[Numpy-discussion] numpy : error with cc compiler

akshar bhosale akshar.bhosale@gmail....
Wed Jun 8 16:21:04 CDT 2011


Hi,

we have RHEL 5.2 x86_64, python 2.6, intel compilers 11.0.69, intel mkl
10.1. We are trying to configure numpy 1.6.0 and we are getting below
errors.
our site.cfg is :
-------------------------
[mkl]
#mkl_libs = mkl_blacs_intelmpi_ilp64, mkl_blacs_intelmpi_lp64, mkl_core,
mkl_def, mkl_gf_ilp64, mkl_gf_lp64, mkl_gnu_thread, mkl_intel_ilp64,
mkl_intel_lp64, mkl_intel_sp2dp, mkl_intel_thread, mkl_lapack, mkl_mc3,
mkl_mc, mkl_p4n,  mkl_scalapack_ilp64, mkl_scalapack_lp64, mkl_sequential,
mkl, iomp, guide, mkl_vml_def, mkl_vml_mc2, mkl_vml_mc3, mkl_vml_mc,
mkl_vml_p4n,mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core, mkl_mc


mkl_libs = mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core, mkl_mc
lapack_libs = mkl_lapack95_lp64

#lapack_libs
=mkl_lapack,mkl_scalapack_ilp64,mkl_scalapack_lp64,mkl_lapack95_lp64
library_dirs =
/opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/intel/Compiler/11.0/069/lib/intel64/
include_dirs =
/opt/intel/Compiler/11.0/069/mkl/include:/opt/intel/Compiler/11.0/069/include/
-------------------------
We are not able to understand what all flags to include with icc and ifort
in intelccompiler.py and intel.py. Also what ll libraries to link for above
configuration is not given. Can somebody guide for with proper guidelines so
that installation goes smooth.

ERRORS :

 DeprecationWarning)
C compiler: cc

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
-Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath
-Inumpy/core/include -I/home/external/unipune/gadre/Python-2.6/Include
-I/home/external/unipune/gadre/Python-2.6 -c
'
cc: _configtest.c
cc _configtest.o -o _configtest
_configtest
failure.
removing: _configtest.c _configtest.o _configtest
building data_files sources
build_src: building npy-pkg config files
customize IntelCCompiler
customize IntelCCompiler using build_clib
building 'npymath' library
compiling C sources
C compiler: cc

creating build/temp.linux-x86_64-2.6
creating build/temp.linux-x86_64-2.6/build
creating build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6
creating build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy
creating build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core
creating
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src
creating
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/npymath
creating build/temp.linux-x86_64-2.6/numpy
creating build/temp.linux-x86_64-2.6/numpy/core
creating build/temp.linux-x86_64-2.6/numpy/core/src
creating build/temp.linux-x86_64-2.6/numpy/core/src/npymath
compile options: '-Inumpy/core/include
-Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy
-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
-Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath
-Inumpy/core/include -I/home/external/un
ipune/gadre/Python-2.6/Include -I/home/external/unipune/gadre/Python-2.6
-Ibuild/src.linux-x86_64-2.6/numpy/core/src/multiarray
-Ibuild/src.linux-x86_64-2.6/numpy/core/src/umath -c'
cc: numpy/core/src/npymath/halffloat.c
cc: build/src.linux-x86_64-2.6/numpy/core/src/npymath/npy_math_complex.c
cc: build/src.linux-x86_64-2.6/numpy/core/src/npymath/npy_math.c
cc: build/src.linux-x86_64-2.6/numpy/core/src/npymath/ieee754.c
ar: adding 4 object files to build/temp.linux-x86_64-2.6/libnpymath.a
running build_ext
customize IntelCCompiler
customize IntelCCompiler using build_ext
building 'numpy.core._sort' extension
compiling C sources
C compiler: cc

compile options: '-Inumpy/core/include
-Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy
-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
-Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath
-Inumpy/core/include -I/home/external/un
ipune/gadre/Python-2.6/Include -I/home/external/unipune/gadre/Python-2.6
-Ibuild/src.linux-x86_64-2.6/numpy/core/src/multiarray
-Ibuild/src.linux-x86_64-2.6/numpy/core/src/umath -c'
cc: build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.c
creating build/lib.linux-x86_64-2.6
creating build/lib.linux-x86_64-2.6/numpy
creating build/lib.linux-x86_64-2.6/numpy/core
cc -shared
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o
-Lbuild/temp.linux-x86_64-2.6 -lnpymath -lm -o
build/lib.linux-x86_64-2.6/numpy/core/_sort.so
/usr/bin/ld:
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o:
relocation R_X86_64_32 against `a local symbol' can not be used when making
a shared object; recompile with -fPIC
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o:
could not read symbols: Bad value
collect2: ld returned 1 exit status
/usr/bin/ld:
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o:
relocation R_X86_64_32 against `a local symbol' can not be used when making
a shared object; recompile with -fPIC
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o:
could not read symbols: Bad value
collect2: ld returned 1 exit status
error: Command "cc -shared
build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o
-Lbuild/temp.linux-x86_64-2.6 -lnpymath -lm -o
build/lib.linux-x86_64-2.6/numpy/core/_sort.so" failed with exit status 1
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