[Numpy-discussion] Numpy installation problem

Jonathan Tu jhtu@princeton....
Sat Jul 24 14:23:19 CDT 2010


On Jul 24, 2010, at 3:08 PM, Benjamin Root wrote:

> On Fri, Jul 23, 2010 at 10:10 AM, Jonathan Tu <jhtu@princeton.edu> wrote:
> 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
> 
> 
> 
> Jonathan,
> 
> Looking at your error logs, I suspect that the issue is that the ATLAS libraries that were installed on your system were probably built using f90, and then your f77-built objects can't link against ATLAS.  Do you have admin access to this machine?  If possible, try using the yum package manager to install f90 (its availability depends on whatever RHEL license you have, though...).
> 
> If you can install f90, I would then remove the numpy build directory and try building it again.
> 
> I hope this helps,
> Ben Root 
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Hi Ben,

I managed to complete my installation.  It required setting up the configure file to reference my local installation of Python, rather than the default /usr/bin/Python.  However, I would like to see whether or not I am using the optimized ATLAS/LAPACK libraries for my matrix computations.  I couldn't figure out how to do this by just Googling.  Does anyone know how to check?  I'm interested in the performance of my algorithms and this could be one of the bottlenecks.



Jonathan Tu

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