Archive from user: James Barnett GROMACS: gmx, version 2016-dev-20160510-e7e35d3-unknown Executable: /usr/sbin/gmx Data prefix: /usr Command line: gmx --version GROMACS version: 2016-dev-20160510-e7e35d3-unknown GIT SHA1 hash: e7e35d318984eb34901f5215482eba8bd71841e7 Branched from: unknown Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: disabled SIMD instructions: AVX2_256 FFT library: fftw-3.3.4-sse2-avx RDTSCP usage: enabled TNG support: enabled Hwloc support: hwloc-1.11.0 Tracing support: disabled Built on: Wed May 11 16:48:38 UTC 2016 Built by: wes@cfe808fa184c [CMAKE] Build OS/arch: Linux 4.5.2-1-ARCH x86_64 Build CPU vendor: Intel Build CPU brand: Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz Build CPU family: 6 Model: 60 Stepping: 3 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/sbin/cc GNU 6.1.1 C compiler flags: -march=core-avx2 -march=native -mtune=generic -O2 -pipe -fstack-protector-strong -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds C++ compiler: /usr/sbin/c++ GNU 6.1.1 C++ compiler flags: -march=core-avx2 -march=native -mtune=generic -O2 -pipe -fstack-protector-strong -std=c++0x -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds GROMACS: gmx grompp, version 2016-dev-20160510-e7e35d3-unknown Executable: /usr/sbin/gmx Data prefix: /usr Command line: gmx grompp -f mdp/min.mdp -v -o min checking input for internal consistency... Setting the LD random seed to -432366476 processing topology... Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... processing coordinates... double-checking input for internal consistency... Cleaning up constraints and constant bonded interactions with virtual sites Removing all charge groups because cutoff-scheme=Verlet renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: There are: 909 Water residues Making dummy/rest group for T-Coupling containing 3636 elements Making dummy/rest group for Acceleration containing 3636 elements Making dummy/rest group for Freeze containing 3636 elements Making dummy/rest group for Energy Mon. containing 3636 elements Making dummy/rest group for VCM containing 3636 elements Number of degrees of freedom in T-Coupling group rest is 5451.00 Making dummy/rest group for User1 containing 3636 elements Making dummy/rest group for User2 containing 3636 elements Making dummy/rest group for Compressed X containing 3636 elements Making dummy/rest group for Or. Res. Fit containing 3636 elements Making dummy/rest group for QMMM containing 3636 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest Compressed X has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Calculating fourier grid dimensions for X Y Z Using a fourier grid of 25x25x25, spacing 0.120 0.120 0.120 Estimate for the relative computational load of the PME mesh part: 0.20 This run will generate roughly 2 Mb of data writing run input file... GROMACS: gmx mdrun, version 2016-dev-20160510-e7e35d3-unknown Executable: /usr/sbin/gmx Data prefix: /usr Command line: gmx mdrun -deffnm min -v Running on 1 node with total 4 cores, 8 logical cores Hardware detected on host cfe808fa184c (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 Hardware topology: Full, with devices Reading file min.tpr, VERSION 2016-dev-20160510-e7e35d3-unknown (single precision) Using 1 MPI process Using 8 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 50000 Step= 0, Dmax= 1.0e-02 nm, Epot= 6.65807e+02 Fmax= 9.95624e+04, atom= 1629 Step= 1, Dmax= 1.0e-02 nm, Epot= -1.22684e+04 Fmax= 4.18033e+04, atom= 1629 Step= 2, Dmax= 1.2e-02 nm, Epot= -2.15497e+04 Fmax= 1.91245e+04, atom= 1629 Step= 3, Dmax= 1.4e-02 nm, Epot= -2.70253e+04 Fmax= 7.58158e+03, atom= 853 Step= 4, Dmax= 1.7e-02 nm, Epot= -3.11160e+04 Fmax= 2.97013e+03, atom= 853 Step= 5, Dmax= 