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

From: Gustaf Olsson <>
Date: Sun, 28 Apr 2019 21:12:38 +0000

I did some spring cleaning and ran through the installation again. This time the serial tests went a lot better.

Finished test suite for AmberTools at Sat Apr 27 21:41:50 CEST 2019.

        2430 file comparisons passed
           4 file comparisons failed ( 4 ignored)
           0 tests experienced errors
    Test log file saved as /amber18/logs/test_at_serial/2019-04-27_20-44-38.log
    Test diffs file saved as /amber18/logs/test_at_serial/2019-04-27_20-44-38.diff

I don't know what may have been different this time, as I already have

test -f $AMBERHOME/ && source $AMBERHOME/

Added to my .profile, just happy it worked this time around.

Using the "homebrew" installed version of openMPI 4.0.1 results in a finished compilation of amber:

$ ./configure -macAccelerate -mpi clang
$ make install

    Installation of AmberTools19 MPI is complete at Sat Apr 27 21:54:55 CEST 2019.

I tried the following after "removing" the homebrew version of openMPI:
$ cd $AMBERHOME/AmberTools/src/
$ wget
$ tar xvf openmpi-4.0.1.tar.gz
$ nps=$(sysctl -h hw.ncpu | awk '{print $2}')
$ ./configure_openmpi -np $nps gnu

Which resulted in the following error:
    ld: library not found for -levent
    collect2: error: ld returned 1 exit status
    make[2]: *** [] Error 1
    make[1]: *** [install-recursive] Error 1
    make: *** [install-recursive] Error 1

Meaning that I could not get the configure_openmpi script to properly install openMPI from source using clang. As the homebrew version seemingly managed to compile sander.MPI I did not dig into solving this or finding the cause either.

I do have to say "seemingly" as I cannot run the "make test" as it triggers something anoying. This is, as far as I can figure out, not in the openMPI as I have now tried to different sources of openMPI, but rather in macOS itself. If I have my firewall active I get one popup for every test asking for permission to use the internet, to many to accept in any reasonable time. If I turn my firewall off, all the test fail silently and instantaneously. I've seen this before on different versions of macOS and AT as well though I cannot remember how I managed this issue before it right now.

Anyway, everything seems to be working right now, except for the clang compatibility issues with the -openmp flag for the cpptraj parallel netcdf stuff and as everything seems to work without issues (exept for MPI make test) using gcc8 and the configure_openmpi script, I am just pretty pleased right now.

Thank you for all the feedback from all and a fantastic product.
Have a fantastic rest of your day
// Gustaf

Från: David Case <>
Skickat: den 28 april 2019 18:49:13
Till: AMBER Mailing List
Ämne: Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang

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.


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