[gmx-users] MPICH or LAM/MPI
Carsten Kutzner
ckutzne at gwdg.de
Tue Jun 27 18:50:37 CEST 2006
Arneh Babakhani wrote:
> Hi Carsten, thanks for the reply, good question.
>
> I can run it fine on as much as 4 processors, but nothing beyond that.
> Any idea why?
Hi Arneh,
which version of mpich are you using? Several people have encountered
hangs on >4 processors when running GROMACS on top of MPICH-1.2.x on
Ethernet (other interconnects are fine, though). The solution on Ethernet
is to switch to MPICH-2-1.0.x - at least on our cluster this works in
principle on up to 64 CPUs.
Regards,
Carsten
>> do you have the same problem on less processors? Can you run on 1, 2
>> and 4
>> procs?
>>
>> Carsten
>>
>>
>> Arneh Babakhani wrote:
>>
>>> Hi All,
>>>
>>> Ok, I've successfully created the mpi version of mdrun. Am now trying to
>>> run my simulation on 32 processors. After processing with grompp and the
>>> option -np 32, I use mdrun with the following script (where CONF is the
>>> input file, NPROC is the number of processors):
>>>
>>>
>>> /opt/mpich/intel/bin/mpirun -v -np $NPROC -machinefile \$TMPDIR/machines
>>> ~/gromacs-mpi/bin/mdrun -np $NPROC -s $CONF -o $CONF -c After$CONF -e
>>> $CONF -g $CONF >& $CONF.job
>>>
>>>
>>> Everything seems to start up ok, but then GMX stalls (it never actually
>>> starts the simulation. It stalls for about 7 minutes then completely
>>> aborts). I've pasted the log file below, which shows that the
>>> simulation stalls at Step 0, but there's no discernible error (only
>>> claims that AMD 3D Now support is not available, which makes sense b/c
>>> I'm not running on AMD).
>>>
>>> If you scroll further down, I've also pasted the job file, FullMD7.job,
>>> which is normally empty if everything is running smoothly. There seems
>>> to be some errors at the end, but they're rather cryptic to me, nor am I
>>> sure if this is a cause or effect. If anyone has any suggestions, I'd
>>> love to hear them.
>>>
>>> Thanks,
>>>
>>> Arneh
>>>
>>>
>>> *****FullMD70.log******
>>>
>>> Log file opened on Mon Jun 26 21:51:55 2006
>>> Host: compute-0-1.local pid: 13353 nodeid: 0 nnodes: 32
>>> The Gromacs distribution was built Wed Jun 21 16:01:01 PDT 2006 by
>>> ababakha at chemcca40.ucsd.edu (Linux 2.6.9-22.ELsmp i686)
>>>
>>>
>>> :-) G R O M A C S (-:
>>>
>>> Groningen Machine for Chemical Simulation
>>>
>>> :-) VERSION 3.3.1 (-:
>>>
>>>
>>> Written by David van der Spoel, Erik Lindahl, Berk Hess, and
>>> others.
>>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>> Copyright (c) 2001-2006, The GROMACS development team,
>>> 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.
>>>
>>> :-) /home/ababakha/gromacs-mpi/bin/mdrun (-:
>>>
>>>
>>> ++++ 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 --- -------- --------
>>>
>>> CPU= 0, lastcg= 515, targetcg= 5799, myshift= 14
>>> CPU= 1, lastcg= 1055, targetcg= 6339, myshift= 15
>>> CPU= 2, lastcg= 1595, targetcg= 6879, myshift= 16
>>> CPU= 3, lastcg= 2135, targetcg= 7419, myshift= 17
>>> CPU= 4, lastcg= 2675, targetcg= 7959, myshift= 18
>>> CPU= 5, lastcg= 3215, targetcg= 8499, myshift= 19
