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
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Received on Tue Apr 17 2012 - 20:00:04 PDT
