Segmentation fault when minimizing box of water - Redmine #1955
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 41ce7792 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