>>> CPU= 6, lastcg= 3755, targetcg= 9039, myshift= 20
>>> CPU= 7, lastcg= 4112, targetcg= 9396, myshift= 20
>>> CPU= 8, lastcg= 4381, targetcg= 9665, myshift= 20
>>> CPU= 9, lastcg= 4650, targetcg= 9934, myshift= 20
>>> CPU= 10, lastcg= 4919, targetcg=10203, myshift= 20
>>> CPU= 11, lastcg= 5188, targetcg=10472, myshift= 20
>>> CPU= 12, lastcg= 5457, targetcg= 174, myshift= 20
>>> CPU= 13, lastcg= 5726, targetcg= 443, myshift= 19
>>> CPU= 14, lastcg= 5995, targetcg= 712, myshift= 19
>>> CPU= 15, lastcg= 6264, targetcg= 981, myshift= 18
>>> CPU= 16, lastcg= 6533, targetcg= 1250, myshift= 18
>>> CPU= 17, lastcg= 6802, targetcg= 1519, myshift= 17
>>> CPU= 18, lastcg= 7071, targetcg= 1788, myshift= 17
>>> CPU= 19, lastcg= 7340, targetcg= 2057, myshift= 16
>>> CPU= 20, lastcg= 7609, targetcg= 2326, myshift= 16
>>> CPU= 21, lastcg= 7878, targetcg= 2595, myshift= 15
>>> CPU= 22, lastcg= 8147, targetcg= 2864, myshift= 15
>>> CPU= 23, lastcg= 8416, targetcg= 3133, myshift= 14
>>> CPU= 24, lastcg= 8685, targetcg= 3402, myshift= 14
>>> CPU= 25, lastcg= 8954, targetcg= 3671, myshift= 13
>>> CPU= 26, lastcg= 9223, targetcg= 3940, myshift= 13
>>> CPU= 27, lastcg= 9492, targetcg= 4209, myshift= 13
>>> CPU= 28, lastcg= 9761, targetcg= 4478, myshift= 13
>>> CPU= 29, lastcg=10029, targetcg= 4746, myshift= 13
>>> CPU= 30, lastcg=10298, targetcg= 5015, myshift= 13
>>> CPU= 31, lastcg=10566, targetcg= 5283, myshift= 13
>>> nsb->shift = 20, nsb->bshift= 0
>>> Listing Scalars
>>> nsb->nodeid: 0
>>> nsb->nnodes: 32
>>> nsb->cgtotal: 10567
>>> nsb->natoms: 25925
>>> nsb->shift: 20
>>> nsb->bshift: 0
>>> Nodeid index homenr cgload workload
>>> 0 0 788 516 516
>>> 1 788 828 1056 1056
>>> 2 1616 828 1596 1596
>>> 3 2444 828 2136 2136
>>> 4 3272 828 2676 2676
>>> 5 4100 828 3216 3216
>>> 6 4928 828 3756 3756
>>> 7 5756 807 4113 4113
>>> 8 6563 807 4382 4382
>>> 9 7370 807 4651 4651
>>> 10 8177 807 4920 4920
>>> 11 8984 807 5189 5189
>>> 12 9791 807 5458 5458
>>> 13 10598 807 5727 5727
>>> 14 11405 807 5996 5996
>>> 15 12212 807 6265 6265
>>> 16 13019 807 6534 6534
>>> 17 13826 807 6803 6803
>>> 18 14633 807 7072 7072
>>> 19 15440 807 7341 7341
>>> 20 16247 807 7610 7610
>>> 21 17054 807 7879 7879
>>> 22 17861 807 8148 8148
>>> 23 18668 807 8417 8417
>>> 24 19475 807 8686 8686
>>> 25 20282 807 8955 8955
>>> 26 21089 807 9224 9224
>>> 27 21896 807 9493 9493
>>> 28 22703 807 9762 9762
>>> 29 23510 804 10030 10030
>>> 30 24314 807 10299 10299
>>> 31 25121 804 10567 10567
>>>
>>> parameters of the run:
>>> integrator = md
>>> nsteps = 1500000
>>> init_step = 0
>>> ns_type = Grid
>>> nstlist = 10
>>> ndelta = 2
>>> bDomDecomp = FALSE
>>> decomp_dir = 0
>>> nstcomm = 1
>>> comm_mode = Linear
>>> nstcheckpoint = 1000
>>> nstlog = 10
>>> nstxout = 500
>>> nstvout = 1000
>>> nstfout = 0
>>> nstenergy = 10
>>> nstxtcout = 0
>>> init_t = 0
>>> delta_t = 0.002
>>> xtcprec = 1000
>>> nkx = 64
>>> nky = 64
>>> nkz = 80
>>> pme_order = 6
>>> ewald_rtol = 1e-05
>>> ewald_geometry = 0
>>> epsilon_surface = 0
>>> optimize_fft = TRUE
>>> ePBC = xyz
>>> bUncStart = FALSE
>>> bShakeSOR = FALSE
>>> etc = Berendsen
>>> epc = Berendsen
>>> epctype = Semiisotropic
>>> tau_p = 1
>>> ref_p (3x3):
>>> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
>>> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
>>> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
>>> compress (3x3):
>>> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
>>> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
>>> compress[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e-30}
>>> andersen_seed = 815131
>>> rlist = 0.9
>>> coulombtype = PME
>>> rcoulomb_switch = 0
>>> rcoulomb = 0.9
>>> vdwtype = Cut-off
>>> rvdw_switch = 0
>>> rvdw = 1.4
>>> epsilon_r = 1
>>> epsilon_rf = 1
>>> tabext = 1
>>> gb_algorithm = Still
>>> nstgbradii = 1
>>> rgbradii = 2
>>> gb_saltconc = 0
>>> implicit_solvent = No
>>> DispCorr = No
>>> fudgeQQ = 1
>>> free_energy = no
>>> init_lambda = 0
>>> sc_alpha = 0
>>> sc_power = 0
>>> sc_sigma = 0.3
>>> delta_lambda = 0
>>> disre_weighting = Conservative
>>> disre_mixed = FALSE
>>> dr_fc = 1000
>>> dr_tau = 0
>>> nstdisreout = 100
>>> orires_fc = 0
>>> orires_tau = 0
>>> nstorireout = 100
>>> dihre-fc = 1000
>>> dihre-tau = 0
>>> nstdihreout = 100
>>> em_stepsize = 0.01
>>> em_tol = 10
>>> niter = 20
>>> fc_stepsize = 0
>>> nstcgsteep = 1000
>>> nbfgscorr = 10
>>> ConstAlg = Lincs
>>> shake_tol = 1e-04
>>> 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}
>>> userint1 = 0
>>> userint2 = 0
>>> userint3 = 0
>>> userint4 = 0
>>> userreal1 = 0
>>> userreal2 = 0
>>> userreal3 = 0
>>> userreal4 = 0
>>> grpopts:
>>> nrdf: 11903.3 39783.7 285.983
>>> ref_t: 310 310 310
>>> tau_t: 0.1 0.1 0.1
>>> anneal: No No No
>>> ann_npoints: 0 0 0
>>> acc: 0 0 0
>>> nfreeze: N N N
>>> energygrp_flags[ 0]: 0
>>> efield-x:
>>> n = 0
>>> efield-xt:
>>> n = 0
>>> efield-y:
>>> n = 0
>>> efield-yt:
>>> n = 0
>>> efield-z:
>>> n = 0
>>> efield-zt:
>>> n = 0
>>> bQMMM = FALSE
>>> QMconstraints = 0
>>> QMMMscheme = 0
>>> scalefactor = 1
>>> qm_opts:
>>> ngQM = 0
>>> Max number of graph edges per atom is 4
>>> Table routines are used for coulomb: TRUE
>>> Table routines are used for vdw: FALSE
>>> Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
>>> Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 1.4
>>> System total charge: 0.000
>>> Generated table with 1200 data points for Ewald.
>>> Tabscale = 500 points/nm
>>> Generated table with 1200 data points for LJ6.
>>> Tabscale = 500 points/nm
>>> Generated table with 1200 data points for LJ12.
>>> Tabscale = 500 points/nm
>>> Generated table with 500 data points for 1-4 COUL.
>>> Tabscale = 500 points/nm
>>> Generated table with 500 data points for 1-4 LJ6.
>>> Tabscale = 500 points/nm
>>> Generated table with 500 data points for 1-4 LJ12.
>>> Tabscale = 500 points/nm
>>>
>>> Enabling SPC water optimization for 6631 molecules.
>>>
>>> Will do PME sum in reciprocal space.
>>>
>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G.
>>> Pedersen
>>> A smooth particle mesh Ewald method
>>> J. Chem. Phys. 103 (1995) pp. 8577-8592
>>> -------- -------- --- Thank You --- -------- --------
>>>
>>> Parallelized PME sum used.
