Hi Tomek –
APBS has weak parallel scaling which means that it is intended to solve bigger systems in approximately the same time as smaller ones (if the right number of processors are used). What are you trying to accomplish with this parallel calculation? If you’re analyzing a bigger system, then I would recommend leaving dime unchanged and just increasing pdime.
Laboratory Fellow and Technical Group Manager
Applied Statistics and Computational Modeling
Pacific Northwest National Laboratory
From: Tomek Wlodarski [mailto:tomek.wlodarski@...]
Sent: Monday, February 10, 2014 3:20 PM
Subject: [apbs-users] dime in mg-para
When I was running APBS for small systems, values for dime, cglen and fglen I took from pdb2pqr webserver.
Now I would like to use more than one processor, with mg-para.
So my question is: how should I change values for dime, cglen and fglen when I am transferring my system from 1 CPU simulations to e.g. 8 CPU.
Should I just divide this number of grid points by 2 (when I have pdime 2 2 2)?