[gmx-developers] Fwd: problem with REMD run continuation. My mistake or bug?
Giovanni Settanni
gs at mrc-lmb.cam.ac.uk
Fri Mar 4 09:26:17 CET 2011
Hi,
(I posted the following message on the users list but, probably it is
appropriate for the developers list)
I am using gromacs 4.5.3 to run a replica exchange md simulations of a
peptide with implicit solvent and noe-distance restraints using 8
replicas and the -maxh option.
The initial run completes successfully with no errors, however, the
continuation run crashes very early with a segmentation fault (mdp file
(for replica 0 only), command lines, stdout and stderr attached below).
mdrun executables compiled with several different compilers (gcc, pgi,
intel) and mpi implementations (platform_mpi, openmpi), provide simular
results (i.,e. very early crash).
I checked the checkpoint files state[0-7].cpt using gmxdump, which are
produced during the initial run, and they look correct in terms of
number of atoms and they have been saved all at the same timestep.
The -noappend option does not help either.
I wonder if I am doing something wrong or this is a genuine bug. In
particular, I wonder how time averaging of distances for the
restraints interacts with a restart from checkpoint.
Can anyone help?
thanks
Gianni
/******** Command line for intial run ***/
mpirun -np 8 mdrun_mpi -maxh 0.5 -cpt 2 -multi 8 -replex 1000 -v -pd
-s gbsa_md1_.tpr -o gbsa_md1_.trr -c gbsa_md1_.gro -e gbsa_md1_.edr
-g gbsa_md1_.log 1> gbsa_md1_.out 2> gbsa_md1_.err
/**************/
/******** Command line for continuation run ***/
mpirun -np 8 mdrun_mpi -cpi state -maxh 0.5 -cpt 2 -multi 8 -replex
1000 -v -pd -s gbsa_md1_.tpr -o gbsa_md1_.trr -c gbsa_md1_.gro -e
gbsa_md1_.edr -g gbsa_md1_.log 1> gbsa_md1_.out 2> gbsa_md1_.err
/************/
/******** gbsa_md1_0.mdp ***********/
; VARIOUS PREPROCESSING OPTIONS
include = -I../top
; e.g.: -DI_Want_Cookies -DMe_Too
define = -DNOERES
; RUN CONTROL PARAMETERS
integrator = sd1
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 50000000
; For exact run continuation or redoing part of a run
init_step = 0
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part = 1
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 0
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed 0.5 less than water
but enough to disperse excessive heat (see gromacs manual)
bd-fric = 0.5
ld-seed = 1993
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1000
nstvout = 1000
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 1000
nstcalcenergy = -1
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 1000
xtc-precision = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc_grps = System
; Selection of energy groups
energygrps = Protein
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 25
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = no
periodic_molecules = no
; nblist cut-off
rlist = 1.4
; long-range cut-off for switched potentials
rlistlong = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = cut-off
