[gmx-users] Re: latest benchmarks (Itanium/Xeon/Opteron)
michel.cuendet at epfl.ch
Mon Jan 19 18:37:00 CET 2004
>>>>> The --disable-software-sqrt option doesn't help. I noted also that
>>>>> gromacs single precision computes wrong results (box exploding
>>>>> systematically), whereas double precision doesn't take more time and
>>>>> gives more reasonable output.
>>> This shouldn't be... What system is that? Is it reproducible, i.e. the
>>> same tpr gives different results in single and double?
My system is a big protein complex, which I'm trying to pull apart to
measure an affinity. Gromos force field, PME, Nose-Hoover. (Explosions
in single precisions also occur when no pulling is done).
Yes it is reproductible, because I ran 64 Jarzynski trajectories in
parallel, which all crashed after a few Ksteps. Running the same 64
trajectories in double precision has been stable for 3 weeks. Also,
copying the same .tpr to an alpha machine or an athlon produced behaved
results in single precision
>I think I've disabled software sqrt by default on ia64, so that
>explains the lack of effect.
In fact, I tried --enable-software-sqrt also, which has no effect either.
>To help isolate the problem, check if it occurs:
>(A) when you use gcc
It doesn't work. Compiles fine, but crashes at runtime because of a PME
>(B) when you use a lower level of optimization (e.g. -O1)
I'm gonna try this out. Tomorrow I will meet an HP guy who was
incredibly enthousiastic about trying to optimize gromacs on his
itaniums. Let's see what comes out of that ;-)
>Using the Intel Fortran compiler might give you slightly better
>performance, otherwise you'll have to wait a *little* while longer for
>the assembly loops.
Option --enable-fortran does not compile. Problem with linking.
Oh, please post these assembly loops as soon as they are ready, can't
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