[Debichem-devel] Bug#732400: Bug#732400: gromacs: Illegal instruction in all programs on Intel Core 2 CPU
Christoph Junghans
junghans at votca.org
Tue Dec 17 22:27:20 UTC 2013
2013/12/17 Andras Szilagyi <sziami at gmail.com>:
> Unfortunately, mdrun crashes before it could create an md.log file.
> All programs, including mdrun, crash while reporting the command line
> arguments (all programs start with this).
> I noticed the crash always occurs before reporting the first command
> line argument (option) with a value that is not an integer or boolean.
> That is, when the type of the next command line argument to be printed
> is real, vector, or time.
>
> If this version is not supposed to run on pre-Sandy Bridge processors,
> maybe this should be indicated in the description.
Gromacs can run on pre-Sandy Bridge processors, but you have to
configure it with
-DGMX_CPU_ACCELERATION=SSE2. Anyhow, this issue seems to be fixed in
bug #725013 already.
>
> Andras
>
> On Tue, Dec 17, 2013 at 10:02 PM, Christoph Junghans <junghans at votca.org> wrote:
>> 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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>>> Debichem-devel at lists.alioth.debian.org
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>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
--
Christoph Junghans
Web: http://www.compphys.de
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