rcoulomb_switch = 0
rcoulomb = 1.4
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdwtype = cut-off
; cut-off lengths
rvdw_switch = 0
rvdw = 1.4
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = gbsa
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 1.4
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = -1
; langevin dynamics (set above with the integrator sd1)
tau_t = 0.2
tc-grps = system
ref_t = 275.00
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = yes
gen-temp = 100
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = hbonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = simple
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre_weighting = equal
; Use sqrt of the time averaged times the instantaneous violation
disre_mixed = no
disre_fc = 100
disre_tau = 10
; Output frequency for pair distances to energy file
nstdisreout = 500
; Dihedral angle restraints: No or Yes
dihre = no
dihre-fc = 1000
/*****************************************/
/******** gbsa_md1_.out *************/
node 0 par_fn 'gbsa_md1_0.tpr'
node 0 par_fn 'gbsa_md1_0.trr'
node 0 par_fn 'traj0.xtc'
node 0 par_fn 'state0.cpt'
node 0 par_fn 'state0.cpt'
node 0 par_fn 'gbsa_md1_0.gro'
node 0 par_fn 'gbsa_md1_0.edr'
node 0 par_fn 'gbsa_md1_0.log'
log
node 0 par_fn 'dhdl0.xvg'
node 0 par_fn 'field0.xvg'
node 0 par_fn 'rerun0.xtc'
node 0 par_fn 'tpi0.xvg'
node 0 par_fn 'tpidist0.xvg'
node 0 par_fn 'sam0.edo'
node 0 par_fn 'bam0.gct'
node 0 par_fn 'gct0.xvg'
node 0 par_fn 'deviatie0.xvg'
node 0 par_fn 'runaver0.xvg'
node 0 par_fn 'pullx0.xvg'
node 0 par_fn 'pullf0.xvg'
node 0 par_fn 'nm0.mtx'
node 0 par_fn 'dipole0.ndx'
node 0 par_fn 'gbsa_md1_1.tpr'
node 0 par_fn 'gbsa_md1_1.trr'
node 0 par_fn 'traj1.xtc'
node 0 par_fn 'state1.cpt'
node 0 par_fn 'state1.cpt'
node 0 par_fn 'gbsa_md1_1.gro'
node 0 par_fn 'gbsa_md1_1.edr'
node 0 par_fn 'gbsa_md1_1.log'
log
node 0 par_fn 'dhdl1.xvg'
node 0 par_fn 'field1.xvg'
node 0 par_fn 'rerun1.xtc'
node 0 par_fn 'tpi1.xvg'
node 0 par_fn 'tpidist1.xvg'
node 0 par_fn 'sam1.edo'
node 0 par_fn 'bam1.gct'
node 0 par_fn 'gct1.xvg'
node 0 par_fn 'deviatie1.xvg'
node 0 par_fn 'runaver1.xvg'
node 0 par_fn 'pullx1.xvg'
node 0 par_fn 'pullf1.xvg'
node 0 par_fn 'nm1.mtx'
node 0 par_fn 'dipole1.ndx'
node 0 par_fn 'gbsa_md1_2.tpr'
node 0 par_fn 'gbsa_md1_2.trr'
node 0 par_fn 'traj2.xtc'
node 0 par_fn 'state2.cpt'
node 0 par_fn 'state2.cpt'
node 0 par_fn 'gbsa_md1_2.gro'
node 0 par_fn 'gbsa_md1_2.edr'
node 0 par_fn 'gbsa_md1_2.log'
log
node 0 par_fn 'dhdl2.xvg'
node 0 par_fn 'field2.xvg'
node 0 par_fn 'rerun2.xtc'
node 0 par_fn 'tpi2.xvg'
node 0 par_fn 'tpidist2.xvg'
node 0 par_fn 'sam2.edo'
node 0 par_fn 'bam2.gct'
node 0 par_fn 'gct2.xvg'
node 0 par_fn 'deviatie2.xvg'
node 0 par_fn 'runaver2.xvg'
node 0 par_fn 'pullx2.xvg'
node 0 par_fn 'pullf2.xvg'
node 0 par_fn 'nm2.mtx'
node 0 par_fn 'dipole2.ndx'
node 0 par_fn 'gbsa_md1_3.tpr'
node 0 par_fn 'gbsa_md1_3.trr'
node 0 par_fn 'traj3.xtc'
node 0 par_fn 'state3.cpt'
node 0 par_fn 'state3.cpt'
