Re: [gmx-users] Problem with OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi
Thanks David and Szilárd. I am attaching a log file that I have got from my experiment. Please have a look. It says, gromacs version 4.6-dev I am using :-) VERSION 4.6-dev-20120820-87e5bcf (-: of Gromacs. I have used the commands: git clone git://git.gromacs.org/gromacs.git cd gromacs git checkout --track -b release-4-6 origin/release-4-6 as written on the gromacs website. to download it and used cmake .. -DGMX_MPI=ON -DGMX_OPENMP=ON to configure it. Is it the case that later version of 4.6 has this feature? Please let me know. Thanks, Jesmin On Wed, Aug 29, 2012 at 4:27 AM, Szilárd Páll szilard.p...@cbr.su.se wrote: On Wed, Aug 29, 2012 at 5:32 AM, jesmin jahan shraba...@gmail.com wrote: Dear All, I have installed gromacs VERSION 4.6-dev-20120820-87e5bcf with -DGMX_MPI=ON . I am assuming as OPENMP is default, it will be automatically installed. My Compiler is /opt/apps/intel11_1/mvapich2/1.6/bin/mpicc Intel icc (ICC) 11.1 20101201 And I am using OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi -s imd.tpr I was hopping this will run 16 processes each with 12 threads. However, in the log file I saw something like this: R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp.16 10.0270.0 1.8 Comm. coord. 16 10.0020.0 0.1 Neighbor search 16 10.1130.1 7.7 Force 16 11.2360.883.4 Wait + Comm. F16 10.0150.0 1.0 Update16 10.0050.0 0.4 Comm. energies16 10.0080.0 0.5 Rest 16 0.0760.0 5.1 --- Total 16 1.4810.9 100.0 --- Its not clear whether each of the 16 nodes runs 12 threads internally or not. No it's not. That out put is not from 4.6, you should have an extra column with the number of threads. -- Szilárd If anyone knows about this, please let me know. Thanks for help. Best Regards, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Problem with incorrect GB-Polarization Energy Value
LJ (SR) Coulomb (SR) PotentialKinetic En. -1.65116e+045.74908e+08 -2.37699e+055.74654e+086.36009e+11 Total EnergyTemperature Pressure (bar) 6.36584e+111.60465e+100.0e+00 == ### == A V E R A G E S == ### == Statistics over 1 steps using 1 frames Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -1.65116e+045.74908e+08 -2.37699e+055.74654e+086.36009e+11 Total EnergyTemperature Pressure (bar) 6.36584e+111.60465e+100.0e+00 Total Virial (kJ/mol) -1.13687e+091.14300e+07 -1.23884e+07 1.14273e+07 -1.15125e+09 -5.31658e+06 -1.23830e+07 -5.31326e+06 -1.16512e+09 Pressure (bar) 0.0e+000.0e+000.0e+00 0.0e+000.0e+000.0e+00 0.0e+000.0e+000.0e+00 Total Dipole (D) 1.35524e+03 -4.39059e+012.16985e+03 M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 0.006162 0.296 0.2 GB Coulomb + LJ 0.446368 27.22819.8 Outer nonbonded loop 0.015554 0.156 0.1 Born radii (HCT/OBC) 0.452530 82.81360.3 Born force chain rule0.452530 6.788 4.9 NS-Pairs 0.940291 19.74614.4 Reset In Box 0.003179 0.010 0.0 CG-CoM 0.006358 0.019 0.0 Virial 0.003899 0.070 0.1 Stop-CM 0.006358 0.064 0.0 Calc-Ekin0.006358 0.172 0.1 - Total 137.361 100.0 - D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 7369.0 R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp.16 10.2100.111.4 Comm. coord. 16 10.0060.0 0.3 Neighbor search 16 10.1180.1 6.4 Force 16 11.3190.871.4 Wait + Comm. F16 10.0160.0 0.9 Update16 10.0030.0 0.2 Comm. energies16 10.0930.1 5.0 Rest 16 0.0820.1 4.4 --- Total 16 1.8471.1 100.0 --- NOTE: 5 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 0.036 0.036100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 12.702 3.856 2.425 9.896 Finished mdrun on node 0 Wed Aug 29 02:32:21 2012 The GB- energy value reported is half of that reported by Amber 11 and Octree based Molecular dynamic package. Although I guess the difference can be due to the difference in algorithms they are using, but there could be some other reason. If anyone knows what are the possible reasons behind this, please let me know. May be fixing them will give me same value for all different Molecular Dynamic Package. Best Regard, Jesmin On Mon, Aug 27, 2012 at 6:25 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/08/2012 2:33 AM, jesmin jahan wrote: Dear All, I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I am not interested to any other energy terms right now, I have set all the non-bonded parameters to 0. I am also calculating GB polarization energy using other available Molecular Dynamic Packages and doing a comparative study between them (say: Accuracy Vs. Speed Up). I have already used Gromacs for calculating GB-energy for 168 different Protein molecules and the energy values reported
Re: [gmx-users] Problem with incorrect GB-Polarization Energy Value
Ops! Thanks Justin for you quick reply. Sorry, I have attached a log file from previous run. I am attaching the correct log file here. Please have a look. Actually, I am a Computer Science student. I do not have enough background of Molecular Dynamics. I am using these three commands and pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr and my .mdp file is like this: constraints = none integrator = md pbc = no dt = 0.001 ; ps nsteps = 0 ; 10 ps = 100 ns rcoulomb= 1 rvdw= 1 rlist =1 nstgbradii = 1 rgbradii= 1 implicit_solvent= GBSA gb_algorithm= HCT ; OBC ; Still sa_algorithm= None What else might go wrong? Thanks, Jesmin On Wed, Aug 29, 2012 at 11:14 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/29/12 11:11 AM, jesmin jahan wrote: Thanks Mark for your reply. For the time being, I admit your claim that I am comparing apple with orange. So, to investigate more, I run the simulation without any modification in parameter fields and force field I am using. My test data is CMV virus shell. I am using the following commands. pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr The log file looks like this: :-) G R O M A C S (-: GROningen MAchine for Chemical Simulation :-) VERSION 4.6-dev-20120820-87e5bcf (-: 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 --- 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 = 0 init-step= 0 ns-type = Grid nstlist = 10 ndelta = 2 nstcomm = 10 comm-mode= Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy= 10 nstenergy= 100 nstxtcout= 0 init-t = 0 delta-t = 0.001 xtcprec = 1000 nkx = 0 nky = 0 nkz = 0 pme-order= 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface = 0 optimize-fft = FALSE ePBC = no bPeriodicMols= FALSE bContinuation= FALSE bShakeSOR= FALSE etc = No bPrintNHChains = FALSE nsttcouple = -1 epc = No epctype
