----- Original Message ----- From: Sebastian Breuers <breue...@uni-koeln.de> Date: Tuesday, September 7, 2010 0:42 Subject: Re: [gmx-users] g_covar & g_anaeig problems To: gmx-users@gromacs.org
> Hey everyone, > > searching the list for the answer to a g_covar problem I've > found this post of Arne who describes the very same problem that > I encounter. > > I'm observing this problem on a linux cluster with 32GB memory > on each node. The g_covar_d application was compiled in double > precision with an intel compiler and works fine up to a number > of atoms of around 15408. In tests I could find out that above > this number +/- 48 atoms I receive the following error output: > > > Calculating the average structure ... > Last frame 50 > time 5000.000 > > Constructing covariance matrix (46368x46368) ... > Reading frame 0 > time 0.000 Segmentation fault > > Meaning a matrix over around 46224x46224 elements starts to > generate this problem. > > Did anyone encounter the same problem or does anyone has a hint > to solve this issue? Get more memory or use fewer atoms :-) The memory needs and run time will scale at least as high as the square of the number of atoms. Probably you can ignore at least your hydrogen atoms... Mark
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