[gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

Mon Jun 10 16:57:02 CEST 2013

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.

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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