[gmx-users] Problem with incorrect GB-Polarization Energy Value
type 'Protein_chain_C20' Excluding 3 bonded neighbours molecule type 'Protein_chain_A21' Excluding 3 bonded neighbours molecule type 'Protein_chain_B21' Excluding 3 bonded neighbours molecule type 'Protein_chain_C21' Excluding 3 bonded neighbours molecule type 'Protein_chain_A22' Excluding 3 bonded neighbours molecule type 'Protein_chain_B22' Excluding 3 bonded neighbours molecule type 'Protein_chain_C22' Excluding 3 bonded neighbours molecule type 'Protein_chain_A23' Excluding 3 bonded neighbours molecule type 'Protein_chain_B23' Excluding 3 bonded neighbours molecule type 'Protein_chain_C23' Excluding 3 bonded neighbours molecule type 'Protein_chain_A24' Excluding 3 bonded neighbours molecule type 'Protein_chain_B24' Excluding 3 bonded neighbours molecule type 'Protein_chain_C24' Excluding 3 bonded neighbours molecule type 'Protein_chain_A25' Excluding 3 bonded neighbours molecule type 'Protein_chain_B25' Excluding 3 bonded neighbours molecule type 'Protein_chain_C25' Excluding 3 bonded neighbours molecule type 'Protein_chain_A26' Excluding 3 bonded neighbours molecule type 'Protein_chain_B26' Excluding 3 bonded neighbours molecule type 'Protein_chain_C26' Excluding 3 bonded neighbours molecule type 'Protein_chain_A27' Excluding 3 bonded neighbours molecule type 'Protein_chain_B27' Excluding 3 bonded neighbours molecule type 'Protein_chain_C27' Excluding 3 bonded neighbours molecule type 'Protein_chain_A28' Excluding 3 bonded neighbours molecule type 'Protein_chain_B28' Excluding 3 bonded neighbours molecule type 'Protein_chain_C28' Excluding 3 bonded neighbours molecule type 'Protein_chain_A29' Excluding 3 bonded neighbours molecule type 'Protein_chain_B29' Excluding 3 bonded neighbours molecule type 'Protein_chain_C29' Excluding 3 bonded neighbours molecule type 'Protein_chain_A30' Excluding 3 bonded neighbours molecule type 'Protein_chain_B30' Excluding 3 bonded neighbours molecule type 'Protein_chain_C30' Excluding 3 bonded neighbours molecule type 'Protein_chain_A31' Excluding 3 bonded neighbours molecule type 'Protein_chain_B31' Excluding 3 bonded neighbours molecule type 'Protein_chain_C31' Excluding 3 bonded neighbours molecule type 'Protein_chain_A32' Excluding 3 bonded neighbours molecule type 'Protein_chain_B32' Excluding 3 bonded neighbours molecule type 'Protein_chain_C32' Excluding 3 bonded neighbours molecule type 'Protein_chain_A33' Excluding 3 bonded neighbours molecule type 'Protein_chain_B33' Excluding 3 bonded neighbours molecule type 'Protein_chain_C33' Excluding 3 bonded neighbours molecule type 'Protein_chain_A34' Excluding 3 bonded neighbours molecule type 'Protein_chain_B34' Excluding 3 bonded neighbours molecule type 'Protein_chain_C34' Excluding 3 bonded neighbours molecule type 'Protein_chain_A35' Excluding 3 bonded neighbours molecule type 'Protein_chain_B35' Excluding 3 bonded neighbours molecule type 'Protein_chain_C35' ... so on. NOTE 5 [file topol.top, line 388]: System has non-zero total charge: 780.04 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Analysing residue names: There are: 32280Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 1529097.00 This run will generate roughly 39 Mb of data There were 5 notes Back Off! I just backed up imd.tpr to ./#imd.tpr.1# gcq#97: The Universe is Somewhere In Here (J.G.E.M. Fraaije) I was only interested in non bonded terms (Specially GB-Energy), so I guess, exclusion of bonded terms is not a problem. Thanks, Jesmin On Wed, Aug 29, 2012 at 12:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/29/12 11:27 AM, jesmin jahan wrote: Ops! Thanks Justin for you quick reply. Sorry, I have attached a log file from previous run. I am attaching the correct log file here. Please have a look. I don't see a new .log file attached anywhere. Actually, I am a Computer Science student. I do not have enough background of Molecular Dynamics. I am using these three commands and pdb2gmx -f 1F15-full.pdb -ter -ignh -ff amber99 -water none grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr OMP_NUM_THREADS=12 mdrun -nt 16 -s imd.tpr and my .mdp file is like this: constraints = none integrator = md pbc = no dt = 0.001 ; ps nsteps = 0 ; 10 ps = 100 ns rcoulomb= 1 rvdw= 1 rlist =1 nstgbradii = 1 rgbradii= 1 implicit_solvent= GBSA gb_algorithm= HCT ; OBC ; Still sa_algorithm= None What else might go wrong? The normal workflow included energy minimization before running MD. Basic tutorial material covers this. Without EM, you assume that whatever structure you're using is suitable for MD, which may or may not be true. -Justin Thanks, Jesmin On Wed, Aug 29, 2012
Re: [gmx-users] Problem with incorrect GB-Polarization Energy Value
5.62500e-01 -2.12500e+00 3.28125e-01 -1.57464e+073.25000e+00 -3.67188e+00 -2.68750e+00 -1.57464e+07 Pressure (bar) 0.0e+000.0e+000.0e+00 0.0e+000.0e+000.0e+00 0.0e+000.0e+000.0e+00 Total Dipole (D) 9.76562e-040.0e+001.95312e-03 M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 1.626204 78.058 0.3 GB Coulomb + LJ 73.6290964491.37517.3 Outer nonbonded loop 1.962706 19.627 0.1 1,4 nonbonded interactions 1.348860 121.397 0.5 Born radii (HCT/OBC)78.053220 14283.73955.0 Born force chain rule 78.0532201170.798 4.5 NS-Pairs 245.0585265146.22919.8 Reset In Box 0.509700 1.529 0.0 CG-CoM 1.019400 3.058 0.0 Bonds0.514800 30.373 0.1 Angles 0.934260 156.956 0.6 Propers 1.742760 399.092 1.5 Virial 0.510420 9.188 0.0 Stop-CM 1.019400 10.194 0.0 Calc-Ekin1.019400 27.524 0.1 - Total 25949.137 100.0 - D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 103046.0 R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp.16 12.8702.0 0.7 Comm. coord. 