On 2013-04-11 17:57, Bryan Roessler wrote:
Hello,
I am running a normal mode analysis on a ~1500AA protein with the following
mdp parameters:
Log file opened on Tue Apr 9 09:55:00 2013
Host: uv1 pid: 128985 nodeid: 0 nnodes: 64
Gromacs version: VERSION 4.6.1
Precision: double
Memory model: 64 bit
MPI library: MPI
OpenMP support: disabled
GPU support: disabled
invsqrt routine: gmx_software_invsqrt(x)
CPU acceleration: AVX_256
FFT library: fftw-3.3.2-sse2
Large file support: enabled
RDTSCP usage: enabled
Built on: Fri Mar 15 09:20:59 CDT 2013
Built by: asndcy@uv [CMAKE]
Build OS/arch: Linux 3.0.58-0.6.6-default x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU E5-2667 0 @ 2.90GHz
Build CPU family: 6 Model: 45 Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
sse4.2 ssse3 tdt x2apic
C compiler: /opt/sgi/mpt/mpt-2.07/bin/mpicc GNU gcc (GCC) 4.7.2
C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
-DNDEBUG
:-) G R O M A C S (-:
Good gRace! Old Maple Actually Chews Slate
:-) 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.
:-) /opt/asn/apps/gromacs_4.6.1/bin/mdrun_mpi_d (double precision) (-:
++++ 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 --- -------- --------
Changing rlist from 1.47 to 1.4 for non-bonded 4x4 atom kernels
Input Parameters:
integrator = nm
nsteps = 100000
init-step = 0
cutoff-scheme = Verlet
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 100
comm-mode = Linear
nstlog = 1000
nstxout = 500
nstvout = 500
nstfout = 500
nstcalcenergy = 100
nstenergy = 500
nstxtcout = 0
init-t = 0
delta-t = 0.002
xtcprec = 1000
fourierspacing = 0.12
nkx = 160
nky = 160
nkz = 216
pme-order = 4
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
bPrintNHChains = FALSE
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
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, 4.50000e-05}
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
verlet-buffer-drift = 0.005
rlist = 1.4
rlistlong = 1.4
nstcalclr = 10
rtpi = 0.05
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 1.2
rcoulomb = 1.4
vdwtype = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 1.2
rvdw = 1.4
epsilon-r = 1
epsilon-rf = inf
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
bSimTemp = FALSE
free-energy = no
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
rotation = FALSE
disre = No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orires-fc = 0
orires-tau = 0
nstorireout = 100
dihre-fc = 0
em-stepsize = 0.01
em-tol = 10
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}
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 71907
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
Non-default thread affinity set, disabling internal thread affinity
Using 64 MPI processes
Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU E5-4640 0 @ 2.40GHz
Family: 6 Model: 45 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc
pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
tdt x2apic
Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: AVX_256
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 0.448228 nm for Ewald
Cut-off's: NS: 1.4 Coulomb: 1.4 LJ: 1.4
System total charge: 19.000
Generated table with 4800 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4800 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4800 data points for LJ12.
Tabscale = 2000 points/nm
Generated table with 4800 data points for 1-4 COUL.
Tabscale = 2000 points/nm
Generated table with 4800 data points for 1-4 LJ6.
Tabscale = 2000 points/nm
Generated table with 4800 data points for 1-4 LJ12.
Tabscale = 2000 points/nm
Using AVX-256 4x4 non-bonded kernels
Using Lorentz-Berthelot Lennard-Jones combination rule
Potential shift: LJ r^-12: 0.018 r^-6 0.133, Ewald 1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 7.81e-04 size: 3076
Removing pbc first time
Initiating Normal Mode Analysis
Started Normal Mode Analysis on node 0 Sun Apr 7 09:55:01 2013
However, my NMA has been running for about 4 days on 64 Xeon nodes with
120GB available memory and GROMACS has not generated any output.
What should I expect to see, and how would I adjust my mdp parameters to
increase the frequency of output of the normal-mode analysis? How long
would a run like this be expected to take?
Thank you,
Bryan
Do you have water too? Otherwise it might be good to turn off PME, then
the problem becomes sparse. With water it will not be likely to get
anything useful.
Your calculation should use about 5-10 Gb core memory but I'm not sure
whether NM works in parallel.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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