On Aug 22, 2014 4:49 PM, "Johnny Lu" <johnny.lu...@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. > 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.abra...@gmail.com> > wrote: > > > On Thu, Aug 21, 2014 at 7:59 PM, Johnny Lu <johnny.lu...@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.abra...@gmail.com> > > > wrote: > > > > > > > On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu <johnny.lu...@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? 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