Bug#581761: libatlas3gf-base: Illegal instructions .... dgemm
For those interested -- I've rebuilt atlas manually in a clean cow chroot on a native architecture -- illegal instruction issue is gone! On Mon, 26 Jul 2010, Yaroslav Halchenko wrote: Package: libatlas3gf-base Version: 3.8.3-24 Severity: normal -- .-. =-- /v\ = Keep in touch// \\ (yoh@|www.)onerussian.com Yaroslav Halchenko /( )\ ICQ#: 60653192 Linux User^^-^^[17] signature.asc Description: Digital signature
Bug#581761: libatlas3gf-base: Illegal instructions .... dgemm
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 0x73303626 in ATL_dmmJIK2 () from /usr/lib/libblas.so.3gf #2 0x73304082 in ATL_dmmJIK () from /usr/lib/libblas.so.3gf #3 0x732f7ad4 in ATL_dgemm () from /usr/lib/libblas.so.3gf #4 0x73703ae8 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. 0x732e1899 in ATL_dJIK52x52x52TN52x52x0_a1_b0 () from /usr/lib/libblas.so.3gf (gdb) bt 30 #0 0x732e1899 in ATL_dJIK52x52x52TN52x52x0_a1_b0 () from /usr/lib/libblas.so.3gf #1 0x73303626 in ATL_dmmJIK2 () from /usr/lib/libblas.so.3gf #2 0x73304082 in ATL_dmmJIK () from /usr/lib/libblas.so.3gf #3 0x732f7ad4 in ATL_dgemm () from /usr/lib/libblas.so.3gf #4 0x73703ae8 in ?? () from /usr/lib/pymodules/python2.5/numpy/core/_dotblas.so #5 0x0048fef6 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 0x004915f9 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 0x004dac19 in function_call (func=0xe8c398, arg=0x2457a28, kw=0x0) at ../Objects/funcobject.c:517 #9 0x00418493 in PyObject_Call (func=0x2552f60, arg=0x1a0, kw=0x25337e0) at ../Objects/abstract.c:1861 #10 0x0042009f in instancemethod_call (func=0xe8c398, arg=0x2457a28, kw=0x0) at ../Objects/classobject.c:2519 #11 0x00418493 in PyObject_Call (func=0x2552f60, arg=0x1a0, kw=0x25337e0) at ../Objects/abstract.c:1861 #12 0x004617a8 in call_maybe (o=value optimized out, name=value optimized out, nameobj=value optimized out, format=0x4f28fa (O)) at ../Objects/typeobject.c:967 #13 0x00462eb4 in slot_nb_multiply (self=0x2486d70, other=0x2486668) at ../Objects/typeobject.c:4393 #14 0x0041913f in binary_op1 (v=0x2486d70,
Bug#581761: libatlas3gf-base: Illegal instructions .... dgemm
ah... and test_plt.py provided in original report works fine for me (via forwarded X to suspect box) ... so it could be a separate issue... sorry for not testing right away On Mon, 26 Jul 2010, Yaroslav Halchenko wrote: 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 0x73303626 in ATL_dmmJIK2 () from /usr/lib/libblas.so.3gf #2 0x73304082 in ATL_dmmJIK () from /usr/lib/libblas.so.3gf #3 0x732f7ad4 in ATL_dgemm () from /usr/lib/libblas.so.3gf #4 0x73703ae8 in ?? () from /usr/lib/pymodules/python2.5/numpy/core/_dotblas.so -- .-. =-- /v\ = Keep in touch// \\ (yoh@|www.)onerussian.com Yaroslav Halchenko /( )\ ICQ#: 60653192 Linux User^^-^^[17] -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#581761: libatlas3gf-base: Illegal instructions .... dgemm
and here is an easy way to reproduce it with even different function as
a victim:
*$ gdb --args /usr/bin/python2.6 -c 'import scipy; scipy.test()'
GNU gdb (GDB) 7.1-debian
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type show copying
and show warranty for details.
This GDB was configured as x86_64-linux-gnu.
For bug reporting instructions, please see:
http://www.gnu.org/software/gdb/bugs/...
Reading symbols from /usr/bin/python2.6...Reading symbols from
/usr/lib/debug/usr/bin/python2.6...done.
done.
(gdb) c
The program is not being run.
(gdb) r
Starting program: /usr/bin/python2.6 -c import\ scipy\;\ scipy.test\(\)
[Thread debugging using libthread_db enabled]
Running unit tests for scipy
NumPy version 1.4.1
NumPy is installed in /usr/lib/pymodules/python2.6/numpy
SciPy version 0.7.2
SciPy is installed in /usr/lib/python2.6/dist-packages/scipy
Python version 2.6.5+ (release26-maint, Jul 6 2010, 12:58:20) [GCC 4.4.4]
nose version 0.11.1
[New Thread 0x7fffee0a8710 (LWP 23988)]
/usr/lib/python2.6/dist-packages/scipy/linsolve/__init__.py:4:
DeprecationWarning: scipy.linsolve has moved to scipy.sparse.linalg.dsolve
warn('scipy.linsolve has moved to scipy.sparse.linalg.dsolve',
DeprecationWarning)
.
