Compile AMBERTOOLS14 on AHPCC.

This blog is just a note. This might be not suitable for your condition.

I found AMBERTOOLS14 would change ./configure when I chose different CPU (eg. SSE4 only…). So I ssh to a AMD cpu node this time (David made me know the cpu had nothing to do with compilers, so I still used intel compiler), and then compiled AMBERTOOLS14. And I can use the compiled AMBERTOOLS14 on any cpu. I extracted files to two folers, amber14_serial and amber14_parallel.

#####################################

export AMBERHOME=’~/amber14_serial’

cd $AMBERHOME

module load python/2.7.5 intel/11.1 mkl/11.1 impi/4.1.0

./configure -noX11 intel

make install

make test

################################################

Then compiler the parallel version

###############################################

export AMBERHOME=’~/amber14_parallel’

cd $AMBERHOME

./configure -noX11 -mpi intel

make install

cp -n ~/amber14_serial/bin/* bin/ #copy the serial compiled files to the parallel bin folder.

export DO_PARALLEL=’mpirun -np 2′

make test

########################################

The test for serial are all ok. The test for parallel had one possible error, never mind!

Add module load python/2.7.5 intel/11.1 mkl/11.1 impi/4.1.0 to the end of ~/amber14_parallel/amber.sh.

When you want to use AMBERTOOLS14, just source ~/amber14_parallel/amber.sh.

The compiled sander.MPI can run parallely. I have tested it by with several nodes.

Enjoy free AMBER14 MD simulation!

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s