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
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@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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