Program received signal SIGILL, Illegal instruction.
0x75a9e327 in ATL_zaxpy_xp1yp1aXbX () from /usr/lib/libblas.so.3gf
(gdb) bt 10
#0 0x75a9e327 in ATL_zaxpy_xp1yp1aXbX () from /usr/lib/libblas.so.3gf
#1 0x7fffec37b38b in zgesl_ () from
/usr/lib/python2.6/dist-packages/scipy/integrate/vode.so
#2 0x7fffec36ad9a in zvsol_ () from
/usr/lib/python2.6/dist-packages/scipy/integrate/vode.so
#3 0x7fffec36f815 in zvnlsd_ () from
/usr/lib/python2.6/dist-packages/scipy/integrate/vode.so
#4 0x7fffec372f61 in zvstep_ () from
/usr/lib/python2.6/dist-packages/scipy/integrate/vode.so
#5 0x7fffec37a6ec in zvode_ () from
/usr/lib/python2.6/dist-packages/scipy/integrate/vode.so
#6 0x7fffec34d838 in f2py_rout_vode_zvode (capi_self=value optimized
out, capi_args=value optimized out, capi_keywds=value optimized out,
f2py_func=value optimized out)
at build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.c:1424
#7 0x0041ef47 in PyObject_Call (func=fortran at remote 0x1ce02d8,
arg=unknown at remote 0x7fff8000, kw=unknown at remote 0x280bef0) at
../Objects/abstract.c:2492
#8 0x004a6215 in ext_do_call (f=
Frame 0x280b8b0, for file
/usr/lib/python2.6/dist-packages/scipy/integrate/ode.py, line 554, in run
(self=zvode(max_step=float at remote 0x2d26108, success=1, first_step=float
at remote 0x2d26108, ml=None, iwork=numpy.ndarray at remote 0x2781d30,
rwork=numpy.ndarray at remote 0x26a8d90, nsteps=500, mu=None,
with_jacobian=0, rtol=float at remote 0x2d4cde0, zwork=numpy.ndarray at
remote 0x26bc1f0, call_args=[float at remote 0x2d4cde0, float at remote
0x2d4cd80, 1, 1, numpy.ndarray at remote 0x26bc1f0, numpy.ndarray at remote
0x26a8d90, numpy.ndarray at remote 0x2781d30, 11], atol=float at remote
0x2d4cd80, min_step=float at remote 0x2d26108, meth=1, order=12) at remote
0x27c6590, args=(function at remote 0x27c32a8, function at remote
0x27c3410, numpy.ndarray at remote 0x2787e60, float at remote 0x2d4ce58,
float at remote 0x2d4cd50, (), (...))), throwflag=value optimized out) at
../Python/ceval.c:4063
#9 PyEval_EvalFrameEx (f=
Frame 0x280b8b0, for file
/usr/lib/python2.6/dist-packages/scipy/integrate/ode.py, line 554, in run
(self=zvode(max_step=float at remote 0x2d26108, success=1, first_step=float
at remote 0x2d26108, ml=None, iwork=numpy.ndarray at remote 0x2781d30,
rwork=numpy.ndarray at remote 0x26a8d90, nsteps=500, mu=None,
with_jacobian=0, rtol=float at remote 0x2d4cde0, zwork=numpy.ndarray at
remote 0x26bc1f0, call_args=[float at remote 0x2d4cde0, float at remote
0x2d4cd80, 1, 1, numpy.ndarray at remote 0x26bc1f0, numpy.ndarray at remote
0x26a8d90, numpy.ndarray at remote 0x2781d30, 11], atol=float at remote
0x2d4cd80, min_step=float at remote 0x2d26108, meth=1, order=12) at remote
0x27c6590, args=(function at remote 0x27c32a8, function at remote
0x27c3410, numpy.ndarray at remote 0x2787e60, float at remote 0x2d4ce58,
float at remote 0x2d4cd50, (), (...))), throwflag=value optimized out) at
../Python/ceval.c:2452
(More stack frames follow...)
On Mon, 26 Jul 2010, Yaroslav Halchenko wrote:
ah... and test_plt.py provided in original report works fine for me (via
forwarded X to suspect box) ...
so it could be a separate issue... sorry for not testing right away
--
.-.
=-- /v\ =
Keep in touch// \\ (yoh@|www.)onerussian.com
Yaroslav Halchenko /( )\ ICQ#: 60653192
