Bug#581761: libatlas3gf-base: Illegal instructions .... dgemm

Yaroslav Halchenko yoh at sandbox.pymvpa.org
Tue Jul 27 02:24:39 UTC 2010 

Package: libatlas3gf-base
Version: 3.8.3-24
Severity: normal


I think I started to experience similar simptoms recently.  Our testbox started
throwing "illegal instructions".  It started to happen after recent upgrades.
Before providing this information I've updated to current sid but nothing
changed... installed also libatlas3gf-amd64sse3 which became used... the
same... 

In both cases (different python modules tested) it seems to boil to (sorry that
I used python2.5 at first... the same with 2.6)

#1  0x00007ffff3303626 in ATL_dmmJIK2 () from /usr/lib/libblas.so.3gf
#2  0x00007ffff3304082 in ATL_dmmJIK () from /usr/lib/libblas.so.3gf
#3  0x00007ffff32f7ad4 in ATL_dgemm () from /usr/lib/libblas.so.3gf
#4  0x00007ffff3703ae8 in ?? () from /usr/lib/pymodules/python2.5/numpy/core/_dotblas.so

Ill Ins started to pop out after following updates which included atlas:

2010-07-15 09:59:22 upgrade fsl-atlases 4.1.5-1 4.1.6-1
2010-07-15 09:59:22 status half-configured fsl-atlases 4.1.5-1
2010-07-15 09:59:22 status unpacked fsl-atlases 4.1.5-1
2010-07-15 09:59:22 status half-installed fsl-atlases 4.1.5-1
2010-07-15 09:59:24 status half-installed fsl-atlases 4.1.5-1
2010-07-15 09:59:29 status unpacked fsl-atlases 4.1.6-1
2010-07-15 09:59:29 status unpacked fsl-atlases 4.1.6-1
2010-07-15 10:00:43 upgrade libatlas3gf-base 3.6.0-24 3.8.3-24
2010-07-15 10:00:43 status half-configured libatlas3gf-base 3.6.0-24
2010-07-15 10:00:43 status unpacked libatlas3gf-base 3.6.0-24
2010-07-15 10:00:44 status half-installed libatlas3gf-base 3.6.0-24
2010-07-15 10:00:44 status half-installed libatlas3gf-base 3.6.0-24
2010-07-15 10:00:45 status unpacked libatlas3gf-base 3.8.3-24
2010-07-15 10:00:45 status unpacked libatlas3gf-base 3.8.3-24
2010-07-15 10:54:30 configure fsl-atlases 4.1.6-1 4.1.6-1
2010-07-15 10:54:30 status unpacked fsl-atlases 4.1.6-1
2010-07-15 10:54:30 status half-configured fsl-atlases 4.1.6-1
2010-07-15 10:54:30 status installed fsl-atlases 4.1.6-1
2010-07-15 10:54:41 configure libatlas3gf-base 3.8.3-24 3.8.3-24
2010-07-15 10:54:41 status unpacked libatlas3gf-base 3.8.3-24
2010-07-15 10:54:41 status half-configured libatlas3gf-base 3.8.3-24
2010-07-15 10:54:41 update-alternatives: run with --install /usr/lib/libblas.so.3gf libblas.so.3gf /usr/lib/atlas-base/atlas/libblas.so.3gf 35 --slave /usr/lib/libcblas.so.3gf libcblas.so.3gf /usr/lib/atlas-base/libcblas.so.3gf --slave /usr/lib/libf77blas.so.3gf libf77blas.so.3gf /usr/lib/atlas-base/libf77blas.so.3gf --slave /usr/lib/libatlas.so.3gf libatlas.so.3gf /usr/lib/atlas-base/libatlas.so.3gf --slave /usr/lib/liblapack_atlas.so.3gf liblapack_atlas.so.3gf /usr/lib/atlas-base/liblapack_atlas.so.3gf
2010-07-15 10:54:41 update-alternatives: link group libblas.so.3gf updated to point to /usr/lib/atlas-base/atlas/libblas.so.3gf
2010-07-15 10:54:41 update-alternatives: run with --install /usr/lib/liblapack.so.3gf liblapack.so.3gf /usr/lib/atlas-base/atlas/liblapack.so.3gf 35
2010-07-15 10:54:41 update-alternatives: link group liblapack.so.3gf updated to point to /usr/lib/atlas-base/atlas/liblapack.so.3gf
2010-07-15 10:54:41 status installed libatlas3gf-base 3.8.3-24