16 10.9430.6 0.2 Neighbor search 16 1 20.102 13.7 5.0 Force 16 1 132.542 90.432.7 Wait + Comm. F16 12.3151.6 0.6 Update16 10.1300.1 0.0 Comm. energies16 10.0900.1 0.0 Rest 16 246.272 167.960.8 --- Total 16 405.265 276.3 100.0 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 8.635 8.635100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 8.715 3.005 0.010 2398.708 Finished mdrun on node 0 Wed Aug 29 09:58:22 2012 Thanks, Jesmin On Wed, Aug 29, 2012 at 1:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/29/12 1:06 PM, jesmin jahan wrote: Dear Justin, Thanks for your reply. Here is the CMV.log file . Please check it. What you've posted is output from grompp. Note that if you're trying to send attachments, the list rejects them. Actually, the .pdb file I am using is already minimized and we are using the same file for amber 11 and Octree based molecular dynamic package. Something doesn't add up. The energy values were indicative of a completely unphysical system. I will also do the minimization step to see what happens. One thing I also want to mention is when I run grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr command, I get following the log. NOTE 1 [file mdr.mdp]: Tumbling and or flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR. For a single-point energy evaluation this probably isn't significant. NOTE 2 [file mdr.mdp]: You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = Shift (possibly with DispCorr) NOTE 3 [file mdr.mdp]: You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = PME-Switch or Reaction-Field-zero Finite cutoffs do have a significant outcome of implicit calculations, but if you're doing this to remain consistent with other software, I suppose you
[gmx-users] Problem with OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi
Dear All, I have installed gromacs VERSION 4.6-dev-20120820-87e5bcf with -DGMX_MPI=ON . I am assuming as OPENMP is default, it will be automatically installed. My Compiler is /opt/apps/intel11_1/mvapich2/1.6/bin/mpicc Intel icc (ICC) 11.1 20101201 And I am using OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi -s imd.tpr I was hopping this will run 16 processes each with 12 threads. However, in the log file I saw something like this: R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp.16 10.0270.0 1.8 Comm. coord. 16 10.0020.0 0.1 Neighbor search 16 10.1130.1 7.7 Force 16 11.2360.883.4 Wait + Comm. F16 10.0150.0 1.0 Update16 10.0050.0 0.4 Comm. energies16 10.0080.0 0.5 Rest 16 0.0760.0 5.1 --- Total 16 1.4810.9 100.0 --- Its not clear whether each of the 16 nodes runs 12 threads internally or not. If anyone knows about this, please let me know. Thanks for help. Best Regards, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Problem with incorrect GB-Polarization Energy Value
Dear All, I am using Gromacs 4.5.3 for GB-Polarization Energy Calculation. As I am not interested to any other energy terms right now, I have set all the non-bonded parameters to 0. I am also calculating GB polarization energy using other available Molecular Dynamic Packages and doing a comparative study between them (say: Accuracy Vs. Speed Up). I have already used Gromacs for calculating GB-energy for 168 different Protein molecules and the energy values reported were more or less the same as reported by others. Now, I am using a virus shell as input in this process. It contains 1.5 million atoms. Unfortunately, this time, the energy reported is almost half of the value reported by others. So, I am a little bit confused. Am I doing something wrong? I have heard previously that there is no max size for Gromacs. If anyone have encountered similar kind of problem or have knowledge about this, please let me know. Thanks, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Question about Multi-level parallelization: MPI and OpenMP
Dear Gromacs Users, I have two questions about the multi-level parallelism of Gromacs. http://www.gromacs.org/Documentation/Acceleration_and_parallelization?highlight=verlet#GPU_acceleration 1. Is this feature is only supported by Gromacs 4.6? Or we can get it in 4.5.3 also? 2. In Gromacs 4.5.3, I have used OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi -s imd.tpr command to run 16 gromacs processes each with 12 threads. In the log file, I can see nodeid: 0 nnodes: 16 Its clear that 16 nodes are being used in work load distribution. But its not clear whether 12 thread is being used in each of those processes /nodes because there is no mention about the number of threads. Does anyone know about this? Sincerely. Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Question about Multi-level parallelization: MPI and OpenMP
Okay Mark, Thanks!. Best Regards, Jesmin On Mon, Aug 27, 2012 at 6:15 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/08/2012 2:40 AM, jesmin jahan wrote: Dear Gromacs Users, I have two questions about the multi-level parallelism of Gromacs. http://www.gromacs.org/Documentation/Acceleration_and_parallelization?highlight=verlet#GPU_acceleration 1. Is this feature is only supported by Gromacs 4.6? Or we can get it in 4.5.3 also? That section of that page is pretty specific about versions. The shiny new stuff is due in 4.6. 2. In Gromacs 4.5.3, I have used OMP_NUM_THREADS=12 mpirun -np 16 mdrun_mpi -s imd.tpr command to run 16 gromacs processes each with 12 threads. In the log file, I can see nodeid: 0 nnodes: 16 Its clear that 16 nodes are being used in work load distribution. But its not clear whether 12 thread is being used in each of those processes /nodes because there is no mention about the number of threads. Does anyone know about this? Again from that page: With GROMACS 4.6 OpenMP multithreading is supported... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Error:The selected GPU (#0, Tesla M2090) is not supported by Gromacs!
Dear all, I got the following error while running mdrun-gpu, I got the following error: The selected GPU (#0, Tesla M2090) is not supported by Gromacs! Although in the Gromacs site , it says that Tesla M2090 is supported. Then, I have used mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -s imd.tpr command. I got the following warning and I am using this for calculating GB-polarization energy, but the result does not contains GB-polarization energy at all. WARNING: Non-supported GPU selected (#0, Tesla M2090), forced continuing.Note, that the simulation can be slow or it migth even crash. Started mdrun on node 0 Sat Aug 25 00:04:18 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) PotentialKinetic En. Total EnergyTemperature -2.22432e+050.0e+00 -2.22432e+050.0e+00 If anyone has ever experienced this kind of problem, or knows the solution, please let me know. Thanks in advance. Thanks, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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] Error:The selected GPU (#0, Tesla M2090) is not supported by Gromacs!
