[Scipy-tickets] [SciPy] #1472: Recent Arpack changes segfaulting in test suite

SciPy Trac scipy-tickets@scipy....
Sun Jul 3 10:47:20 CDT 2011


#1472: Recent Arpack changes segfaulting in test suite
---------------------------------+------------------------------------------
 Reporter:  rgommers             |       Owner:  pv    
     Type:  defect               |      Status:  new   
 Priority:  high                 |   Milestone:  0.10.0
Component:  scipy.sparse.linalg  |     Version:  0.9.0 
 Keywords:  arpack               |  
---------------------------------+------------------------------------------

Comment(by rgommers):

 Okay, getting something more useful out of Valgrind:
 {{{
 $ valgrind --trace-children=yes --leak-check=yes --suppressions=valgrind-
 python.supp --dsymutil=yes python -c "from scipy.sparse import linalg;
 linalg.eigen.test()"
 ==76670== Memcheck, a memory error detector
 ==76670== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
 ==76670== Using Valgrind-3.7.0.SVN and LibVEX; rerun with -h for copyright
 info
 ==76670== Command: python -c from\ scipy.sparse\ import\ linalg;\
 linalg.eigen.test()
 ==76670==
 ==76670== Memcheck, a memory error detector
 ==76670== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
 ==76670== Using Valgrind-3.7.0.SVN and LibVEX; rerun with -h for copyright
 info
 ==76670== Command:
 /Library/Frameworks/Python.framework/Versions/2.6/Resources/Python.app/Contents/MacOS/Python
 -c from\ scipy.sparse\ import\ linalg;\ linalg.eigen.test()
 ==76670==
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/numpy/numpy/core/multiarray.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/numpy/numpy/core/umath.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/numpy/numpy/core/_dotblas.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/numpy/numpy/core/scalarmath.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/numpy/numpy/lib/_compiled_base.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/numpy/numpy/linalg/lapack_lite.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/numpy/numpy/fft/fftpack_lite.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/numpy/numpy/random/mtrand.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/sparsetools/_csr.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/sparsetools/_csc.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/sparsetools/_coo.so"
 warning: invalid DWARF generated by the compiler: DIE 0x000026df has
 multiple  AT_byte_size attributes in
 '/Users/rgommers/Code/scipy/build/scons/scipy/sparse/sparsetools/coo_wrap.os'.
 warning: invalid DWARF generated by the compiler: DIE 0x000026df has
 multiple  AT_decl_file attributes in
 '/Users/rgommers/Code/scipy/build/scons/scipy/sparse/sparsetools/coo_wrap.os'.
 warning: invalid DWARF generated by the compiler: DIE 0x000026df has
 multiple  AT_decl_line attributes in
 '/Users/rgommers/Code/scipy/build/scons/scipy/sparse/sparsetools/coo_wrap.os'.
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/sparsetools/_dia.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/sparsetools/_bsr.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/sparsetools/_csgraph.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/linalg/isolve/_iterative.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/linalg/_flinalg.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/linalg/flapack.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/linalg/clapack.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/linalg/calc_lwork.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/linalg/cblas.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/linalg/fblas.so"
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/linalg/dsolve/_superlu.so"
 /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-
 packages/scikits.statsmodels-0.3.0rc1-py2.6.egg/scikits/__init__.py:1:
 UserWarning: Module numpy was already imported from
 /Users/rgommers/Code/numpy/numpy/__init__.pyc, but
 /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-
 packages is being added to sys.path
   __import__('pkg_resources').declare_namespace(__name__)
 /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-
 packages/scikits.statsmodels-0.3.0rc1-py2.6.egg/scikits/__init__.py:1:
 UserWarning: Module scipy was already imported from
 /Users/rgommers/Code/scipy/scipy/__init__.pyc, but
 /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-
 packages is being added to sys.path
   __import__('pkg_resources').declare_namespace(__name__)
 --76670-- run: /usr/bin/dsymutil
 "/Users/rgommers/Code/scipy/scipy/sparse/linalg/eigen/arpack/_arpack.so"
 Running unit tests for scipy.sparse.linalg.eigen
 NumPy version 2.0.0.dev-5e4a407
 NumPy is installed in /Users/rgommers/Code/numpy/numpy
 SciPy version 0.10.0.dev
 SciPy is installed in /Users/rgommers/Code/scipy/scipy
 Python version 2.6.4 (r264:75821M, Oct 27 2009, 19:48:32) [GCC 4.0.1
 (Apple Inc. build 5493)]
 nose version 1.0.0
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE3AA2E: ATL_dgemvT_a1_x1_b1_y1 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE69C7A: ATL_dger1_a1_x1_yX (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE359B7: ATL_sgemvT_a1_x1_b0_y1 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE34DA7: ATL_sgemvN_a1_x1_b1_y1 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE348F7: ATL_sgemvN_a1_x1_b0_y1 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Use of uninitialised value of size 4
 ==76670==    at 0xE34792: dp2dpNb0m_N_42dpNb0m (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Use of uninitialised value of size 4
 ==76670==    at 0xE3479F: dp2dpNb0m_N_42dpNb0m (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE348FB: ATL_sgemvN_a1_x1_b0_y1 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE3490E: ATL_sgemvN_a1_x1_b0_y1 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Use of uninitialised value of size 4
 ==76670==    at 0xE3459D: dp1dpNb0_N_41dpNb0 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE678D4: ATL_sger1_a1_x1_yX (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ....==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE39529: ATL_dgemvT_a1_x1_b0_y1 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE395DE: ATL_dgemvT_a1_x1_b0_y1 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ........................................................==76670==
 Conditional jump or move depends on uninitialised value(s)
 ==76670==    at 0xE69CB5: ATL_dger1_a1_x1_yX (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ............................................................==76670== Use
 of uninitialised value of size 4
 ==76670==    at 0xE347C9: dp2dpNb0m_N_22dpNb0m (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Use of uninitialised value of size 4
 ==76670==    at 0xE347D5: dp2dpNb0m_N_22dpNb0m (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Use of uninitialised value of size 4
 ==76670==    at 0xE347FA: dp2dpNb0m_N_12dpNb0m (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Use of uninitialised value of size 4
 ==76670==    at 0xE34806: dp2dpNb0m_N_12dpNb0m (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Use of uninitialised value of size 4
 ==76670==    at 0xE345EA: dp1dpNb0_N_11dpNb0 (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ..........................................................................................................................==76670==
 Use of uninitialised value of size 4
 ==76670==    at 0xBBC8F4: ATL_zaxpy (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== Invalid read of size 8
 ==76670==    at 0xBBC8F4: ATL_zaxpy (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==  Address 0x1 is not stack'd, malloc'd or (recently) free'd
 ==76670==
 ==76670==
 ==76670== Process terminating with default action of signal 10 (SIGBUS)
 ==76670==  Non-existent physical address at address 0x1
 ==76670==    at 0xBBC8F4: ATL_zaxpy (in
 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib)
 ==76670==
 ==76670== HEAP SUMMARY:
 ==76670==     in use at exit: 11,997,114 bytes in 11,130 blocks
 ==76670==   total heap usage: 1,333,804 allocs, 1,322,674 frees,
 91,621,294 bytes allocated
 }}}

 Trac is not letting me upload the rest, so cutting it off here.

-- 
Ticket URL: <http://projects.scipy.org/scipy/ticket/1472#comment:8>
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