lib/liblapack.so.3.0. Numpy used to detect/use only this debian version of lapack. I never had a cusomized version of site.cfg. I have seen some recent changes (svn commits) on the way numpy detects the libs so it looks like we have a bug here when both libmkl_lapack32.so and liblapack.so (debian) are installed. I just would like to be able to tell numpy to use liblapack.so instead of this non free libmkl_lapack32.so Xavier
If not, and without any modification to the site.cfg of numpy, I don't see why numpy would try to detect the mkl. Maybe some really recent (eg a few days) changes in the trunk ? I build quite regularly the lastest numpy (several times / week) on Ubuntu without problems.
ImportError: /usr/lib/python2.4/site-packages/numpy/linalg/lapack_lite.so: undefined symbol: zgesdd_
Looks like the procedure to detect the lapack version is fully buggy (or maybe the lapack debian pacakges??)
Quite the contrary: debian LAPACK packages were the only ones working properly for a long time.
David _______________________________________________ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
-- ############################################ Xavier Gnata CRAL - Observatoire de Lyon 9, avenue Charles André 69561 Saint Genis Laval cedex Phone: +33 4 78 86 85 28 Fax: +33 4 78 86 83 86 E-mail: gnata@obs.univ-lyon1.fr ############################################
Pearu Peterson wrote:
Xavier Gnata wrote:
I just would like to be able to tell numpy to use liblapack.so instead of this non free libmkl_lapack32.so
For that set the following environment variable when building numpy/scipy:
export MKL=None
Hth, Pearu
ok it works with export MKL=None but IMHO there is something wrong in the mkl detection code on i386. Xavier -- ############################################ Xavier Gnata CRAL - Observatoire de Lyon 9, avenue Charles André 69561 Saint Genis Laval cedex Phone: +33 4 78 86 85 28 Fax: +33 4 78 86 83 86 E-mail: gnata@obs.univ-lyon1.fr ############################################
participants (3)
-
David Cournapeau -
Pearu Peterson -
Xavier Gnata