On Sun, Jul 25, 2010 at 4:23 AM, Jonathan Tu <[email protected]> wrote: > > On Jul 24, 2010, at 3:08 PM, Benjamin Root wrote: > > On Fri, Jul 23, 2010 at 10:10 AM, Jonathan Tu <[email protected]> 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 > _______________________________________________ > NumPy-Discussion mailing list > [email protected] > http://mail.scipy.org/mailman/listinfo/numpy-discussion > > > 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.
Run ldd on the concerned extensions: numpy/linalg/lapack_lite.so and numpy/core/_dotblas.so David _______________________________________________ NumPy-Discussion mailing list [email protected] http://mail.scipy.org/mailman/listinfo/numpy-discussion
