On Thursday, November 5, 2015, Jason Swails <jason.swails.gmail.com> wrote:
>
> This doesn't seem like it should blow memory. For the unsolvated dimer,
> you have 6307*2=12614 atoms, right? The covariance matrix for that will be
> (3x)^2 = 1.432e9 doubles. At 8 bytes per number, this is about 10.7 GB of
> space needed to store the full matrix. Since it's symmetric, you need ~1/2
> of this, plus workspace (I'm not sure whether cpptraj allocates the full
> matrix or just the triangular half-matrix).
For symmetric matrices (1 mask) cpptraj allocates a half matrix (i.e.
diagonal plus upper right triangle).
-Dan
>
> When you're running in parallel, you have to add the memory requirements of
> every thread together. The quasi-harmonic analysis is always run on a
> single core, but if it runs at the same time as the PB calculations (which
> might require a large grid), it's possible that the program actually
> *needs* that much memory to run 4 threads.
>
> So start small -- run in serial without entropy=1 and see what the memory
> requirements are. Add entropy=1 back in and see how the memory requirement
> changes (just keep in mind for 15 frames you can only get 15 non-zero
> eigenvalues).
>
> HTH,
> Jason
>
> Suggestions welcomed.
> > Nic out
> > ==============
> > &general
> > keep_files=2, endframe=15, entropy=1,
> > /
> > &gb
> > igb=2, saltcon=0.100,
> > /
> > &pb
> > istrng=0.100, inp=1, radiopt=0,
> > /
> > =============
> > mpirun -np 4 --bind-to-none $AMBERHOME/bin/MMPBSA.py.MPI -O -i qha.in
> \
> > -o qha_15frames.dat\
> > -sp ../complex-wat.top \
> > -srp ../protein-wat.top \
> > -slp ../ligand-wat.top \
> > -cp ../complex.top \
> > -rp ../protein.top \
> > -lp ../ligand.top \
> > -y ../complex_prodc.mdcrd.gz \
> > -yr ../protein_prodc.mdcrd.gz \
> > -yl ../ligand_prodc.mdcrd.gz
> > --
> > ================================
> > C. Nicklaus Steussy, M.D., Ph.D.
> > Purdue University
> > [1]csteussy.purdue.edu <javascript:;>
> > ================================
> >
> > References
> >
> > 1. mailto:csteussy.purdue.edu <javascript:;>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Nov 05 2015 - 15:00:04 PST
