I am not running in parallel. Right now I just changed links order from 12 to 4. It is still slow. While I change to shift, not Ewald, it finished 10000 steps in 10 mins. In the paper:
J Comput Chem. <javascript:AL_get(this,%20'jour',%20'J%20Comput%20Chem.');> 2005 Dec;26(16):1701-18. GROMACS: fast, flexible, and free.<http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.103.418&rep=rep1&type=pdf> Van Der Spoel D<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Van%20Der%20Spoel%20D%22%5BAuthor%5D> , Lindahl E<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Lindahl%20E%22%5BAuthor%5D> , Hess B<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Hess%20B%22%5BAuthor%5D> , Groenhof G<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Groenhof%20G%22%5BAuthor%5D> , Mark AE<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Mark%20AE%22%5BAuthor%5D> , Berendsen HJ<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Berendsen%20HJ%22%5BAuthor%5D> . The performance there is around 10000 ps/day. I do not understand why my speed is so slow and it seems that Ewald option makes it slow. Thanks, Shuangxing Dai On Thu, Apr 15, 2010 at 10:18 AM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. slow speed (Shuangxing Dai) > 2. Re: slow speed (Justin A. Lemkul) > 3. Re: slow speed (XAvier Periole) > 4. Re: slow speed (Mark Abraham) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 15 Apr 2010 10:02:47 -0400 > From: Shuangxing Dai <shuangxing...@gmail.com> > Subject: [gmx-users] slow speed > To: gmx-users@gromacs.org > Message-ID: > <q2ka8381c791004150702ye4007304pa2156201ca4b5...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, gmx-users: > I am using latest version of gromacs and found it was really slow. I was > wondering anyone got the same experience and can point out where the > problem > is. > I was running double precision for MD. But for each dynamics simulation, > it takes 4 days. I should only take two or three hours. > Here is the .mdp file: > define = > ; RUN CONTROL PARAMETERS = > integrator = sd > ; start time and timestep in ps = > tinit = 0 > dt = 0.001 > nsteps = 200000 > ; number of steps for center of mass motion removal = > nstcomm = 100 > ; OUTPUT CONTROL OPTIONS = > ; Output frequency for coords (x), velocities (v) and forces (f) = > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Output frequency for energies to log file and energy file = > nstlog = 100 > nstenergy = 100 > ; Output frequency and precision for xtc file = > nstxtcout = 100 > xtc-precision = 1000 > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 50 > ; ns algorithm (simple or grid) = > ns_type = grid > > ;OPTIONS FOR PRESSURE COUPLING > Pcoupl = berendsen > tau_p = 1 > compressibility = 4.5e-05 > ref_p = 0.1 > ;OPTIONS FOR TEMPERATURE COUPLING > tc_grps = system > tau_t = 0.1 > ref_t = 300 > ; OPTIONS FOR BONDS = > constraints = hbonds > ; Type of constraint algorithm = > constraint-algorithm = Lincs > ; Do not constrain the start configuration = > unconstrained-start = no > ; Relative tolerance of shake = > shake-tol = 0.0001 > ; Highest order in the expansion of the constraint coupling matrix = > lincs-order = 12 > ; Lincs will write a warning to the stderr if in one step a bond = > ; rotates over more degrees than = > lincs-warnangle = 30 > ; Periodic boundary conditions: xyz, no, xy > pbc = xyz > periodic_molecules = no > ; nblist cut-off > rlist = 1 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = Ewald > rcoulomb = 1 > ; Method for doing Van der Waals > vdw-type = Cut-off > ; cut-off lengths > rvdw = 1 > > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order = 6 > ewald_rtol = 1e-4 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > Can anyone help me? Thank you in advance. > Thanks, > Shuangxing Dai > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100415/73eee331/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 15 Apr 2010 10:09:58 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] slow speed > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4bc71e36.6050...