[gmx-users] Numerical Stability of Gromacs Implementation

Mon Aug 25 20:36:50 CEST 2014

> Date: Fri, 22 Aug 2014 17:05:31 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Numerical Stability of Gromacs Implementation
> Message-ID:
>         <CAMNuMASKYJP_HnVtPWykP9VkMnQczc+YKD1M=DJOMs72crQd8A at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Aug 22, 2014 4:49 PM, "Johnny Lu" <johnny.lu128 at gmail.com> wrote:
>>
>> 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.
>
> 6.1 was released 7 years ago, but if you have a functional xlc, then you
> should be able to build GROMACS. It won't run fast, though.
>
>>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.
>
> It doesn't.
>
>> Somehow, gcc can't find affinity support on aix ld, so I specified that in
>> the job script of llqueue.
A recent version of gcc (~4.7) for aix is available through Gentoo Prefix:
<https://www.gentoo.org/proj/en/gentoo-alt/prefix/>
Once you have bootstrapped Gentoo Prefix on your AIX machine, you will
most likely be able to use the Gromacs package (4.6.6 or 5.0) therein!

Cheers,

Christoph

>> 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.
>
> Not surprising, that Intel hardware has been the target of a lot of
> optimization.
>
> Mark
>
>> 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
>> > > > >
>> > > > > * Please search the archive at
>> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > > > posting!
>> > > > >
>> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > > > >
>> > > > > * For (un)subscribe requests visit
>> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> > or
>> > > > > send a mail to gmx-users-request at gromacs.org.
>> > > > >
>> > > > --
>> > > > Gromacs Users mailing list
>> > > >
>> > > > * Please search the archive at
>> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > > posting!
>> > > >
>> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > > >
>> > > > * For (un)subscribe requests visit
>> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
>> > > > send a mail to gmx-users-request at gromacs.org.
>> > > >
>> > > --
>> > > Gromacs Users mailing list
>> > >
>> > > * Please search the archive at
>> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > > posting!
>> > >
>> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> > > * For (un)subscribe requests visit
>> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > > send a mail to gmx-users-request at gromacs.org.
>> > >
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-request at gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

-- 
Christoph Junghans
Web: http://www.compphys.de