Hi Mark,
with FE, without PR : same error
without FE, with PR: stable
without FE, without PR: stable
I've never had this error before.
Logfile says:
[...]
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761
multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686
Minimum cell size due to bonded interactions: 3.675 nm
Using 0 separate PME nodes
Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm
The maximum allowed number of cells is: X 1 Y 1 Z 2
Domain decomposition grid 1 x 1 x 2, separate PME nodes 0
PME domain decomposition: 2 x 1 x 1
Domain decomposition nodeid 0, coordinates 0 0 0
[...]
Linking all bonded interactions to atoms
There are 55376 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: Z 1
The initial domain decomposition cell size is: Z 5.09 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.200 nm
two-body bonded interactions (-rdd) 4.213 nm
multi-body bonded interactions (-rdd) 4.213 nm
There it stops. In the 1-thread case, the second part is replaced by
"Initiating Steepest Descents" and then writing out the energies for
every step.
Gromacs version is 4.5.5.
I also attached the whole logfile.
Cheers
Sabine
On 03/23/2012 11:52 AM, Mark Abraham wrote:
On 23/03/2012 9:17 PM, Sabine Reisser wrote:
Dear gromacs users/developers,
when trying to couple in a peptide into a membrane with:
; Define position restraints for peptide
define = -DPOSRES
; couple in peptide
free_energy = yes
init_lambda = 0.05
sc_alpha = 0.7
sc_power = 1
couple-moltype = Protein
couple-lambda0 = none
couple-lambda1 = vdw-q
grompp works fine, but mdrun (2 threads) gives me
Making 1D domain decomposition 1 x 1 x 2
*** glibc detected *** mdrun: realloc(): invalid next size:
0x00007f0f30305810 ***
and breaks up.
When running "mdrun -nt 1 " on only one thread, it works fine.
Is this a known bug?
First, is it likely not to be a problem with your setup... is your
system stable in parallel without FE code? Without position restraints?
What does your .log file say? What GROMACS version is it?
Mark
Log file opened on Fri Mar 23 12:07:20 2012
Host: tcbpc170 pid: 4388 nodeid: 0 nnodes: 1
The Gromacs distribution was built Fri Feb 24 15:27:34 CET 2012 by
sabine@tcbpc170 (Linux 2.6.30.10-105.2.23.fc11.x86_64 x86_64)
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) 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.
:-) mdrun (-:
++++ 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 = 100
init_step = 0
ns_type = Grid
nstlist = 1
ndelta = 2
nstcomm = 10
comm_mode = Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstcalcenergy = -1
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 45
nky = 45
nkz = 90
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
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
andersen_seed = 815131
rlist = 1.2
rlistlong = 1.2
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.2
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.2
epsilon_r = 1
epsilon_rf = 1
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
free_energy = yes
init_lambda = 0.05
delta_lambda = 0
n_foreign_lambda = 0
sc_alpha = 0.7
sc_power = 1
sc_sigma = 0.3
sc_sigma_min = 0.3
nstdhdl = 10
separate_dhdl_file = yes
dhdl_derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
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
disre = Simple
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
em_stepsize = 0.01
em_tol = 1000
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}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 50427
ref_t: 0
tau_t: 0
anneal: No
ann_npoints: 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
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761
multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686
Minimum cell size due to bonded interactions: 3.675 nm
Using 0 separate PME nodes
Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm
The maximum allowed number of cells is: X 1 Y 1 Z 2
Domain decomposition grid 1 x 1 x 2, separate PME nodes 0
PME domain decomposition: 2 x 1 x 1
Domain decomposition nodeid 0, coordinates 0 0 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, 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 --- -------- --------
Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge, top. A: -0.000 top. B: 5.000
Generated table with 1100 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1100 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC-like water optimization for 5953 molecules.
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE2 support... present.
There are 304 atoms and 304 charges for free energy perturbation
Removing pbc first time
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Linking all bonded interactions to atoms
There are 55376 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: Z 1
The initial domain decomposition cell size is: Z 5.09 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.200 nm
two-body bonded interactions (-rdd) 4.213 nm
multi-body bonded interactions (-rdd) 4.213 nm
--
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