Hi,
Thanks Guanglei. I shall forward your analysis to the
reflector for closure.
I have added this to the shake section of sander.me:
For parallel versions of \fIsander\fR only intramolecular atoms
can be constrained. Thus, such atoms must be in the same chain of
the originating PDB file.
Scott
On Sat, 24 Apr 2004, Guanglei Cui wrote:
> Hi, Scott
>
> I think I know what's going on with the partition error in shake. For a
> multi-molecule system, sander assumes/requires that atoms of the same
> molecule are in the same block of the PDB file (I don't remember if this
> is documented anywhere). But my PDB file has a metal ion bonded to one
> of the monomer, but this metal ion is not located in the same block as
> the monomer. This created the partition error in shake. Reordering this
> atom solved the problem.
>
> Regards,
>
> Guanglei
>
> Scott Brozell wrote:
> > Hi Guanglei,
> >
> > This indicates that a constrained pair of atoms are on different
> > processors.
> > I have slightly cleaned up the amber9/src/sander/shake.f and
> > added a more detailed error message. If this is really a bug
> > then you will probably have to trace back to the creation of the
> > ib and jb arguments.
> >
> > Scott
> >
> > ---------- Forwarded message ----------
> > Date: Fri, 23 Apr 2004 11:18:19 -0400
> > From: Guanglei Cui <cuigl.csb.sunysb.edu>
> > Reply-To: amber.scripps.edu
> > To: amber.scripps.edu
> > Subject: AMBER: partition error in shake
> >
> > Dear all,
> >
> > After I managed to get SCALI to work with AMBER8, I found I can't use
> > more than 4 CPUs for one of my systems (80,000 atoms), but it worked
> > fine with a regular DNA test case (10 base pairs). It failed because
of
> > "partition error in shake". Before I dive into shake.f, I wonder if
> > anyone has a quick guess what might be the problem. Thanks in advance.
>
Received on Wed Apr 05 2006 - 23:50:03 PDT