Hi Justin, Thanks for your reply. Do you mean that Gromacs does not support tesla M2090? I have used the force-device=yes option. But the problem is, it runs but does not give me GB-polarization energy, It only gives the the potential energy. I intention was to calculate the GB-Energy. In .mdp file I added constraints = none integrator = md pbc = no dt = 0.001 ; ps nsteps = 0 ; 10 ps = 100 ns rcoulomb= 1 rvdw= 1 rlist =1 nstgbradii = 1 rgbradii= 1 implicit_solvent= GBSA gb_algorithm= OBC ; Still sa_algorithm= None Thanks, Jesmin On Sat, Aug 25, 2012 at 11:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/25/12 10:57 AM, jesmin jahan wrote: Dear all, I got the following error while running mdrun-gpu, I got the following error: The selected GPU (#0, Tesla M2090) is not supported by Gromacs! Although in the Gromacs site , it says that Tesla M2090 is supported. Then, I have used mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes -s imd.tpr command. I got the following warning and I am using this for calculating GB-polarization energy, but the result does not contains GB-polarization energy at all. WARNING: Non-supported GPU selected (#0, Tesla M2090), forced continuing.Note, that the simulation can be slow or it migth even crash. Started mdrun on node 0 Sat Aug 25 00:04:18 2012 Step Time Lambda 00.00.0 Energies (kJ/mol) PotentialKinetic En. Total EnergyTemperature -2.22432e+050.0e+00 -2.22432e+050.0e+00 If anyone has ever experienced this kind of problem, or knows the solution, please let me know. Thanks in advance. The list is simply outdated and will be updated in the next version. Your command line (using force-device=yes) is the only workaround. -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 -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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] Problem with The requested platform CUDA could not be found
Dear Friends, I have download the pre-compiled binary version of openmm4.1.1 form https://simtk.org/. It is the precompiled OpenMM libraries for 64 bit Linux supported on NVIDIA GPUs with CUDA Toolkit 4.1 and on AMD GPUs with APP SDK 2.4. I have compiled Gromacs 4.5.5 with cuda 4.1 and linked with this pre-compiled library. export PATH=$PATH:/home1//OpenMM4.1.1-Linux64/OpenMM4.1.1-Linux64 export OPENMM_ROOT_DIR=/home1//OpenMM4.1.1-Linux64/OpenMM4.1.1-Linux64 export OPENMM_PLUGIN_DIR=/home1//OpenMM4.1.1-Linux64/OpenMM4.1.1-Linux64/lib/plugins export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home1//OpenMM4.1.1-Linux64/OpenMM4.1.1-Linux64/lib But If I run mdrun-gpu with some .tpr file, I get the following error -- Program mdrun-gpu, VERSION 4.5.5-dev Source code file: /home1/01945/jesmin/gromacs/src/kernel/openmm_wrapper.cpp, line: 1272 Fatal error: The requested platform CUDA could not be found. --- I saw in gromacs users email archive that lots of people has faced similar kind of problem and the most probable reason is mismatching cuda version for openmm and Gromacs. But I think for my case, I am using the same version. what else might go wrong. If there is anyone who knows about the problem, please reply me. Thanks, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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] Problem with Gromacs 4.6 installation
Dear All, I am trying to install Gromacs 4.6 with -DGMX_OPENMM=ON I am getting the following errors in make install-mdrun ../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_thread_num' ../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_num_threads' ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_parallel_start' ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_loop_end_nowait' ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_loop_ordered_static_start' ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_parallel_end' ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_barrier' ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_loop_ordered_static_next' collect2: ld returned 1 exit status make[3]: *** [src/kernel/mdrun-openmm] Error 1 make[2]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/install-mdrun.dir/rule] Error 2 make: *** [install-mdrun] Error 2 Is there anyone out there who has faced the same kind of problem and know the solution? Any kind of help will be highly appreciated. Thanks, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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] Problem with Gromacs installation with GPU.
Dear All, I have installed gromacs 4.5.3 on a cluster. I downloaded the gromacs-4.5-GPU-beta2-X86_64 binaries and followed the following instructions: * INSTALLING FROM BINARY DISTRIBUTION: 0. Prerequisites: - OpenMM (included in the binary release) - NVIDIA CUDA libraries (version =3.0); - NVIDIA driver (for details on compatiblity consult http://www.nvidia.com/Download/index5.aspx); - NVIDIA CUDA-enabled GPU (for compatiblity list see http://www.gromacs.org/gpu). 1. Download and unpack the binary package for the respective OS and architecture. Copy the content of the package to your normal GROMACS installation directory (or to a custom location). Note that as the distributed Gromacs-GPU packages do not contain the entire set of tools and utilities included in a full GROAMCS installation. Therefore, it is recommended to have a ≥v4.5 standard Gromacs installation along the GPU accelerated one. e.g. on unix: tar -xvf gromacs-4.5-GPU.tar.gz cp -R gromacs-4.5-GPU/* PATH_TO_GROMACS_INSTALLATION 2. Add the openmm/lib directory to your library path, e.g. in bash: export LD_LIBRARY_PATH=PATH_TO_GROMACS/openmm/lib:$LD_LIBRARY_PATH If there are other OpenMM versions installed, make sure that the supplied libraries have preference when running mdrun-gpu. Also, make sure that the CUDA libraries installed match the version of CUDA with which GROMACS-GPU is compiled. 3. Set the OPENMM_PLUGIN_DIR environment variable to contain the path to the openmm/lib/plugins directory, e.g. in bash: export OPENMM_PLUGIN_DIR=PATH_TO_GROMACS/openmm/lib/plugins 4. At this point, running the command: PATH_TO_GROMACS/bin/mdrun-gpu -h should display the standard mdrun help which means that all the necessary libraries are accessible. But running the PATH_TO_GROMACS/bin/mdrun-gpu -h command gives me /home1/01945/jesmin/Gromacs/4.5.3/bin/mdrun-gpu: error while loading shared libraries: libcudart.so.3: cannot open shared object file: No such file or directory So, if I actually look into the cuda library directory I found the following files: libcublas.solibcudart.solibcufft.solibcuinj.so libcurand.solibcusparse.solibnpp.so libcublas.so.4 libcudart.so.4 libcufft.so.4 libcuinj.so.4 libcurand.so.4 libcusparse.so.4 libnpp.so.4 libcublas.so.4.2.9 libcudart.so.4.2.9 libcufft.so.4.2.9 libcuinj.so.4.2.9 libcurand.so.4.2.9 libcusparse.so.4.2.9 libnpp.so.4.2.9 Is there anyone who knows about how to fix this problem? Please let me know. Then, I installed the Gromacs-openmm precompiled version which used cuda 4.1 following the instructions To install Gromacs-OpenMM, follow these steps. 1. Install Gromacs 4. 2. Install OpenMM. 3. Copy mdrun-openmm to gromacs/bin, where gromacs is the root directory of your Gromacs installation (e.g. /usr/local/gromacs). 4. Copy params.agb to gromacs/share/gromacs/top. 5. Add the OpenMM lib directory to your library path (PATH on Windows, DYLD_LIBRARY_PATH on Mac OS X, LD_LIBRARY_PATH on Linux). 6. If you have an Nvidia GPU, install CUDA (http://www.nvidia.com/object/cuda_get.html). Make sure the CUDA lib directory is in your library path. 7. If you installed OpenMM in the default location (/usr/local/openmm on Mac OS X or Linux, Program Files\OpenMM on Windows), no further steps are required. If you installed it in a different location, set the environment variable OPENMM_PLUGIN_DIR to point to the OpenMM plugin directory (e.g. /usr/local/openmm/lib/plugins). Note that I do not have any /usr/local directory. my home is /home1/01945/jesmin. Now if I type mdrun-openmm -h, I get the following error: /home1/01945/jesmin/Gromacs/4.5.3/bin/mdrun-openmm: /home1/01945/jesmin/cilk/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /home1/01945/jesmin/Gromacs/4.5.3/openmm/lib/libOpenMM.so) Can anyone help me to about how to solve this problem? Thanks, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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] Problem with Gromacs installation with GPU.
