[gmx-users] gmx 4.6.2 segementation fault (core dump)

Johannes Wagner johannes.wagner at h-its.org
Mon Jun 3 16:12:28 CEST 2013


hi, thanks for the prompt replies

~/programs/gromacs-4.6.2/bin$ ./mdrun -version

Program: ./mdrun
Gromacs version:    VERSION 4.6.2
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled
GPU support:        enabled
invsqrt routine:    gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:        fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage:       enabled
Built on:           Fri May 31 18:44:32 CEST 2013
Built by:           xxxxx at xxxx-its.org [CMAKE]
Build OS/arch:      Linux 3.8.8-100.fc17.x86_64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:    Intel(R) Core(TM) i5-3550 CPU @ 3.30GHz
Build CPU family:   6   Model: 58   Stepping: 9
Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:         /usr/lib64/ccache/cc GNU cc (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2)
C compiler flags:   -mavx    -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value  -march=core-avx-i  -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG
C++ compiler:       /usr/lib64/ccache/c++ GNU c++ (GCC) 4.7.2 20120921 (Red Hat 4.7.2-2)
C++ compiler flags: -mavx   -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value   -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG
CUDA compiler:      nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221
CUDA driver:        5.0
CUDA runtime:       5.0


~/programs/gromacs-4.6.2/bin/mdrun -o gpu.log -s gpu.tpr -v

Back Off! I just backed up md.log to ./#md.log.1#
Reading file gpu.tpr, VERSION 4.6.2 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads

1 GPU detected:
  #0: NVIDIA GeForce GT 640, compute cap.: 3.0, ECC:  no, stat: compatible

1 GPU auto-selected for this run: #0


Back Off! I just backed up traj.xtc to ./#traj.xtc.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'triazole'
100000 steps,    100.0 ps.
Segmentation fault (core dumped)



.log file:

                                                                                                                                                                                  1,1        Anfang
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's:   NS: 1.004   Coulomb: 1   LJ: 1
System total charge: 0.000
Generated table with 1002 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1002 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1002 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1002 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1002 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1002 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Using CUDA 8x8 non-bonded kernels

Potential shift: LJ r^-12: 1.000 r^-6 1.000, Ewald 1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 6.52e-04 size: 1536

Removing pbc first time
Pinning threads with an auto-selected logical core stride of 1
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 18206 Atoms
Initial temperature: 299.372 K

Started mdrun on node 0 Mon Jun  3 16:09:59 2013

           Step           Time         Lambda
              0        0.00000        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    2.04376e+04    2.58927e+04    9.76653e+00    1.50764e+02   -5.89359e+02
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
   -2.69867e+05   -3.86496e+04   -4.94959e+04    3.97160e+03   -3.08139e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    6.80836e+04   -2.40055e+05    2.99864e+02   -1.42021e+02




thats basically it. not much information, hence my email here in this list…

cheers, Johannes


--
Dipl. Phys. Johannes Wagner
PhD Student, MBM Group

Klaus Tschira Lab (KTL)
Max Planck Partner Institut for Computational Biology (PICB)
320 YueYang Road
200031 Shanghai, China

phone: +86-21-54920475
email: Johannes at picb.ac.cn

and

Heidelberg Institut for Theoretical Studies
HITS gGmbH
Schloß-Wolfsbrunnenweg 35
69118 Heidelberg
Germany

phone: +49-6221-533254
fax: +49 6221 533298
email: johannes.wagner at h-its.org

http://www.h-its.org
_________________________________________________

Amtsgericht Mannheim / HRB 337446
Managing Directors:
Dr. h.c. Klaus Tschira
Prof. Dr.-Ing. Andreas Reuter

On 03.06.2013, at 16:01, Szilárd Páll <szilard.pall at cbr.su.se> wrote:

> Thanks for reporting this.
> 
> he best would be a redmine bug with a tpr, command line invocation for
> reproduction as well log output to see what software and hardware
> configuration are you using.
> 
> Cheers,
> --
> Szilárd
> 
> 
> On Mon, Jun 3, 2013 at 2:46 PM, Johannes Wagner
> <johannes.wagner at h-its.org> wrote:
>> Hi there,
>> trying to set up gmx-4.6.2, compiled with cuda 5.0.35 and gcc 4.7.2 on fedora linux, but it only gives me a "segementation fault (core dump)" on mdrun startup. Same compiling options on gmx 4.6.1 gives me a running mdrun. Did anyone encounter the same problem?
>> 
>> Thanks, Johannes
>> 
>> --
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