[gmx-users] problem with g_cluster
feenstra at few.vu.nl
Tue Jun 21 17:57:46 CEST 2005
sridhar at cdfd.org.in wrote:
> Can anybody help me out from the following problem?
> I am using g_cluster to cluster my trajectory of 20000 structures
> (20000ps). I am using the matrix file as input using option -dm. The
> program gave error indicating memory fault initially. Later I ran the same
> program using -skip 1000 option, thereby effectively reading only 20
> structures, to check if it runs. Surprisingly the same problem repeats
> even with this option.
20001^2 = 400040001 with 4 bytes per real makes 1600160004 Gb of memory
for reading your matrix file. That pretty much uses up what you have.
The -skip option is for the trajectory, not for the matrix. You may be
able to 'trim' the matrix in the same fashion using xpm2ps, but it may
not work, and it may be faster to generate the 20x20 matrix separately
(for testing, that is).
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