Dear Szilárd I have downloaded Gromacs 4.6 from git. But I saw that implicit solvent feature is still not supported. Features currently not supported by the new GPU and SSE kernels: Implicit solvent (but this will still be supported on the GPU through OpenMM) But I need the implicit solvent feature for my experiments. I went to https://simtk.org/project/ where I found GromacsOpenmm2.0. But that one is also deprecated! So, its not clear to me what does it meant by but this will still be supported on the GPU through OpenMM How to add this feature with Gromacs4.6? Or is there any version of Gromacs which supports implicit solvent simulation on GPU? Please let me know. Thanks, Jesmin On Tue, Aug 21, 2012 at 4:24 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: Dear Jesmin, On Tue, Aug 21, 2012 at 7:21 PM, jesmin jahan shraba...@gmail.com wrote: Dear All, I have installed gromacs 4.5.3 on a cluster. I downloaded the gromacs-4.5-GPU-beta2-X86_64 binaries and followed the following instructions: Those binaries are extremely outdated. Please compile Gromacs form the last source release or the latest git version from release-4-5-patches. Cheers, -- Szilárd * INSTALLING FROM BINARY DISTRIBUTION: 0. Prerequisites: - OpenMM (included in the binary release) - NVIDIA CUDA libraries (version =3.0); - NVIDIA driver (for details on compatiblity consult http://www.nvidia.com/Download/index5.aspx); - NVIDIA CUDA-enabled GPU (for compatiblity list see http://www.gromacs.org/gpu). 1. Download and unpack the binary package for the respective OS and architecture. Copy the content of the package to your normal GROMACS installation directory (or to a custom location). Note that as the distributed Gromacs-GPU packages do not contain the entire set of tools and utilities included in a full GROAMCS installation. Therefore, it is recommended to have a ≥v4.5 standard Gromacs installation along the GPU accelerated one. e.g. on unix: tar -xvf gromacs-4.5-GPU.tar.gz cp -R gromacs-4.5-GPU/* PATH_TO_GROMACS_INSTALLATION 2. Add the openmm/lib directory to your library path, e.g. in bash: export LD_LIBRARY_PATH=PATH_TO_GROMACS/openmm/lib:$LD_LIBRARY_PATH If there are other OpenMM versions installed, make sure that the supplied libraries have preference when running mdrun-gpu. Also, make sure that the CUDA libraries installed match the version of CUDA with which GROMACS-GPU is compiled. 3. Set the OPENMM_PLUGIN_DIR environment variable to contain the path to the openmm/lib/plugins directory, e.g. in bash: export OPENMM_PLUGIN_DIR=PATH_TO_GROMACS/openmm/lib/plugins 4. At this point, running the command: PATH_TO_GROMACS/bin/mdrun-gpu -h should display the standard mdrun help which means that all the necessary libraries are accessible. But running the PATH_TO_GROMACS/bin/mdrun-gpu -h command gives me /home1/01945/jesmin/Gromacs/4.5.3/bin/mdrun-gpu: error while loading shared libraries: libcudart.so.3: cannot open shared object file: No such file or directory So, if I actually look into the cuda library directory I found the following files: libcublas.solibcudart.solibcufft.solibcuinj.so libcurand.solibcusparse.solibnpp.so libcublas.so.4 libcudart.so.4 libcufft.so.4 libcuinj.so.4 libcurand.so.4 libcusparse.so.4 libnpp.so.4 libcublas.so.4.2.9 libcudart.so.4.2.9 libcufft.so.4.2.9 libcuinj.so.4.2.9 libcurand.so.4.2.9 libcusparse.so.4.2.9 libnpp.so.4.2.9 Is there anyone who knows about how to fix this problem? Please let me know. Then, I installed the Gromacs-openmm precompiled version which used cuda 4.1 following the instructions To install Gromacs-OpenMM, follow these steps. 1. Install Gromacs 4. 2. Install OpenMM. 3. Copy mdrun-openmm to gromacs/bin, where gromacs is the root directory of your Gromacs installation (e.g. /usr/local/gromacs). 4. Copy params.agb to gromacs/share/gromacs/top. 5. Add the OpenMM lib directory to your library path (PATH on Windows, DYLD_LIBRARY_PATH on Mac OS X, LD_LIBRARY_PATH on Linux). 6. If you have an Nvidia GPU, install CUDA (http://www.nvidia.com/object/cuda_get.html). Make sure the CUDA lib directory is in your library path. 7. If you installed OpenMM in the default location (/usr/local/openmm on Mac OS X or Linux, Program Files\OpenMM on Windows), no further steps are required. If you installed it in a different location, set the environment variable OPENMM_PLUGIN_DIR to point to the OpenMM plugin directory (e.g. /usr/local/openmm/lib/plugins). Note that I do not have any /usr/local directory. my home is /home1/01945/jesmin. Now if I type mdrun-openmm -h, I get the following error: /home1/01945/jesmin/Gromacs/4.5.3/bin/mdrun-openmm: /home1
Re: [gmx-users] Questions regarding Polarization Energy Calculation
Hi Mark, Thanks for your reply. In the ffnonbonded.itp, I set all sigma and epsilon values to zero. So, the the LJ energy is coming as zero. But the coulomb potential is non zero. What should I do to make it zero? Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+030.0e+00 -3.47729e+04 -3.70041e+040.0e+00 Total EnergyTemperature Pressure (bar) -3.70041e+040.0e+000.0e+00 One more point: I am not sure whether getting the 0 for an energy does mean that it is not being calculated at all! It seems, the energy value was calculated but the result was zero because the sigma and epsilon were zero. In that case, the time reported by the program will also include the time of the extra calculation (unless the program is smart enough to know before hand that the result is going to be zero and return from the top!). So, while comparing with other molecular dynamic packages, its not fair to report that time for gromacs which also includes non GB time (as that can make Gromacs slower than others who do not include non GB-time). Any suggestions about this? What is the fair approach for gromacs? Thanks, Jesmin On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 17/08/2012 1:14 PM, jesmin jahan wrote: Hi Mark, According to your advice remove the the bonded terms and zero the VDW parameters, I removed everything under [ bond] , [angles], [pairs] and [ dihedrals ], This only removes the bonded terms (in the sense of those atoms that interact because of the presence of bonds). The VDW parameters for non-bonded interactions are in ffnonbonded.itp for your force field. You should probably follow the advice here http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Modifying_a_force_field to get a local copy you can change conveniently. and run the simulation mdrun rerun. I got output something like the following: Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+037.54287e+07 -3.47729e+047.53917e+07 0.0e+00 Total EnergyTemperature Pressure (bar) 7.53917e+070.0e+000.0e+00 where the previous output was something like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 2.12480e+034.80088e+021.06648e+039.04861e+01 -2.23122e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+00 -1.45483e+030.0e+000.0e+00 Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+034.17621e+13 -3.47729e+044.17621e+13 0.0e+00 Total EnergyTemperature Pressure (bar) 4.17621e+130.0e+000.0e+00 So, you can see, although it has managed to remove some extra terms, the LJ and Columb potential are still there. I searched for VWD parameters. Although I saw various options for VWD, its not clear from the options, how to turn it off. Could you kindly tell me more clearly about it? I was also looking into the forcefield.itp file. I set the gen-pairs to no , fudgeLJ 1 and fudgeQQ to 1 which were yes, .5 and .83 respectively originally. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1 1 Please let me know how to get rid of calculation of other energies (LJ, Culumb and Total Potential) and how to set the parameters for this properly. You can't get rid of the total. It's the total. You're trying to keep the (GB) Coulomb. Mark Thanks for your help. Sincerely, Jesmin On Thu, Aug 16, 2012 at 3:27 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:08 PM, jesmin jahan wrote: Hi Mark, Thanks for your reply. If I open the .tpr file using notepad, it seems to be a binary file. Then, how to remove the the bonded terms and zero the VDW parameters? In the .top file from which you made the .tpr. (And contributing .itp files) Parts of chapter 5 may help with this process. Mark I really need to compare how fast different well known package can compute GB-polarization energy and how good the energy values are? That's why time is an important factor me my experiments and I really want to measure the time for GB energy in isolation ! Thanks, Jesmin On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 4:26 PM, jesmin jahan wrote: Hi Mark, Thanks for your previous reply. I tried to run single point energy simulation with some proteins. I got .log files with content like this: Energies (kJ/mol
