Re: [Numpy-discussion] [SciPy-Dev] numpy.test hangs
Hi, i changed site.cfg : ####site.cfg#### [MKL} mkl_libs = mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core, mkl_mc lapack_libs = mkl_lapack95_lp64, mkl_lapack, mkl_scalapack_ilp64, mkl_scalapack_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/ and now numpy.test hangs at : python Python 2.6 (r26:66714, May 29 2011, 15:10:47) [GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.test(verbose=3) Running unit tests for numpy NumPy version 1.6.0 NumPy is installed in /home/aksharb/Python-2.6/lib/python2.6/site-packages/numpy Python version 2.6 (r26:66714, May 29 2011, 15:10:47) [GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] nose version 1.0.0 nose.config: INFO: Excluding tests matching ['f2py_ext', 'f2py_f90_ext', 'gen_ext', 'pyrex_ext', 'swig_ext'] nose.selector: INFO: /home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/multiarray.so is executable; skipped nose.selector: INFO: /home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/scalarmath.so is executable; skipped nose.selector: INFO: /home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/umath.so is executable; skipped nose.selector: INFO: /home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/multiarray_tests.so is executable; skipped nose.selector: INFO: /home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/core/umath_tests.so is executable; skipped nose.selector: INFO: /home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/fft/fftpack_lite.so is executable; skipped nose.selector: INFO: /home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/linalg/lapack_lite.so is executable; skipped nose.selector: INFO: /home/external/unipune/gadre/Python-2.6/lib/python2.6/site-packages/numpy/random/mtrand.so is executable; skipped test_api.test_fastCopyAndTranspose ... ok test_arrayprint.TestArrayRepr.test_nan_inf ... ok test_str (test_arrayprint.TestComplexArray) ... ok Ticket 844. ... ok test_blasdot.test_blasdot_used ... ok test_blasdot.test_dot_2args ... ok test_blasdot.test_dot_3args ... ok test_blasdot.test_dot_3args_errors ... ok . . . Test if an appropriate exception is raised when passing bad values to ... ok Test whether equivalent subarray dtypes hash the same. ... ok Test whether different subarray dtypes hash differently. ... ok Test some data types that are equal ... ok Test some more complicated cases that shouldn't be equal ... ok Test some simple cases that shouldn't be equal ... ok test_single_subarray (test_dtype.TestSubarray) ... ok test_einsum_errors (test_einsum.TestEinSum) ... ok test_einsum_sums_cfloat128 (test_einsum.TestEinSum) ...
####################### On Sat, Oct 22, 2011 at 1:46 PM, <numpy-discussion-owner@scipy.org> wrote:
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---------- Forwarded message ---------- From: akshar bhosale <akshar.bhosale@gmail.com> To: SciPy Developers List <scipy-dev@scipy.org>, Discussion of Numerical Python <numpy-discussion@scipy.org> Date: Sat, 22 Oct 2011 13:46:49 +0530 Subject: Re: [SciPy-Dev] numpy.test hangs <charlesr.harris@gmail.com>Hi,
python Python 2.6 (r26:66714, May 29 2011, 15:10:47) [GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
import numpy numpy.show_config() lapack_opt_info: libraries = ['mkl_lapack95_lp64', 'mkl_def', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_mc', 'pthread'] library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include', '/opt/intel/Compiler/11.0/069/include/'] blas_opt_info: libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_mc', 'pthread'] library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include', '/opt/intel/Compiler/11.0/069/include/'] lapack_mkl_info: libraries = ['mkl_lapack95_lp64', 'mkl_def', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_mc', 'pthread'] library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include', '/opt/intel/Compiler/11.0/069/include/'] blas_mkl_info: libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_mc', 'pthread'] library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include', '/opt/intel/Compiler/11.0/069/include/'] mkl_info: libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'mkl_mc', 'pthread'] library_dirs = ['/opt/intel/Compiler/11.0/069/mkl/lib/em64t'] define_macros = [('SCIPY_MKL_H', None)] include_dirs = ['/opt/intel/Compiler/11.0/069/mkl/include', '/opt/intel/Compiler/11.0/069/include/']
