[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1
Mark Abraham
mark.j.abraham at gmail.com
Mon Jun 10 19:51:34 CEST 2013
On Mon, Jun 10, 2013 at 4:57 PM, Amil Anderson <aanderson at wittenberg.edu>wrote:
> Roland,
>
> Here is the output from the debug run with the stack trace:
>
> [aanderson at warp2-login gmxdemo]$ gdb mdrun
> GNU gdb Fedora (6.8-27.el5)
> Copyright (C) 2008 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <
> http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law. Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu"...
> (gdb) run -nt 1 -s cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v
> Starting program: /shared/software/gromacs-4.6.1/bin/mdrun -nt 1 -s
> cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v
> [Thread debugging using libthread_db enabled]
> :-) G R O M A C S (-:
>
> Gromacs Runs On Most of All Computer Systems
>
> :-) VERSION 4.6.1 (-:
> ...
>
> Back Off! I just backed up md.log to ./#md.log.18#
> Reading file cpeptide_em.tpr, VERSION 4.6.1 (single precision)
> Using 1 MPI thread
> [New Thread 0x2b5fe6188ee0 (LWP 19572)]
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00002b5fe3865479 in omp_set_num_threads ()
> from /shared/software/intel/Compiler/11.1/046/lib/intel64/libguide.so
> (gdb) bt
> #0 0x00002b5fe3865479 in omp_set_num_threads ()
> from /shared/software/intel/Compiler/11.1/046/lib/intel64/libguide.so
> #1 0x00002b5fe514c7f8 in gmx_omp_set_num_threads (num_threads=1)
> at /shared/software/temp/gromacs-4.6.1/include/vec.h:885
> #2 0x00002b5fe5199862 in gmx_omp_nthreads_init (fplog=0x17e14b70,
> cr=0x17e14010, nthreads_hw_avail=16, omp_nthreads_req=1,
> omp_nthreads_pme_req=1, bThisNodePMEOnly=0, bFullOmpSupport=0)
> at /shared/software/temp/gromacs-4.6.1/include/vec.h:885
> #3 0x0000000000410a6a in mdrunner (hw_opt=0x7fff7f3d78c0,
> fplog=0x17e14b70,
> cr=0x17e14010, nfile=36, fnm=0x7fff7f3d7a50, oenv=0x17e146d0,
> bVerbose=1,
> bCompact=1, nstglobalcomm=-1, ddxyz=0x7fff7f3d7310, dd_node_order=1,
> rdd=0, rconstr=0, dddlb_opt=0x438449 "auto", dlb_scale=0.800000012,
> ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nbpu_opt=0x438449 "auto",
> nsteps_cmdline=-2, nstepout=100, resetstep=-1, nmultisim=0,
> repl_ex_nst=0,
> repl_ex_nex=0, repl_ex_seed=-1, pforce=-1, cpt_period=15, max_hours=-1,
> deviceOptions=0x43846c "", Flags=1055744)
> at /shared/software/temp/gromacs-4.6.1/include/vec.h:885
> #4 0x0000000000429cd1 in cmain (argc=1, argv=0x7fff7f3d8c18)
> at /shared/software/temp/gromacs-4.6.1/include/vec.h:885
> #5 0x0000000000430fd8 in main (argc=10, argv=0x7fff7f3d8c18)
> at /shared/software/temp/gromacs-4.6.1/src/kernel/main.c:29
> (gdb)
>
>
> I compiled with gcc-4.7.0 so I'm surprised to see a reference to the Intel
> compiler.
>
Thanks, I think that does resolve the issue, though not in the way any of
us supposed. There is a known issue with icc 11.1 (
http://bugzilla.gromacs.org/issues/1126), though its symptoms were
different from yours. I suspect the only way GROMACS can get to link
libguide is from the CMake FindBLAS and/or FindLAPACK packages finding MKL
libraries via your environment. If so, you can work around the issue by
using cmake -DGMX_EXTERNAL_BLAS=off -D GMX_EXTERNAL_LAPACK=off, which will
build internal versions of the fraction of these libraries needed by the
fraction of GROMACS non-mdrun tools that need them. This circumvents the
mechanism by which I think CMake detection lets your libguide become
available for linking. Now whatever gcc library provides
omp_set_num_threads() will get used and that should be fine.
Mark
>
> Amil
>
> On Jun 9, 2013, at 6:08 PM, Roland Schulz [via GROMACS] wrote:
>
> Hi,
>
> based on Mark's idea I would have thought that the cpu detection would
> have already failed during cmake. But it seems it detected SSE4.1
> correctly.
> Could you post the stack trace for the crash? (see previous mail for
> instructions)
>
> Roland
>
> On Sun, Jun 9, 2013 at 4:42 PM, Amil Anderson <[hidden
> email]<x-msg://16/user/SendEmail.jtp?type=node&node=5008945&i=0>> wrote:
>
> > Roland,
> >
> > I have posted the cmake output (cmake-4.6.1) and the file CMakeError.log
> at
> > the usual
> >
> > https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP
> >
> > I see there are some errors but don't know what to make of them.
> >
> > Thanks,
> > Amil
> >
> >
> >
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