Re: [gmx-users] Questions regarding Polarization Energy Calculation
Okay thanks. I got it. :-) Best Regards, Jesmin On Fri, Aug 17, 2012 at 11:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 18/08/12, *jesmin jahan * shraba...@gmail.com wrote: Hi Mark, Thanks for your reply. In the ffnonbonded.itp, I set all sigma and epsilon values to zero. So, the the LJ energy is coming as zero. But the coulomb potential is non zero. What should I do to make it zero? Each charge-charge interaction contributes both a Coulomb term and a GB polarization term. They're computed at nearly the same time, because both need the distance, so both contribute to the same timing stats. They show up in the different energy terms that you see. There's no way to separate them - and any code that can do so is probably still slower than GROMACS doing both. Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) Potential Kinetic En. -2.23121e+030.0e+00 -3.47729e+04 -3.70041e+04 0.0e+00 Total EnergyTemperature Pressure (bar) -3.70041e+040.0e+000.0e+00 One more point: I am not sure whether getting the 0 for an energy does mean that it is not being calculated at all! Most of GROMACS is supposed to avoid computing zero interactions. It's not true for the all-vs-all GB loops, which you're not using, and currently not true for bonded interactions. Since nobody seems likely would compute without LJ in a real calculation, this is not a big deal from GROMACS point of view. I'm still skeptical about what you're trying to measure. Performance of well-written code is generally not additive from its components. If you're later going to be computing on a real molecular system, you're going to have LJ and/or bonded terms, and how well the codes compute them *together with the Coulomb terms* is what you really want to measure. It's like measuring how long a top chef takes to prepare a meal, and then wondering how they manage to feed a whole restaurant on time. They do lots of time-slicing and get lots of efficiencies of scale that are not available if you're doing just one meal. It seems, the energy value was calculated but the result was zero because the sigma and epsilon were zero. In that case, the time ...or that the LJ component of the energy is always present even if there are no interactions to compute for it, which I expect is the case. reported by the program will also include the time of the extra calculation (unless the program is smart enough to know before hand that the result is going to be zero and return from the top!). IIRC neighbour searching detects there's no LJ and so doesn't trigger loops that compute LJ. So, while comparing with other molecular dynamic packages, its not fair to report that time for gromacs which also includes non GB time (as that can make Gromacs slower than others who do not include non GB-time). Any suggestions about this? What is the fair approach for gromacs? Look at the flop break-down to see if GROMACS thinks it is computing LJ any more. Or do some real timing measurements and compare before and after. Mark Thanks, Jesmin On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 17/08/2012 1:14 PM, jesmin jahan wrote: Hi Mark, According to your advice remove the the bonded terms and zero the VDW parameters, I removed everything under [ bond] , [angles], [pairs] and [ dihedrals ], This only removes the bonded terms (in the sense of those atoms that interact because of the presence of bonds). The VDW parameters for non-bonded interactions are in ffnonbonded.itp for your force field. You should probably follow the advice here http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Modifying_a_force_field to get a local copy you can change conveniently. and run the simulation mdrun rerun. I got output something like the following: Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+037.54287e+07 -3.47729e+04 7.53917e+07 0.0e+00 Total EnergyTemperature Pressure (bar) 7.53917e+070.0e+000.0e+00 where the previous output was something like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 2.12480e+034.80088e+021.06648e+03 9.04861e+01 -2.23122e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+00 -1.45483e+030.0e+00 0.0e+00 Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+034.17621e+13 -3.47729e+04 4.17621e+13 0.0e+00 Total EnergyTemperature Pressure (bar
Re: [gmx-users] Questions regarding Polarization Energy Calculation
Hi Mark, Thanks for your previous reply. I tried to run single point energy simulation with some proteins. I got .log files with content like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+042.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+00 ... Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 0.005711 0.274 0.2 GB Coulomb + LJ 0.416308 25.39518.5 Outer nonbonded loop 0.016367 0.164 0.1 1,4 nonbonded interactions 0.008410 0.757 0.6 Born radii (HCT/OBC) 0.439486 80.42658.5 Born force chain rule0.439486 6.592 4.8 NS-Pairs 0.943653 19.81714.4 Reset In Box 0.003179 0.010 0.0 CG-CoM 0.006358 0.019 0.0 Bonds0.003219 0.190 0.1 Angles 0.005838 0.981 0.7 Propers 0.011273 2.582 1.9 Virial 0.003899 0.070 0.1 Stop-CM 0.003179 0.032 0.0 Calc-Ekin0.006358 0.172 0.1 - Total 137.479 100.0 - D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 6859.0 R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp.16 10.0430.0 1.4 Comm. coord. 16 10.0030.0 0.1 Neighbor search 16 10.1030.0 3.5 Force 16 11.5300.551.5 Wait + Comm. F16 10.2640.1 8.9 Write traj. 16 10.0620.0 2.1 Update16 10.0010.0 0.0 Comm. energies16 20.9330.331.4 Rest 16 0.0310.0 1.1 --- Total 16 2.9700.9 100.0 --- NOTE: 31 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 0.056 0.056100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 7.497 2.442 1.535 15.637 From the log file, it seems, the time includes the time for LJ and Columb Potential Energy. But as I said before, I am only interested to GB-energy times. I am doing a comparative study of GB-energy performance (values vs time) for different molecular dynamic packages. That's why I was trying to deduct the time for any other extra energy computation time from it. Can anyone tell me how to get the exact time of GB-polarization energy (including Born radii) and excluding the times for any other additional energy (like LJ and Columb etc) from gromacs simutation? Thanks, Jesmin On Tue, Aug 14, 2012 at 10:16 AM, jesmin jahan shraba...@gmail.com wrote: Thanks Mark for your reply. I was trying to use Single-Point Energy Calculation as you advised in your first reply but for most of the files the simulation failed because I was using the original .pdb files in the mdrun command. Anyways. I really appreciate your help. Thanks again, Jesmin On Tue, Aug 14, 2012 at 1:26 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 14/08/2012 7:38 AM, jesmin jahan wrote: Dear Gromacs Users, I have some questions regarding GB-Polarization Energy Calculation with Gromacs. I will be grateful if someone can help me with the answers. I am trying to calculate GB-Polarization energy for different Protein molecules. I am
Re: [gmx-users] Questions regarding Polarization Energy Calculation
