<div dir="ltr">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: <div><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; font-size: 12px; line-height: 18px; "><p class="citation" style="margin-top: 0.5em; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; font-size: 0.91666em; line-height: 1.45em; ">
<a href="javascript:AL_get(this,%20'jour',%20'J%20Comput%20Chem.');" title="Journal of computational chemistry." style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">J Comput Chem.</a> 2005 Dec;26(16):1701-18.</p>
<h1 class="title" style="font-size: 1.3333em; line-height: 1.125em; font-weight: bold; margin-top: 0.375em; margin-right: 0px; margin-bottom: 0.375em; margin-left: 0px; "><a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.103.418&rep=rep1&type=pdf">GROMACS: fast, flexible, and free.</a></h1>
<p class="auth_list" style="margin-top: 0.5em; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; "><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Van%20Der%20Spoel%20D%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Van Der Spoel D</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Lindahl%20E%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Lindahl E</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Hess%20B%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Hess B</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Groenhof%20G%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Groenhof G</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Mark%20AE%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Mark AE</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Berendsen%20HJ%22%5BAuthor%5D" style="color: black; font-weight: normal; border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: black; text-decoration: none; ">Berendsen HJ</a>.</p>
<p class="auth_list" style="margin-top: 0.5em; margin-right: 0px; margin-bottom: 0.5em; margin-left: 0px; "> 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. </p>
</span></div><div>Thanks,<br>Shuangxing Dai<br>
<br><br><div class="gmail_quote">On Thu, Apr 15, 2010 at 10:18 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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Today's Topics:<br>
<br>
1. slow speed (Shuangxing Dai)<br>
2. Re: slow speed (Justin A. Lemkul)<br>
3. Re: slow speed (XAvier Periole)<br>
4. Re: slow speed (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 15 Apr 2010 10:02:47 -0400<br>
From: Shuangxing Dai <<a href="mailto:shuangxingdai@gmail.com">shuangxingdai@gmail.com</a>><br>
Subject: [gmx-users] slow speed<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:q2ka8381c791004150702ye4007304pa2156201ca4b5635@mail.gmail.com">q2ka8381c791004150702ye4007304pa2156201ca4b5635@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi, gmx-users:<br>
I am using latest version of gromacs and found it was really slow. I was<br>
wondering anyone got the same experience and can point out where the problem<br>
is.<br>
I was running double precision for MD. But for each dynamics simulation,<br>
it takes 4 days. I should only take two or three hours.<br>
Here is the .mdp file:<br>
define =<br>
; RUN CONTROL PARAMETERS =<br>
integrator = sd<br>
; start time and timestep in ps =<br>
tinit = 0<br>
dt = 0.001<br>
nsteps = 200000<br>
; number of steps for center of mass motion removal =<br>
nstcomm = 100<br>
; OUTPUT CONTROL OPTIONS =<br>
; Output frequency for coords (x), velocities (v) and forces (f) =<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
; Output frequency for energies to log file and energy file =<br>
nstlog = 100<br>
nstenergy = 100<br>
; Output frequency and precision for xtc file =<br>
nstxtcout = 100<br>
xtc-precision = 1000<br>
; NEIGHBORSEARCHING PARAMETERS =<br>
; nblist update frequency =<br>
nstlist = 50<br>
; ns algorithm (simple or grid) =<br>
ns_type = grid<br>
<br>
;OPTIONS FOR PRESSURE COUPLING<br>
Pcoupl = berendsen<br>
tau_p = 1<br>
compressibility = 4.5e-05<br>
ref_p = 0.1<br>
