From owner-chemistry@ccl.net Wed Feb 1 17:36:00 2006 From: "Jozsef Csontos jozsefcsontos~~creighton.edu" To: CCL Subject: CCL: PES vs. # of CPUs Message-Id: <-30748-060201171851-9495-pZU31dnbQER9LD3vfBYgSQ|-|server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 01 Feb 2006 14:57:14 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos]|[creighton.edu] Hi, my short question is: is it possible to get different optimized final structures using the same input and architecture, OS, software (and so on), but different number of processors? My longer comments are: I understand that we use approximations (in QM and in life too:) and there might be error accumulations and our number representation depends on the hardware etc. But, I'm quite sure the answer is no. Maybe I'm wrong, so I tell you the story. The story: I have been using a commercial quantum package, which uses the MPI libraries (MPICH) for parallelization. I was about to map the PES of several tripeptides in water using DFT. (Of course, the molecules are flexible and the PESs are flat and more more approximations) I'm not totally surprised that the results are different on 1 node with 1 processor and 6 node with 6 processors. (In the first case there is no MPI and in the second one there is.) Interestingly, the results are different on 3 nodes with 6 processors (2CPUs/node) and on 6 nodes with 6 processors (1CPU/node), in addition the calculation using the previous 6 processor configuration (2CPUs/node) differs from the 4 CPUs config (2CPUs/node) ones. The energy differences between the structures are small about 1kcal/mol, however, the rmsd is quite large 1.9 Angstrom considering heavy atoms and one of these structures is the deepest minimum on the PES, so these structures belong to the low energy region. I haven't checked all the structures whether they are minima or other stationary points. I guess this is not related to the question, but if all of them were minima my question would be louder. I'm wondering what your opinions are? Best wishes, Jozsef -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE