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Today's Topics:
1. Re: Re: gmx-users Digest, Vol 62, Issue 57 (Justin A. Lemkul)
2. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Thamu)
3. Alternative TRP residue (abelius)
4. Re: Issues regarding exclusions and Charge group distribution
(Manik Mayur)
----------------------------------------------------------------------
Message: 1
Date: Thu, 11 Jun 2009 10:50:29 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 62, Issue 57
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a3119b5.30...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Thamu wrote:
Hi Mark,
Yes I have compared the runtime for single as well as 8 processor .
Could you please tell me the right steps to configure GROMACS-MPI
version?.
The full installation procedure is here:
http://oldwww.gromacs.org/content/view/23/33/
...as well as Appendix A of the manual.
-Justin
Thanks.
thamu
2009/6/11 <gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
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Today's Topics:
1. Re: gromacs-4.0.5 parallel run in 8 cpu: slow speed (Mark
Abraham)
----------------------------------------------------------------------
Message: 1
Date: Thu, 11 Jun 2009 13:56:15 +0000 (GMT)
From: Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
Subject: Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow
speed
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <fbe6b07c8ea.4a310...@anu.edu.au
<mailto:fbe6b07c8ea.4a310...@anu.edu.au>>
Content-Type: text/plain; charset="iso-8859-1"
On 06/11/09, Thamu <asth...@gmail.com <mailto:asth...@gmail.com>>
wrote:
Hi Mark,
The top md.log is below. The mdrun command was "mpirun -np 8
~/software/bin/mdrun_mpi -deffnm md"
In my experience, correctly-configured MPI gromacs running in
parallel reports information about the number of nodes and the
identity of the node writing the .log file. This is missing, so
something is wrong with your setup.
I've assumed that you've compared this "8-processor" runtime
with a
single-processor runtime and found them comparable...
Mark
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess,
and others.
Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org
(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/thamu/software/bin/mdrun_mpi (-:
++++ 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 = md
nsteps = 10000000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 1000
nstvout = 0
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 70
nky = 70
nkz = 70
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 = V-rescale
epc = Parrinello-Rahman
epctype = Isotropic
tau_p = 0.5
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
andersen_seed = 815131
rlist = 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
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 = 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 = 1000
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}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 6706.82 106800
ref_t: 300 300
tau_t: 0.1 0.1
anneal: No No
ann_npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0 0 0
energygrp_flags[ 1]: 0 0 0
energygrp_flags[ 2]: 0 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
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. 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 --- -------- --------
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 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 1200 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1200 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1200 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling TIP4p water optimization for 17798 molecules.
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Removing pbc first time
Initializing LINear Constraint Solver
++++ 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 --- -------- --------
The number of constraints is 3439
++++ 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 --- -------- --------
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
There are: 56781 Atoms
There are: 17798 VSites
Max number of connections per atom is 59
Total number of connections is 216528
Max number of graph edges per atom is 4
Total number of graph edges is 113666
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 3.77e-05
Initial temperature: 299.838 K
Recently I successfully installed the gromacs-4.0.5 mpi version.
I could run in 8 cpu. but the speed is very slow.
Total number of atoms in the system is 78424.
while running all 8 cpu showing 95-100% CPU.
How to speed up the calculation.
Thanks
That's normal for a system that atoms/cpu ratio.
What's your system and what mdp file are you using?
--
------------------------------------------------------
You haven't given us any diagnostic information. The problem
could be
that you're not running an MPI GROMACS (show us your configure
line,
your mdrun command line and the top 50 lines of your .log file).
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 2
Date: Thu, 11 Jun 2009 22:53:54 +0800
From: Thamu <asth...@gmail.com>
Subject: [gmx-users] Re: gromacs-4.0.5 parallel run in 8 cpu: slow
speed
To: gmx-users@gromacs.org
Message-ID:
<ca6f18140906110753r3acfd68wefc313a65f5a...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
i am using openmpi, how to build hostfile and where keep that file
thamu
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------------------------------
Message: 3
Date: Thu, 11 Jun 2009 17:09:41 +0200
From: abelius <abel...@gmail.com>
Subject: [gmx-users] Alternative TRP residue
To: gmx-users@gromacs.org
Message-ID: <4a311e35.7090...@gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear All,
I have AmberFF parameters for a TRP excited state and I was
wondering if
it was possible to create an alternative TRP residue for gromacs?
Things I've done so far:
* Download and install amber99 for gromacs
* Add a new residue [ ETRP ] with adapted charges to the amber99.rtp
file
* Add ETRP to aminoacids.dat
My question is where do I go from here, how can I add distances (bond
lengths) and angles?
Thank you very much,
Abel
------------------------------
Message: 4
Date: Thu, 11 Jun 2009 21:00:02 +0530
From: Manik Mayur <manik.ma...@gmail.com>
Subject: [gmx-users] Re: Issues regarding exclusions and Charge group
distribution
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<7e56bc410906110830g2208ebcak4a42fa9fb3177...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
The last mail supposedly bounced from the server due to attachments.
So
please excuse in case you find this as a repetition.
I am trying to simulate a system where I want to exclude all nb
interactions
between frozen groups. So I followed the manual and defined them in
energygrp_excl. But upon doing that it throws the following warning.
WARNING 1 [file topol.top, line 1583]:
Can not exclude the lattice Coulomb energy between energy groups
What is the reason of the warning and should I be worried about it
or safely
ignore it.
Next, I am facing a strange problem with mdrun_mpi. If I run it on 4
nodes
then it throws up the following error. Which I traced to md.log
where I saw:
There are: 15923 Atoms
Charge group distribution at step 0: 0 3264 3185 0 (why these zeroes?)
Grid: 3 x 4 x 5 cells
However with 2 nodes it has and runs fine:
There are: 15923 Atoms
Charge group distribution at step 0: 3226 3223
Grid: 4 x 5 x 25 cells
The error-
Making 1D domain decomposition 1 x 1 x 4
starting mdrun 'TransverseElectrode'
100000 steps, 200.0 ps.
step 0
NOTE: Turning on dynamic load balancing
[md-comp1:32374] *** Process received signal ***
[md-comp1:32377] *** Process received signal ***
[md-comp1:32377] Signal: Segmentation fault (11)
[md-comp1:32377] Signal code: Address not mapped (1)
[md-comp1:32377] Failing at address: (nil)
[md-comp1:32374] Signal: Segmentation fault (11)
[md-comp1:32374] Signal code: Address not mapped (1)
[md-comp1:32374] Failing at address: (nil)
[md-comp1:32377] [ 0] [0xb7fd8440]
[md-comp1:32374] [ 0] [0xb7ef0440]
[md-comp1:32374] *** End of error message ***
[md-comp1:32377] *** End of error message ***
I would be extremely thankful, if somebody points me to the source
of the
error and the workaround.
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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