I might be wrong here, as I haven't been able to play around with AMBER 12,
but I believe that when using the GPU, all the work is done on the GPU,
hence only 1 cpu per 1 gpu is ever used (the cpu just acts as an overseer
of sorts). So you won't be able to get a benefit from all those CPU
cores.
~Aron
On Tue, Apr 17, 2012 at 10:37 PM, Vijay Manickam Achari <
vjrajamany.yahoo.com> wrote:
> Thanks for Dac and Jason.
> I could install the AMBER12 GPU version successfully.
>
> Well now I have another question to ask.
> Our GPU simulation box have 2 CPUs (each with 12 cores, so total 24 cores)
> and 4 units of GPU.
>
> What I want to know is how to submit job with choosing lets say 12 cores
> of cpus and 2 units of GPU? We dont use PBS or any other job scheduler
> package yet. I would like to know how to submit job without scheduler?
>
> Thanks in advance.
>
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <
> amber.ambermd.org>
> Sent: Wednesday, 18 April 2012, 2:38
> Subject: Re: [AMBER] error installing Amber12-gpu version
>
> On Tue, Apr 17, 2012 at 12:06 PM, Vijay Manickam Achari <
> vjrajamany.yahoo.com> wrote:
>
> > Hi Jason,
> >
> > Thanks for the reply.
> > For my surprise, I still get the same error even after I run the
> > installation start from beginning.
> > The problem occur when I try to compile at
> > Building CUDA-enabled Amber in parallel
> > as described in the website you mentioned above.
> >
> > Is there any other way to fix this issue?
> >
>
> This is because old versions of OpenMPI don't support the features that
> pmemd.cuda.MPI require. As a result, you'll need to upgrade to a newer
> OpenMPI (try the 1.5 series), or switch to something like mpich2 that
> supports them.
>
> HTH,
> Jason
>
>
> > Regards
> >
> >
> > Vijay Manickam Achari
> > (Phd Student c/o Prof Rauzah Hashim)
> > Chemistry Department,
> > University of Malaya,
> > Malaysia
> > vjramana.gmail.com
> >
> >
> > ________________________________
> > From: Jason Swails <jason.swails.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Sent: Tuesday, 17 April 2012, 2:53
> > Subject: Re: [AMBER] error installing Amber12-gpu version
> >
> > As Dave mentioned, the problem is that the MPI libraries can't be found
> in
> > any directories listed in LD_LIBRARY_PATH. I have updated the procedure
> on
> > http://jswails.wikidot.com/installing-amber12-and-ambertools-12 to
> reflect
> > this new instruction.
> >
> > HTH,
> > Jason
> >
> > On Mon, Apr 16, 2012 at 9:19 AM, David A Case <case.biomaps.rutgers.edu
> > >wrote:
> >
> > > On Mon, Apr 16, 2012, Vijay Manickam Achari wrote:
> > >
> > > >
> > > > I tried to compile the serial version of amber12 and I installed
> > > > openmpi-1.5.4. from Ambertools/src by executing ./configure-openmpi
> > > > script. All the installation went on smoothly.
> > > >
> > >
> > > > Then in execute 'make install' command to install amber12 parallel
> > > > version and I got stuck again. The errors are as below;
> > >
> > > > /usr/local/apps/amber12/bin/yacc -d nabgrm.y
> > > > /usr/local/apps/amber12/bin/yacc: error while loading shared
> libraries:
> > > libmpi.so.1: cannot open shared object file: No such file or directory
> > >
> > > Does your LD_LIBRARY_PATH variable include $AMBERHOME/lib? Or have you
> > set
> > > MPI_HOME to $AMBERHOME? Also, make sure that "which mpicc" returns the
> > > executable in $AMBERHOME/bin.
> > >
> > > ...good luck...dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Apr 17 2012 - 20:00:06 PDT
