[SciPy-user] numpy linking issue

Gary pajer at iname.com
Wed Nov 22 09:24:18 CST 2006


Friedrich, Robin K wrote:
>
> I'm trying to build Numpy from source on a Red Hat Enterprise Linux 3
> system. But it doesn't seem to be linking the way I need it to. I have a
> scratch built ATLAS installation (libatlas.a  libcblas.a  libf77blas.a
> liblapack.a etc.) in our CM location (not /usr/lib) that I want to link
> with. Importing numpy throws an exception from lapack_lite for an
> undefined symbol. Regardless of whatever problem the
> /usr/lib/liblapack.so might have I chose via site.cfg to use the ATLAS
> libraries.  The configtest.c seems to have picked it up and was OK with
> it.  Why does the main numpy lapack_lite not use the same libs?
> Is there some way of forcing these libs to be picked up in preference to
> /usr/lib stuff?
> Thanks!
> -Robin
>
Your problem seems similar (?) to the problem I'm having.  See 
yesterday's thread "Windows build help".
config reports that the libraries are found, but when the compiler needs 
them, it complains about undefined symbols.  Different symbols in my 
case, btw.

-gary




>
>
> ==============================
> Python 2.5 (r25:51908, Oct 17 2006, 11:07:50)
> [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-53)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import numpy
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/ips/fd/sw/csw/oss/lib/python2.5/site-packages/numpy/__init__.py", line
> 40, in <module>
>     import linalg
>   File
> "/ips/fd/sw/csw/oss/lib/python2.5/site-packages/numpy/linalg/__init__.py", 
> line 4, in <module>
>     from linalg import *
>   File
> "/ips/fd/sw/csw/oss/lib/python2.5/site-packages/numpy/linalg/linalg.py",
> line 25, in <module>
>     from numpy.linalg import lapack_lite
> ImportError: /usr/lib/libblas.so.3: undefined symbol: e_wsfe
> >>>
>
> ===========================
> ldd -r lapack_lite.so
>         liblapack.so.3 => /usr/lib/liblapack.so.3 (0x00965000)
>         libblas.so.3 => /usr/lib/libblas.so.3 (0x005cf000)
>         libpthread.so.0 => /lib/tls/libpthread.so.0 (0x00575000)
>         libc.so.6 => /lib/tls/libc.so.6 (0x00111000)
>         libm.so.6 => /lib/tls/libm.so.6 (0x0024a000)
>         /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x00541000)
> undefined symbol: e_wsfe        (/usr/lib/libblas.so.3)
> undefined symbol: z_abs (/usr/lib/libblas.so.3)
> undefined symbol: do_fio        (/usr/lib/libblas.so.3)
> undefined symbol: s_stop        (/usr/lib/libblas.so.3)
> undefined symbol: c_abs (/usr/lib/libblas.so.3)
> undefined symbol: s_wsfe        (/usr/lib/libblas.so.3)
> undefined symbol: e_wsfe        (/usr/lib/liblapack.so.3)
> undefined symbol: z_abs (/usr/lib/liblapack.so.3)
> undefined symbol: c_sqrt        (/usr/lib/liblapack.so.3)
> undefined symbol: s_cmp (/usr/lib/liblapack.so.3)
> undefined symbol: z_exp (/usr/lib/liblapack.so.3)
> undefined symbol: c_exp (/usr/lib/liblapack.so.3)
> undefined symbol: etime_        (/usr/lib/liblapack.so.3)
> undefined symbol: do_fio        (/usr/lib/liblapack.so.3)
> undefined symbol: z_sqrt        (/usr/lib/liblapack.so.3)