ATM they look like following while testing nitime

Program received signal SIGILL, Illegal instruction.
0x00007ffff32e1899 in ATL_dJIK52x52x52TN52x52x0_a1_b0 () from /usr/lib/libblas.so.3gf
(gdb) bt 30
#0  0x00007ffff32e1899 in ATL_dJIK52x52x52TN52x52x0_a1_b0 () from /usr/lib/libblas.so.3gf
#1  0x00007ffff3303626 in ATL_dmmJIK2 () from /usr/lib/libblas.so.3gf
#2  0x00007ffff3304082 in ATL_dmmJIK () from /usr/lib/libblas.so.3gf
#3  0x00007ffff32f7ad4 in ATL_dgemm () from /usr/lib/libblas.so.3gf
#4  0x00007ffff3703ae8 in ?? () from /usr/lib/pymodules/python2.5/numpy/core/_dotblas.so
#5  0x000000000048fef6 in call_function (f=0x24990f0, throwflag=<value optimized out>) at ../Python/ceval.c:3612
#6  PyEval_EvalFrameEx (f=0x24990f0, throwflag=<value optimized out>) at ../Python/ceval.c:2304
#7  0x00000000004915f9 in PyEval_EvalCodeEx (co=0xe85eb8, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=21632, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at ../Python/ceval.c:2875
#8  0x00000000004dac19 in function_call (func=0xe8c398, arg=0x2457a28, kw=0x0) at ../Objects/funcobject.c:517
#9  0x0000000000418493 in PyObject_Call (func=0x2552f60, arg=0x1a0, kw=0x25337e0) at ../Objects/abstract.c:1861
#10 0x000000000042009f in instancemethod_call (func=0xe8c398, arg=0x2457a28, kw=0x0) at ../Objects/classobject.c:2519
#11 0x0000000000418493 in PyObject_Call (func=0x2552f60, arg=0x1a0, kw=0x25337e0) at ../Objects/abstract.c:1861
#12 0x00000000004617a8 in call_maybe (o=<value optimized out>, name=<value optimized out>, nameobj=<value optimized out>, format=0x4f28fa "(O)") at ../Objects/typeobject.c:967
#13 0x0000000000462eb4 in slot_nb_multiply (self=0x2486d70, other=0x2486668) at ../Objects/typeobject.c:4393
#14 0x000000000041913f in binary_op1 (v=0x2486d70, w=0x2486668, op_slot=16) at ../Objects/abstract.c:398
#15 0x0000000000419c68 in PyNumber_Multiply (v=0x2552f60, w=0x1a0) at ../Objects/abstract.c:669
#16 0x000000000048dd50 in PyEval_EvalFrameEx (f=0x2498880, throwflag=<value optimized out>) at ../Python/ceval.c:1094
#17 0x0000000000490ad6 in fast_function (f=0x24953d0, throwflag=<value optimized out>) at ../Python/ceval.c:3698
#18 call_function (f=0x24953d0, throwflag=<value optimized out>) at ../Python/ceval.c:3633
#19 PyEval_EvalFrameEx (f=0x24953d0, throwflag=<value optimized out>) at ../Python/ceval.c:2304
#20 0x0000000000490ad6 in fast_function (f=0x21b6a50, throwflag=<value optimized out>) at ../Python/ceval.c:3698
#21 call_function (f=0x21b6a50, throwflag=<value optimized out>) at ../Python/ceval.c:3633
#22 PyEval_EvalFrameEx (f=0x21b6a50, throwflag=<value optimized out>) at ../Python/ceval.c:2304
#23 0x00000000004915f9 in PyEval_EvalCodeEx (co=0x1c28dc8, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=21632, kws=0x0, kwcount=0, defs=0x1c01ba8, defcount=1, 
    closure=0x0) at ../Python/ceval.c:2875
#24 0x00000000004dac19 in function_call (func=0x195c1b8, arg=0x2446370, kw=0x0) at ../Objects/funcobject.c:517
#25 0x000000000041c7ab in PyObject_Call (callable=0x195c1b8) at ../Objects/abstract.c:1861
#26 PyObject_CallFunctionObjArgs (callable=0x195c1b8) at ../Objects/abstract.c:2091
#27 0x0000000000448e6e in PyObject_GenericGetAttr (obj=0x2484350, name=0x2601b10) at ../Objects/object.c:1356
#28 0x000000000048c953 in PyEval_EvalFrameEx (f=0x21918d0, throwflag=<value optimized out>) at ../Python/ceval.c:2016
#29 0x00000000004915f9 in PyEval_EvalCodeEx (co=0x2440468, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=21632, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
    at ../Python/ceval.c:2875
(More stack frames follow...)