node 0 par_fn 'gbsa_md1_3.gro'
node 0 par_fn 'gbsa_md1_3.edr'
node 0 par_fn 'gbsa_md1_3.log'
log
node 0 par_fn 'dhdl3.xvg'
node 0 par_fn 'field3.xvg'
node 0 par_fn 'rerun3.xtc'
node 0 par_fn 'tpi3.xvg'
node 0 par_fn 'tpidist3.xvg'
node 0 par_fn 'sam3.edo'
node 0 par_fn 'bam3.gct'
node 0 par_fn 'gct3.xvg'
node 0 par_fn 'deviatie3.xvg'
node 0 par_fn 'runaver3.xvg'
node 0 par_fn 'pullx3.xvg'
node 0 par_fn 'pullf3.xvg'
node 0 par_fn 'nm3.mtx'
node 0 par_fn 'dipole3.ndx'
node 0 par_fn 'gbsa_md1_5.tpr'
node 0 par_fn 'gbsa_md1_5.trr'
node 0 par_fn 'traj5.xtc'
node 0 par_fn 'state5.cpt'
node 0 par_fn 'state5.cpt'
node 0 par_fn 'gbsa_md1_5.gro'
node 0 par_fn 'gbsa_md1_5.edr'
node 0 par_fn 'gbsa_md1_5.log'
log
node 0 par_fn 'dhdl5.xvg'
node 0 par_fn 'field5.xvg'
node 0 par_fn 'rerun5.xtc'
node 0 par_fn 'tpi5.xvg'
node 0 par_fn 'tpidist5.xvg'
node 0 par_fn 'sam5.edo'
node 0 par_fn 'bam5.gct'
node 0 par_fn 'gct5.xvg'
node 0 par_fn 'deviatie5.xvg'
node 0 par_fn 'runaver5.xvg'
node 0 par_fn 'pullx5.xvg'
node 0 par_fn 'pullf5.xvg'
node 0 par_fn 'nm5.mtx'
node 0 par_fn 'dipole5.ndx'
node 0 par_fn 'gbsa_md1_6.tpr'
node 0 par_fn 'gbsa_md1_6.trr'
node 0 par_fn 'traj6.xtc'
node 0 par_fn 'state6.cpt'
node 0 par_fn 'state6.cpt'
node 0 par_fn 'gbsa_md1_6.gro'
node 0 par_fn 'gbsa_md1_6.edr'
node 0 par_fn 'gbsa_md1_6.log'
log
node 0 par_fn 'dhdl6.xvg'
node 0 par_fn 'field6.xvg'
node 0 par_fn 'rerun6.xtc'
node 0 par_fn 'tpi6.xvg'
node 0 par_fn 'tpidist6.xvg'
node 0 par_fn 'sam6.edo'
node 0 par_fn 'bam6.gct'
node 0 par_fn 'gct6.xvg'
node 0 par_fn 'deviatie6.xvg'
node 0 par_fn 'runaver6.xvg'
node 0 par_fn 'pullx6.xvg'
node 0 par_fn 'pullf6.xvg'
node 0 par_fn 'nm6.mtx'
node 0 par_fn 'dipole6.ndx'
node 0 par_fn 'gbsa_md1_7.tpr'
node 0 par_fn 'gbsa_md1_7.trr'
node 0 par_fn 'traj7.xtc'
node 0 par_fn 'state7.cpt'
node 0 par_fn 'state7.cpt'
node 0 par_fn 'gbsa_md1_7.gro'
node 0 par_fn 'gbsa_md1_7.edr'
node 0 par_fn 'gbsa_md1_7.log'
log
node 0 par_fn 'dhdl7.xvg'
node 0 par_fn 'field7.xvg'
node 0 par_fn 'rerun7.xtc'
node 0 par_fn 'tpi7.xvg'
node 0 par_fn 'tpidist7.xvg'
node 0 par_fn 'sam7.edo'
node 0 par_fn 'bam7.gct'
node 0 par_fn 'gct7.xvg'
node 0 par_fn 'deviatie7.xvg'
node 0 par_fn 'runaver7.xvg'
node 0 par_fn 'pullx7.xvg'
node 0 par_fn 'pullf7.xvg'
node 0 par_fn 'nm7.mtx'
node 0 par_fn 'dipole7.ndx'
node 0 par_fn 'gbsa_md1_4.tpr'
node 0 par_fn 'gbsa_md1_4.trr'
node 0 par_fn 'traj4.xtc'
node 0 par_fn 'state4.cpt'
node 0 par_fn 'state4.cpt'
node 0 par_fn 'gbsa_md1_4.gro'
node 0 par_fn 'gbsa_md1_4.edr'
node 0 par_fn 'gbsa_md1_4.log'
log
node 0 par_fn 'dhdl4.xvg'
node 0 par_fn 'field4.xvg'
node 0 par_fn 'rerun4.xtc'
node 0 par_fn 'tpi4.xvg'
node 0 par_fn 'tpidist4.xvg'
node 0 par_fn 'sam4.edo'
node 0 par_fn 'bam4.gct'
node 0 par_fn 'gct4.xvg'
node 0 par_fn 'deviatie4.xvg'
node 0 par_fn 'runaver4.xvg'
node 0 par_fn 'pullx4.xvg'
node 0 par_fn 'pullf4.xvg'
node 0 par_fn 'nm4.mtx'
node 0 par_fn 'dipole4.ndx'
/**********************************/
/******** gbsa_md1_.err **************/
