[Numpy-discussion] compile process of numpy-1.5.0 fails in Itanium cluster with icc

Miguel Pan Fidalgo mpan@cesga...
Tue Sep 21 01:33:35 CDT 2010


hi,

I'm trying to install numpy-1.5.0 in our Itanium (IA-64) supercomputer 
[http://www.cesga.es/content/view/917/115/lang,en/ ].

This is my site.cfg (I have to install umfpack but I think this is not the 
problem): 

$ cat site.cfg
[DEFAULT]
library_dirs = 
/opt/cesga/fftw-3.2.2/lib:/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64  
include_dirs = 
/opt/cesga/fftw-3.2.2/include:/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include 

#[umfpack]
#umfpack_libs = umfpack

[fftw]
libraries = fftw3

[mkl]
library_dirs = /opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64  
lapack_libs = mkl_lapack
mkl_libs = mkl_core

The only hacks that I made: 

$ diff numpy/distutils/system_info.py  ../numpy-
scipy/numpy-1.5.0/numpy/distutils/system_info.py
818c818
<     _lib_mkl = ['mkl','mkl_lapack','guide']
---
>     _lib_mkl = ['mkl','vml','guide']

$ diff numpy/distutils/intelccompiler.py  ../numpy-
scipy/numpy-1.5.0/numpy/distutils/intelccompiler.py
11c11
<     cc_exe = 'icc -O3 -openmp -lpthread -fPIC'
---
>     cc_exe = 'icc'

 
And I have used this script to launch the compilation process: 

$ cat compilar.sh 
#!/bin/bash

module load nose/0.10.4 fftw/3.2.2 ifort/11.1.056 icc/11.1.056 mkl/10.2.2

python setup.py config --compiler=intele --fcompiler=intele build install --
prefix=/home/cesga/mpan/numpy-1.5.0

exit 0

blas and lapack are detected properly:

$ head -n 40 compilar.log 
Running from numpy source directory.F2PY Version 1
blas_opt_info:
blas_mkl_info:
  FOUND:
    libraries = ['mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include']

  FOUND:
    libraries = ['mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include']

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  FOUND:
    libraries = ['mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include']

  FOUND:
    libraries = ['mkl_lapack', 'mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include']

  FOUND:
    libraries = ['mkl_lapack', 'mkl_core', 'pthread']
    library_dirs = ['/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/lib/64']
    define_macros = [('SCIPY_MKL_H', None)]
    include_dirs = ['/opt/cesga/fftw-3.2.2/include', 
'/opt/cesga/intel/intel11.0/Compiler/11.1/056/mkl/include']

running config
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler 
options

but, unfortunately, the compilation process ends with an unexpected 
realocation problem: 

$ tail -n 11 compilar.log 

/opt/cesga/intel/intel11.0/Compiler/11.1/056/bin/ia64/icc -shared 
build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o -Lbuild/temp.linux-ia64-2.4 -o 
build/lib.linux-ia64-2.4/numpy/core/umath_tests.so
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol inner1d_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol innerwt_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol matrix_multiply_signature
ld: final link failed: Nonrepresentable section on output
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol inner1d_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol innerwt_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol matrix_multiply_signature
ld: final link failed: Nonrepresentable section on output
error: Command "/opt/cesga/intel/intel11.0/Compiler/11.1/056/bin/ia64/icc -
shared build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o -Lbuild/temp.linux-ia64-2.4 -o 
build/lib.linux-ia64-2.4/numpy/core/umath_tests.so" failed with exit status 1

I have tried to link this files manually but I haven't any success: 

$ /opt/cesga/intel/intel11.0/Compiler/11.1/056/bin/ia64/icc -shared 
build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o -Lbuild/temp.linux-ia64-2.4 -o 
build/lib.linux-ia64-2.4/numpy/core/umath_tests.so
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol inner1d_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol innerwt_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol matrix_multiply_signature
ld: final link failed: Nonrepresentable section on output
$ /opt/cesga/intel/intel11.0/Compiler/11.1/056/bin/ia64/icc -fPIC -shared 
build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o -Lbuild/temp.linux-ia64-2.4 -o 
build/lib.linux-ia64-2.4/numpy/core/umath_tests.so
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol inner1d_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol innerwt_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol matrix_multiply_signature
ld: final link failed: Nonrepresentable section on output
$ /opt/cesga/intel/intel11.0/Compiler/11.1/056/bin/ia64/icc -i-dynamic -shared 
build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o -Lbuild/temp.linux-ia64-2.4 -o 
build/lib.linux-ia64-2.4/numpy/core/umath_tests.so
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol inner1d_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol innerwt_signature
ld: build/temp.linux-ia64-2.4/build/src.linux-
ia64-2.4/numpy/core/src/umath/umath_tests.o: @gprel relocation against dynamic 
symbol matrix_multiply_signature
ld: final link failed: Nonrepresentable section on output

with differents combinations (MKL 9.1, no optimatazions flags, no hacks.....) 
I have the same problem.

any idea?

-- 

Atentamente,

Miguel Pan Fidalgo (Applications Technician)
mail: mpan at cesga.es
web: http://www.cesga.es
Avda. de Vigo s/n 15705, Santiago de Compostela
Telf.: +34 981 569810 - Fax: 981 594616


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