Hi,
Thanks for the instruction, I have difficulty understanding the following
steps
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
you separated ln with ";" , what do I do with each command? when I type in
the last command line, it gave me error :
user.ubuntu:~/bin$ ln -s gcc-6 gcc
user.ubuntu:~/bin$ ln -s gcc-ar-6 gcc-ar
user.ubuntu:~/bin$ ln -s gcc-nm-6 gcc-nm
user.ubuntu:~/bin$ ln -s
ln: missing file operand
Try 'ln --help' for more information.
user.ubuntu:~/bin$ ln -s gcc-ranlib-6 gcc-ranlib
user.ubuntu:~/bin$ ln -s g++-6 g++
user.ubuntu:~/bin$ ln -s /usr/bin/gfortran-6 /usr/bin/gfortran
ln: failed to create symbolic link '/usr/bin/gfortran': File exists
user.ubuntu:~/bin$ ls
Can you be more specific?
Thanks
On Thu, Jun 14, 2018 at 10:10 AM, BERGY <nucleic81.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 18 2018 - 19:30:02 PDT