NNODES=8, MYRANK=6, HOSTNAME=homer2
NNODES=8, MYRANK=0, HOSTNAME=homer2
NNODES=8, MYRANK=3, HOSTNAME=homer2
NNODES=8, MYRANK=4, HOSTNAME=homer2
NNODES=8, MYRANK=5, HOSTNAME=homer2
NNODES=8, MYRANK=2, HOSTNAME=homer2
NODEID=2 argc=23
NODEID=0 argc=23
NNODES=8, MYRANK=7, HOSTNAME=homer2
NODEID=6 argc=23
NNODES=8, MYRANK=1, HOSTNAME=homer2
NODEID=1 argc=23
NODEID=5 argc=23
NODEID=3 argc=23
NODEID=7 argc=23
:-) G R O M A C S (-:
NODEID=4 argc=23
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.5.3 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, 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) 2001-2010, 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 General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_mpi (-:
Option Filename Type Description
------------------------------------------------------------
-s gbsa_md1_.tpr Input Run input file: tpr tpb tpa
-o gbsa_md1_.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-cpi state.cpt Input, Opt! Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c gbsa_md1_.gro Output Structure file: gro g96 pdb etc.
-e gbsa_md1_.edr Output Energy file
-g gbsa_md1_.log Output Log file
-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-tpid tpidist.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-px pullx.xvg Output, Opt. xvgr/xmgr file
-pf pullf.xvg Output, Opt. xvgr/xmgr file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-deffnm string Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool yes Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or
cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions
with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no
or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-gcom int -1 Global communication frequency
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 2 Checkpoint interval (minutes)
-[no]cpnum bool no Keep and number checkpoint files
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxh real 0.5 Terminate after 0.99 times this time (hours)
-multi int 8 Do multiple simulations in parallel
-replex int 1000 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
[homer2:25821] *** Process received signal ***
[homer2:25821] Signal: Segmentation fault (11)
[homer2:25821] Signal code: Address not mapped (1)
[homer2:25821] Failing at address: 0x14
[homer2:25815] *** Process received signal ***
[homer2:25815] Signal: Segmentation fault (11)
[homer2:25815] Signal code: Address not mapped (1)
[homer2:25815] Failing at address: 0x14
[homer2:25818] *** Process received signal ***
[homer2:25818] Signal: Segmentation fault (11)
[homer2:25818] Signal code: Address not mapped (1)
[homer2:25818] Failing at address: 0x14
[homer2:25816] *** Process received signal ***
[homer2:25816] Signal: Segmentation fault (11)
[homer2:25816] Signal code: Address not mapped (1)
[homer2:25816] Failing at address: 0x14
[homer2:25817] *** Process received signal ***
[homer2:25817] Signal: Segmentation fault (11)
[homer2:25817] Signal code: Address not mapped (1)
