Re: [AMBER] problem of srun

From: David A Case <>
Date: Wed, 29 May 2019 09:45:22 -0400

On Wed, May 29, 2019, Albert wrote:
>I am trying to compile amber 18 in a small cluster, which uses srun instead
>of mpi for the system. However, Amber cannot recognize it.

My understanding is that srun uses MPI behind the scenes. I've always
been able to configure Amber with the "-mpi" flag in the usual way, then
use srun later. Or, as an alternative, just use "mpirun" in batch
scripts, rather than "srun".

You may need to consult the srun documentation for more information.
You don't say how you tried to run configure, but you will need to know
where the underlying mpi commands are, and have them in your PATH, in
order to configure Amber in parallel.

>if I installed
>FFTW in somewhere else instead of system default path, how shall I specify
>the FFTW path?

Amber builds fftw from source inside it's directory tree, and doesn't
use a "system" FFTW. This is because our code requires various options
(like Fortran linking) that are often not present in standard
installations. (The code can find the Intel MKL interface to FFTW, but,
for now, only when Intel compilers are used). Other than that, there is
no built-in option to use some othe FFTW libraries. You'd have to edit
the configure2 script to get this, but I'm not sure what the advantage
would be.


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Received on Wed May 29 2019 - 07:00:02 PDT
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