View source for Using AMBER 14 on the GPU and compute clusters

===Using the pre-compiled AMBER 14 source===

We have a site license for [[AMBER]] 14, and it has been pre-compiled for you to use on the GPU and compute clusters. You can find the AMBER 14 manual [http://ambermd.org/doc12/Amber14.pdf here].

In order to use [[AMBER]] 14, you need to add a few lines to your ~/.bashrc file on the machine you are working on:

'''volkhan/sinister/dexter'''
<pre>
# Adding support for AMBER 14
export AMBERHOME=/home/csw34/amber14
if [ -z "${LD_LIBRARY_PATH}" ]; then
   export LD_LIBRARY_PATH="${AMBERHOME}/lib"
else
   export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${AMBERHOME}/lib"
fi
# PATH
export PATH=$AMBERHOME/bin:$PATH
</pre>

You should then be able to access all of the AMBER 14 binaries (pmemd, ptraj, tleap etc) from anywhere.

'''GPU cluster (pat)'''
<pre>
# Adding support for AMBER 14
export AMBERHOME=/home/csw34/amber14
if [ -z "${LD_LIBRARY_PATH}" ]; then
   export LD_LIBRARY_PATH="${AMBERHOME}/lib"
else
   export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${AMBERHOME}/lib"
fi
# PATH
export PATH=$AMBERHOME/bin:$PATH
</pre>

On the GPU cluster pat, both pmemd and pmemd.cuda have been compiled for you to use. If you are planning to use CUDA, make sure you have loaded the cuda/7.0 module:

<pre>
module load cuda/7.0
</pre>

===Compiling AMBER 14 for yourself===

If you want to compile and use [[AMBER]] 14 with special options e.g. MPI, or a different level of CUDA precision, you can find the source code on quartz:

<pre>
pat:/sharedscratch/csw34/AmberTools14.tar.bz2 
pat:/sharedscratch/csw34/Amber14.tar.bz2
</pre>

You can find compilation instructions in the [http://ambermd.org/doc12/Amber14.pdf AMBER 14 manual]. Obviously - please don't distribute the source code beyond the group.