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. > 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 > > > > > > > > -- > > 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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