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Shuangxing Dai wrote: > > Hi, gmx-users: > > I am using latest version of gromacs and found it was really slow. I > > was wondering anyone got the same experience and can point out where the > > problem is. > > I was running double precision for MD. But for each dynamics > > simulation, it takes 4 days. I should only take two or three hours. > > How did you establish this benchmark? Are you running in serial or in > parallel? > If you're running in parallel, what type of interconnect do the processors > have? If they're high-latency (like gigabit ethernet) you will not get > very > good performance. > > -Justin > > > Here is the .mdp file: > > define = > > ; RUN CONTROL PARAMETERS = > > integrator = sd > > ; start time and timestep in ps = > > tinit = 0 > > dt = 0.001 > > nsteps = 200000 > > ; number of steps for center of mass motion removal = > > nstcomm = 100 > > ; OUTPUT CONTROL OPTIONS = > > ; Output frequency for coords (x), velocities (v) and forces (f) = > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > ; Output frequency for energies to log file and energy file = > > nstlog = 100 > > nstenergy = 100 > > ; Output frequency and precision for xtc file = > > nstxtcout = 100 > > xtc-precision = 1000 > > ; NEIGHBORSEARCHING PARAMETERS = > > ; nblist update frequency = > > nstlist = 50 > > ; ns algorithm (simple or grid) = > > ns_type = grid > > > > ;OPTIONS FOR PRESSURE COUPLING > > Pcoupl = berendsen > > tau_p = 1 > > compressibility = 4.5e-05 > > ref_p = 0.1 > > ;OPTIONS FOR TEMPERATURE COUPLING > > tc_grps = system > > tau_t = 0.1 > > ref_t = 300 > > ; OPTIONS FOR BONDS = > > constraints = hbonds > > ; Type of constraint algorithm = > > constraint-algorithm = Lincs > > ; Do not constrain the start configuration = > > unconstrained-start = no > > ; Relative tolerance of shake = > > shake-tol = 0.0001 > > ; Highest order in the expansion of the constraint coupling matrix = > > lincs-order = 12 > > ; Lincs will write a warning to the stderr if in one step a bond = > > ; rotates over more degrees than = > > lincs-warnangle = 30 > > ; Periodic boundary conditions: xyz, no, xy > > pbc = xyz > > periodic_molecules = no > > ; nblist cut-off > > rlist = 1 > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype = Ewald > > rcoulomb = 1 > > ; Method for doing Van der Waals > > vdw-type = Cut-off > > ; cut-off lengths > > rvdw = 1 > > > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing = 0.12 > > ; FFT grid size, when a value is 0 fourierspacing will be used > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > ; EWALD/PME/PPPM parameters > > pme_order = 6 > > ewald_rtol = 1e-4 > > ewald_geometry = 3d > > epsilon_surface = 0 > > optimize_fft = no > > > > Can anyone help me? Thank you in advance. > > Thanks, > > Shuangxing Dai > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Thu, 15 Apr 2010 16:11:15 +0200 > From: XAvier Periole <x.peri...@rug.nl> > Subject: Re: [gmx-users] slow speed > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <04339834-5e09-4a83-86dc-7dca920e5...@rug.nl> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > What makes you think it should be so fast? > > Nothing appears obviously wrong in the mdp file. > > May be this though! > > lincs-order = 12 > > On Apr 15, 2010, at 4:02 PM, Shuangxing Dai wrote: > > > Hi, gmx-users: > > I am using latest version of gromacs and found it was really > > slow. I was wondering anyone got the same experience and can point > > out where the problem is. > > I was running double precision for MD. But for each dynamics > > simulation, it takes 4 days. I should only take two or three hours. > > Here is the .mdp file: > > define = > > ; RUN CONTROL PARAMETERS = > > integrator = sd > > ; start time and timestep in ps = > > tinit = 0 > > dt = 0.001 > > nsteps = 200000 > > ; number of steps for center of mass motion removal = > > nstcomm = 100 > > ; OUTPUT CONTROL OPTIONS = > > ; Output frequency for coords (x), velocities (v) and forces (f) = > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > ; Output frequency for energies to log file and energy file = > > nstlog = 100 > > nstenergy = 100 > > ; Output frequency and precision for xtc file = > > nstxtcout = 100 > > xtc-precision = 1000 > > ; NEIGHBORSEARCHING PARAMETERS = > > ; nblist update frequency = > > nstlist = 50 > > ; ns algorithm (simple or grid) = > > ns_type = grid > > > > ;OPTIONS FOR PRESSURE COUPLING > > Pcoupl = berendsen > > tau_p = 1 > > compressibility = 4.5e-05 > > ref_p = 0.1 > > ;OPTIONS FOR TEMPERATURE COUPLING > > tc_grps = system > > tau_t = 0.1 > > ref_t = 300 > > ; OPTIONS FOR BONDS = > > constraints = hbonds > > ; Type of constraint algorithm = > > constraint-algorithm = Lincs > > ; Do not constrain the start configuration = > > unconstrained-start = no > > ; Relative tolerance of shake = > > shake-tol = 0.0001 > > ; Highest order in the expansion of the constraint