[gmx-users] Re: equilibrium stage runs for too long
Dear Justin, I just tried running it using one node with 12 cores, and it's been completed successfully within a short time! Yes you are right, the system is under reparation and this probably causes those problems. I'm really grateful for your and Vitaly's help. Thank you very much!!! Clare -- View this message in context: http://gromacs.5086.n6.nabble.com/equilibrium-stage-runs-for-too-long-tp5000461p5000488.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: equilibrium stage runs for too long
On 8/24/12 6:01 AM, Clare wrote: Dear Vitaly, Thank you so much for your suggestion!! I've run the simultion using one core as you suggested, and I can see two outputs on step 0 and step 100 now ( shown on the bottom), but it still took a while to only generate these two outputs. Maybe it is indeed the problem of scaling as mentioned by Justin? There are: 34001 Atoms The reason that it is slow now is that you have 34001 atoms being calculated on one core. What that demonstrates is that your simulation is stable and likely did not crash when run in parallel. My previous comments about scaling issues were simply a guess based on incomplete information. Your log file from the MPI run indicated the job never even started. That's not an issue of scaling; it's an issue of functionality. It looks to me like either mdrun_mpi or your MPI implementation is broken or not being invoked properly. Try the test case I suggested before, something that doesn't involve Gromacs. -Justin Charge group distribution at step 0: 1953 1973 2103 2032 2044 2072 2063 1967 Grid: 3 x 7 x 18 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 1.99e-05 Initial temperature: 300.057 K Started mdrun on node 0 Fri Aug 24 10:37:20 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 6.66008e+033.06081e+037.94034e+022.55031e+028.61710e+02 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 2.40538e+035.11091e+04 -3.00143e+03 -4.49637e+05 -8.11103e+04 Position Rest. PotentialKinetic En. Total Energy Conserved En. 5.53187e+01 -4.68547e+058.57672e+04 -3.82780e+05 -3.82780e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00450e+02 -9.73436e+01 -2.97627e+033.74608e-05 DD step 4 load imb.: force 6.0% DD step 99 load imb.: force 6.1% Step Time Lambda 1000.20.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.10274e+042.82478e+031.23525e+032.24466e+021.54991e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 4.67051e+036.34091e+04 -3.00143e+03 -4.31792e+05 -8.19081e+04 Position Rest. PotentialKinetic En. Total Energy Conserved En. 1.44619e+04 -4.17298e+057.13854e+04 -3.45913e+05 -3.82303e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.50069e+02 -9.73436e+01 -3.79866e+023.45085e-06 -- View this message in context: http://gromacs.5086.n6.nabble.com/equilibrium-stage-runs-for-too-long-tp5000461p5000483.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: equilibrium stage runs for too long
Dear Vitaly, Thank you so much for your suggestion!! I've run the simultion using one core as you suggested, and I can see two outputs on step 0 and step 100 now ( shown on the bottom), but it still took a while to only generate these two outputs. Maybe it is indeed the problem of scaling as mentioned by Justin? There are: 34001 Atoms Charge group distribution at step 0: 1953 1973 2103 2032 2044 2072 2063 1967 Grid: 3 x 7 x 18 cells Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 1.99e-05 Initial temperature: 300.057 K Started mdrun on node 0 Fri Aug 24 10:37:20 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 6.66008e+033.06081e+037.94034e+022.55031e+028.61710e+02 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 2.40538e+035.11091e+04 -3.00143e+03 -4.49637e+05 -8.11103e+04 Position Rest. PotentialKinetic En. Total Energy Conserved En. 5.53187e+01 -4.68547e+058.57672e+04 -3.82780e+05 -3.82780e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 3.00450e+02 -9.73436e+01 -2.97627e+033.74608e-05 DD step 4 load imb.: force 6.0% DD step 99 load imb.: force 6.1% Step Time Lambda 1000.20.0 Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.10274e+042.82478e+031.23525e+032.24466e+021.54991e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 4.67051e+036.34091e+04 -3.00143e+03 -4.31792e+05 -8.19081e+04 Position Rest. PotentialKinetic En. Total Energy Conserved En. 1.44619e+04 -4.17298e+057.13854e+04 -3.45913e+05 -3.82303e+05 Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd 2.50069e+02 -9.73436e+01 -3.79866e+023.45085e-06 -- View this message in context: http://gromacs.5086.n6.nabble.com/equilibrium-stage-runs-for-too-long-tp5000461p5000483.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: equilibrium stage runs for too long
> Dear Vitaly, > > here's the log file of the nvt simulation, and it was killed due to > exceeding the wall time. Hopefully it could still provide some useful > information. Thank you so much indeed! > > The initial number of communication pulses is: X 1 Y 1 Z 1 > The initial domain decomposition cell size is: X 1.33 nm Y 2.00 nm Z 8.00 nm > > The maximum allowed distance for charge groups involved in interactions is: > non-bonded interactions 0.900 nm > two-body bonded interactions (-rdd) 0.900 nm > multi-body bonded interactions (-rdd) 0.900 nm > atoms separated by up to 5 constraints (-rcon) 1.333 nm > > When dynamic load balancing gets turned on, these settings will change to: > The maximum number of communication pulses is: X 1 Y 1 Z 1 > The minimum size for domain decomposition cells is 0.900 nm > The requested allowed shrink of DD cells (option -dds) is: 0.80 > The allowed shrink of domain decomposition cells is: X 0.67 Y 0.45 Z 0.11 > The maximum allowed distance for charge groups involved in interactions is: > non-bonded interactions 0.900 nm > two-body bonded interactions (-rdd) 0.900 nm > multi-body bonded interactions (-rdd) 0.900 nm > atoms separated by up to 5 constraints (-rcon) 0.900 nm > > > Making 3D domain decomposition grid 6 x 4 x 2, home cell index 0 0 0 > 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 --- Dear Clare - So, we now see that the run freezes at its every beginning without even writing the information for STEP 0. Please, try to run your system using just one processor, i.e. no MPI in the invocation like (or maybe even faster, using a command line and see what the MDRUN says). Cheers, Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: equilibrium stage runs for too long
On 8/23/12 5:10 PM, Clare wrote:
Dear Vitaly,
here's the log file of the nvt simulation, and it was killed due to
exceeding the wall time. Hopefully it could still provide some useful
information. Thank you so much indeed!
