[gmx-users] single vs double precision issues

[David van der Spoel]

Adrien Leygue wrote:
> Dear Gromacs users,
> 
> I am experiencing several problems which all seem to relate to single
> vs. double precision.
> 
> 1-) I am doing simulations of a liquid crystal system using a custom
> force field but whenever I try to run them in parallel they all crash
> after some time (238 ps) unless I run them in single precision. The
> error message tend to vary but it is usually something like:

please run tpbconv_d -f -s -e -time 230 -o test.tpr

test whether this tpr crashes in double but not in single, and if it 
still crashes please submit a bugzilla.

Have you done make distclean between compilations?


> 
> 2-) I am also doing simulations of coarse grained molecules using
> virtual sites and home-made tabulated potentials (using several
> table_X_Y.xvg files). I haven't tried parallel runs. These simulations
> run prefectly in double precision but whenerver I try to go to single
> precision they crash almost immediately (prior energy minimization is
> performed in double precision). I have tried to re-run some energy
> minimization on the system in single precision but this stops
> immediately as well. Looking at the output I see huge forces and
> potential energy which are not present in double precision. However if
> I remove all non-bonded interactions (I do not have charges) in the
> topology file the energy minimization works fine in single precision.
> 
> I can however simulate a LJ fluid using any of the above tabulated
> potential. I assume there must be some coupling between constraints,
> virtual sites, and tabulated potentials but then why does it work in
> single precision.
The spacing in single precision tables is usually different than in 
double, but this should be taken care of automatically.

Again if you have a tpr that crashes in single but not in double then 
you are welcome to submit a bugzilla.



> 
> I welcome any help or suggestion on how to investigate these issues. I
> haven't attached any file (mdp, topology,...) but I can send them.
> 
> Thanks a lot for your help.
> 
> 
> Adrien.
> 


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se