Can you try installing the latest OpenMPI and use that instead? I am seeing all sorts of sensitivity to MPI libraries and even specific builds of them.
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Sunday, December 05, 2010 11:13
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] more pmemd.cuda.MPI issues
Hi Ross,
A couple differences between our config.h files. It doesn't appear that you
set MPI_HOME. Where you have -I/include, I have
-I/usr/local/mvapich2-1.2-intel-ofed-1.2.5.5/include . Also, I set
-DNO_NTT3_SYNC, would this break things? Using my config.h file, I'm
getting 20 ns/day in serial (compared to your 23), and in parallel, I was
getting junk at a rate of ~35 ns/day, which is considerably different than
your 23.
I'm trying again without -DNO_NTT3_SYNC, but I'm curious as to what affect
not setting MPI_HOME has on your build, although the fortran compiler should
be picking up the mpif.h includes... Is MPI_HOME completely unnecessary for
pmemd?
Thanks!
Jason
On Sat, Dec 4, 2010 at 11:33 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jason,
>
> Works fine for me. Files I used to build along with my environmental config
> files are attached.
>
> I did.
>
> tar xvjf AmberTools-1.4.tar.bz
> tar xvjf Amber11.tar.bz2
> cd $AMBERHOME
> wget http://ambermd.org/bugfixes/AmberTools/1.4/bugfix.all
> patch -p0 < bugfix.all
> rm -f bugfix.all
> wget http://ambermd.org/bugfixes/11.0/bugfix.all
> wget http://ambermd.org/bugfixes/apply_bugfix.x
> chmod 755 apply_bugfix.x
> ./apply_bugfix.x bugfix.all
> cd AmberTools/src/
> ./configure -cuda -mpi intel
> cd ../../src
> make cuda_parallel
>
> cd ~/
> mkdir parallel_fail
> cd parallel_fail
> tar xvzf ../parallel_fail.tgz
>
> qsub -I -l walltime=0:30:00 -q Lincoln_debug
>
> cd parallel_fail
>
> mpirun -np 2 ~/amber11/bin/pmemd.cuda.MPI -O -p hairpin_0.mbondi2.parm7
> -ref
> hairpin_0.mbondi2.heat.rst7 -c hairpin_0.mbondi2.heat.rst7 </dev/null
>
> Output file is attached.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Jason Swails [mailto:jason.swails.gmail.com]
> > Sent: Saturday, December 04, 2010 3:21 PM
> > To: AMBER Developers Mailing List
> > Subject: [AMBER-Developers] more pmemd.cuda.MPI issues
> >
> > Hello,
> >
> > I ran a GB simulation on NCSA Lincoln using 2 GPUs with a standard
> nucleic
> > acid system, and every energy term was ***********. Running in serial,
> all
> > results were reasonable. I've attached the mdin, restart, and prmtop
> files
> > for this error.
> >
> > All the best,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Dec 05 2010 - 11:30:04 PST