Hi Mark, Thanks for your reply. If I open the .tpr file using notepad, it seems to be a binary file. Then, how to remove the the bonded terms and zero the VDW parameters? I really need to compare how fast different well known package can compute GB-polarization energy and how good the energy values are? That's why time is an important factor me my experiments and I really want to measure the time for GB energy in isolation ! Thanks, Jesmin On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 4:26 PM, jesmin jahan wrote: Hi Mark, Thanks for your previous reply. I tried to run single point energy simulation with some proteins. I got .log files with content like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+042.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+00 ... Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 0.005711 0.274 0.2 GB Coulomb + LJ 0.416308 25.39518.5 Outer nonbonded loop 0.016367 0.164 0.1 1,4 nonbonded interactions 0.008410 0.757 0.6 Born radii (HCT/OBC) 0.439486 80.42658.5 Born force chain rule0.439486 6.592 4.8 NS-Pairs 0.943653 19.81714.4 Reset In Box 0.003179 0.010 0.0 CG-CoM 0.006358 0.019 0.0 Bonds0.003219 0.190 0.1 Angles 0.005838 0.981 0.7 Propers 0.011273 2.582 1.9 Virial 0.003899 0.070 0.1 Stop-CM 0.003179 0.032 0.0 Calc-Ekin0.006358 0.172 0.1 - Total 137.479 100.0 - D O M A I N D E C O M P O S I T I O N S T A T I S T I C S av. #atoms communicated per step for force: 2 x 6859.0 R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp.16 10.0430.0 1.4 Comm. coord. 16 10.0030.0 0.1 Neighbor search 16 10.1030.0 3.5 Force 16 11.5300.551.5 Wait + Comm. F16 10.2640.1 8.9 Write traj. 16 10.0620.0 2.1 Update16 10.0010.0 0.0 Comm. energies16 20.9330.331.4 Rest 16 0.0310.0 1.1 --- Total 16 2.9700.9 100.0 --- NOTE: 31 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 0.056 0.056100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 7.497 2.442 1.535 15.637 From the log file, it seems, the time includes the time for LJ and Columb Potential Energy. But as I said before, I am only interested to GB-energy times. I am doing a comparative study of GB-energy performance (values vs time) for different molecular dynamic packages. Since the LJ calculation also needs the distances, GROMACS does them in the same loops and makes no apology for being efficient. :-) If you're really trying to measure the time for the GB energy in isolation, then you will need to construct a different model physics that lacks LJ interactions. Or perhaps you don't really want to measure the time for GB energy in isolation. Depends what
Re: [gmx-users] Questions regarding Polarization Energy Calculation
Hi Mark, According to your advice remove the the bonded terms and zero the VDW parameters, I removed everything under [ bond] , [angles], [pairs] and [ dihedrals ], and run the simulation mdrun rerun. I got output something like the following: Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+037.54287e+07 -3.47729e+047.53917e+070.0e+00 Total EnergyTemperature Pressure (bar) 7.53917e+070.0e+000.0e+00 where the previous output was something like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 2.12480e+034.80088e+021.06648e+039.04861e+01 -2.23122e+03 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+00 -1.45483e+030.0e+000.0e+00 Energies (kJ/mol) GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En. -2.23121e+034.17621e+13 -3.47729e+044.17621e+130.0e+00 Total EnergyTemperature Pressure (bar) 4.17621e+130.0e+000.0e+00 So, you can see, although it has managed to remove some extra terms, the LJ and Columb potential are still there. I searched for VWD parameters. Although I saw various options for VWD, its not clear from the options, how to turn it off. Could you kindly tell me more clearly about it? I was also looking into the forcefield.itp file. I set the gen-pairs to no , fudgeLJ 1 and fudgeQQ to 1 which were yes, .5 and .83 respectively originally. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1 1 Please let me know how to get rid of calculation of other energies (LJ, Culumb and Total Potential) and how to set the parameters for this properly. Thanks for your help. Sincerely, Jesmin On Thu, Aug 16, 2012 at 3:27 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:08 PM, jesmin jahan wrote: Hi Mark, Thanks for your reply. If I open the .tpr file using notepad, it seems to be a binary file. Then, how to remove the the bonded terms and zero the VDW parameters? In the .top file from which you made the .tpr. (And contributing .itp files) Parts of chapter 5 may help with this process. Mark I really need to compare how fast different well known package can compute GB-polarization energy and how good the energy values are? That's why time is an important factor me my experiments and I really want to measure the time for GB energy in isolation ! Thanks, Jesmin On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 4:26 PM, jesmin jahan wrote: Hi Mark, Thanks for your previous reply. I tried to run single point energy simulation with some proteins. I got .log files with content like this: Energies (kJ/mol) Bond AngleProper Dih. Improper Dih.GB Polarization 1.54109e+043.84351e+038.47152e+033.58425e+02 -1.69666e+04 LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential 4.29664e+033.63997e+042.22900e+05 -5.18818e+04 2.22832e+05 Kinetic En. Total EnergyTemperature Pressure (bar) 1.08443e+091.08465e+092.73602e+070.0e+00 ... Computing: M-Number M-Flops % Flops - Generalized Born Coulomb 0.005711 0.274 0.2 GB Coulomb + LJ 0.416308 25.395 18.5 Outer nonbonded loop 0.016367 0.164 0.1 1,4 nonbonded interactions 0.008410 0.757 0.6 Born radii (HCT/OBC) 0.439486 80.426 58.5 Born force chain rule0.439486 6.592 4.8 NS-Pairs 0.943653 19.817 14.4 Reset In Box 0.003179 0.010 0.0 CG-CoM 0.006358 0.019 0.0 Bonds0.003219 0.190 0.1 Angles 0.005838 0.981 0.7 Propers 0.011273 2.582 1.9 Virial 0.003899 0.070 0.1 Stop-CM 0.003179 0.032 0.0 Calc-Ekin0.006358 0.172 0.1 - Total 137.479 100.0
Re: [gmx-users] Questions regarding Polarization Energy Calculation
Thanks Mark for your reply. I was trying to use Single-Point Energy Calculation as you advised in your first reply but for most of the files the simulation failed because I was using the original .pdb files in the mdrun command. Anyways. I really appreciate your help. Thanks again, Jesmin On Tue, Aug 14, 2012 at 1:26 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 14/08/2012 7:38 AM, jesmin jahan wrote: Dear Gromacs Users, I have some questions regarding GB-Polarization Energy Calculation with Gromacs. I will be grateful if someone can help me with the answers. I am trying to calculate GB-Polarization energy for different Protein molecules. I am interested both in energy values with the time required to calculate the Born Radii and Polarization Energy. I am not doing any energy minimization step as the files I am using as input are already minimized. Here is the content of my mdrun.mdp file: constraints = none integrator= md pbc = no dt = 0.001 nsteps = 0 implicit_solvent= GBSA gb_algorithm= HCT sa_algorithm= None And I am using following three steps for all the .pdb files I have: let x is the name of the .pdb file. pdb2gmx -f x.pdb -ter -ignh -ff amber99sb -water none grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr mpirun -np 8 mdrun_mpi -deffnm imd -v -g x.log So you're not using the advice I gave you about how to calculate single point energies. OK. 1 .Now the running time reported by a log file also includes other times. Its also not clear to me whether the time includes the time for Born Radii calculations. The timing breakdown is printed at the end of the .log file. Likely your time is heavily dominated by the GB calculation and communication cost. Born radii calculation are part of the former, and not reported separately. You should not bother with timing measurements unless your run goes for at least several minutes, else your time will be dominated by I/O and setup costs. So, to get the GB-energy time I am doing the following: I am also running a simulation