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.
> > _______________________________________________
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> >
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> >
>
>
>
> --
> With kind regards,
> G. Sreemol
> M.Tech (Computational Biology)
> Anna university
> Chennai.
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Received on Mon Apr 04 2016 - 04:00:03 PDT
