[Numpy-discussion] Numpy installation problem
Jonathan Tu
jhtu at Princeton.EDU
Fri Jul 23 11:10:24 EDT 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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