Yes, you would have to use sander.MPI if you plan to run in parallel and you would configure the build in the way you say.
If there is a problem in the configuration step you would need to provide all of the output from configure, tell us what the exact command line was and also what operating system version and compiler version you are using. Only then will it be possible for the developers to find out what was going wrong.
________________________________________
From: Sreemol G [sreemolinfo.gmail.com]
Sent: 04 April 2016 11:39
To: AMBER Mailing List
Subject: Re: [AMBER] General question
I'm not using sander.MPI. To use this do we need to configure using -mpi
while installing amber??? I have tried "configure -mpi gnu" but I got
error "fftw-3.3 configuration failed"
On 04-Apr-2016 3:47 pm, <hannes.loeffler.stfc.ac.uk> wrote:
> There is no OpenMP version of sander. It may be a good idea to read
> through the first chapter of the manual to understand the build procedure.
>
> If you want to run sander in parallel you have to make the MPI version and
> run it according to the MPI library you are using, typicall through a
> program called "mpirun" (but may also be a very different name, see the
> respective documentation).
>
> I think MDOUT always tells you how many nodes you use when you use
> sander.MPI. Are you sure that you were using the right executable and are
> calling it correclty?
>
> ________________________________________
> From: Sreemol G [sreemolinfo.gmail.com]
> Sent: 04 April 2016 10:57
> To: AMBER Mailing List
> Subject: Re: [AMBER] General question
>
> I have uninstalled that program and reinstalled again. In the second time i
> used -openmp flag instead of -mpi. After this I was not able to run make
> test. It is giving this error
> "[root.Kronos amber14]# make test
> make: *** No rule to make target 'test.openmp', needed by 'test'. Stop."
>
>
> On Mon, Apr 4, 2016 at 12:38 PM, <hannes.loeffler.stfc.ac.uk> wrote:
>
> > Have you compiled and are you running sander.MPI?
> > ________________________________________
> > From: Sreemol G [sreemolinfo.gmail.com]
> > Sent: 04 April 2016 07:47
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] General question
> >
> > I'm using sander for running simulation.. I already checked mdout file
> but
> > I didn't find line "Running AMBER/MPI version on 4 nodes" in mdout
> file.
> > If I want to run the program in parallel what should I do???
> > Both sander and pmemd report what version is running and how many
> "nodes"
> > have been used. Look into the MDOUT file.
> >
> > ________________________________________
> > From: Sreemol G [sreemolinfo.gmail.com]
> > Sent: 04 April 2016 07:04
> > To: AMBER Mailing List
> > Subject: [AMBER] General question
> >
> > Hi all,
> >
> > Can anyone tell me the command to check whether amber simulation
> > is running in parallely in all core (N=4). For running 500ps simulation
> it
> > took almost 19 hrs of wall clock time. Since, I want to check whether its
> > running in serial or parallel.
> > _______________________________________________
> > 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
> > _______________________________________________
> > 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
> >
>
>
>
> --
> With kind regards,
> G. Sreemol
> M.Tech (Computational Biology)
> Anna university
> Chennai.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 04 2016 - 04:00:04 PDT