> undefined symbol: s_cat (/usr/lib/liblapack.so.3)
> undefined symbol: s_stop        (/usr/lib/liblapack.so.3)
> undefined symbol: c_abs (/usr/lib/liblapack.so.3)
> undefined symbol: s_wsfe        (/usr/lib/liblapack.so.3)
> undefined symbol: s_copy        (/usr/lib/liblapack.so.3)
> undefined symbol: PyExc_RuntimeError    (./lapack_lite.so)
> undefined symbol: PyExc_ImportError     (./lapack_lite.so)
> undefined symbol: PyCObject_Type        (./lapack_lite.so)
> undefined symbol: PyDict_SetItemString  (./lapack_lite.so)
> undefined symbol: Py_BuildValue (./lapack_lite.so)
> undefined symbol: PyErr_SetString       (./lapack_lite.so)
> undefined symbol: Py_InitModule4        (./lapack_lite.so)
> undefined symbol: PyObject_GetAttrString        (./lapack_lite.so)
> undefined symbol: PyImport_ImportModule (./lapack_lite.so)
> undefined symbol: PyCObject_AsVoidPtr   (./lapack_lite.so)
> undefined symbol: PyModule_GetDict      (./lapack_lite.so)
> undefined symbol: PyErr_Format  (./lapack_lite.so)
> undefined symbol: PyType_IsSubtype      (./lapack_lite.so)
> undefined symbol: PyErr_Print   (./lapack_lite.so)
> undefined symbol: PyArg_ParseTuple      (./lapack_lite.so)
> undefined symbol: PyErr_NewException    (./lapack_lite.so)
>
> =============================
> gcc: _configtest.c
> gcc -pthread _configtest.o -L/ips/fd/cm/cmg/rel/csw/oss/lib/ATLAS/
> -llapack -lcblas -lf77blas -latlas -o _configtest
> ATLAS version 3.6.0 built by bloom on Tue Aug  9 18:36:17 CDT 2005:
>    UNAME    : Linux fdx-401 2.4.21-20.0.1.EL #1 Wed Nov 24 20:45:03 EST
> 2004 i686 i686 i386 GNU/Linux
>    INSTFLG  :
>    MMDEF    :
> /ips/fd/cm/cmg/bld/csw/oss/atlas3_6/ATLAS/CONFIG/ARCHS/P4SSE2/gcc/gemm
>    ARCHDEF  :
> /ips/fd/cm/cmg/bld/csw/oss/atlas3_6/ATLAS/CONFIG/ARCHS/P4SSE2/gcc/misc
>    F2CDEFS  : -DAdd__ -DStringSunStyle
>    CACHEEDGE: 1048576
>    F77      : /usr/bin/g77, version GNU Fortran (GCC 3.2.3 20030502 (Red
> Hat Linux 3.2.3-42)) 3.2.3 20030502 (Red Hat Linux 3.2.3-42)
>    F77FLAGS : -fomit-frame-pointer -O
>    CC       : /usr/bin/gcc, version gcc (GCC) 3.2.3 20030502 (Red Hat
> Linux 3.2.3-42)
>    CC FLAGS : -fomit-frame-pointer -O3 -funroll-all-loops
>    MCC      : /usr/bin/gcc, version gcc (GCC) 3.2.3 20030502 (Red Hat
> Linux 3.2.3-42)
>    MCCFLAGS : -fomit-frame-pointer -O
> success!
>
>
> ==============================
> ldd -r /usr/lib/libblas.so.3
>         libm.so.6 => /lib/tls/libm.so.6 (0x00178000)
>         libc.so.6 => /lib/tls/libc.so.6 (0x001b1000)
>         /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x00958000)
> undefined symbol: e_wsfe        (/usr/lib/libblas.so.3)
> undefined symbol: z_abs (/usr/lib/libblas.so.3)
> undefined symbol: do_fio        (/usr/lib/libblas.so.3)
> undefined symbol: s_stop        (/usr/lib/libblas.so.3)
> undefined symbol: c_abs (/usr/lib/libblas.so.3)
> undefined symbol: s_wsfe        (/usr/lib/libblas.so.3)
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> SciPy-user mailing list
> SciPy-user at scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>   



More information about the SciPy-user mailing list