coupling matrix = > > lincs-order = 12 > > ; Lincs will write a warning to the stderr if in one step a bond = > > ; rotates over more degrees than = > > lincs-warnangle = 30 > > ; Periodic boundary conditions: xyz, no, xy > > pbc = xyz > > periodic_molecules = no > > ; nblist cut-off > > rlist = 1 > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype = Ewald > > rcoulomb = 1 > > ; Method for doing Van der Waals > > vdw-type = Cut-off > > ; cut-off lengths > > rvdw = 1 > > > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing = 0.12 > > ; FFT grid size, when a value is 0 fourierspacing will be used > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > ; EWALD/PME/PPPM parameters > > pme_order = 6 > > ewald_rtol = 1e-4 > > ewald_geometry = 3d > > epsilon_surface = 0 > > optimize_fft = no > > > > Can anyone help me? Thank you in advance. > > Thanks, > > Shuangxing Dai > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > > ------------------------------ > > Message: 4 > Date: Fri, 16 Apr 2010 00:18:05 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] slow speed > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4bc7201d.4010...@anu.edu.au> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 16/04/2010 12:02 AM, Shuangxing Dai wrote: > > Hi, gmx-users: > > I am using latest version of gromacs and found it was really slow. I > > was wondering anyone got the same experience and can point out where the > > problem is. > > I was running double precision for MD. But for each dynamics > > simulation, it takes 4 days. I should only take two or three hours. > > Well, double precisions is slower - possibly very much so. You need > twice the bus and cache bandwidth because you are throwing around twice > the memory. Otherwise, we can't say much because we don't know anything > about your hardware or where you got your benchmark from. > > Other comments below. It looks very much like you've gone and made a > bunch of semi-random changes to things. That's not normally a good idea. > > > Here is the .mdp file: > > define = > > ; RUN CONTROL PARAMETERS = > > integrator = sd > > ; start time and timestep in ps = > > tinit = 0 > > dt = 0.001 > > nsteps = 200000 > > ; number of steps for center of mass motion removal = > > nstcomm = 100 > > ; OUTPUT CONTROL OPTIONS = > > ; Output frequency for coords (x), velocities (v) and forces (f) = > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > ; Output frequency for energies to log file and energy file = > > nstlog = 100 > > nstenergy = 100 > > ; Output frequency and precision for xtc file = > > nstxtcout = 100 > > xtc-precision = 1000 > > ; NEIGHBORSEARCHING PARAMETERS = > > ; nblist update frequency = > > nstlist = 50 > > ; ns algorithm (simple or grid) = > > ns_type = grid > > > > ;OPTIONS FOR PRESSURE COUPLING > > Pcoupl = berendsen > > tau_p = 1 > > compressibility = 4.5e-05 > > ref_p = 0.1 > > ;OPTIONS FOR TEMPERATURE COUPLING > > tc_grps = system > > tau_t = 0.1 > > ref_t = 300 > > ; OPTIONS FOR BONDS = > > constraints = hbonds > > ; Type of constraint algorithm = > > constraint-algorithm = Lincs > > ; Do not constrain the start configuration = > > unconstrained-start = no > > ; Relative tolerance of shake = > > shake-tol = 0.0001 > > ; Highest order in the expansion of the constraint coupling matrix = > > lincs-order = 12 > > That's huge, and the use of lincs is somewhat inconsistent with a 1fs > timestep. > > > ; Lincs will write a warning to the stderr if in one step a bond = > > ; rotates over more degrees than = > > lincs-warnangle = 30 > > ; Periodic boundary conditions: xyz, no, xy > > pbc = xyz > > periodic_molecules = no > > ; nblist cut-off > > rlist = 1 > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing electrostatics > > coulombtype = Ewald > > This could be a correct decision, but it's unlikely. > > > rcoulomb = 1 > > ; Method for doing Van der Waals > > vdw-type = Cut-off > > ; cut-off lengths > > rvdw = 1 > > > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing = 0.12 > > ; FFT grid size, when a value is 0 fourierspacing will be used > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > ; EWALD/PME/PPPM parameters > > pme_order = 6 > > ewald_rtol = 1e-4 > > Again, could be correct, or could just be killing you. > > > ewald_geometry = 3d > > epsilon_surface = 0 > > optimize_fft = no > > Mark > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 72, Issue 82 > ***************************************** >
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