[SciPy-dev] patch for scsl support

Arnd Baecker arnd.baecker at web.de
Mon Dec 19 04:36:03 CST 2005


Hi,

the attached patch allows to detect the scsl
(Scientific Computing Software Library,
http://www.sgi.com/products/software/scsl.html
)
via system_info.py.
Here we have used the OpenMP variant scs_mp.
This library allows (among other stuff)
to perform linear algebra operations
using several CPUs in parallel.

On our machine we have scsl, ATLAS and MKL , so
  export ATLAS=None
  export MKL=None
enforces scsl.
Build and install work without problems (with gcc)
and almost all tests of scipy.test(10,10) pass, apart from

  ERROR: check_nils (scipy.linalg.matfuncs.test_matfuncs.test_logm)
  FAIL: check_tandg (scipy.special.basic.test_basic.test_cephes)
  FAIL: check_nils (scipy.linalg.matfuncs.test_matfuncs.test_signm)

Full output below. Not sure what is going on with those ...
In addition one gets during the test:

****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by scipy/system_info.py,
  then scipy uses flapack instead of clapack.
****************************************************************

Questions
- how crucial are these warnings?
- what is the best way to support both scsl and scsl_mp?

I am not sure if we managed to add everything in the right way,
so it would be great if someone more experienced with this
(Pearu?!) could have a look at the patch.

Many thanks,

Arnd and Jan


======================================================================
ERROR: check_nils (scipy.linalg.matfuncs.test_matfuncs.test_logm)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/baecker/python2/scipy_lintst_scsl/lib/python2.4/site-packages/scipy/linalg/tests/test_matfuncs.py",
line 82, in check_nils
    logm((identity(7)*3.1+0j)-a)
  File
"/home/baecker/python2//scipy_lintst_scsl/lib/python2.4/site-packages/scipy/linalg/matfuncs.py",
line 230, in logm
    temp = mat(solve(E.T,(E-A).T))
  File
"/home/baecker/python2//scipy_lintst_scsl/lib/python2.4/site-packages/scipy/linalg/basic.py",
line 103, in solve
    a1, b1 = map(asarray_chkfinite,(a,b))
  File
"/home/baecker/python2//scipy_lintst_scsl/lib/python2.4/site-packages/scipy/base/function_base.py",
line 211, in asarray_chkfinite
    raise ValueError, "array must not contain infs or NaNs"
ValueError: array must not contain infs or NaNs

======================================================================
FAIL: check_tandg (scipy.special.basic.test_basic.test_cephes)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/baecker/python2/scipy_lintst_scsl/lib/python2.4/site-packages/scipy/special/tests/test_basic.py",
line 440, in check_tandg
    assert_equal(cephes.tandg(45),1.0)
  File
"/home/baecker/python2//scipy_lintst_scsl/lib/python2.4/site-packages/scipy/test/testing.py",
line 666, in assert_equal
    assert desired == actual, msg
AssertionError:
Items are not equal:
DESIRED: 1.0
ACTUAL: 1.0000000000000002

======================================================================
FAIL: check_nils (scipy.linalg.matfuncs.test_matfuncs.test_signm)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/baecker/python2/scipy_lintst_scsl/lib/python2.4/site-packages/scipy/linalg/tests/test_matfuncs.py",
line 44, in check_nils
    assert_array_almost_equal(r,cr)
  File
"/home/baecker/python2//scipy_lintst_scsl/lib/python2.4/site-packages/scipy/test/testing.py",
line 763, in assert_array_almost_equal
    assert cond,\
AssertionError:
Arrays are not almost equal (mismatch 100.0%):
        Array 1: [[  5.5434479e+146 -3.0932899e+146j   1.0704570e+147
+2.4698621e+146j
    2.1300115e+146 -1.8113002e+147j   7.0783749e+1...
        Array 2: [[ 11.9493333  -2.2453333  15.3173333  21.6533333
-2.2453333]
 [ -3.8426667   0.4986667  -4.5906667  -7.1866667   0.498...
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