2.1e-02 nm, Epot= -3.47536e+04 Fmax= 1.27441e+03, atom= 2386 Step= 6, Dmax= 2.5e-02 nm, Epot= -3.82821e+04 Fmax= 7.38159e+02, atom= 2234 Step= 7, Dmax= 3.0e-02 nm, Epot= -4.05334e+04 Fmax= 3.61420e+03, atom= 525 Step= 8, Dmax= 3.6e-02 nm, Epot= -4.12646e+04 Fmax= 1.10815e+03, atom= 525 Step= 9, Dmax= 4.3e-02 nm, Epot= -4.21067e+04 Fmax= 6.32448e+03, atom= 525 Step= 10, Dmax= 5.2e-02 nm, Epot= -4.24086e+04 Fmax= 1.38419e+03, atom= 525 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates [cfe808fa184c:19480] *** Process received signal *** [cfe808fa184c:19480] Signal: Segmentation fault (11) [cfe808fa184c:19480] Signal code: Address not mapped (1) [cfe808fa184c:19480] Failing at address: 0xfffffffe02618420 [cfe808fa184c:19480] [ 0] /usr/bin/../lib/libc.so.6(+0x33310)[0x7f7e3ba78310] [cfe808fa184c:19480] [ 1] /usr/bin/../lib/libgromacs.so.2(+0xe48af8)[0x7f7e3d7b3af8] [cfe808fa184c:19480] [ 2] /usr/bin/../lib/libgromacs.so.2(+0xe4917a)[0x7f7e3d7b417a] [cfe808fa184c:19480] [ 3] /usr/bin/../lib/../lib/libgomso.1(GOMP_parallel+0x3f)[0x7f7e39f1115f] [cfe808fa184c:19480] [ 4] /usr/bin/../lib/libgromacs.so.2(_Z17nbnxn_put_on_gridP12nbnxn_searchiPA3_fiPfS3_iifPKiS2_iPiiP16nbnxn_atomdata_t+0x1269)[0x7f7e3d7b72a9] [cfe808fa184c:19480] [ 5] /usr/bin/../lib/libgromacs.so.2(_Z19do_force_cutsVERLETP8_IO_FILEP9t_commrecP10t_inputreclP6t_nrnbP13gmx_wallcycleP14gmx_localtop_tP12gmx_groups_tPA3_fSE_P9history_tSE_SE_P9t_mdatomsP14gmx_enerdata_tP8t_fcdataPfP7t_graphP10t_forcerecP19interaction_const_tP11gmx_vsite_tSN_dS0_P9gmx_edsamii+0x1015)[0x7f7e3d7fa625] [cfe808fa184c:19480] [ 6] /usr/bin/../lib/libgromacs.so.2(_Z8do_forceP8_IO_FILEP9t_commrecP10t_inputreclP6t_nrnbP13gmx_wallcycleP14gmx_localtop_tP12gmx_groups_tPA3_fSE_P9history_tSE_SE_P9t_mdatomsP14gmx_enerdata_tP8t_fcdataPfP7t_graphP10t_forcerecP11gmx_vsite_tSN_dS0_P9gmx_edsamii+0x272)[0x7f7e3d7fb6a2] [cfe808fa184c:19480] [ 7] /usr/bin/../lib/libgromacs.so.2(_ZN3gmx8do_steepEP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiP11gmx_vsite_tP10gmx_constriP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP9t_mdatomsP6t_nrnbP13gmx_wallcycleP9gmx_edsamP10t_forcereciiiffimP23gmx_walltime_accounting+0x5f9)[0x7f7e3d7a8049] [cfe808fa184c:19480] [ 8] gmx(_ZN3gmx8mdrunnerEP12gmx_hw_opt_tP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiPiiiffPKcfSE_SE_SE_SE_iliiiiiifffim+0x1870)[0x430930] [cfe808fa184c:19480] [ 9] gmx(_Z9gmx_mdruniPPc+0x1650)[0x417bf0] [cfe808fa184c:19480] [10] /usr/bin/../lib/libgromacs.so.2(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x324)[0x7f7e3caff3f4] [cfe808fa184c:19480] [11] gmx(main+0x8c)[0x40c67c] [cfe808fa184c:19480] [12] /usr/bin/../lib/libc.so.6(__libc_start_main+0xf1)[0x7f7e3ba65741] [cfe808fa184c:19480] [13] gmx(_start+0x29)[0x40c759] [cfe808fa184c:19480] *** End of error message *** Segmentation fault (core dumped) This is in an Arch Linux docker container, but I have the same problem in a normal installation. *(from redmine: issue id 1955, created on 2016-05-11 by gmxdefault, closed on 2016-06-22)* * Changesets: * Revision 41ce77920fd28160fe8f2f1deea37e5f25f75d07 by Berk Hess on 2016-06-13T07:41:39Z: ``` Handle constraint errors with EM All energy minimizers could fail with random errors when constraining produced NaN coordinates. Steepest descents now rejects steps with a constraint error. All other minimizer produce a fatal error with the suggestion to use steepest descents first. Fixes #1955. Change-Id: Ie2f7ad4039634d3c5f2597171ec47d6a145c5fcb ``` * Uploads: * [min.tpr](/uploads/add925fd7833354dd7c49520e8e3ec34/min.tpr) * [min.mdp](/uploads/4d281feef7ed4a981167de5a26162405/min.mdp) * [topol.top](/uploads/fb8b898a23f5bda75a9622e8681b2e70/topol.top) * [conf.gro](/uploads/1026d2a3a5e9f58ffe45912e3c241c50/conf.gro)