I am trying to do some nmode calculations with nab (mpinab) on a system of
11,795 atoms.
>From what i understand, the nmode calculations would calculate a Hessian of
3Nx3N elements, and each element would take 8 bytes.
Therefore, my system of 11,795 atoms, 35,385 coordinates, and 1.25 million
matrix elements would need ~10 GB of memory. However, my testing on
supercomputer nodes with 48 GB of physical memory have been confusing. Some
of these jobs fail once they pass to the Newton Raphson part of the
calculation and memory requirements exceed 48 GB. However some of my jobs
are successful in completing a couple iterations of NR minimization before
walltime runs out. When monitoring these successful jobs, i see that they
are using ~211 GB of memory to complete these calculations.
Is my estimation of required memory off by ~200 GB or is there a potential
problem with the mpinab executable i am using?
Thanks for your help,
ryan
input file, nmode_complex.nab:
molecule m;
float x[35385], fret;
m = getpdb("../../../com1.pdb");
readparm(m, "../../../complex.prmtop");
getxyz("../../../snaps/BigD_2_1_com.crd.1",11795,x);
mm_options("cut=999.0, ntpr=1, nsnb=99999, diel=C, gb=1, dielc=1.0");
mme_init(m, NULL, "::Z", x, NULL);
setxyz_from_mol(m, NULL, x);
//conjugate gradient minimization
conjgrad(x,3*m.natoms,fret,mme,0.001,0.001,20000);
//newton-raphson minimization
newton(x,3*m.natoms,fret,mme,mme2,0.0000001,0.0,1000);
//get normal modes
nmode(x,3*m.natoms,mme2,0,0,0.0,0.0,0);
batch execution:
$AMBERHOME/bin/mpinab -o nmode_complex nmode_complex.nab
mpiexec ./nmode_complex > nmode_com1.out
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Received on Mon Dec 10 2012 - 10:00:02 PST