;OPTIONS FOR TEMPERATURE COUPLING<br>
tc_grps = system<br>
tau_t = 0.1<br>
ref_t = 300<br>
; OPTIONS FOR BONDS =<br>
constraints = hbonds<br>
; Type of constraint algorithm =<br>
constraint-algorithm = Lincs<br>
; Do not constrain the start configuration =<br>
unconstrained-start = no<br>
; Relative tolerance of shake =<br>
shake-tol = 0.0001<br>
; Highest order in the expansion of the constraint coupling matrix =<br>
lincs-order = 12<br>
; Lincs will write a warning to the stderr if in one step a bond =<br>
; rotates over more degrees than =<br>
lincs-warnangle = 30<br>
; Periodic boundary conditions: xyz, no, xy<br>
pbc = xyz<br>
periodic_molecules = no<br>
; nblist cut-off<br>
rlist = 1<br>
<br>
; OPTIONS FOR ELECTROSTATICS AND VDW<br>
; Method for doing electrostatics<br>
coulombtype = Ewald<br>
rcoulomb = 1<br>
; Method for doing Van der Waals<br>
vdw-type = Cut-off<br>
; cut-off lengths<br>
rvdw = 1<br>
<br>
; Spacing for the PME/PPPM FFT grid<br>
fourierspacing = 0.12<br>
; FFT grid size, when a value is 0 fourierspacing will be used<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; EWALD/PME/PPPM parameters<br>
pme_order = 6<br>
ewald_rtol = 1e-4<br>
ewald_geometry = 3d<br>
epsilon_surface = 0<br>
optimize_fft = no<br>
<br>
Can anyone help me? Thank you in advance.<br>
Thanks,<br>
Shuangxing Dai<br>
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Message: 2<br>
Date: Thu, 15 Apr 2010 10:09:58 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] slow speed<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4BC71E36.6050102@vt.edu">4BC71E36.6050102@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
<br>
Shuangxing Dai wrote:<br>
> Hi, gmx-users:<br>
> I am using latest version of gromacs and found it was really slow. I<br>
> was wondering anyone got the same experience and can point out where the<br>
> problem is.<br>
> I was running double precision for MD. But for each dynamics<br>
> simulation, it takes 4 days. I should only take two or three hours.<br>
<br>
How did you establish this benchmark? Are you running in serial or in parallel?<br>
If you're running in parallel, what type of interconnect do the processors<br>
have? If they're high-latency (like gigabit ethernet) you will not get very<br>
good performance.<br>
<br>
-Justin<br>
<br>
> Here is the .mdp file:<br>
> define =<br>
> ; RUN CONTROL PARAMETERS =<br>
> integrator = sd<br>
> ; start time and timestep in ps =<br>
> tinit = 0<br>
> dt = 0.001<br>
> nsteps = 200000<br>
> ; number of steps for center of mass motion removal =<br>
> nstcomm = 100<br>
> ; OUTPUT CONTROL OPTIONS =<br>
> ; Output frequency for coords (x), velocities (v) and forces (f) =<br>
> nstxout = 0<br>
> nstvout = 0<br>
> nstfout = 0<br>
> ; Output frequency for energies to log file and energy file =<br>
> nstlog = 100<br>
> nstenergy = 100<br>
> ; Output frequency and precision for xtc file =<br>
> nstxtcout = 100<br>
> xtc-precision = 1000<br>
> ; NEIGHBORSEARCHING PARAMETERS =<br>
> ; nblist update frequency =<br>
> nstlist = 50<br>
> ; ns algorithm (simple or grid) =<br>
> ns_type = grid<br>
><br>
> ;OPTIONS FOR PRESSURE COUPLING<br>
> Pcoupl = berendsen<br>
> tau_p = 1<br>
> compressibility = 4.5e-05<br>
> ref_p = 0.1<br>
> ;OPTIONS FOR TEMPERATURE COUPLING<br>
> tc_grps = system<br>
> tau_t = 0.1<br>
> ref_t = 300<br>
> ; OPTIONS FOR BONDS =<br>
> constraints = hbonds<br>
> ; Type of constraint algorithm =<br>
> constraint-algorithm = Lincs<br>
> ; Do not constrain the start configuration =<br>
> unconstrained-start = no<br>
> ; Relative tolerance of shake =<br>
> shake-tol = 0.0001<br>
> ; Highest order in the expansion of the constraint coupling matrix =<br>
> lincs-order = 12<br>
> ; Lincs will write a warning to the stderr if in one step a bond =<br>
> ; rotates over more degrees than =<br>
> lincs-warnangle = 30<br>
> ; Periodic boundary conditions: xyz, no, xy<br>
> pbc = xyz<br>
> periodic_molecules = no<br>
> ; nblist cut-off<br>
> rlist = 1<br>
><br>
