[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 20:10:33 CEST 2013 

On Mon, Jun 10, 2013 at 6:11 PM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:

> 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.
>

It was fixed just after 4.6.1, and leads to this aspect of the symptoms
Amil sees here.

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.
>

Right. Sorry for duplicate post, my email hadn't synced yet :-)

Mark


>
> 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
> >>
> >>
> >>
> >> --
> >> View this message in context:
> http://gromacs.5086.x6.nabble.com/mdrun-segmentation-fault-for-new-build-of-gromacs-4-6-1-tp5008873p5008944.html
> >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com<
> http://Nabble.com>.
> >> --
> >> gmx-users mailing list    [hidden
> email]<x-msg://16/user/SendEmail.jtp?type=node&node=5008945&i=1>
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to [hidden
> email]<x-msg://16/user/SendEmail.jtp?type=node&node=5008945&i=2>.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >>
> >>
> >>
> >
> >
> >
> > --
> > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov<http://cmb.ornl.gov
> >
> > 865-241-1537, ORNL PO BOX 2008 MS6309
> > --
> > gmx-users mailing list    [hidden
> email]<x-msg://16/user/SendEmail.jtp?type=node&node=5008945&i=3>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to [hidden
> email]<x-msg://16/user/SendEmail.jtp?type=node&node=5008945&i=4>.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> > ________________________________
> > If you reply to this email, your message will be added to the discussion
> below:
> >
> http://gromacs.5086.x6.nabble.com/mdrun-segmentation-fault-for-new-build-of-gromacs-4-6-1-tp5008873p5008945.html
> > To unsubscribe from mdrun segmentation fault for new build of gromacs
> 4.6.1, click here<
> http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=5008873&code=YWFuZGVyc29uQHdpdHRlbmJlcmcuZWR1fDUwMDg4NzN8NTI5NTk5MTIw
> >.
> > NAML<
> http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml
> >
> >
> >
> >
> >
> >
> > --
> > View this message in context:
> http://gromacs.5086.x6.nabble.com/mdrun-segmentation-fault-for-new-build-of-gromacs-4-6-1-tp5008873p5008986.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

More information about the gromacs.org_gmx-users mailing list