Hi everyone,
I was hoping you could help me with a further problem regarding Amber20. I've managed to compile Amber20, and I'm able to run sander with Plumed; however, when I try running pmemd.MPI with sander (once trying to compile it with and without the plumed library), I have to specify the PLUMED_KERNEL variable. In addition, once I do that, I get an error message saying that plumed isn't compiled for usage with MPI. However, I've followed all of the instructions given on the Amber website, and I am stuck as to how I can get Amber20 to use plumed with pmemd.MPI. Could you help please?
Best wishes
Amanda
________________________________
From: Amanda Buyan <Amanda.Buyan.anu.edu.au>
Sent: 28 July 2020 08:50
To: AMBER Mailing List <amber.ambermd.org>; david.case.rutgers.edu <david.case.rutgers.edu>
Subject: Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
Hi DAC,
I just checked, and I've got cmake in my path (under /usr/local/bin, which I have added to my PATH in my .bashrc file, and I had to add it in the run_cmake as well). It's also version 3.14.5, if that helps.
Best wishes
Amanda
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 27 July 2020 23:10
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
On Mon, Jul 27, 2020, Amanda Buyan wrote:
>
>I'm currently having trouble with compiling even the serial version of
>Amber20 on the second cluster of ours. When I run the "make install"
>command (following the same procedure as on the other cluster), I get the
>following error:
>
>---
>Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
>Detecting Python version... 3.6
>Detecting Python root... /usr
>Unicode/ICE support for Boost.Regex?... not foud.
>Generating Boost.Build configuration in project-config.jam...
>
>Bootstrapping is done. To build, run:
>
>./b2
>
>to adjust configuration, edit 'project-config.jam'.
>
>[ Further information about boost.build]
>
>/bin/sh: cmake: command not found
I think this is the problem: you have to have cmake in your PATH: it's not
enough to just specify the location in the run_cmake script.
This is not documented in our installation instructions. And, it might not be
the only problem. But check on the second cluster to see if cmake is in your
PATH.
...dac
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Received on Wed Jul 29 2020 - 17:00:02 PDT