> ; OPTIONS FOR ELECTROSTATICS AND VDW<br>
> ; Method for doing electrostatics<br>
> coulombtype = Ewald<br>
> rcoulomb = 1<br>
> ; Method for doing Van der Waals<br>
> vdw-type = Cut-off<br>
> ; cut-off lengths<br>
> rvdw = 1<br>
><br>
> ; Spacing for the PME/PPPM FFT grid<br>
> fourierspacing = 0.12<br>
> ; FFT grid size, when a value is 0 fourierspacing will be used<br>
> fourier_nx = 0<br>
> fourier_ny = 0<br>
> fourier_nz = 0<br>
> ; EWALD/PME/PPPM parameters<br>
> pme_order = 6<br>
> ewald_rtol = 1e-4<br>
> ewald_geometry = 3d<br>
> epsilon_surface = 0<br>
> optimize_fft = no<br>
><br>
> Can anyone help me? Thank you in advance.<br>
> Thanks,<br>
> Shuangxing Dai<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 15 Apr 2010 16:11:15 +0200<br>
From: XAvier Periole <<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>><br>
Subject: Re: [gmx-users] slow speed<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:04339834-5E09-4A83-86DC-7DCA920E53BE@rug.nl">04339834-5E09-4A83-86DC-7DCA920E53BE@rug.nl</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br>
<br>
<br>
What makes you think it should be so fast?<br>
<br>
Nothing appears obviously wrong in the mdp file.<br>
<br>
May be this though!<br>
<br>
lincs-order = 12<br>
<br>
On Apr 15, 2010, at 4:02 PM, Shuangxing Dai wrote:<br>
<br>
> Hi, gmx-users:<br>
> I am using latest version of gromacs and found it was really<br>
> slow. I was wondering anyone got the same experience and can point<br>
> out where the problem is.<br>
> I was running double precision for MD. But for each dynamics<br>
> simulation, it takes 4 days. I should only take two or three hours.<br>
> Here is the .mdp file:<br>
> define =<br>
> ; RUN CONTROL PARAMETERS =<br>
> integrator = sd<br>
> ; start time and timestep in ps =<br>
> tinit = 0<br>
> dt = 0.001<br>
> nsteps = 200000<br>
> ; number of steps for center of mass motion removal =<br>
> nstcomm = 100<br>
> ; OUTPUT CONTROL OPTIONS =<br>
> ; Output frequency for coords (x), velocities (v) and forces (f) =<br>
> nstxout = 0<br>
> nstvout = 0<br>
> nstfout = 0<br>
> ; Output frequency for energies to log file and energy file =<br>
> nstlog = 100<br>
> nstenergy = 100<br>
> ; Output frequency and precision for xtc file =<br>
> nstxtcout = 100<br>
> xtc-precision = 1000<br>
> ; NEIGHBORSEARCHING PARAMETERS =<br>
> ; nblist update frequency =<br>
> nstlist = 50<br>
> ; ns algorithm (simple or grid) =<br>
> ns_type = grid<br>
><br>
> ;OPTIONS FOR PRESSURE COUPLING<br>
> Pcoupl = berendsen<br>
> tau_p = 1<br>
> compressibility = 4.5e-05<br>
> ref_p = 0.1<br>
> ;OPTIONS FOR TEMPERATURE COUPLING<br>
> tc_grps = system<br>
> tau_t = 0.1<br>
> ref_t = 300<br>
> ; OPTIONS FOR BONDS =<br>
> constraints = hbonds<br>
> ; Type of constraint algorithm =<br>
> constraint-algorithm = Lincs<br>
> ; Do not constrain the start configuration =<br>
> unconstrained-start = no<br>
> ; Relative tolerance of shake =<br>
> shake-tol = 0.0001<br>
> ; Highest order in the expansion of the constraint coupling matrix =<br>
> lincs-order = 12<br>
> ; Lincs will write a warning to the stderr if in one step a bond =<br>
> ; rotates over more degrees than =<br>
> lincs-warnangle = 30<br>
> ; Periodic boundary conditions: xyz, no, xy<br>
> pbc = xyz<br>
> periodic_molecules = no<br>
> ; nblist cut-off<br>
> rlist = 1<br>
><br>
> ; OPTIONS FOR ELECTROSTATICS AND VDW<br>
> ; Method for doing electrostatics<br>
> coulombtype = Ewald<br>
> rcoulomb = 1<br>
> ; Method for doing Van der Waals<br>
> vdw-type = Cut-off<br>
> ; cut-off lengths<br>
> rvdw = 1<br>
><br>
> ; Spacing for the PME/PPPM FFT grid<br>
> fourierspacing = 0.12<br>
> ; FFT grid size, when a value is 0 fourierspacing will be used<br>
> fourier_nx = 0<br>
> fourier_ny = 0<br>
> fourier_nz = 0<br>
> ; EWALD/PME/PPPM parameters<br>
> pme_order = 6<br>
> ewald_rtol = 1e-4<br>
> ewald_geometry = 3d<br>
> epsilon_surface = 0<br>
> optimize_fft = no<br>
><br>
> Can anyone help me? Thank you in advance.<br>
> Thanks,<br>
