Dear Users,
I have a system that has been running under gromacs 4.5.5. I can restart it
fine from
a checkpoint file with gromacs 4.5.5 but not with gromacs 4.6.1.
The long description follows, but the short answer seems to be that 4.5.5
recorded My-X/Y/Z values (the internet tells me these relate to dipole
information) in the .edr file but 4.6.1 does not for my system so there is an
incompatibility that I can only get around by using mdrun -noappend.
I'm not sure if this is known or not, or if it is a minor bug or if I am doing
something wrong.
Thank you,
Chris.
Here is what I get if I try to run under gromacs 4.5.5:
[cneale@seawolf3 12]$ ~/gromacs_links/mdrun -deffnm popc -cpi popc.cpt
NNODES=1, MYRANK=0, HOSTNAME=seawolf3
:-) G R O M A C S (-:
߼߬
¸°ß²¾ß
:-) VERSION 4.5.5 (-:
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.
:-) /home/cneale/gromacs_links/mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s popc.tpr Input Run input file: tpr tpb tpa
-o popc.trr Output Full precision trajectory: trr trj cpt
-x popc.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi popc.cpt Input, Opt! Checkpoint file
-cpo popc.cpt Output, Opt. Checkpoint file
-c popc.gro Output Structure file: gro g96 pdb etc.
-e popc.edr Output Energy file
-g popc.log Output Log file
-dhdl popc.xvg Output, Opt. xvgr/xmgr file
-field popc.xvg Output, Opt. xvgr/xmgr file
-table popc.xvg Input, Opt. xvgr/xmgr file
-tablep popc.xvg Input, Opt. xvgr/xmgr file
-tableb popc.xvg Input, Opt. xvgr/xmgr file
-rerun popc.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi popc.xvg Output, Opt. xvgr/xmgr file
-tpid popc.xvg Output, Opt. xvgr/xmgr file
-ei popc.edi Input, Opt. ED sampling input
-eo popc.edo Output, Opt. ED sampling output
-j popc.gct Input, Opt. General coupling stuff
-jo popc.gct Output, Opt. General coupling stuff
-ffout popc.xvg Output, Opt. xvgr/xmgr file
-devout popc.xvg Output, Opt. xvgr/xmgr file
-runav popc.xvg Output, Opt. xvgr/xmgr file
-px popc.xvg Output, Opt. xvgr/xmgr file
-pf popc.xvg Output, Opt. xvgr/xmgr file
-mtx popc.mtx Output, Opt. Hessian matrix
-dn popc.ndx Output, Opt. Index file
-multidir popc Input, Opt., Mult. Run directory
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 popc Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no 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 no 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 15 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 -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 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
Reading file popc.tpr, VERSION 4.5.4 (single precision)
Reading checkpoint file popc.cpt generated: Wed Mar 6 11:05:41 2013
NOTE: The checkpoint file was for 40 nodes doing SD or BD,
while the simulation uses 1 SD or BD nodes,
continuation will be exact, except for the random state
Build time mismatch,
current program: Fri Mar 2 15:27:56 PST 2012
checkpoint file: Sun May 6 08:50:24 EDT 2012
Build user mismatch,
current program: root@elder2
checkpoint file: cneale@gpc-logindm02 [CMAKE]
Build machine mismatch,
current program: Linux 2.6.18-194.el5 x86_64
checkpoint file: Linux 2.6.32-220.7.1.el6.x86_64 x86_64
Program name mismatch,
current program: /home/cneale/gromacs_links/mdrun
checkpoint file: mdrun_mpi
#nodes mismatch,
current program: 1
checkpoint file: 56
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.
starting mdrun 'GROup of MAchos and Cynical Suckers in water'
2500000000 steps, 5000000.0 ps (continuing from step 49665920, 99331.8 ps).
# i.e., it runs fine.
###############################
And here is what i get if I try to run under gromacs 4.6.1:
[cneale@seawolf3 12]$ mdrun -deffnm popc -cpi popc.cpt
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.6.1 (-:
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.
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s popc.tpr Input Run input file: tpr tpb tpa
-o popc.trr Output Full precision trajectory: trr trj cpt
-x popc.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi popc.cpt Input, Opt! Checkpoint file
-cpo popc.cpt Output, Opt. Checkpoint file
-c popc.gro Output Structure file: gro g96 pdb etc.
