Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang

From: David Case <>
Date: Sun, 28 Apr 2019 16:49:13 +0000

On Sat, Apr 27, 2019, Gustaf Olsson wrote:
>The parallell installation using external and global openMPI version
>4.0.1. also proceeded with some warnings though without errors.

A note: Amber only supports openMPI version 4 if it was built with the
"--enable-mpi1-compatibility" flag. This is unlikely to have been
specified in most "official" or "global" versions. If that is the case,
then you can use the configure_openmpi script in AmberTools/src, which
sets this flag.

Other notes:

1. The "" script sets your PYTHONPATH variable, which is needed
for python programs installed with AmberTools. Here is what you can put
in a .bashrc (or similar) file:

export AMBERHOME=<....>
test -f $AMBERHOME/ && source $AMBERHOME/

2. I'm not familiar with firewall protections in openMPI: that may be a
feature turned on in your openMPI that we haven't yet tested.

3. We are aware that some sites have trouble with the PerlMol extension
required for FEW. But we haven't figured out yet what the fix is: so
far, the people who see this problem (it never shows up for me) have not
been able to either figure out what is different about their
installations, or to propose a fix.


AMBER mailing list
Received on Sun Apr 28 2019 - 10:00:02 PDT
Custom Search