[homer2:25817] Failing at address: 0x14
[homer2:25820] *** Process received signal ***
[homer2:25820] Signal: Segmentation fault (11)
[homer2:25820] Signal code: Address not mapped (1)
[homer2:25820] Failing at address: 0x14
[homer2:25822] *** Process received signal ***
[homer2:25822] Signal: Segmentation fault (11)
[homer2:25822] Signal code: Address not mapped (1)
[homer2:25822] Failing at address: 0x14
[homer2:25821] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7f71c9e278f0]
[homer2:25821] [ 1] /lib/libc.so.6(xdr_float+0x5c) [0x7f71c9bab7fc]
[homer2:25821] [ 2] /lib/libc.so.6(xdr_vector+0x44) [0x7f71c9bab5e4]
[homer2:25821] [ 3] mdrun_mpi() [0x5a9f15]
[homer2:25821] [ 4] mdrun_mpi() [0x5acb8a]
[homer2:25821] [ 5] mdrun_mpi() [0x5b06a3]
[homer2:25821] [ 6] mdrun_mpi(read_checkpoint_simulation_part+0x1dd)
[0x5b0bdd]
[homer2:25821] [ 7] mdrun_mpi(main+0xe82) [0x445e42]
[homer2:25821] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f71c9ab3c4d]
[homer2:25821] [ 9] mdrun_mpi() [0x419c09]
[homer2:25821] *** End of error message ***
[homer2:25815] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7fecc9b0e8f0]
[homer2:25815] [ 1] /lib/libc.so.6(xdr_float+0x5c) [0x7fecc98927fc]
[homer2:25815] [ 2] /lib/libc.so.6(xdr_vector+0x44) [0x7fecc98925e4]
[homer2:25815] [ 3] mdrun_mpi() [0x5a9f15]
[homer2:25815] [ 4] mdrun_mpi() [0x5acb8a]
[homer2:25815] [ 5] mdrun_mpi() [0x5b06a3]
[homer2:25815] [ 6] mdrun_mpi(read_checkpoint_simulation_part+0x1dd)
[0x5b0bdd]
[homer2:25815] [ 7] mdrun_mpi(main+0xe82) [0x445e42]
[homer2:25815] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7fecc979ac4d]
[homer2:25815] [ 9] mdrun_mpi() [0x419c09]
[homer2:25815] *** End of error message ***
[homer2:25822] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7f5cc01e98f0]
[homer2:25822] [ 1] /lib/libc.so.6(xdr_float+0x5c) [0x7f5cbff6d7fc]
[homer2:25822] [ 2] /lib/libc.so.6(xdr_vector+0x44) [0x7f5cbff6d5e4]
[homer2:25822] [ 3] mdrun_mpi() [0x5a9f15]
[homer2:25822] [ 4] mdrun_mpi() [0x5acb8a]
[homer2:25822] [ 5] mdrun_mpi() [0x5b06a3]
[homer2:25822] [ 6] mdrun_mpi(read_checkpoint_simulation_part+0x1dd)
[0x5b0bdd]
[homer2:25822] [ 7] mdrun_mpi(main+0xe82) [0x445e42]
[homer2:25822] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f5cbfe75c4d]
[homer2:25822] [ 9] mdrun_mpi() [0x419c09]
[homer2:25822] *** End of error message ***
[homer2:25818] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7f11d30238f0]
[homer2:25818] [ 1] /lib/libc.so.6(xdr_float+0x5c) [0x7f11d2da77fc]
[homer2:25818] [ 2] /lib/libc.so.6(xdr_vector+0x44) [0x7f11d2da75e4]
[homer2:25818] [ 3] mdrun_mpi() [0x5a9f15]
[homer2:25818] [ 4] mdrun_mpi() [0x5acb8a]
[homer2:25818] [ 5] mdrun_mpi() [0x5b06a3]
[homer2:25818] [ 6] mdrun_mpi(read_checkpoint_simulation_part+0x1dd)
[0x5b0bdd]
[homer2:25818] [ 7] mdrun_mpi(main+0xe82) [0x445e42]
[homer2:25818] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f11d2cafc4d]
[homer2:25818] [ 9] mdrun_mpi() [0x419c09]
[homer2:25818] *** End of error message ***
