[Numpy-discussion] building numpy locally but get error: undefined symbol: zgesdd_

Francis F.Drossaert at googlemail.com
Tue Sep 16 07:28:17 EDT 2008 

On 16 Sep, 10:18, David Cournapeau <da... at ar.media.kyoto-u.ac.jp>
wrote:
> Francis wrote:
>
> > I don't really need Python2.5. Python2.4 is actually available on the
> > network but I think I will run into problems using the network one and
> > try using local libraries.
>
> No, it is perfectly supported (I do it all the time, even on my own
> machines where I have root rights). You use --prefix when installing
> packages, and you need to make sure that PYTHONPATH is correctly set up,
> e.g.:
>
> python setup.py install --prefix=$HOME/local # will install in
> $HOME/local/lib/python2.4/site-packages for python2.4
>
> And set PYTHONPATH to:
> PYTHONPATH=$HOME/local/lib/python2.4/site-packages:$PYTHONPATH.
>
> You can check which path you use by doing: python -c "import numpy;
> print numpy.__file__".

Okay. That should not be much of a problem.

> >  I assume one would need to change the paths
> > on a file which I can't change. Anyway I installed Python2.5 without
> > any problems.
>
> The problem is that when building software, you generally don't know
> whether you did it right or wrong before much later, by building other
> softwares on the top of it. For numpy/scipy, it is not too much of a
> problem, because they only depend on the interpreter, but for
> matplotlib, you will have to build pygtk/pyqt/etc... Since it does not
> make a difference to use your own python or the included python, you
> should use it. I personally use python2.4 on Centos to build numpy/scipy
> myself.
>
>
>
> > Output:
>
> >         libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b4187472000)
> >         libc.so.6 => /lib64/libc.so.6 (0x00002b418768c000)
> >         /lib64/ld-linux-x86-64.so.2 (0x00000036b8800000)
>
> For some reason, lapack has not been linked. Can you build numpy from
> scratch and give us the build.log ? For example, in the source tree:
>
> rm -rf ./build && python setup.py build &> build.log
>
> cheers,
>
> David

I only included the first and last part which I think are relevant.

F2PY Version 2_5585
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/users/francisd/local/lib/atlas']
    language = c

customize GnuFCompiler
Found executable /usr/bin/g77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -
Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --
param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/users/francisd/local/lib/atlas -llapack -
lf77blas -lcblas -latlas -o _configtest
ATLAS version 3.8.2 built by francisd on Mon Sep 15 15:20:08 BST 2008:
   UNAME    : Linux red-67 2.6.18-92.el5 #1 SMP Tue Jun 10 18:51:06
EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_PIII -DATL_CPUMHZ=2500 -
DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 262144
   F77      : gfortran, version GNU Fortran (GCC) 4.1.2 20071124 (Red
Hat 4.1.2-42)
   F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -
fPIC -m64
   SMC      : gcc, version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
   SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -
fPIC -m64
   SKC      : gcc, version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
   SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -
fPIC -m64
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/users/francisd/local/lib/atlas']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.2\\""')]

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not found in /users/francisd/local/lib/atlas
numpy.distutils.system_info.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/users/francisd/local/lib/atlas']
    language = f77

customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -
Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --
param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/users/francisd/local/lib/atlas -llapack -
llapack -lf77blas -lcblas -latlas -o _configtest
ATLAS version 3.8.2 built by francisd on Mon Sep 15 15:20:08 BST 2008:
   UNAME    : Linux red-67 2.6.18-92.el5 #1 SMP Tue Jun 10 18:51:06
EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_PIII -DATL_CPUMHZ=2500 -
DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 262144
   F77      : gfortran, version GNU Fortran (GCC) 4.1.2 20071124 (Red
Hat 4.1.2-42)
   F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -
fPIC -m64
   SMC      : gcc, version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
   SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -
fPIC -m64
   SKC      : gcc, version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42)
   SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -
fPIC -m64
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/users/francisd/local/lib/atlas']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.8.2\\""')]

running build
running scons
.
.
.
.
.
creating build/temp.linux-x86_64-2.4/numpy/fft
compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.4/
numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/usr/
include/python2.4 -I/usr/include/python2.4 -c'
gcc: numpy/fft/fftpack_litemodule.c
gcc: numpy/fft/fftpack.c
gcc -pthread -shared build/temp.linux-x86_64-2.4/numpy/fft/
fftpack_litemodule.o build/temp.linux-x86_64-2.4/numpy/fft/fftpack.o -
o build/lib.linux-x86_64-2.4/numpy/fft/fftpack_lite.so
building 'numpy.linalg.lapack_lite' extension
compiling C sources
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -
Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --
param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC

creating build/temp.linux-x86_64-2.4/numpy/linalg
compile options: '-DATLAS_INFO="\"3.8.2\"" -Inumpy/core/include -
Ibuild/src.linux-x86_64-2.4/numpy/core/include/numpy -Inumpy/core/src -
Inumpy/core/include -I/usr/include/python2.4 -I/usr/include/python2.4 -
c'
gcc: numpy/linalg/lapack_litemodule.c
gcc: numpy/linalg/python_xerbla.c
/usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.4/
numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.4/numpy/
linalg/python_xerbla.o -L/users/francisd/local/lib/atlas -llapack -
llapack -lf77blas -lcblas -latlas -lg2c -o build/lib.linux-x86_64-2.4/
numpy/linalg/lapack_lite.so
building 'numpy.random.mtrand' extension
compiling C sources
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -
Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --
param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC

creating build/temp.linux-x86_64-2.4/numpy/random
creating build/temp.linux-x86_64-2.4/numpy/random/mtrand
compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.4/
numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/usr/
include/python2.4 -I/usr/include/python2.4 -c'
gcc: numpy/random/mtrand/initarray.c
gcc: numpy/random/mtrand/distributions.c
gcc: numpy/random/mtrand/randomkit.c
gcc: numpy/random/mtrand/mtrand.c
gcc -pthread -shared build/temp.linux-x86_64-2.4/numpy/random/mtrand/
mtrand.o build/temp.linux-x86_64-2.4/numpy/random/mtrand/randomkit.o
build/temp.linux-x86_64-2.4/numpy/random/mtrand/initarray.o build/
temp.linux-x86_64-2.4/numpy/random/mtrand/distributions.o -o build/
lib.linux-x86_64-2.4/numpy/random/mtrand.so
running build_scripts
creating build/scripts.linux-x86_64-2.4
Creating build/scripts.linux-x86_64-2.4/f2py
  adding 'build/scripts.linux-x86_64-2.4/f2py' to scripts
changing mode of build/scripts.linux-x86_64-2.4/f2py from 664 to 775

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