[Debichem-devel] Bug#732400: gromacs: Illegal instruction in all programs on Intel Core 2 CPU

[Andras Szilagyi]

Package: gromacs
Version: 4.6.5-1
Severity: important

All gromacs programs crash right at the start, reporting an illegal hardware 
instruction while printing the program options. 
E.g. "g_angle -h" results in the following output:

::::::
                         :-)  G  R  O  M  A  C  S  (-:

                   Groningen Machine for Chemical Simulation

                            :-)  VERSION 4.6.5  (-:

(lots of text omitted)

Option     Filename  Type         Description
------------------------------------------------------------
  -f       traj.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
  -n      angle.ndx  Input        Index file
 -od    angdist.xvg  Output       xvgr/xmgr file
 -ov    angaver.xvg  Output, Opt. xvgr/xmgr file
 -of    dihfrac.xvg  Output, Opt. xvgr/xmgr file
 -ot   dihtrans.xvg  Output, Opt. xvgr/xmgr file
 -oh    trhisto.xvg  Output, Opt. xvgr/xmgr file
 -oc    dihcorr.xvg  Output, Opt. xvgr/xmgr file
 -or       traj.trr  Output, Opt. Trajectory in portable xdr format

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   yes     Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    19      Set the nicelevel
zsh: illegal hardware instruction  g_angle -h
:::::::

Debugging with gdb indicates that the error occurs in pa_val() in
libgmx.so.8:

:::::::
Program received signal SIGILL, Illegal instruction.
0x00007ffff6801d8e in pa_val () from /usr/lib/libgmx.so.8
(gdb) bt
#0  0x00007ffff6801d8e in pa_val () from /usr/lib/libgmx.so.8
#1  0x00007ffff6802020 in pargs_print_line () from /usr/lib/libgmx.so.8
#2  0x00007ffff680251a in print_pargs () from /usr/lib/libgmx.so.8
#3  0x00007ffff67cc143 in ?? () from /usr/lib/libgmx.so.8
#4  0x00007ffff67ce71f in write_man () from /usr/lib/libgmx.so.8
#5  0x00007ffff67720b8 in parse_common_args () from /usr/lib/libgmx.so.8
#6  0x00007ffff79ccd43 in gmx_g_angle () from /usr/lib/libgmxana.so.8
#7  0x00007ffff7ffe7e9 in main ()
:::::::

This occurs on an Intel Core 2 Quad Q6600 CPU. /proc/cpuinfo gives this for
each core:

:::::::
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 15
model name      : Intel(R) Core(TM)2 Quad CPU    Q6600  @ 2.40GHz
stepping        : 11
cpu MHz         : 1600.000
cache size      : 4096 KB
physical id     : 0
siblings        : 4
core id         : 0
cpu cores       : 4
apicid          : 0
initial apicid  : 0
fpu             : yes
fpu_exception   : yes
cpuid level     : 10
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm
constant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor
ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm lahf_lm tpr_shadow vnmi flexpriority
bogomips        : 4799.50
clflush size    : 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual
power management:
::::::


-- System Information:
Debian Release: 6.0.8
  APT prefers oldstable
  APT policy: (990, 'oldstable'), (500, 'unstable'), (500, 'testing'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 2.6.32-5-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash

Versions of packages gromacs depends on:
ii  atlas3-base [liblapack.s 3.6.0-20.6      Automatically Tuned Linear Algebra
ii  gromacs-data             4.6.5-1         GROMACS molecular dynamics sim, da
ii  lapack3 [liblapack.so.3] 3.0.20000531a-6 library of linear algebra routines
ii  libatlas3-base [liblapac 3.8.4-9.1       Automatically Tuned Linear Algebra
ii  libblas3 [libblas.so.3]  1.2.20110419-5  Basic Linear Algebra Reference imp
ii  libc6                    2.17-5          Embedded GNU C Library: Shared lib
ii  libfftw3-double3         3.3.3-3         Library for computing Fast Fourier
ii  libfftw3-single3         3.3.3-3         Library for computing Fast Fourier
ii  libgomp1                 4.8.0-7         GCC OpenMP (GOMP) support library
ii  liblapack3 [liblapack.so 3.4.2+dfsg-1    Library of linear algebra routines
ii  libx11-6                 2:1.5.0-1       X11 client-side library
ii  refblas3 [libblas.so.3]  1.2-8           Basic Linear Algebra Subroutines 3

Versions of packages gromacs recommends:
ii  cpp                           4:4.4.5-1  The GNU C preprocessor (cpp)

Versions of packages gromacs suggests:
ii  pymol                         1.5.0.1-2  Molecular Graphics System

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