On Mon, Jun 10, 2013 at 6:11 PM, Szilárd Páll <szilard.p...@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 <aander...@wittenberg.edu> > wrote: > > Roland, > > > > Here is the output from the debug run with the stack trace: > > > > [aanderson@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. 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