[SciPy-User] building numpy + scipy with MKL 10.3 and icc + ifort 12.1
Steve Schmerler
elcortogm at googlemail.com
Thu Jul 5 07:20:39 EDT 2012
Hello
I built numpy 1.6.2 and scipy 0.10.1 with MKL 10.3, using ifort+icc or
ifort+gcc, following [1,2] on a Red Hat based box. Build details are at
the end of this mail.
numpy
-----
Using gcc, all tests pass. Using icc, I get some messages like::
.../numpy/core/tests/test_umath.py:570: RuntimeWarning: invalid value encountered in fmax
assert_equal(np.fmax(arg1, arg2), out)
all in test_umath.py. No test fails however. Is this a problem?
scipy
-----
With both gcc and icc, I get 3 errors.
======================================================================
ERROR: test_simple_fat (test_decomp.TestRQ)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/schmerler/soft/lib/python2.7/site-packages/scipy/linalg/tests/test_decomp.py", line 1155, in test_simple_fat
r,q = rq(a)
File "/home/schmerler/soft/lib/python2.7/site-packages/scipy/linalg/decomp_qr.py", line 293, in rq
rq, tau, work, info = gerqf(a1, lwork=lwork, overwrite_a=overwrite_a)
error: (lwork>=n||lwork==-1) failed for 1st keyword lwork: dgerqf:lwork=2
======================================================================
ERROR: test_simple_trap (test_decomp.TestRQ)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/schmerler/soft/lib/python2.7/site-packages/scipy/linalg/tests/test_decomp.py", line 1143, in test_simple_trap
r,q = rq(a)
File "/home/schmerler/soft/lib/python2.7/site-packages/scipy/linalg/decomp_qr.py", line 293, in rq
rq, tau, work, info = gerqf(a1, lwork=lwork, overwrite_a=overwrite_a)
error: (lwork>=n||lwork==-1) failed for 1st keyword lwork: dgerqf:lwork=2
and one which says ".../atlas_version.so: undefined symbol:
ATL_buildinfo" but that's probably because I don't have ATLAS.
Have others seen the TestRQ error with MKL? I haven't built against
normal blas/lapack yet to check if this may be a scipy issue.
Thanks.
----------------------------------------------------------------------
Build details
----------------------------------------------------------------------
python 2.7.1
numpy 1.6.2
scipy 0.10.1
MKL 10.3,
ifort/icc 12.1
gcc 4.1.2 (same was used to build python)
numpy site.cfg:
[DEFAULT]
library_dirs = /usr/lib64
include_dirs = /usr/include
[mkl]
library_dirs = /cm/shared/apps/intel-cs/composer_xe_2011_sp1.9.293/mkl/lib/intel64
include_dirs = /cm/shared/apps/intel-cs/composer_xe_2011_sp1.9.293/mkl/include
lapack_libs = mkl_intel_lp64, mkl_sequential, mkl_core
mkl_libs = mkl_intel_lp64, mkl_sequential, mkl_core, mkl_mc3, mkl_def
modified:
numpy/distutils/intelccompiler.py (IntelEM64TCCompiler)
icc -O2 -xhost -fPIC -fp-model strict -fomit-frame-pointer
numpy/distutils/fcompiler/intel.py
ifort -O2 -xhost -fp-model strict -fPIC
install (numpy,scipy):
gcc + ifort
python setup.py build --fcompiler=intelem
icc + ifort
python setup.py build --compiler=intelem --fcompiler=intelem
[1] http://software.intel.com/en-us/articles/numpy-scipy-with-mkl/
[2] http://www.scipy.org/Installing_SciPy/Linux#head-0b5ce001569a20ddbbdb2187578000372a09acb1
best,
Steve
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