[gmx-users] Segmentation Fault with mdrun_mpi
Pavan Kumar
kumar.pavan006 at gmail.com
Thu Feb 20 13:46:15 CET 2014
Hello,
I am using gromacs 4.6.5.
I am running my code on the cluster providing 8 nodes and 4 processor each.
I am getting "Segmentation Fault" while running mdrunmpi
My command
*mpirun -n 8 mdrunmpi.4.6.5 -v -deffnm em*
More Details:
*Machine : GNU/Linux x86_64*
*gcc (GCC) 4.3.3*
*cmake version 2.8.3*
Compilation Details:
*I have compiled my code using mpich compiler *
*cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON
-DCMAKE_C_COMPILER=/opt/mpich2/gnu/bin/mpicc -DGMX_BUILD_OWN_FFTW=ON
-DGMX_CPU_ACCELERATION=SSE2
-DCMAKE_INSTALL_PREFIX=/home/garuda/garuda3/gromacs465*
mdrun log file is attached. Please find the attachment.
If there is any problem in compiling the code itself, what is the error and
how it could be corrected.
Please give me any solutions, why i am getting the above error.
--
Thanks & Regards,
Pavan Kumar
Project Engineer
CDAC -KP
Ph +91-7676367646
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Log file opened on Thu Feb 20 17:52:25 2014
Host: compute-1-21.local pid: 7187 nodeid: 0 nnodes: 8
Gromacs version: VERSION 4.6.5
Precision: single
Memory model: 64 bit
MPI library: MPI
OpenMP support: enabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: SSE2
FFT library: fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage: disabled
Built on: Tue Feb 4 14:40:23 IST 2014
Built by: garuda3 at compute-1-0.local [CMAKE]
Build OS/arch: Linux 2.6.18-53.1.4.el5 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU X5460 @ 3.16GHz
Build CPU family: 6 Model: 23 Stepping: 6
Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2 sse3 sse4.1 ssse3
C compiler: /opt/mpich2/gnu/bin/mpicc GNU gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)
C compiler flags: -msse2 -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG
:-) G R O M A C S (-:
GROtesk MACabre and Sinister
:-) VERSION 4.6.5 (-:
Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
:-) ./bin/mdrun_mpi (-:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
Input Parameters:
integrator = steep
nsteps = 500
init-step = 0
cutoff-scheme = Verlet
ns_type = Grid
nstlist = 1
ndelta = 2
nstcomm = 100
comm-mode = Linear
nstlog = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy = 100
nstenergy = 1000
nstxtcout = 0
init-t = 0
delta-t = 0.001
xtcprec = 1000
fourierspacing = 0.12
nkx = 64
nky = 64
nkz = 64
pme-order = 4
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
bPrintNHChains = FALSE
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
tau-p = 1
ref-p (3x3):
ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.00000e+00
posres-com[1]= 0.00000e+00
posres-com[2]= 0.00000e+00
posres-comB (3):
posres-comB[0]= 0.00000e+00
posres-comB[1]= 0.00000e+00
posres-comB[2]= 0.00000e+00
verlet-buffer-drift = 0.005
rlist = 1
rlistlong = 1
nstcalclr = 1
rtpi = 0.05
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
vdwtype = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
epsilon-r = 1
epsilon-rf = inf
tabext = 1
implicit-solvent = No
gb-algorithm = Still
gb-epsilon-solvent = 80
nstgbradii = 1
rgbradii = 1
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
DispCorr = No
bSimTemp = FALSE
free-energy = no
nwall = 0
wall-type = 9-3
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = no
rotation = FALSE
disre = No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orires-fc = 0
orires-tau = 0
nstorireout = 100
dihre-fc = 0
em-stepsize = 0.01
em-tol = 100
niter = 20
fc-stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake-tol = 0.0001
lincs-order = 4
lincs-warnangle = 30
lincs-iter = 1
bd-fric = 0
ld-seed = 1993
cos-accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 78138
ref-t: 0
tau-t: 0
anneal: No
ann-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
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