CCL: PES vs. # of CPUs

 Sent to CCL by: "Alex. A. Granovsky" [gran . classic.chem.msu.su]
 Jan,
 your statement is actually not always true.
     More precisely, this is true for single-point calculations.
 The problem is that almost all energy minimization algorithms are not
 numerically stable on the complicated PES having non-trivial structure,
 and initially very close "trajectories" of minimization completely
 diverges
 over time. In this case, it is almost normal situation to get different answers
 (local minima) even with single-processor runs using different binaries
 (e.g., produced by different compilers).
 Best regards,
 Alex Granovsky
 > Sent to CCL by: janl ~ speakeasy.net
 > While very small differences (truncation errors) are allowed
 > between single processor and parallel runs (they may be due to
 > some rounding errors when data are being sent between processors
 > or machines), they should be below 0.001 kcal/mol. The differences
 > 1000x larger indicate one or more:
 >   1) Bug in the program
 >   2) Bug in the compilation or compiler
 >   3) Bug in the MPICH libraries
 >   4) Faults in configuration
 >   5) Errors in communications, e.g., lost packets, or connectionless
 >      protocol (use TCP for testing, rather then UDP if you have
 >      a choice of configuration).
 >
 > Jan Labanowski
 > jkl]^[ccl.net
 >
 >
 > > -----Original Message-----
 > > From: Jozsef Csontos jozsefcsontos~~creighton.edu [mailto:owner-chemistry]^[ccl.net]
 > > Sent: Wednesday, February 1, 2006 10:52 PM
 > > To: 'Labanowski, Jan -
 > > Subject: CCL: PES vs. # of CPUs
 > >
 > > 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>
 >
 >
 >