>>> PARALLEL FFT DATA:
>>> local_nx: 2 local_x_start: 0
>>> local_ny_after_transpose: 2 local_y_start_after_transpose 0
>>> Removing pbc first time
>>> Done rmpbc
>>> Center of mass motion removal mode is Linear
>>> We have the following groups for center of mass motion removal:
>>> 0: rest, initial mass: 207860
>>> There are: 788 Atoms
>>>
>>> Constraining the starting coordinates (step -2)
>>>
>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
>>> Molecular dynamics with coupling to an external bath
>>> J. Chem. Phys. 81 (1984) pp. 3684-3690
>>> -------- -------- --- Thank You --- -------- --------
>>>
>>>
>>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
>>> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
>>> LINCS: A Linear Constraint Solver for molecular simulations
>>> J. Comp. Chem. 18 (1997) pp. 1463-1472
>>> -------- -------- --- Thank You --- -------- --------
>>>
>>>
>>> Initializing LINear Constraint Solver
>>> number of constraints is 776
>>> average number of constraints coupled to one constraint is 2.5
>>>
>>> Rel. Constraint Deviation: Max between atoms RMS
>>> Before LINCS 0.008664 87 88 0.003001
>>> After LINCS 0.000036 95 96 0.000005
>>>
>>>
>>> Constraining the coordinates at t0-dt (step -1)
>>> Rel. Constraint Deviation: Max between atoms RMS
>>> Before LINCS 0.093829 12 13 0.009919
>>> After LINCS 0.000131 11 14 0.000021
>>>
>>> Started mdrun on node 0 Mon Jun 26 21:52:34 2006
>>> Initial temperature: 310.388 K
>>> Step Time Lambda
>>> 0 0.00000 0.00000
>>>
>>> Grid: 8 x 8 x 13 cells
>>> Configuring nonbonded kernels...
>>> Testing AMD 3DNow support... not present.
>>> Testing ia32 SSE support... present.
>>>
>>>
>>>
>>>
>>>
>>>
>>> ********FullMD7.job***************
>>>
>>> *running /home/ababakha/gromacs-mpi/bin/mdrun on 32 LINUX ch_p4
>>> processors
>>> Created /home/ababakha/SMDPeptideSimulation/CapParSMD/FullMD/PI12637
>>> NNODES=32, MYRANK=0, HOSTNAME=compute-0-1.local
>>> NNODES=32, MYRANK=1, HOSTNAME=compute-0-1.local
>>> NNODES=32, MYRANK=30, HOSTNAME=compute-0-29.local
>>> NNODES=32, MYRANK=24, HOSTNAME=compute-0-12.local
>>> NNODES=32, MYRANK=28, HOSTNAME=compute-0-30.local
>>> NNODES=32, MYRANK=3, HOSTNAME=compute-0-26.local
>>> NNODES=32, MYRANK=14, HOSTNAME=compute-0-22.local
>>> NNODES=32, MYRANK=6, HOSTNAME=compute-0-31.local
>>> NNODES=32, MYRANK=8, HOSTNAME=compute-0-20.local
>>> NNODES=32, MYRANK=7, HOSTNAME=compute-0-31.local
>>> NNODES=32, MYRANK=18, HOSTNAME=compute-0-27.local
>>> NNODES=32, MYRANK=2, HOSTNAME=compute-0-26.local
>>> NNODES=32, MYRANK=23, HOSTNAME=compute-0-4.local
>>> NNODES=32, MYRANK=31, HOSTNAME=compute-0-29.local
>>> NNODES=32, MYRANK=5, HOSTNAME=compute-0-21.local
>>> NNODES=32, MYRANK=27, HOSTNAME=compute-0-3.local
>>> NNODES=32, MYRANK=4, HOSTNAME=compute-0-21.local
>>> NNODES=32, MYRANK=20, HOSTNAME=compute-0-8.local
>>> NNODES=32, MYRANK=11, HOSTNAME=compute-0-7.local
>>> NNODES=32, MYRANK=9, HOSTNAME=compute-0-20.local
>>> NNODES=32, MYRANK=12, HOSTNAME=compute-0-19.local
>>> NNODES=32, MYRANK=13, HOSTNAME=compute-0-19.local
>>> NNODES=32, MYRANK=21, HOSTNAME=compute-0-8.local
>>> NNODES=32, MYRANK=22, HOSTNAME=compute-0-4.local
>>> NNODES=32, MYRANK=10, HOSTNAME=compute-0-7.local
>>> NNODES=32, MYRANK=17, HOSTNAME=compute-0-25.local
>>> NNODES=32, MYRANK=25, HOSTNAME=compute-0-12.local
>>> NNODES=32, MYRANK=15, HOSTNAME=compute-0-22.local
>>> NNODES=32, MYRANK=29, HOSTNAME=compute-0-30.local
>>> NNODES=32, MYRANK=19, HOSTNAME=compute-0-27.local
>>> NNODES=32, MYRANK=26, HOSTNAME=compute-0-3.local
>>> NNODES=32, MYRANK=16, HOSTNAME=compute-0-25.local
>>> NODEID=26 argc=13
>>> NODEID=25 argc=13
>>> NODEID=24 argc=13
>>> NODEID=23 argc=13
>>> NODEID=22 argc=13
>>> NODEID=21 argc=13
>>> NODEID=20 argc=13
>>> NODEID=19 argc=13
>>> NODEID=18 argc=13
>>> NODEID=13 argc=13
>>> NODEID=17 argc=13
>>> NODEID=15 argc=13
>>> NODEID=14 argc=13
>>> NODEID=16 argc=13
>>> NODEID=0 argc=13
>>> NODEID=12 argc=13
>>> NODEID=6 argc=13
>>> NODEID=11 argc=13
>>> NODEID=1 argc=13
>>> NODEID=10 argc=13
>>> NODEID=5 argc=13
>>> NODEID=30 argc=13
>>> NODEID=7 argc=13
>>> NODEID=27 argc=13
>>> NODEID=31 argc=13
>>> NODEID=2 argc=13
>>> NODEID=9 argc=13
>>> NODEID=28 argc=13
>>> NODEID=4 argc=13
>>> NODEID=29 argc=13
>>> NODEID=8 argc=13
>>> NODEID=3 argc=13
>>> :-) G R O M A C S (-:
>>>
>>> Groningen Machine for Chemical Simulation
>>>
>>> :-) VERSION 3.3.1 (-:
>>>
>>>
>>> Written by David van der Spoel, Erik Lindahl, Berk Hess, and
>>> others.