[homer2:25816] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7f3ccbe228f0]
[homer2:25816] [ 1] /lib/libc.so.6(xdr_float+0x5c) [0x7f3ccbba67fc]
[homer2:25816] [ 2] /lib/libc.so.6(xdr_vector+0x44) [0x7f3ccbba65e4]
[homer2:25816] [ 3] mdrun_mpi() [0x5a9f15]
[homer2:25816] [ 4] mdrun_mpi() [0x5acb8a]
[homer2:25816] [ 5] mdrun_mpi() [0x5b06a3]
[homer2:25816] [ 6] mdrun_mpi(read_checkpoint_simulation_part+0x1dd)
[0x5b0bdd]
[homer2:25816] [ 7] mdrun_mpi(main+0xe82) [0x445e42]
[homer2:25816] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f3ccbaaec4d]
[homer2:25816] [ 9] mdrun_mpi() [0x419c09]
[homer2:25816] *** End of error message ***
[homer2:25817] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7fd37be128f0]
[homer2:25817] [ 1] /lib/libc.so.6(xdr_float+0x5c) [0x7fd37bb967fc]
[homer2:25817] [ 2] /lib/libc.so.6(xdr_vector+0x44) [0x7fd37bb965e4]
[homer2:25817] [ 3] mdrun_mpi() [0x5a9f15]
[homer2:25817] [ 4] mdrun_mpi() [0x5acb8a]
[homer2:25817] [ 5] mdrun_mpi() [0x5b06a3]
[homer2:25817] [ 6] mdrun_mpi(read_checkpoint_simulation_part+0x1dd)
[0x5b0bdd]
[homer2:25817] [ 7] mdrun_mpi(main+0xe82) [0x445e42]
[homer2:25817] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7fd37ba9ec4d]
[homer2:25817] [ 9] mdrun_mpi() [0x419c09]
[homer2:25817] *** End of error message ***
[homer2:25820] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7f1e059c28f0]
[homer2:25820] [ 1] /lib/libc.so.6(xdr_float+0x5c) [0x7f1e057467fc]
[homer2:25820] [ 2] /lib/libc.so.6(xdr_vector+0x44) [0x7f1e057465e4]
[homer2:25820] [ 3] mdrun_mpi() [0x5a9f15]
[homer2:25820] [ 4] mdrun_mpi() [0x5acb8a]
[homer2:25820] [ 5] mdrun_mpi() [0x5b06a3]
[homer2:25820] [ 6] mdrun_mpi(read_checkpoint_simulation_part+0x1dd)
[0x5b0bdd]
[homer2:25820] [ 7] mdrun_mpi(main+0xe82) [0x445e42]
[homer2:25820] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7f1e0564ec4d]
[homer2:25820] [ 9] mdrun_mpi() [0x419c09]
[homer2:25820] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 6 with PID 25821 on node homer2
exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
[homer2:25819] *** Process received signal ***
[homer2:25819] Signal: Segmentation fault (11)
[homer2:25819] Signal code: Address not mapped (1)
[homer2:25819] Failing at address: 0x14
[homer2:25819] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x7fb8add688f0]
[homer2:25819] [ 1] /lib/libc.so.6(xdr_float+0x5c) [0x7fb8adaec7fc]
[homer2:25819] [ 2] /lib/libc.so.6(xdr_vector+0x44) [0x7fb8adaec5e4]
[homer2:25819] [ 3] mdrun_mpi() [0x5a9f15]
[homer2:25819] [ 4] mdrun_mpi() [0x5acb8a]
[homer2:25819] [ 5] mdrun_mpi() [0x5b06a3]
[homer2:25819] [ 6] mdrun_mpi(read_checkpoint_simulation_part+0x1dd)
[0x5b0bdd]
[homer2:25819] [ 7] mdrun_mpi(main+0xe82) [0x445e42]
[homer2:25819] [ 8] /lib/libc.so.6(__libc_start_main+0xfd) [0x7fb8ad9f4c4d]
[homer2:25819] [ 9] mdrun_mpi() [0x419c09]
[homer2:25819] *** End of error message ***
/********************************************************************/
More information about the gromacs.org_gmx-developers
mailing list