Re: Tolerance Data 2007-1 Keygen Free Download
Chrystal Dueno
I am trying to run LAMMPS compiled with the single-precision FFTW (2.1.5) libraries on the Cray XT3, however, when I do this I get 'nan' for the long-range kspace energy on the first step and the simulation fails (please see log file at the end of this email for simulation parameters and output). I am changing FFT_PRECISION to 1 in fft3d.h. Some things I have tried:
1. I have tried this with both the apoa1 benchmark system and my own protein system. In both cases when LAMMPS is compiled with double-precision fftw libraries it runs fine but with sfftw it fails.
2. I have tried compiling with both pgi (6.1.4) and gcc (4.1.2) compilers, and also with all gcc optimization flags turned off, and 'pair modify table 0' still with the same result.
3. I also tried this on my intel core2 desktop with fftw and gcc, again, same result.
P.S. The reason that I am interested in using single-precision, is that in order to use grid spacings of 1 angstrom, the de facto standard for PME in biosimulations, I need to use a tolerance of 1e-6 for pppm. However, this results in half of the calculation being devoted to the kspace calculation, and a significant portion of that is in the FFT:
I notice that generally LAMMPS takes pppm 1e-4 as the accuracy standard, but in this case that results in a grid that is spaced at over 2 angstroms along each coordinate direction. Can pppm use a grid spacing that is 2 to 2.5 times more sparse than PME and achieve similar accuracy? I plan to look into this more closely, but I thought I would mention it here since, at a pppm tolerance of 1e-4, the FFT doesn't take up much of the calculation, hence there would be little benefit to using the single precision fft.
I've never tried to run/build LAMMPS with single-precision FFTs
so can't help you there. I don't think its a good idea if
you want 1.0e-6 accuracy since single-precision only carries
7 or 8 digits of accuracy. So it seems like you'd be close to
the edge. Paul may want to comment on PPPM vs PME
accuracy. But the general rule-of-thumb is don't worry about
the grid spacing. Rather trust the accuracy criterion you
set. If you want 1.0e-4 then PPPM in LAMMPS will choose
an appropriate grid spacing, whatever it ends up to be.
Just thought of an issue with single-precision FFTs from LAMMPS.
The FFT package (fft3d.cpp) doesn't own the data, it just
provides an interface to the FFTW library. So the storage
of all the data is in LAMMPS and is still double precision,
including how it stores complex datums. So you would have
to change data storage in LAMMPS if you expect FFTs with
floats to work instead of doubles.
Thanks Steve. Your points are well-taken. Actually, the bigger picture is that I am trying to make an apples-to-apples comparison of LAMMPS to NAMD for biomolecular simulation, inasmuch as that is possible, and NAMD uses single-precision FFTs. So I am looking to compare performance for a given level of accuracy. NAMD does not report PME accuracy directly, but I believe that I will need close to 1e-6 accuracy to approach the accuracy of PME in NAMD with a 1 angstrom grid.
Incidentally, after I wrote my original email I discovered that if I use 'kspace_style ewald' instead of pppm then the single-precision FFT works. I will dig into the code as you suggest, but if anyone has experience or comments to share (on any of these matters) they are welcome.
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