[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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