[gmx-users] Numerical Stability of Gromacs Implementation

[Johnny Lu]

it has many (relatively) power7 cores and aix 6.1.0.0 with no gpu, and I
compiled single precision gromacs 4.6.6 with open mp on it.
I tried xlc or mpcc for 30+ times. The gcc on it doesn't support openmp,
and I compiled another one with openmp, and also gnu cmake.
Linker is aix ld, with -lmass, and -lm flags. I am not sure if the mass
library helped in compilation of fftw3 library.
Somehow, gcc can't find affinity support on aix ld, so I specified that in
the job script of llqueue.
May be next time I would try the mass simd library(-lmass_simdp7) or vector
library (-lmassvp4)
(http://www-01.ibm.com/support/docview.wss?uid=swg27005375)

Somehow, 24 intel xeon cpu (compiled with intel compiler, and mkl library)
seems 4 times faster than 32 power7, when I run gromacs 4.6.6.


On Thu, Aug 21, 2014 at 7:28 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Thu, Aug 21, 2014 at 7:59 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > Sorry for asking this. Is it possible for me to get some references about
> > the claims of instability of gromacs simulations, and their debunk?
> >
>
> Not really. You can find a paper from some of the Desmond authors that
> correctly observes some issues in GROMACS 3.x. People occasionally refer to
> it here as if it is current news. These issues are long fixed, but not
> worth writing about - journal articles should be about delivering quality
> science. More commonly, an issue would be handled via private email, though
> even these are rare. Overall, the biomolecular MD community is quite good
> at finding problems with their own and each other's algorithms and
> implementations and getting them fixed constructively. People saying
> "someone said x was bad but gave me no details" need to talk to the
> someone, not just the authors of x ;-) If people start being evasive or
> secretive about possible problems with their code... be concerned.
>
> From the few papers that I read, I guess algorithms of molecular dynamics
> > do not treat all observables equally well.
> > Some old papers say that the velocity in velocity verlet is not
> symplectic,
> > but rather follows some shadow hamiltonian or generalized equipartition
>
> theorem.
> >
>
> This is common to all methods with a finite time step - see
> http://en.wikipedia.org/wiki/Energy_drift. There are certainly a variety
> of
> ways of estimating the velocity with common integrators, and they have
> different quality attributes. You can read about how GROMACS handles this
> in the manual.
>
> Then another one mentioned force splitting can reduce the resonance effect
> > caused by integrator.
> > That said, very few papers talk about this.
> >
>
> There are lots of papers that discuss details of multiple time-stepping
> algorithms that seek to deal with this issue directly.
>
>  I don't know much about the effect of MD on the observables that I try to
> > look at.
> >
>
> It's not an easy topic - generating converged sampling to assess whether an
> integration scheme correctly samples a complex observable is still a
> non-trivial matter. That needs to happen before questions of "how much
> algorithmic energy drift is acceptable" can be satisfactorily addressed.
> Until then, claims of "my energy conservation is better than yours" need to
> be considered alongside "my number of independent converged-ensemble
> samples is better than yours."
>
>  And, sorry for replying this late, I have been installing gromacs on aix
> > for a week.
> > Compiling gcc took 3 days of computer time.
> >
>
> Seriously, don't bother. I don't think there is any system that would have
> AIX, with no gcc package available, and which GROMACS 5.0 would run
> decently on (which would require SIMD support, which currently means x86 or
> BlueGene/Q). I'd guess your laptop will get equivalent performance.
>
> Mark
>
>
> >
> > On Thu, Aug 14, 2014 at 2:29 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu <johnny.lu128 at gmail.com>
> > wrote:
> > >
> > > > Hi again.
> > > >
> > > > Some of my friends said that gromacs had lower numerical stability
> than
> > > > amber, and occasionally has mysterious error in energy.
> > > >
> > >
> > > Show us a result and we'll discuss fixing it ;-)
> > >
> > >
> > > > Is that still true? Does the implementation of Integrator cause more
> > > > resonance effect?
> > > >
> > >
> > > Any numerical software can be used poorly. Any numerical software can
> > have
> > > bugs. Give them the same input to two implementations of the same
> > algorithm
> > > and they should give results that are similar (whatever that means in
> the
> > > problem domain).
> > >
> > >
> > > > I am trying to run NVE simulation with the single precision version,
> > and
> > > so
> > > > I guess the implementation of thermostats is not my most immediate
> > > concern
> > > > at the moment.
> > > >
> > > > I searched online, and haven't found much about numerical instability
> > of
> > > > gromacs using amber forcefield (I mean for version 4.6, which
> supports
> > > the
> > > > amber force-fields without modification.)
> > > >
> > >
> > > What do you mean by numerical stability? Should you actually be
> concerned
> > > about getting a correct physical observable? People look at energy
> > > conservation because it is easy to do, but connecting that to the
> quality
> > > of the resulting physics is non-trivial. Even if you can (say) deliver
> > > state-of-the-art energy conservation (and most packages can do this in
> > some
> > > mode), you still need to measure the price in simulation throughput
> > > incurred by running in that mode. The overall objective is to deliver
> > > science of sufficient quality with minimal time to solution. In some
> > cases,
> > > it is right to let some energy leak and let the thermostat fix it, if
> you
> > > generate many more samples by so doing.
> > >
> > > Why do people still use and paid for amber, when gromacs is free?
> > > > I look online and the number of papers that use amber is about twice
> of
> > > the
> > > > number of paper that use gromacs. There are very few papers that
> > > mentioned
> > > > both gromacs and amber.
> > > >
> > >
> > > Inertia is a big effect. You tend to adopt the package used by the
> local
> > MD
> > > expert so you have a low-latency person of whom to ask questions. They
> > tend
> > > to still use the package they used in their doctoral work, regardless
> of
> > > current technical merit, because learning to use such software well is
> > > tricky and discarding your old workflows is not a cheap proposition.
> The
> > > next biggest effect is what functionality is available, and at what
> > > performance.
> > >
> > > Mark
> > >
> > > Thank you.
> > > > --
> > > > Gromacs Users mailing list
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