AMBER Archive (2005)

Subject: Re: AMBER: mpirun sander8 problem

From: S. Frank Yan (syan_at_gnf.org)
Date: Thu Feb 24 2005 - 10:30:23 CST

They're just the test cases in the package. For example, the cytosine
and dhfr test cases.

Guanglei Cui wrote:
> Hi, Frank
>
> How many molecules are there in your system? What kind of simulation are
> you running? Can you upload your input file?
>
> Guanglei
>
> S. Frank Yan wrote:
> > Hi all,
> >
> > I ran many test cases. When single CPU is used (mpirun -np 1), sander
> > runs fine. But when two CPUs are used, sander hangs right before:
> >
> > | Atom division among processors:
> > | 0 1271
> >
> > Only the sentence:
> >
> > Number of triangulated 3-point waters found: 0
> >
> > is in the output file.
> >
> > The processes go on though without any additional output and it doesn't
> > stop. Any idea what might have caused this problem?
> >
> > Thanks,
> > Frank
> >
> >
> >
> >
> >>-----Original Message-----
> >>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
> >
> > Behalf
> >
> >>Of Carlos Simmerling
> >>Sent: Wednesday, February 23, 2005 5:05 AM
> >>To: amber_at_scripps.edu
> >>Subject: Re: AMBER: mpirun sander8 problem
> >>
> >>does the mpi code work for a single processor? are you sure that the
> >>input you are using works properly? mpi runs do not always give the
> >>proper error message if the error occurs on a cpu other than the
> >
> > master.
> >
> >>S. Frank Yan wrote:
> >>
> >>
> >>>Hi,
> >>>
> >>>I was able to recompile MPI using gcc and ifort with ch_shmem and
> >>>compiled sander8 on a 2-CPU Linux box. I tested it with the dhfr
> >>>testing case. The program runs in parallel but it stops spitting out
> >>>output after "3. ATOMIC COORDINATES AND VELOCITIES... " section. I
> >
> > can
> >
> >>>see the CPU usage is around 100% for both CPUs, but sander seems to
> >
> > be
> >
> >>>stuck in a loop. Using mpirun -v yields "running ../../exe/sander on
> >
> > 2
> >
> >>>LINUX smp processors". Does anyone have the same experience like
> >
> > this?
> >
> >>>Thanks a lot.
> >>>Frank
> >>>
> >>>
> >>>
> >>>
> >>
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