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

Szilárd Páll szilard.pall at cbr.su.se
Mon Jun 10 18:11:14 CEST 2013 

Amil,

It looks like there is a mixup in your software configuration and
mdrun is linked against libguide.so, the OpenMP library part of the
Intel compiler v11 which gets loaded early and is probably causing the
crash. This library was probably pulled in implicitly by MKL which the
build system detected and tried to use for BLAS/LAPACK (note that you
have "FFT library:        FFTW 3.2 wrappers to MKL" in the log and I
assume you intended to use FFTW). I was under the impression that this
issue was solved in 4.6.1 (http://redmine.gromacs.org/issues/1067),
but perhaps that's not the case.

I suggest you make sure that mdrun is not linked against any Intel
library. The easiest way to achieve this is to either:
- set -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF so that
the internal BLAS/LAPACK is used or
- make sure that the Intel Compilers/MKL installation is not in the
path so that the build system does not detect it.

Check the mdrun -version output, specifically the reported "FFT
library", after you recompile mdrun.

Cheers,
--
Szilárd


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.
>
> 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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