So for this one I am using Homebrew GCC 8.3.0_2 and the official openMPI 4.0.1 installed using the $AMBERHOME/AmberTools/src/configure_openmpi script. Using the homebrew version of openMPI 4.0.1 results in an “architecture not supported” error and ld issues so I assume this has to do with the build being based on clang and not gcc, though this is a guess.
$ sudo xcode-select --install
# As I have already done this, I cannot comment on the step being needed or not
$ open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
$ ln -s /usr/local/bin/gcc-8 /usr/local/bin/gcc && ln -s /usr/local/bin/g++-8 /usr/local/bin/g++ && ln -s /usr/local/bin/c++-8 /usr/local/bin/c++
# TO UNDO: rm /usr/local/bin/gcc /usr/local/bin/g++ /usr/local/bin/c++
$ tar xvf AmberTools19.tar.bz2
$ export AMBERHOME=/path/to/amber18
$ export PATH=${AMBERHOME}:$PATH
$ cd $AMBERHOME
$ ./configure -macAccelerate gnu
# For macOS default BASH/SH users - Otherwise (csh/tcsh…) follow the instructions printed
$ echo “test -f /path/to/amber18/amber.sh && source /path/to/SOFTWARE/amber18/amber.sh” >> $HOME/.profile
# Replacing /path/to with the correct path as outputted by the configure script.
$ make install
—> Installation of AmberTools19 serial is complete at Sat Apr 27 15:20:30 CEST 2019.
$ make test
—> Finished test suite for AmberTools at Sat Apr 27 16:17:37 CEST 2019.
—>
—> 2432 file comparisons passed
—> 2 file comparisons failed ( 2 ignored)
—> 0 tests experienced errors
—> Test log file saved as /amber18/logs/test_at_serial/2019-04-27_15-21-34.log
—> Test diffs file saved as /amber18/logs/test_at_serial/2019-04-27_15-21-34.diff
$ cd $AMBERHOME/AmberTools/src
$ sysctl -h hw.ncpu
$ wget
https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.1.tar.gz
$ tar xvf openmpi-4.0.1.tar.gz
$ ./configure_openmpi -np 4 gnu
$ cd $AMBERHOME
$ make clean
$ ./configure -macAccelerate -mpi gnu
$ make install
—> Installation of AmberTools19 MPI is complete at Sat Apr 27 18:56:43 CEST 2019.
# !!! CANNOT RUN TEST
# export DO_PARALLEL="mpirun -np 4"
# make test
$ ./configure -macAccelerate -openmp gnu
$ make install
—> Installation of AmberTools19 OpenMP is complete at Sat Apr 27 19:12:53 CEST 20
Hope someone finds this useful and wish you all a fantastic rest of your weekend!
// Gustaf
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Received on Sat Apr 27 2019 - 12:00:02 PDT