>>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>> Copyright (c) 2001-2006, The GROMACS development team,
>>> 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.
>>>
>>> :-) /home/ababakha/gromacs-mpi/bin/mdrun (-:
>>>
>>> Option Filename Type Description
>>> ------------------------------------------------------------
>>> -s FullMD7.tpr Input Generic run input: tpr tpb tpa xml
>>> -o FullMD7.trr Output Full precision trajectory: trr trj
>>> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr
>>> format)
>>> -c AfterFullMD7.gro Output Generic structure: gro g96 pdb xml
>>> -e FullMD7.edr Output Generic energy: edr ene
>>> -g FullMD7.log Output Log file
>>> -dgdl dgdl.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
>>> -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro
>>> g96 pdb
>>> -tpi tpi.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
>>> -pi pull.ppa Input, Opt. Pull parameters
>>> -po pullout.ppa Output, Opt. Pull parameters
>>> -pd pull.pdo Output, Opt. Pull data output
>>> -pn pull.ndx Input, Opt. Index 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]X bool no Use dialog box GUI to edit command line
>>> options
>>> -nice int 19 Set the nicelevel
>>> -deffnm string Set the default filename for all file options
>>> -[no]xvgr bool yes Add specific codes (legends etc.) in the
>>> output
>>> xvg files for the xmgrace program
>>> -np int 32 Number of nodes, must be the same as used for
>>> grompp
>>> -nt int 1 Number of threads to start on each node
>>> -[no]v bool no Be loud and noisy
>>> -[no]compact bool yes Write a compact log file
>>> -[no]sepdvdl bool no Write separate V and dVdl terms for each
>>> interaction type and node to the log file(s)
>>> -[no]multi bool no Do multiple simulations in parallel (only
>>> with
>>> -np > 1)
>>> -replex int 0 Attempt replica exchange every # steps
>>> -reseed int -1 Seed for replica exchange, -1 is generate
>>> a seed
>>> -[no]glas bool no Do glass simulation with special long range
>>> corrections
>>> -[no]ionize bool no Do a simulation including the effect of an
>>> X-Ray
>>> bombardment on your system
>>>
>>> Reading file FullMD7.tpr, VERSION 3.3.1 (single precision)
>>> starting mdrun 'My membrane with peptides in water'
>>> 1500000 steps, 3000.0 ps.
>>>
>>> p30_10831: p4_error: Timeout in establishing connection to remote
>>> process: 0
>>> rm_l_30_10832: (341.608281) net_send: could not write to fd=5, errno
>>> = 32
>>> rm_l_31_10896: (341.269706) net_send: could not write to fd=5, errno
>>> = 32
>>> p30_10831: (343.634411) net_send: could not write to fd=5, errno = 32
>>> p31_10895: (343.296105) net_send: could not write to fd=5, errno = 32
>>> p0_13353: p4_error: net_recv read: probable EOF on socket: 1
>>> Killed by signal 2.
>>> Killed by signal 2.
>>> Killed by signal 2.
>>> Killed by signal 2.
>>> Killed by signal 2.
>>> p0_13353: (389.926083) net_send: could not write to fd=4, errno = 32
>>>
>>>
>>> _______________________________________________
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>>
>>
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne
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