I've tried without the wrapped boundaries, and also looked at neighbors of
the atoms listed in the mdout (i.e. H559 and O2500) still without any luck.
All the atoms are wrapped into the central image to begin with so I'd
imagine that any overlap would be apparent.
~Eric Shamay
On 3/14/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> try looking at the atom with Gmax: atom O #2500. maybe you can see
> something
> in the coordinates, or maybe the box is not large enough? have you
> tried without iwrap? I have not used that in minimization.
>
> On 3/14/07, Eric Shamay <eric.shamay.gmail.com> wrote:
> > I've had no success in running through a minimization of a system of
> water
> > and nitric acid molecules. 2670 atoms in a 30x30x30 cubic periodic box.
> >
> > I'm attaching a few files for the interested:
> > -topology
> > -input coords
> > -mdout of the run
> >
> > The input (mdin) of the run is a rather simple one:
> > -----
> > General minimization script
> > &cntrl
> > IMIN = 1,
> > IWRAP = 1,
> > NTPR = 250,
> > NTMIN = 1,
> > MAXCYC = 100000, NCYC = 3500,
> > /
> > -----
> >
> >
> >
> > the specific error I get (when running sander.MPI) is:
> > -----
> > Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
> > Failing at addr:0x7dfabde0
> > [0] func:/usr/local/lib/libopal.so.0 [0x400f5b38]
> > [1] func:[0x40000440]
> > [2] func:sander.MPI(ewald_force_+0x1a63) [0x8131d83]
> > [3] func:sander.MPI(force_+0x1270) [0x8254ed8]
> > [4] func:sander.MPI(runmin_+0x598) [0x80fdc68]
> > [5] func:sander.MPI(sander_+0x5427) [0x80f17a3]
> > [6] func:sander.MPI(MAIN__+0x14ab) [0x80e8053]
> > [7] func:sander.MPI(main+0x42) [0x806a4da]
> > [8] func:/lib/tls/libc.so.6(__libc_start_main+0xd3)
> > [0x8a5e23]
> > [9] func: sander.MPI [0x806a411]
> > *** End of error message ***
> > -----
> >
> > When running a serial version (sander) the following error is produced:
> > -----
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image PC Routine Line Source
> > sander 08103B3C Unknown Unknown Unknown
> > sander 08102E10 Unknown Unknown Unknown
> > sander 08219F37 Unknown Unknown Unknown
> > sander 080D2CA7 Unknown Unknown Unknown
> > sander 080C6B43 Unknown Unknown Unknown
> > sander 080C36D1 Unknown Unknown Unknown
> > sander 0804B1BA Unknown Unknown Unknown
> > libc.so.6 008A5E23 Unknown Unknown Unknown
> > sander 0804B0F1 Unknown Unknown Unknown
> > -----
> >
> > Changing the NCYC will allow the run to proceed until that number (i.e.
> if
> > NCYC = 500, the run crashes at 500, if NCYC = 2500, it crashes at 2500,
> > etc.) What I notice is that the energies listed in the mdout are rather
> > large, but I'm at a loss for how to reduce the initial values as I've
> got no
> > overlaps of atoms, and I've checked out the force field parameters and
> they
> > seem kosher. I've read through a number of the segfault topics on the
> > reflector that come close and it doesn't seem that anyone has come up
> with a
> > solution beyond blaming the compiler. I've been able to successfully
> > minimize a different system (similar, but all water molecules without
> any
> > nitric acid), so something tells me that this segmentation fault is
> indeed
> > system-specific: an artifact of the initial conditions and not the
> compiled
> > code.
> >
> > The system used is a dual-processor athlon (32-bit), and the amber 9
> source
> > was compiled with ifort 9.1.040. Openmpi 1.1.4 compiled with the same
> ifort.
> > Intel MKL 9.0 libraries were used.
> >
> > Any help is greatly appreciated. I'm at a loss for whether the
> installation
> > was done correctly or not, and would like to pinpoint where the problem
> may
> > be. Please feel free to ask for further information on anything I've
> > forgotten to include.
> > --
> > ~Eric Shamay
> > eric.shamay.gmail.com
> >
> >
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--
~E
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Received on Sun Mar 18 2007 - 06:07:16 PDT
