Hi Amil,
On Mon, Jun 10, 2013 at 11:03 PM, Amil Anderson <aander...@wittenberg.edu> wrote: > Szilárd, > > I tried the build using a PATH without the Intel compilers and NOT including > the directives -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and it > used the FFTW 3.2 wrappers to MKL. Here is the output from mdrun -version: Note that the aim of both workarounds is to stop the build system from picking up the MKL BLAS/LAPACK libraries. Hence, I suspect that you may have not been successful at preventing cmake to pick up the Intel Compilers' location. I may very well be (have not looked at the code, though) that the cmake find module looks at the standard installation location (e.g. /opt/intel) and picks up automatically if something is found there. Hence, removing MKL form the path may not help at all. In any case, I suppose this should be fixed in 4.6.2, but you should wait for the imminent bugfix release, 4.6.3. Cheers, Szilard > > Program: mdrun > Gromacs version: VERSION 4.6.1 > Precision: single > Memory model: 64 bit > MPI library: thread_mpi > OpenMP support: enabled > GPU support: disabled > invsqrt routine: gmx_software_invsqrt(x) > CPU acceleration: SSE4.1 > FFT library: FFTW 3.2 wrappers to MKL > Large file support: enabled > RDTSCP usage: enabled > Built on: Mon Jun 10 15:34:03 CDT 2013 > Built by: > softwaremgmt@warp2-login.cluster<mailto:softwaremgmt@warp2-login.cluster> > [CMAKE] > Build OS/arch: Linux 2.6.18-308.20.1.el5 x86_64 > Build CPU vendor: GenuineIntel > Build CPU brand: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz > Build CPU family: 6 Model: 26 Stepping: 5 > Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc > pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 > C compiler: /opt/centos/devtoolset-1.0/root/usr/bin/gcc GNU gcc (GCC) > 4.7.0 20120507 (Red Hat 4.7.0-5) > C compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers > -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer > -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG > > > All the regressiontests failed. So it appears that, at least for my system, > I need to include the directives to not use the external BLAS/LAPACK. > > Amil > > > > On Jun 10, 2013, at 12:12 PM, Szilárd Páll [via GROMACS] 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. > > 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 <[hidden > email]<x-msg://32/user/SendEmail.jtp?type=node&node=5008989&i=0>> 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<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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