David Mobley wrote:
Hi,
This doesn't sound like normal behavior. In fact, this is not what I
typically observe. While there may be a small performance difference,
it is probably at the level of a few percent. Certainly not a factor
of more than 10.
I see about a 50% reduction in speed when decoupling small molecules in water.
For me, I don't care if a nanosecond takes 2 or 3 hours. For larger systems
such as the ones considered here, it seems that the performance loss is much
more dramatic.
I can reproduce the poor performance with a simple water box with the free
energy code on. Decoupling the whole system (or at least, a large part of it,
as was the original intent of this thread, as I understand it) results in a
1500% slowdown. Some observations:
1. Water optimizations are turned off when decoupling the water, but this only
accounts for 20% of the slowdown, which is relatively insignificant.
2. Using lambda=0.9 (from a previous post) in my water box results in even worse
performance, but much of this is due to DD instability. The system I used has a
few hundred water molecules in it, and after about 10-12 ps, they collapse in on
one another and form clusters, dramatically shifting the balance of atoms
between DD cells. DLB gets activated but the force imbalances are around 40%,
and the total slowdown (relative to non-perturbed trajectories) is 2000%.
3. Using lambda=0 results in stable trajectories with very low imbalance, but
also poor performance. It seems that mdrun spends all of its time in the free
energy innerloops:
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
Free energy innerloop 19064.187513 2859628.127 89.1
Outer nonbonded loop 325.153806 3251.538 0.1
Calc Weights 231.754635 8343.167 0.3
Spread Q Bspline 9888.197760 19776.396 0.6
Gather F Bspline 9888.197760 59329.187 1.8
3D-FFT 24406.688124 195253.505 6.1
Solve PME 485.109702 31047.021 1.0
NS-Pairs 521.616615 10953.949 0.3
Reset In Box 2.575515 7.727 0.0
CG-CoM 7.728090 23.184 0.0
Virial 8.176635 147.179 0.0
Update 77.251545 2394.798 0.1
Stop-CM 0.774045 7.740 0.0
Calc-Ekin 77.253090 2085.833 0.1
Constraint-V 77.253090 618.025 0.0
Constraint-Vir 7.726545 185.437 0.0
Settle 51.502060 16635.165 0.5
-----------------------------------------------------------------------------
Total 3209687.978 100.0
-----------------------------------------------------------------------------
You may want to provide an mdp file and topology, etc. so someone can
see if they can reproduce your problem.
I agree that would be useful. I can contribute my water box system if it would
help, as well.
-Justin
Thanks.
On Wed, Apr 6, 2011 at 7:59 AM, Luca Bellucci <lcbl...@gmail.com> wrote:
I followed your suggestions and i tried to perform a MD run wit GROMACS and
NAMD for dialanine peptide in a water box. The cell side cubic box was 40 A.
GROMACS:
With the free energy module there is a drop in gromacs performance of about
10/20 fold.
Standard MD: Time: 6.693 6.693 100.0
Free energy MD: Time: 136.113 136.113 100.0
NAMD:
With free energy module there is not a drop in performance so evident as in
gromacs.
Standard MD 6.900000
Free energy MD 9.600000
I would like to point out that this kind of calculation is common, in fact in
the manual of gromacs 4.5.3 it is reported " There is a special option system
that couples all molecules types in the system. This can be useful for
equilibrating a system [..] ".
Actually, I would understand if there is a solution to resolve the drop in
gromacs performance for this kind of calculation.
Luca
I don't know if it is possible or not. I think that you can enhance
your chances of developer attention if you develop a small and simple
test system that reproduces the slowdown and very explicitly state
your case for why you can't use some other method. I would suggest
posting that to the mailing list and, if you don't get any response,
post it as an enhancement request on the redmine page (or whatever has
taken over from bugzilla).
Good luck,
Chris.
-- original message --
Yes i am testing the possibility to perform an Hamiltonian-REMD
Energy barriers can be overcome increasing the temperature system or
scaling potential energy with a lambda value, these methods are
"equivalent". Both have advantages and disavantages, at this stage it is
not the right place to debate on it. The main problem seems to be how to
overcome to the the loss of gromacs performance in such calculation. At
this moment it seems an intrinsic code problem.
Is it possible?
>> Dear Chris and Justin
/ Thank you for your precious suggestions
/>>/ This is a test that i perform in a single machine with 8 cores
/>>/ and gromacs 4.5.4.
/>>/
/>>/ I am trying to enhance the sampling of a protein using the
decoupling scheme />>/ of the free energy module of gromacs. However
when i decouple only the />>/ protein, the protein collapsed. Because i
simulated in NVT i thought that />>/ this was an effect of the solvent.
I was trying to decouple also the solvent />>/ to understand the system
behavior.
/>>/
/>
Rather than suspect that the solvent is the problem, it's more likely
that decoupling an entire protein simply isn't stable. I have never
tried
anything that enormous, but the volume change in the system could be
unstable, along with any number of factors, depending on how you
approach it.
If you're looking for better sampling, REMD is a much more robust
approach
than trying to manipulate the interactions of huge parts of your system
using the free energy code.
Presumably Luca is interested in some type of hamiltonian exchange where
lambda represents the interactions between the protein and the solvent?
This can actually be a useful method for enhancing sampling. I think it's
dangerous if we rely to heavily on "try something else". I still see no
methodological reason a priori why there should be any actual slowdown,
so that makes me think that it's an implementation thing, and there is
at least the possibility that this is something that could be fixed as
an enhancement.
Chris.
-Justin
/ I expected a loss of performance, but not so drastic.
/>/ Luca
/>/
/>>/ Load balancing problems I can understand, but why would it take
longer />>/ in absolute time? I would have thought that some nodes would
simple be />>/ sitting idle, but this should not cause an increase in
the overall />>/ simulation time (15x at that!).
/>>/
/>>/ There must be some extra communication?
/>>/
/>>/ I agree with Justin that this seems like a strange thing to do, but
/>>/ still I think that there must be some underlying coding issue
(probably />>/ one that only exists because of a reasonable assumption
that nobody />>/ would annihilate the largest part of their system).
/>>/
/>>/ Chris.
/>>/
/>>/ Luca Bellucci wrote:
/>>>/ / Hi Chris,
/>>/ />/ thank for the suggestions,
/>>/ />/ in the previous mail there is a mistake because
/>>/ />/ couple-moltype = SOL (for solvent) and not "Protein_chaim_P".
/>>/ />/ Now the problem of the load balance seems reasonable, because
/>>/ />/ the water box is large ~9.0 nm.
/>>/ /
/>>/ Now your outcome makes a lot more sense. You're decoupling all of
the />>/ solvent? I don't see how that is going to be physically stable
or terribly /
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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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