AMBER16+CUDA Installation in Ubuntu 18.04 (BIONIC)
I will attempt to explain the setups involved in install amber16 +
Ambertools 17 in Ubuntu 18.04 LTS with cuda 9.0 and nvidia-driver-390
Installing Prerequisites on a fresh installation of Ubuntu 18.04 LTS
aptitude install vim
apt install csh flex patch gfortran g++ make xorg-dev bison libbz2-dev
Parallel MPI packages
apt-get install openmpi-bin libopenmpi-dev
Python packages
apt install python-numpy python-matplotlib python-scipy ipython
python-notebook cython python-dev python-pip
GNU GCC 6 Installation
Ubuntu 18.04 LTS comes with GCC 7 and AMBER16 requires GCC 6.
apt install gcc-6 g++-6
ln -s gcc-6 gcc; ln -s gcc-ar-6 gcc-ar; ln -s gcc-nm-6 gcc-nm; ln -s
gcc-ranlib-6 gcc-ranlib; ln -s g++-6 g++
ln -s /usr/bin/gfortran-6 /usr/bin/gfortran
CUDA 9.0 Installation
user.machine$ ./cuda_9.0.176_384.81_linux.run
user.machine$ echo "include /usr/local/cuda-9.0/lib64" >> /etc/ld.so.conf
user.machine$ ldconfig
add PATH and environment updates
export PATH="/usr/software/anaconda2/bin:$PATH"test -f
/usr/software/amber16/amber.sh && source
/usr/software/amber16/amber.shexport
PATH=/usr/local/cuda-9.0/bin${PATH:+:${PATH}}export
LD_LIBRARY_PATH=/usr/local/cuda/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
PNETCDF installation
#Download parallel-netcdf-1.9.0 .
user.machine$ cd parallel-netcdf-1.9.0/
user.machine$ make
user.machine$ make install
Compiling AMBER 16 and AMBERTOOLS17
user.machine$ tar xvvf /tmp/Amber16.tar.bz2
user.machine$ tar xvvf /tmp/AmberTools17.tar.bz2
user.machine$ cd /usr/software/amber16
user.machine$ ./configure gnu
user.machine$ make install
user.machine$ ./configure -mpi --with-pnetcdf /usr/software/parallel-netcdf gnu
user.machine$ make install
user.machine$ ./configure -cuda gnu
user.machine$ make install
user.machine$ ./configure -mpi -cuda --with-pnetcdf
/usr/soft/parallel-netcdf gnu
user.machine$ make install
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Received on Thu Jun 14 2018 - 10:30:01 PDT