> Shuangxing Dai<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
> posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
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<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 16 Apr 2010 00:18:05 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] slow speed<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4BC7201D.4010304@anu.edu.au">4BC7201D.4010304@anu.edu.au</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
On 16/04/2010 12:02 AM, Shuangxing Dai wrote:<br>
> Hi, gmx-users:<br>
> I am using latest version of gromacs and found it was really slow. I<br>
> was wondering anyone got the same experience and can point out where the<br>
> problem is.<br>
> I was running double precision for MD. But for each dynamics<br>
> simulation, it takes 4 days. I should only take two or three hours.<br>
<br>
Well, double precisions is slower - possibly very much so. You need<br>
twice the bus and cache bandwidth because you are throwing around twice<br>
the memory. Otherwise, we can't say much because we don't know anything<br>
about your hardware or where you got your benchmark from.<br>
<br>
Other comments below. It looks very much like you've gone and made a<br>
bunch of semi-random changes to things. That's not normally a good idea.<br>
<br>
> Here is the .mdp file:<br>
> define =<br>
> ; RUN CONTROL PARAMETERS =<br>
> integrator = sd<br>
> ; start time and timestep in ps =<br>
> tinit = 0<br>
> dt = 0.001<br>
> nsteps = 200000<br>
> ; number of steps for center of mass motion removal =<br>
> nstcomm = 100<br>
> ; OUTPUT CONTROL OPTIONS =<br>
> ; Output frequency for coords (x), velocities (v) and forces (f) =<br>
> nstxout = 0<br>
> nstvout = 0<br>
> nstfout = 0<br>
> ; Output frequency for energies to log file and energy file =<br>
> nstlog = 100<br>
> nstenergy = 100<br>
> ; Output frequency and precision for xtc file =<br>
> nstxtcout = 100<br>
> xtc-precision = 1000<br>
> ; NEIGHBORSEARCHING PARAMETERS =<br>
> ; nblist update frequency =<br>
> nstlist = 50<br>
> ; ns algorithm (simple or grid) =<br>
> ns_type = grid<br>
><br>
> ;OPTIONS FOR PRESSURE COUPLING<br>
> Pcoupl = berendsen<br>
> tau_p = 1<br>
> compressibility = 4.5e-05<br>
> ref_p = 0.1<br>
> ;OPTIONS FOR TEMPERATURE COUPLING<br>
> tc_grps = system<br>
> tau_t = 0.1<br>
> ref_t = 300<br>
> ; OPTIONS FOR BONDS =<br>
> constraints = hbonds<br>
> ; Type of constraint algorithm =<br>
> constraint-algorithm = Lincs<br>
> ; Do not constrain the start configuration =<br>
> unconstrained-start = no<br>
> ; Relative tolerance of shake =<br>
> shake-tol = 0.0001<br>
> ; Highest order in the expansion of the constraint coupling matrix =<br>
> lincs-order = 12<br>
<br>
That's huge, and the use of lincs is somewhat inconsistent with a 1fs<br>
timestep.<br>
<br>
> ; Lincs will write a warning to the stderr if in one step a bond =<br>
> ; rotates over more degrees than =<br>
> lincs-warnangle = 30<br>
> ; Periodic boundary conditions: xyz, no, xy<br>
> pbc = xyz<br>
> periodic_molecules = no<br>
> ; nblist cut-off<br>
> rlist = 1<br>
><br>
> ; OPTIONS FOR ELECTROSTATICS AND VDW<br>
> ; Method for doing electrostatics<br>
> coulombtype = Ewald<br>
<br>
This could be a correct decision, but it's unlikely.<br>
<br>
> rcoulomb = 1<br>
> ; Method for doing Van der Waals<br>
> vdw-type = Cut-off<br>
> ; cut-off lengths<br>
> rvdw = 1<br>
><br>
> ; Spacing for the PME/PPPM FFT grid<br>
> fourierspacing = 0.12<br>
> ; FFT grid size, when a value is 0 fourierspacing will be used<br>
> fourier_nx = 0<br>
> fourier_ny = 0<br>
> fourier_nz = 0<br>
> ; EWALD/PME/PPPM parameters<br>
> pme_order = 6<br>
> ewald_rtol = 1e-4<br>
<br>
Again, could be correct, or could just be killing you.<br>
<br>
> ewald_geometry = 3d<br>
> epsilon_surface = 0<br>
> optimize_fft = no<br>
<br>
Mark<br>
<br>
<br>
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End of gmx-users Digest, Vol 72, Issue 82<br>
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