OK. So if the AVX issue is already fixed in 4.6.5-1 then the bug I found is not related to AVX; it is something else, and we still don't know what it is.
Andras On Wed, Dec 18, 2013 at 12:09 AM, Christoph Junghans <jungh...@votca.org> wrote: > 2013/12/17 Andras Szilagyi <szi...@gmail.com>: >> I may not have been clear enough here. My bug report was intended for >> the debian binary package, not Gromacs itself. The binary package >> cannot be "configured", it's already compiled, there is nothing you >> can configure about it. Also, I'm not asking for support, I'm filing a >> bug report. I can compile Gromacs from source, that is not the issue. > Clear and I meant to configure Gromacs inside debian/rules with > -DGMX_CPU_ACCELERATION=SSE2 so that the binary package only uses sse2 > instructions. > >> >> No, this bug is not fixed in #725013. I reported the bug for the >> latest debian binary package, 4.6.5-1. > And the fix for #725013 ended in 4.6.5-1. > >> >> I guess the package maintainer should decide which processors the >> binary package is intended to support. If only certain CPUs are >> supported then this should be indicated in the package name or title. >> Or if the purpose is to provide a generic version that will run on >> most processors then it should not depend on AVX. > The maintainer already did that or at least the debian changelog claims so: > * rules: Override autodetection of CPU extensions on amd64 and i386; > force to SSE2 only, and provide new DEB_BUILD_OPTIONS=cpuopt flag to > re-enable autodetection for local builds. (Closes: #725013) > > Also debian/rules contains: > ifneq (,$(findstring cpuopt,$(DEB_BUILD_OPTIONS))) > ifneq (,$(findstring $(DEB_HOST_ARCH),i386 amd64)) > COMMON_CONFIG_PARAMS += -DGMX_CPU_ACCELERATION=SSE2 > endif > endif > > >> >> Andras >> >> On Tue, Dec 17, 2013 at 11:27 PM, Christoph Junghans <jungh...@votca.org> >> wrote: >>> 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 > > > > -- > Christoph Junghans > Web: http://www.compphys.de -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
