Re: [AMBER-Developers] more pmemd.cuda.MPI issues

From: Ross Walker <>
Date: Sat, 4 Dec 2010 20:33:13 -0800

Hi Jason,

Works fine for me. Files I used to build along with my environmental config
files are attached.

I did.

tar xvjf
tar xvjf Amber11.tar.bz2
patch -p0 < bugfix.all
rm -f bugfix.all
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

> -----Original Message-----
> From: Jason Swails []
> 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,
> results were reasonable. I've attached the mdin, restart, and prmtop
> for this error.
> All the best,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032

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Received on Sat Dec 04 2010 - 21:00:03 PST
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