Hi Qi,
You probably don’t have enough memory in your machine to run the simulation.
Thus it is probably swapping like crazy. You either need to buy more memory
or find a machine with more memory. You might also consider getting a
development allocation of 30,000 SUs on the NSF’s SGI Altix at NCSA
(Cobalt). This sort of machine is ideal for such simulations.
See: https://pops-submit.teragrid.org/
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Qi Yan
Sent: Wednesday, May 07, 2008 11:26 AM
To: amber.scripps.edu
Subject: AMBER: nmode: number of atoms limitation
Hi,all:
I'm using amber9 to do nmode analysis. The atoms in my system are 8454 which
are more than maxatom=8000 written in sizes2.h.
Therefore I did some modification as below
parameter (memdrv=10000000)
parameter (maxatom=9000)
parameter (maxint=500)
parameter (maxvec=500)
parameter (maxdih = 55000)
parameter (maxdia = 35000)
parameter (maxinb = 90000)
parameter (maxbon = 26000)
parameter (maxbnh = 20000)
parameter (maxang = 30000)
parameter (maxanh = 30000)
and then I recompiled nmode. Actually, nmode can work after this
modification, but when I check the process of CPU, I found that %CPU is ~4
which is too small and %MEM is ~90 which is very high. The nmode with 8454
atoms has been running for a whole day and I still can not get result. When
I use a system with 3244 atoms to test this recompiled system, it worked
very well and I can get the result within 20 minutes.
Does anybody know what is the reason?
Thanks in advance,
Qi
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Received on Sun May 11 2008 - 06:07:16 PDT
