[gmx-users] Re: slow speed
Shuangxing Dai
shuangxingdai at gmail.com
Fri Apr 16 01:40:54 CEST 2010
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-request at gromacs.org> wrote:
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> Today's Topics:
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> 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 <shuangxingdai at gmail.com>
> Subject: [gmx-users] slow speed
> To: gmx-users at gromacs.org
> Message-ID:
> <q2ka8381c791004150702ye4007304pa2156201ca4b5635 at 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
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> ------------------------------
>
> Message: 2
> Date: Thu, 15 Apr 2010 10:09:58 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] slow speed
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4BC71E36.6050102 at 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.periole at rug.nl>
> Subject: Re: [gmx-users] slow speed
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <04339834-5E09-4A83-86DC-7DCA920E53BE at 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 at 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-request at 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.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] slow speed
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4BC7201D.4010304 at 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 at 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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