with implicit_solvent set to no and I am taking the difference of these two (with GB and Without GB). Is that a right approach? No, that measures the weight difference between an apple and an orange, not whether the apple's seeds are heavy. I also want to be sure that it also includes Born-Radii calculation time. It's part of the GB calculation, so it's included in its timing. Is there any other approach to do this? 2. I was trying to run the simulations on 192 cores (16 nodes each with 12 codes). But I got There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 2.90226 nm error for some pdb files. Can anyone explain what is happening. Is there any restriction on number of nodes can be used? Yes. See discussion linked from http://www.gromacs.org/Documentation/Errors 3. I run the simulations with 1 way 96 (8 nodes each with 12 cores). Its not clear to me from the log file whether Gromacs is able to utilize all the 92 cores. It seems, it is using only 8 nodes. Does Gromacs use both shared and distributed memory parallelism? Not at the moment. Look at the top of your .log file for clues about what your configuration is making available to GROMACS. It is likely that mpirun -np 8 makes only 8 MPI processes available to GROMACS. Using more will require you to use your MPI installation correctly (and we can't help with that). 4. In the single-point energy calculation mdrun -s input.tpr -rerun configuration.pdb, is the configuration.pdb mentioned is the original pdb file used on pdb2gmx with -f option? Or its a modified pdb file? I am asking because if I use the original file that does not work always :-( It can be any configuration that matches the .top file you gave to grompp. That's the point - you only need one run input file to compute the energy of any such configuration you later want. The configuration you gave to grompp (or any other tool) doesn't matter. 5. Is there any known speedup factor of Gromacs on multicores? That depends on your simulation system, hardware, network and algorithm. Don't bother with fewer than hundreds of atoms per core. Mark -- 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 -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx
[gmx-users] Questions regarding Polarization Energy Calculation
Dear Gromacs Users, I have some questions regarding GB-Polarization Energy Calculation with Gromacs. I will be grateful if someone can help me with the answers. I am trying to calculate GB-Polarization energy for different Protein molecules. I am interested both in energy values with the time required to calculate the Born Radii and Polarization Energy. I am not doing any energy minimization step as the files I am using as input are already minimized. Here is the content of my mdrun.mdp file: constraints = none integrator= md pbc = no dt = 0.001 nsteps = 0 implicit_solvent= GBSA gb_algorithm= HCT sa_algorithm= None And I am using following three steps for all the .pdb files I have: let x is the name of the .pdb file. pdb2gmx -f x.pdb -ter -ignh -ff amber99sb -water none grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr mpirun -np 8 mdrun_mpi -deffnm imd -v -g x.log 1 .Now the running time reported by a log file also includes other times. Its also not clear to me whether the time includes the time for Born Radii calculations. So, to get the GB-energy time I am doing the following: I am also running a simulation with implicit_solvent set to no and I am taking the difference of these two (with GB and Without GB). Is that a right approach? I also want to be sure that it also includes Born-Radii calculation time. Is there any other approach to do this? 2. I was trying to run the simulations on 192 cores (16 nodes each with 12 codes). But I got There is no domain decomposition for 12 nodes that is compatible with the given box and a minimum cell size of 2.90226 nm error for some pdb files. Can anyone explain what is happening. Is there any restriction on number of nodes can be used? 3. I run the simulations with 1 way 96 (8 nodes each with 12 cores). Its not clear to me from the log file whether Gromacs is able to utilize all the 92 cores. It seems, it is using only 8 nodes. Does Gromacs use both shared and distributed memory parallelism? 4. In the single-point energy calculation mdrun -s input.tpr -rerun configuration.pdb, is the configuration.pdb mentioned is the original pdb file used on pdb2gmx with -f option? Or its a modified pdb file? I am asking because if I use the original file that does not work always :-( 5. Is there any known speedup factor of Gromacs on multicores? Thanks for your help. Best Regards, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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] About getting running time from a Gromacs Run
Dear Gromacs Users, I am a new user of Gromacs and I am using gromacs to calculate GB-polarization energy . I have a couple of questions about it. It would be great if someone can answer them. Thanks in advance. Questions: 1: I got an output like this in log file from a protein simulation: R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Comm. coord. 24 10.2350.1 1.0 Force 24 1 17.3695.271.9 Wait + Comm. F24 10.2580.1 1.1 Write traj. 24 10.2960.1 1.2 Update24 10.0050.0 0.0 Comm. energies24 27.2522.230.0 --- Total 24 24.1577.3 100.0 --- NOTE: 30 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 0.303 0.303100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 0.000 54.029 0.285 84.257 Now my question is: What is the time to calculate the GB-polarization Energy that is shown in log? Or How to get the time? 2. I have a protein with 1.5 million atoms. I tried to run it with gromacs on 16 machines each with 12 cores. It generated a segmentation fault. Is there any size limit to run in gromacs? 3. Can I only calculate the GB-polarization energy without calculating any Forces? How? 4. What are the good tools to get the GB- energy values along with the time to calculate the GB-energy? Thanks, Jesmin -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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] About getting running time from a Gromacs Run
Hi Mark, Thanks for your reply. I will try to follow your instructions. Thanks, Jesmin On Thu, Aug 9, 2012 at 9:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 10/08/2012 3:06 AM, jesmin jahan wrote: Dear Gromacs Users, I am a new user of Gromacs and I am using gromacs to calculate GB-polarization energy . I have a couple of questions about it. It would be great if someone can answer them. Thanks in advance. Questions: 1: I got an output like this in log file from a protein simulation: R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Comm. coord. 24 10.2350.1 1.0 Force 24 1 17.3695.271.9 Wait + Comm. F24 10.2580.1 1.1 Write traj. 24 10.2960.1 1.2 Update24 10.0050.0 0.0 Comm. energies24 27.2522.230.0 --- Total 24 24.1577.3 100.0 --- NOTE: 30 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 0.303 0.303 100.0 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 0.000 54.029 0.285 84.257 Now my question is: What is the time to calculate the GB-polarization Energy that is shown in log? Or How to get the time? It's a side-effect of the Force component of the timing breakdown. 2. I have a protein with 1.5 million atoms. I tried to run it with gromacs on 16 machines each with 12 cores. It generated a segmentation fault. Is there any size limit to run in gromacs? No, but if you run yourself out of memory results are unpredictable. Consult your .log and stdout files for clues what is going on. 3. Can I only calculate the GB-polarization energy without calculating any Forces? How? http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy 4. What are the good tools to get the GB- energy values along with the time to calculate the GB-energy? As above. Mark -- 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 -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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