Akshar
On Sat, Oct 22, 2011 at 11:54 AM, akshar bhosale <akshar.bhosale@gmail.com
wrote:
yes sure.. i have intel cluster toolkit installed on my system. (11/069 version and mkl 10.3). i have machine having intel xeon processor and rhel 5.2 x86_64 platform. i am trying with intel compilers. if i do
python -c 'import numpy;numpy.matrix([[1, 5, 10], [1.0, 3j, 4]], numpy.complex128).T.I.H' python: symbol lookup error: /opt/intel/Compiler/11.0/069/mkl/lib/em64/libmkl_lapack.so: undefined symbol: mkl_lapack_zgeqrf
my site.cfg is : #################### [mkl]
mkl_libs = mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core, mkl_mc lapack_libs = 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/ #################### and intelcompiler.py is : ############################ from distutils.unixccompiler import UnixCCompiler from numpy.distutils.exec_command import find_executable import sys
class IntelCCompiler(UnixCCompiler): """ A modified Intel compiler compatible with an gcc built Python.""" compiler_type = 'intel' cc_exe = 'icc' cc_args = 'fPIC'
def __init__ (self, verbose=0, dry_run=0, force=0): sys.exit(0) UnixCCompiler.__init__ (self, verbose,dry_run, force) self.cc_exe = 'icc -fPIC ' compiler = self.cc_exe self.set_executables(compiler=compiler, compiler_so=compiler, compiler_cxx=compiler, linker_exe=compiler, linker_so=compiler + ' -shared -lstdc++')
class IntelItaniumCCompiler(IntelCCompiler): compiler_type = 'intele'
# On Itanium, the Intel Compiler used to be called ecc, let's search for # it (now it's also icc, so ecc is last in the search). for cc_exe in map(find_executable,['icc','ecc']): if cc_exe: break
class IntelEM64TCCompiler(UnixCCompiler): """ A modified Intel x86_64 compiler compatible with a 64bit gcc built Python. """ compiler_type = 'intelem' cc_exe = 'icc -m64 -fPIC' cc_args = "-fPIC -openmp" def __init__ (self, verbose=0, dry_run=0, force=0): UnixCCompiler.__init__ (self, verbose,dry_run, force) self.cc_exe = 'icc -m64 -fPIC -openmp ' compiler = self.cc_exe self.set_executables(compiler=compiler, compiler_so=compiler, compiler_cxx=compiler, linker_exe=compiler, linker_so=compiler + ' -shared -lstdc++') ########################## LD_LIBRARY_PATH is : #########################
/opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/scalasca-1.3.3/lib:/opt/PBS/lib:/opt/intel/mpi/lib64:/opt/maui/lib:/opt/jdk1.6.0_23/lib:/opt/intel/Compiler/11.0/069/ipp/em64t/sharedlib:/opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/intel/Compiler/11.0/069/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.0/069/lib/intel64:/opt/intel/Compiler/11.0/069/ipp/em64t/sharedlib:/opt/intel/Compiler/11.0/069/mkl/lib/em64t:/opt/intel/Compiler/11.0/069/tbb/em64t/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.0/069/lib/intel64:/usr/local/lib #########################
-AKSHAR
On Sat, Oct 22, 2011 at 11:32 AM, Charles R Harris < charlesr.harris@gmail.com> wrote:
On Fri, Oct 21, 2011 at 11:49 PM, akshar bhosale < akshar.bhosale@gmail.com> wrote:
Hi,
unfortunately 1.6.1 also hangs on the same place. Can i move ahead with installing scipy?
Hmm. Well, give scipy a try, but it would be nice to know what the problem is with einsum. I'm thinking compiler, GCC 4.1.2 might be a bit old, but it could easily be something else. Can you give us more information about your system?
Chuck
On Sat, Oct 22, 2011 at 12:19 AM, Charles R Harris < charlesr.harris@gmail.com> wrote:
On Fri, Oct 21, 2011 at 5:25 AM, akshar bhosale < akshar.bhosale@gmail.com> wrote:
Hi, does this mean that numpy is not configured properly or i can ignore this and go ahead with scipy installation?
Scipy will probably work, but you should really install numpy 1.6.1 instead of 1.6.0.
<snip>
Chuck
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