Amber12 with AmberTools13 on CentOS 6

This is a very quick note for install on your own small cluster or single server. If you need more information, please leave a comment.

The destination is /opt/local/amber12 and the shell is /bin/bash.

# yum install libXdmcp-devel python-devel

# mkdir -p /opt/local
# tar jxf AmberTools13.tar.bz2 -C /opt/local
# tar jxf Amber12.tar.bz2 -C /opt/local

# export AMBERHOME=/opt/local/amber12

# cd $AMBERHOME
# ./update_amber --update

Update once again due to the update of update.py.

# ./update_amber --update

Serial version

Configure, compile, install, and test.

# ./configure gnu
# make install
# make test.serial

There are 5 file comparisons failed. However,  they seem to be bugs which are fixed with update.21 (published on Nov. 4, 2013) of AmberTools13 without updates to the saved test output files (run on Mar. 19, 2013).

Parallel version

Install and active required and optional packages.

# yum install openmpi-devel blacs-openmpi-devel blacs-openmpi-static ga-openmpi-devel ga-openmpi-static hdf5-openmpi-devel hdf5-openmpi-static scalapack-openmpi-devel scalapack-openmpi-static mpi4py-openmpi
# module load openmpi-x86_64

Configure and install.

# cd $AMBERHOME
# make clean
# ./configure -mpi gnu
# make install

Test.

# export DO_PARALLEL="mpirun -np 16"
# make test.parallel