Shuangxing Dai wrote:
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.
The greatest performance obtained in the paper you quote uses virtual sites,
long time steps, and plain cutoff (or RF) for electrostatics. Ewald summation
methods are going to be slower. The system size will also be a major factor.
The benchmarks are based on relatively small systems (10,000 atoms for the
best-performing systems). If you have many more atoms, you can't expect the
same performance. You're simply comparing apples to oranges.
-Justin
Thanks,
Shuangxing Dai
On Thu, Apr 15, 2010 at 10:18 AM, <[email protected]
<mailto:[email protected]>> wrote:
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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 <[email protected]
<mailto:[email protected]>>
Subject: [gmx-users] slow speed
To: [email protected] <mailto:[email protected]>
Message-ID:
<[email protected]
<mailto:[email protected]>>
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" <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] slow speed
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected] <mailto:[email protected]>>
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 <http://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 <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] slow speed
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
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 [email protected]
<mailto:[email protected]>
> 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 [email protected]
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------------------------------
Message: 4
Date: Fri, 16 Apr 2010 00:18:05 +1000
From: Mark Abraham <[email protected]
<mailto:[email protected]>>
Subject: Re: [gmx-users] slow speed
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
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
------------------------------
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*****************************************
--
========================================
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
========================================
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