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) 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_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
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 = 5
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 10
comm_mode= Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstcalcenergy= 5
nstenergy= 100
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 50
nky = 50
nkz = 100
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 = V-rescale
nsttcouple = 5
epc = No
epctype = Isotropic
nstpcouple = -1
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 0.9
rlistlong= 0.9
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 0.9
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.9
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_ga
[gmx-users] Re: equilibrium stage runs for too long
Dear Vitaly,
here's the log file of the nvt simulation, and it was killed due to
exceeding the wall time. Hopefully it could still provide some useful
information. Thank you so much indeed!
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) 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_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
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 = 5
init_step= 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 10
comm_mode= Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstcalcenergy= 5
nstenergy= 100
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 50
nky = 50
nkz = 100
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 = V-rescale
nsttcouple = 5
epc = No
epctype = Isotropic
nstpcouple = -1
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 0.9
rlistlong= 0.9
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 0.9
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.9
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
[gmx-users] Re: equilibrium stage runs for too long
> Dear all, > > I'm performing NVT on a system consisting a water layer, a decane layer > and a lipid layer in between those two layers. There are 40 lipids, 627 > decane molecules and 8577 water molecules in total. > > The EM was conducted successfully, however, when I try to run NVT on > this system, it seems to take forever. I'm using 48 cores on a super > computer and the report suggests it has token 367 hours already for the > performance of one core, and it still has not finished yet. > > So I'm wondering does it really require so much time to run or is there > something wrong in my system which prevents it to converge? > Additionally, there's a running time specified in the mdp file which in > my case is 100 ps, so I suppose the simulation should end when the time > limit is reached regardless of whether the pressure converges to the > reference value? > > I'm new to gromacs, could anyone help me with this? Your efforts are > very much appreciated! > Thanks a lot! Dear Clare - I believe there is a problem with your particular run. Your system should sample its 100ps for one day even using just one processor. Please, look at your MD.LOG file and report it here. Cheers, Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: equilibrium stage runs for too long
On 8/23/12 2:37 PM, Clare wrote: Hi Justin, Thank you so much for your reply! what could be the fundamental things that went wrong? for example, is it the problem of the parameters I used in my mdp file or the problem in the system itself? Either, both, or neither. Slow run times are generally incorrect .mdp parameters (which you haven't shown), incorrect use of mdrun (you haven't shown your command), or some problem external to Gromacs (MPI/threading environment, hardware, etc). The way I built my system is that, firstly I created three boxes containing water, lipid and decane respectively using random insertion, and I performed EM,NVT and NPT on each box. After this, I built a new box and placed the three boxes in it one by one, and finally EM was performed on this big box. The result from EM was: Steepest Descents converged to Fmax < 1000 in 168 steps Potential Energy = -4.7134688e+05 Maximum force = 8.5041827e+02 on atom 634 Norm of force = 4.4439018e+01 Does that show any clue? None of that indicates anything that would give rise to the problem at hand. Your EM appears entirely normal. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: equilibrium stage runs for too long
Hi Justin, Thank you so much for your reply! what could be the fundamental things that went wrong? for example, is it the problem of the parameters I used in my mdp file or the problem in the system itself? The way I built my system is that, firstly I created three boxes containing water, lipid and decane respectively using random insertion, and I performed EM,NVT and NPT on each box. After this, I built a new box and placed the three boxes in it one by one, and finally EM was performed on this big box. The result from EM was: Steepest Descents converged to Fmax < 1000 in 168 steps Potential Energy = -4.7134688e+05 Maximum force = 8.5041827e+02 on atom 634 Norm of force = 4.4439018e+01 Does that show any clue? Thanks Clare -- View this message in context: http://gromacs.5086.n6.nabble.com/equilibrium-stage-runs-for-too-long-tp5000461p5000466.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
