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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--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
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Received on Mon Apr 04 2016 - 03:30:05 PDT
