2013/12/17 Andras Szilagyi <szi...@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 <jungh...@votca.org> > wrote: >> 2013/12/17 Andras Szilagyi <szi...@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 >>> >>> _______________________________________________ >>> Debichem-devel mailing list >>> debichem-de...@lists.alioth.debian.org >>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debichem-devel >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de -- Christoph Junghans Web: http://www.compphys.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". 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