On Feb 24, 2014 11:01 PM, "Christopher Neale" <chris.ne...@alum.utoronto.ca> wrote: > > Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread pinning issue?
Yes, but part of the larger problem of over-loading the physical cores. > I run on a Nehalem system with 8 cores/node but, because of the Nehalem hyperthreading (I think), gromacs always complains if I run "mpirun -np $N mdrun" where $N is the number of cores > > NOTE: The number of threads is not equal to the number of (logical) cores > and the -pin option is set to auto: will not pin thread to cores. > This can lead to significant performance degradation. > Consider using -pin on (and -pinoffset in case you run multiple jobs). > > However, if I use $N = 2 times the number of cores, then I don't get that note, instead getting: > > "Pinning threads with a logical core stride of 1" > > Aside, if anybody has a suggestion about how I should handle the thread pinning in my case, or if it matters, then I would be happy to hear it (my throughput seems to be good though). Hyper-threading is good for applications that are memory- or user-bound (so enabled by default on consumer machines), so they can take advantage of CPU instruction-issue opportunities while stalled. GROMACS kernels are already CPU-bound, so there is little to gain and it generally does not pay for the overhead. Generally, one should not use HT; turning it off can be emulated with the right use of -pinoffset and using half the number of threads. > Finally, this comment is off topic, but you might want to reconsider having the CL ions in a separate temperature coupling group. Indeed. Mark > Chris. > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Singam Karthick <sikar...@yahoo.in> > Sent: 24 February 2014 02:32 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] REMD slow's down drastically > > Dear members, > I am trying to run REMD simulation for poly Alanine (12 residue) system. I used remd generator to get the range of temperature with the exchange probability of 0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its drastically slow down the simulation time (for 70 pico seconds it took around 17 hours ) could anyone please tell me how to solve this issue. > > Following is the MDP file > > title = G4Ga3a4a5 production. > ;define = ;-DPOSRES ; position restrain the protein > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 12500000 ; 2 * 5000000 = 3ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 0 ; save coordinates every 0.2 ps > nstvout = 10000 ; save velocities every 0.2 ps > nstxtcout = 500 ; save xtc coordinate every 0.2 ps > nstenergy = 500 ; save energies every 0.2 ps > nstlog = 100 ; update log file every 0.2 ps > ; Bond parameters > continuation = yes ; Restarting after NVT > constraint_algorithm = lincs ; holonomic constraints > constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > morse = no > ; Neighborsearching > ns_type = grid ; search neighboring grid cels > nstlist = 5 ; 10 fs > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) > rvdw = 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling is on > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = protein SOL Cl ;two coupling groups - more accurate > tau_t = 0.1 0.1 0.1 ; time constant, in ps > ref_t = XXXXX XXXXX XXXXX ; reference temperature, one for each group, in K > ; Pressure coupling is on > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > pcoupltype = isotropic ; uniform scaling of box vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > > DispCorr = EnerPres ; account for cut-off vdW scheme > > > regards > singam > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.