[Numpy-discussion] Numpy installation problem

Jonathan Tu jhtu@Princeton....
Fri Jul 23 10:10:24 CDT 2010


Hi,

I am trying to install Numpy on a Linux cluster running RHEL4.  I installed a local copy of Python 2.7 because RHEL4 uses Python 2.3.4 for various internal functionalities.  I downloaded the Numpy source code using

svn co http://svn.scipy.org/svn/numpy/trunk numpy

and then I tried to build using

python setup.py build

This resulted in the following error:

gcc: numpy/linalg/lapack_litemodule.c
gcc: numpy/linalg/python_xerbla.c
/usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so
/usr/bin/ld: /usr/lib64/ATLAS/liblapack.a(dgeev.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/lib64/ATLAS/liblapack.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
/usr/bin/ld: /usr/lib64/ATLAS/liblapack.a(dgeev.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/lib64/ATLAS/liblapack.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: Command "/usr/bin/g77 -g -Wall -g -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/lib64/ATLAS -Lbuild/temp.linux-x86_64-2.7 -llapack -lptf77blas -lptcblas -latlas -lg2c -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1
 
Full details of the output are attached in stdout.txt and stderr.txt.  I thought maybe it was a compiler error so I tried 

python setup.py build -fcompiler=gnu

but this also resulted in errors as well (stdout_2.txt, stderr_2.txt).

I just noticed that on both attempts, it is complaining that it can't find a Fortran 90 compiler.  I'm not sure if I have the right compiler available.  On this cluster I have the following modules:

------------ /usr/share/Modules/modulefiles ------------ 
dot         module-cvs  module-info modules     null        use.own     
------------ /usr/local/share/Modules/modulefiles ------------ 
mpich/gcc/1.2.7p1/64           openmpi/gcc-ib/1.2.3/64        
mpich/intel/1.2.7dmcrp1/64     openmpi/gcc-ib/1.2.5/64        
mpich/intel/1.2.7p1/64         openmpi/intel/1.2.3/64         
mpich/pgi-7.1/1.2.7p1/64       openmpi/intel-11.0/1.2.8/64    
mpich-debug/gcc/1.2.7p1/64     openmpi/intel-9.1/1.2.8/64     
mpich-debug/intel/1.2.7p1/64   openmpi/intel-ib/1.1.5/64      
mpich-debug/pgi-7.1/1.2.7p1/64 openmpi/intel-ib/1.2.3/64      
mvapich/gcc/0.9.9/64           openmpi/intel-ib/1.2.5/64      
mvapich/pgi-7.1/0.9.9/64       openmpi/pgi-7.0/1.2.3/64       
openmpi/gcc/1.2.8/64           openmpi/pgi-7.1/1.2.5/64       
openmpi/gcc/1.3.0/64           openmpi/pgi-7.1/1.2.8/64       
openmpi/gcc-ib/1.1.5/64        openmpi/pgi-8.0/1.2.8/64       
------------ /opt/share/Modules/modulefiles ------------ 
intel/10.0/64/C/10.0.026       intel/9.1/64/default           
intel/10.0/64/Fortran/10.0.026 intel-mkl/10/64                
intel/10.0/64/Iidb/10.0.026    intel-mkl/10.1/64              
intel/10.0/64/default          intel-mkl/9/32                 
intel/11.1/64/11.1.038         intel-mkl/9/64                 
intel/11.1/64/11.1.072         pgi/7.0/64                     
intel/9.1/64/C/9.1.045         pgi/7.1/64                     
intel/9.1/64/Fortran/9.1.040   pgi/8.0/64                     
intel/9.1/64/Iidb/9.1.045      

If anyone has any ideas, they would be greatly appreciated!  I am new to Linux and am unsure how to fix this problem.





Jonathan Tu







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