[MMTK] Hang in DomainFinder code

Gisle Sælensminde Gisle.Salensminde at bccs.uib.no
Wed Apr 5 11:04:39 CEST 2006


We have a problem in our normal mode web application server at 
ww.bioinfo.no. The processes of the server will often hang, using all 
available CPU. This eventually cause the server to go down. We have 
tracked the problem to some code from the DomainfinderLib of 
Domainfinder. The function rigidMovement in DomainAnalysis.py calls a 
function generalized_inverse in Numeric. This hangs somewhere down in 
the numeric code (Lapack).

The problem is only present on our dual PIII application server running 
Linux, and we have not been able to reproduce it anywhere else, 
including a sun solaris server and my own P4-based linux comuter. We 
have tried several versions of Numeric, all of them have the same 
problem, which is not surprising since the relevant pieces of code have 
not changed.

Have anyone else experienced a similar problem?

The code below reproduce the problem on the application server:

import Numeric; N = Numeric
import LinearAlgebra; LA = LinearAlgebra

a = N.array([[ 1.    ,  0.    ,  0.    ,  0.    ,  1.8795,  0.0064],
       [ 0.    ,  1.    ,  0.    , -1.8795,  0.    ,  2.7611],
       [ 0.    ,  0.    ,  1.    , -0.0064, -2.7611,  0.    ],
       [ 1.    ,  0.    ,  0.    ,  0.    ,  1.7985,  0.1705],
       [ 0.    ,  1.    ,  0.    , -1.7985,  0.    ,  3.094 ],
       [ 0.    ,  0.    ,  1.    , -0.1705, -3.094 ,  0.    ],
       [ 1.    ,  0.    ,  0.    ,  0.    ,  1.2889,  0.3984],
       [ 0.    ,  1.    ,  0.    , -1.2889,  0.    ,  2.8891],
       [ 0.    ,  0.    ,  1.    , -0.3984, -2.8891,  0.    ],
       [ 1.    ,  0.    ,  0.    ,  0.    ,  1.201 ,  0.4347],
       [ 0.    ,  1.    ,  0.    , -1.201 ,  0.    ,  2.5211],
       [ 0.    ,  0.    ,  1.    , -0.4347, -2.5211,  0.    ]])

#The function below never return:
LA.generalized_inverse(a)

#generalized inverse calls singular_value_decomposition(), so this hangs 
too:
LA.singular_value_decomposition(a)




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