Tsjerk Wassenaar wrote:
Hi,
I wonder if there a way to run g_cover in paralel in order to make
things run faster?
No. Obviously you can use -dt to reduce the number of frames you analyze.
In most cases it's not the reading of frames, but the diagonalization
of the covariance matrix that consumes most of the time.
True, such an algorithm for N atoms over F frames is either something
like O(F) or O(N^3) according to whether the I/O-and-compute phase or
the diagonalization phase dominates. Once could also reduce N by
coarse-graining the covariance matrix.
It might be
interesting to have it MPI enabled, especially since systems are
getting bigger and bigger.
Someone would have to identify a candidate MPI diagonalization algorithm
that can be readily added. That doesn't sound like a easy algorithm to
write with numerical stability :-)
ScaLAPACK http://www.netlib.org/scalapack/html/scalapack_single.html
might work - how about http://www.netlib.org/scalapack/single/pssyevd.f
? It would add further dependency to the build process, unless we
incorporated it as with BLAS and LAPACK.
Mark
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