-e popc.edr Output Energy file
-g popc.log Output Log file
-dhdl popc.xvg Output, Opt. xvgr/xmgr file
-field popc.xvg Output, Opt. xvgr/xmgr file
-table popc.xvg Input, Opt. xvgr/xmgr file
-tabletf popc.xvg Input, Opt. xvgr/xmgr file
-tablep popc.xvg Input, Opt. xvgr/xmgr file
-tableb popc.xvg Input, Opt. xvgr/xmgr file
-rerun popc.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi popc.xvg Output, Opt. xvgr/xmgr file
-tpid popc.xvg Output, Opt. xvgr/xmgr file
-ei popc.edi Input, Opt. ED sampling input
-eo popc.xvg Output, Opt. xvgr/xmgr file
-j popc.gct Input, Opt. General coupling stuff
-jo popc.gct Output, Opt. General coupling stuff
-ffout popc.xvg Output, Opt. xvgr/xmgr file
-devout popc.xvg Output, Opt. xvgr/xmgr file
-runav popc.xvg Output, Opt. xvgr/xmgr file
-px popc.xvg Output, Opt. xvgr/xmgr file
-pf popc.xvg Output, Opt. xvgr/xmgr file
-ro popc.xvg Output, Opt. xvgr/xmgr file
-ra popc.log Output, Opt. Log file
-rs popc.log Output, Opt. Log file
-rt popc.log Output, Opt. Log file
-mtx popc.mtx Output, Opt. Hessian matrix
-dn popc.ndx Output, Opt. Index file
-multidir popc Input, Opt., Mult. Run directory
-membed popc.dat Input, Opt. Generic data file
-mp popc.top Input, Opt. Topology file
-mn popc.ndx Input, 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 popc Set the default filename for all file options
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-nt int 0 Total number of threads to start (0 is guess)
-ntmpi int 0 Number of thread-MPI threads to start (0 is guess)
-ntomp int 0 Number of OpenMP threads per MPI process/thread
to start (0 is guess)
-ntomp_pme int 0 Number of OpenMP threads per MPI process/thread
to start (0 is -ntomp)
-pin enum auto Fix threads (or processes) to specific cores:
auto, on or off
-pinoffset int 0 The starting logical core number for pinning to
cores; used to avoid pinning threads from
different mdrun instances to the same core
-pinstride int 0 Pinning distance in logical cores for threads,
use 0 to minimize the number of threads per
physical core
-gpu_id string List of GPU id's to use
-[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
-nb enum auto Calculate non-bonded interactions on: auto, cpu,
gpu or gpu_cpu
-[no]tunepme bool yes Optimize PME load between PP/PME nodes or GPU/CPU
-[no]testverlet bool no Test the Verlet non-bonded scheme
-[no]v bool no 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 15 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
-nsteps int -2 Run this number of steps, overrides .mdp file
option
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange periodically with this
period (steps)
-nex int 0 Number of random exchanges to carry out each
exchange interval (N^3 is one suggestion). -nex
zero or not specified gives neighbor replica
exchange.
-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
Reading file popc.tpr, VERSION 4.5.4 (single precision)
Note: file tpx version 73, software tpx version 83
Reading checkpoint file popc.cpt generated: Thu Mar 7 17:52:58 2013
NOTE: The checkpoint file was for 1 nodes doing SD or BD,
while the simulation uses -1 SD or BD nodes,
continuation will be exact, except for the random state
Version mismatch,
current program: 4.6.1
checkpoint file: 4.5.5
Build time mismatch,
current program: Thu Mar 7 12:51:28 PST 2013
checkpoint file: Fri Mar 2 15:27:56 PST 2012
Build user mismatch,
current program: cneale@seawolf3 [CMAKE]
checkpoint file: root@elder2
Double prec. mismatch,
current program: 0
checkpoint file: -1
Program name mismatch,
current program: mdrun
checkpoint file: /home/cneale/gromacs_links/mdrun
#nodes mismatch,
current program: 12
checkpoint file: 1
#PME-nodes mismatch,
current program: -1
checkpoint file: 0
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not guaranteed to be binary identical.
Using 12 MPI threads
-------------------------------------------------------
Program mdrun, VERSION 4.6.1
Source code file: /home/cneale/exe/gromacs-4.6.1/source/src/mdlib/mdebin.c,
line: 1637
Fatal error:
Mismatch between number of energies in run input (45) and checkpoint file (48).
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Let Me Do This" (Urban Dance Squad)
######################
If I look at the pre-existing .edr file (created by my original 4.5.5 run),
gromacs 4.6.1 or 4.5.5 g_energy lists:
1 U-B 2 Proper-Dih. 3 Improper-Dih. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr.
9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En.
13 Total-Energy 14 Temperature 15 Pres.-DC 16 Pressure
17 Constr.-rmsd 18 Constr.2-rmsd 19 Box-X 20 Box-Y
21 Box-Z 22 Volume 23 Density 24 pV
25 Enthalpy 26 Vir-XX 27 Vir-XY 28 Vir-XZ
29 Vir-YX 30 Vir-YY 31 Vir-YZ 32 Vir-ZX
33 Vir-ZY 34 Vir-ZZ 35 Pres-XX 36 Pres-XY
37 Pres-XZ 38 Pres-YX 39 Pres-YY 40 Pres-YZ
41 Pres-ZX 42 Pres-ZY 43 Pres-ZZ 44 #Surf*SurfTen
45 Mu-X 46 Mu-Y 47 Mu-Z 48 T-System
I can get the simulation to proceed with gromacs 4.6.1 by adding the -noappend
option to mdrun
Then, if I use g_energy to look at the new .edr file, I see:
1 U-B 2 Proper-Dih. 3 Improper-Dih. 4 LJ-14
5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr.
9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En.
13 Total-Energy 14 Temperature 15 Pres.-DC 16 Pressure
17 Constr.-rmsd 18 Constr.2-rmsd 19 Box-X 20 Box-Y
21 Box-Z 22 Volume 23 Density 24 pV
25 Enthalpy 26 Vir-XX 27 Vir-XY 28 Vir-XZ
29 Vir-YX 30 Vir-YY 31 Vir-YZ 32 Vir-ZX
33 Vir-ZY 34 Vir-ZZ 35 Pres-XX 36 Pres-XY
37 Pres-XZ 38 Pres-YX 39 Pres-YY 40 Pres-YZ
41 Pres-ZX 42 Pres-ZY 43 Pres-ZZ 44 #Surf*SurfTen
45 T-System
So the 3 energies that were recorded by gromacs 4.5.5 but not by 4.6.1 are:
45 Mu-X 46 Mu-Y 47 Mu-Z
Thank you,
Chris.
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