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

[Christoph Junghans]

2013/12/17 Andras Szilagyi <sziami at gmail.com>:
> 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.
My guess is that the deb package is compiled with some hardware
acceleration, which is not available on your machine.

To check, could you run:
$ grep "CPU acceleration" md.log
on some md.log file?

If it says something like:
CPU acceleration:   AVX_256
we know why.

> 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
>
> -- no debconf information
>
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-- 
Christoph Junghans
Web: http://www.compphys.de