numpy-discussion

[Numpy-discussion] Compile with atlas 3.7.17 fails

[Hanno K. <kl...@ph...>]

Hi, 

I don't know if this is a bug or just me doing something wrong (I
suspect the latter). I try to compile numpy-1.0rc1 with python2.5 and
atlas 3.7.17.

I have build the atlas library myself, it doesn't give any errors
under make test or make pttest, so it seems to be okay. if I try to
build numpy I get the following error:

creating build/temp.linux-x86_64-2.5/numpy/core/blasdot
compile options: '-DATLAS_INFO="\"3.7.17\"" -Inumpy/core/blasdot
-I/scratch/python2.5/include -Inumpy/core/include
-Ibuild/src.linux-x86_64-2.5/numpy/core -Inumpy/core/src
-Inumpy/core/include -I/scratch/python2.5/include/python2.5 -c'
gcc: numpy/core/blasdot/_dotblas.c
gcc -pthread -shared
build/temp.linux-x86_64-2.5/numpy/core/blasdot/_dotblas.o
-L/scratch/python2.5/lib -lcblas -latlas -o
build/lib.linux-x86_64-2.5/numpy/core/_dotblas.so
/usr/bin/ld: /scratch/python2.5/lib/libcblas.a(cblas_dgemm.o):
relocation R_X86_64_32 can not be used when making a shared object;
recompile with -fPIC
/scratch/python2.5/lib/libcblas.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
/usr/bin/ld: /scratch/python2.5/lib/libcblas.a(cblas_dgemm.o):
relocation R_X86_64_32 can not be used when making a shared object;
recompile with -fPIC
/scratch/python2.5/lib/libcblas.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: Command "gcc -pthread -shared
build/temp.linux-x86_64-2.5/numpy/core/blasdot/_dotblas.o
-L/scratch/python2.5/lib -lcblas -latlas -o
build/lib.linux-x86_64-2.5/numpy/core/_dotblas.so" failed with exit
status 1

I then tried to recompile atlas with the configure options as:

configure --cflags=-fPIC
--with-netlib-lapack=/scratch/src/python_dist/LAPACK
--prefix=/scratch/python2.5

but the error still remains. I'm on a 2 CPU Intel Xeon machine with
gcc 3.2.3.

Any hints?

Hanno

-- 
Hanno Klemm
kl...@ph...

Re: [Numpy-discussion] Compile with atlas 3.7.17 fails

[Travis O. <oli...@ee...>]

Hanno Klemm wrote:

>Hi, 
>
>I don't know if this is a bug or just me doing something wrong (I
>suspect the latter). I try to compile numpy-1.0rc1 with python2.5 and
>atlas 3.7.17.
>
>I have build the atlas library myself, it doesn't give any errors
>under make test or make pttest, so it seems to be okay. if I try to
>build numpy I get the following error:
>
>creating build/temp.linux-x86_64-2.5/numpy/core/blasdot
>compile options: '-DATLAS_INFO="\"3.7.17\"" -Inumpy/core/blasdot
>-I/scratch/python2.5/include -Inumpy/core/include
>-Ibuild/src.linux-x86_64-2.5/numpy/core -Inumpy/core/src
>-Inumpy/core/include -I/scratch/python2.5/include/python2.5 -c'
>gcc: numpy/core/blasdot/_dotblas.c
>gcc -pthread -shared
>build/temp.linux-x86_64-2.5/numpy/core/blasdot/_dotblas.o
>-L/scratch/python2.5/lib -lcblas -latlas -o
>build/lib.linux-x86_64-2.5/numpy/core/_dotblas.so
>/usr/bin/ld: /scratch/python2.5/lib/libcblas.a(cblas_dgemm.o):
>relocation R_X86_64_32 can not be used when making a shared object;
>recompile with -fPIC
>  
>

This may be part of your problem.  It's looks like the linker is having 
a hard time making use of your compiled extension in a shared library.  
Perhaps you should make sure -fPIC is on when you compile atlas (I'm not 
sure how to do that --- perhaps setting CCFLAGS environment variable to 
include -fPIC would help).

-Travis

Re: [Numpy-discussion] Compile with atlas 3.7.17 fails

[Hanno K. <kl...@ph...>]

Travis, 

thank you, setting the -fPIC option indeed solved my problem. Just for
future reference (if anybody else needs it), I added the -fPIC flag to
the compiler flags in Make.inc in the atlas build directory, as
setting CCFLAGS somehwo didn't seem to be successful. This might not
be elegant but it worked. 

Best regards,
Hanno


Travis Oliphant <oli...@ee...> said:

> Hanno Klemm wrote:
> 
> >Hi, 
> >
> >I don't know if this is a bug or just me doing something wrong (I
> >suspect the latter). I try to compile numpy-1.0rc1 with python2.5 and
> >atlas 3.7.17.
> >
> >I have build the atlas library myself, it doesn't give any errors
> >under make test or make pttest, so it seems to be okay. if I try to
> >build numpy I get the following error:
> >
> >creating build/temp.linux-x86_64-2.5/numpy/core/blasdot
> >compile options: '-DATLAS_INFO="\"3.7.17\"" -Inumpy/core/blasdot
> >-I/scratch/python2.5/include -Inumpy/core/include
> >-Ibuild/src.linux-x86_64-2.5/numpy/core -Inumpy/core/src
> >-Inumpy/core/include -I/scratch/python2.5/include/python2.5 -c'
> >gcc: numpy/core/blasdot/_dotblas.c
> >gcc -pthread -shared
> >build/temp.linux-x86_64-2.5/numpy/core/blasdot/_dotblas.o
> >-L/scratch/python2.5/lib -lcblas -latlas -o
> >build/lib.linux-x86_64-2.5/numpy/core/_dotblas.so
> >/usr/bin/ld: /scratch/python2.5/lib/libcblas.a(cblas_dgemm.o):
> >relocation R_X86_64_32 can not be used when making a shared object;
> >recompile with -fPIC
> >  
> >
> 
> This may be part of your problem.  It's looks like the linker is having 
> a hard time making use of your compiled extension in a shared library.  
> Perhaps you should make sure -fPIC is on when you compile atlas (I'm
not 
> sure how to do that --- perhaps setting CCFLAGS environment variable to 
> include -fPIC would help).
> 
> -Travis
> 
> 
>
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-- 
Hanno Klemm
kl...@ph...