[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