or like following while testing mvpa module

*(gdb) bt 10
#0  0x00007ffff52eb7d2 in ATL_dupKBmm20_2_1_b0 () from /usr/lib/libblas.so.3gf
#1  0x00007ffff52b36db in ATL_dmmJIK2 () from /usr/lib/libblas.so.3gf
#2  0x00007ffff52b4082 in ATL_dmmJIK () from /usr/lib/libblas.so.3gf
#3  0x00007ffff52a7ad4 in ATL_dgemm () from /usr/lib/libblas.so.3gf
#4  0x00007ffff56b3ae8 in ?? () from /usr/lib/pymodules/python2.6/numpy/core/_dotblas.so
#5  0x00000000004a7b35 in call_function (f=
    Frame 0x3081e30, for file /home/yoh/proj/pymvpa/pymvpa/mvpa/clfs/kernel.py, line 201, in compute (self=<KernelLinear(_Sigma_p=<float at remote 0x3617d70>, _Sigma_p_orig=<float at remote 0x3617d70>, sigma_0=<float at remote 0x36157b8>, kernel_matrix=None) at remote 0x2ed2ed0>, data1=<numpy.ndarray at remote 0x1e3b2a0>, data2=<numpy.ndarray at remote 0x1e3b2a0>, Sigma_p=<float at remote 0x3617d70>, data2_sc=<numpy.ndarray at remote 0x3004e20>), throwflag=<value optimized out>) at ../Python/ceval.c:3750
#6  PyEval_EvalFrameEx (f=
    Frame 0x3081e30, for file /home/yoh/proj/pymvpa/pymvpa/mvpa/clfs/kernel.py, line 201, in compute (self=<KernelLinear(_Sigma_p=<float at remote 0x3617d70>, _Sigma_p_orig=<float at remote 0x3617d70>, sigma_0=<float at remote 0x36157b8>, kernel_matrix=None) at remote 0x2ed2ed0>, data1=<numpy.ndarray at remote 0x1e3b2a0>, data2=<numpy.ndarray at remote 0x1e3b2a0>, Sigma_p=<float at remote 0x3617d70>, data2_sc=<numpy.ndarray at remote 0x3004e20>), throwflag=<value optimized out>) at ../Python/ceval.c:2412
#7  0x00000000004a9551 in PyEval_EvalCodeEx (co=0x2641a08, globals=<value optimized out>, locals=<value optimized out>, args=0x3, argcount=<value optimized out>, kws=<value optimized out>, kwcount=0, defs=0x264e228, 
    defcount=1, closure=0x0) at ../Python/ceval.c:3000
#8  0x00000000004a76e2 in fast_function (f=


-- System Information:
Debian Release: squeeze/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 2.6.32-5-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages libatlas3gf-base depends on:
ii  libc6                         2.11.2-2   Embedded GNU C Library: Shared lib
ii  libgcc1                       1:4.4.4-7  GCC support library
ii  libgfortran3                  4.4.4-7    Runtime library for GNU Fortran ap

libatlas3gf-base recommends no packages.

Versions of packages libatlas3gf-base suggests:
ii  libblas3gf                    1.2-7      Basic Linear Algebra Reference imp
ii  liblapack3gf                  3.2.2-1    library of linear algebra routines

-- no debconf information

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