[SciPy-user] installation problem

Johann Cohen-Tanugi cohen@slac.stanford....
Thu Dec 27 23:06:05 CST 2007


hmm I don't have this symbol in my version of this shared lib, and I am 
no expert here :) But did you make sure that you  compiled ATLAS and 
scipy with gfortran? I could imagine something like that happening if 
scipy was built with g77 and ATLAS with gfortran.... You can use the 
fcompiler option to setup.py to ensure that gfortran is picked up as the 
fortran compiler.
Maybe an expert will kick in here...
hth,
Johann

Vinu Vikram wrote:
> I worked . Thanks!!
> there was no error during the installation. But when I tried to import 
> scipy.signal, I got the following error
>
> >>> import scipy.signal
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File 
> "/usr/local/lib/python2.5/site-packages/scipy/signal/__init__.py", 
> line 10, in <module>
>     from filter_design import *
>   File 
> "/usr/local/lib/python2.5/site-packages/scipy/signal/filter_design.py", 
> line 9, in <module>
>     from scipy import special, optimize
>   File 
> "/usr/local/lib/python2.5/site-packages/scipy/optimize/__init__.py", 
> line 11, in <module>
>     from lbfgsb import fmin_l_bfgs_b
>   File 
> "/usr/local/lib/python2.5/site-packages/scipy/optimize/lbfgsb.py", 
> line 30, in <module>
>     import _lbfgsb
> ImportError: 
> /usr/local/lib/python2.5/site-packages/scipy/optimize/_lbfgsb.so: 
> undefined symbol: _gfortran_st_write_done
>
> How I can fix it?
> Thanks
> Vinu V
>
> On Dec 27, 2007 8:46 PM, Johann Cohen-Tanugi <cohen@slac.stanford.edu 
> <mailto:cohen@slac.stanford.edu>> wrote:
>
>     hi Vinu,
>     you seem to have an installation of ATLAS which has not been built
>     with
>     the -Fa alg -fPIC flags (forcing position independent code for each
>     compiler). See
>     http://math-atlas.sourceforge.net/atlas_install/atlas_install.html#SECTION00043000000000000000
>
>     Johann
>
>     Vinu Vikram wrote:
>     > Hi all
>     > I am facing problem when trying to install scipy0.6.0. The error
>     I am
>     > getting is
>     > building 'scipy.integrate._odepack' extension
>     > compiling C sources
>     > C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
>     > -Wstrict-prototypes -fPIC
>     >
>     > compile options: '-DATLAS_INFO="\"3.6.0\""
>     > -I/usr/local/lib/python2.5/site-packages/numpy/core/include
>     > -I/usr/local/include/python2.5 -c'
>     > /usr/bin/g77 -g -Wall -shared build/temp.linux-x86_64-
>     > 2.5/scipy/integrate/_odepackmodule.o
>     > -L/home/vinu/ATLAS/lib/Linux_UNKNOWNSSE2_2
>     > -Lbuild/temp.linux-x86_64-2.5 -lodepack -llinpack_lite -lmach
>     > -lptf77blas -lptcblas -latlas -lg2c -o
>     > build/lib.linux-x86_64- 2.5/scipy/integrate/_odepack.so
>     > /usr/bin/ld:
>     >
>     /home/vinu/ATLAS/lib/Linux_UNKNOWNSSE2_2/libptf77blas.a(ATL_F77wrap_dptscal.o):
>     > relocation R_X86_64_32 against `a local symbol' can not be used
>     when
>     > making a shared object; recompile with -fPIC
>     > /home/vinu/ATLAS/lib/Linux_UNKNOWNSSE2_2/libptf77blas.a: could not
>     > read symbols: Bad value
>     > collect2: ld returned 1 exit status
>     > /usr/bin/ld:
>     >
>     /home/vinu/ATLAS/lib/Linux_UNKNOWNSSE2_2/libptf77blas.a(ATL_F77wrap_dptscal.o):
>     > relocation R_X86_64_32 against `a local symbol' can not be used when
>     > making a shared object; recompile with -fPIC
>     > /home/vinu/ATLAS/lib/Linux_UNKNOWNSSE2_2/libptf77blas.a: could not
>     > read symbols: Bad value
>     > collect2: ld returned 1 exit status
>     > error: Command "/usr/bin/g77 -g -Wall -shared
>     > build/temp.linux-x86_64- 2.5/scipy/integrate/_odepackmodule.o
>     > -L/home/vinu/ATLAS/lib/Linux_UNKNOWNSSE2_2
>     -Lbuild/temp.linux-x86_64-
>     > 2.5 -lodepack -llinpack_lite -lmach -lptf77blas -lptcblas -latlas
>     > -lg2c -o build/lib.linux-x86_64- 2.5/scipy/integrate/_odepack.so"
>     > failed with exit status 1
>     >
>     > Please help me to solve this.
>     > thanks
>     > Vinu V
>     >
>     > --
>     > VINU VIKRAM
>     > http://iucaa.ernet.in/~vvinuv/
>     <http://iucaa.ernet.in/%7Evvinuv/> <http://iucaa.ernet.in/%7Evvinuv/>
>     >
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>
>
> -- 
> VINU VIKRAM
> http://iucaa.ernet.in/~vvinuv/ <http://iucaa.ernet.in/%7Evvinuv/>
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