Octopus TDDFT code installation on the comet cluster at XSEDE, San Diego

Image credit: Octopus website

Load Modules:

I chose Intel compiler and intelmpi to compile the mpi version of octopus on Comet (after the Rocks OS upgrade to Rocks 7).

The following modules need to be loaded first.

  • intel/2018.1.163
  • intelmpi/2018.1.163
  • gsl/2.5
  • mkl/2018.1.163

Install dependencies/libraries:

Install libxc-4.3.4 or above

Download the latest package of libxc. Use the following configure line:

./configure --prefix=/home/neelravi CC=mpicc FC=mpif90 FCFLAGS=-O3 CFLAGS=-O3
make 
make install
make check

Install fftw-3.3.8 or above

Do not use the pre-installed fftw package. Download the latest fftw package. Use the following configure line to compile.

I chose fftw-3.3.8.

./configure --prefix=/home/neelravi CC=mpicc CFLAGS=-O3 F77=mpif90 F77FLAGS=-O3
make 
make install
make check

Install octopus code

Download the stable version of the octopus. (i.e. octopus 9.1) Use the following configure script.

./configure --prefix=$HOME \
  CC=mpicc FC=mpif90 CFLAGS="-O3" FCFLAGS="-O3" \
--enable-mpi --enable-openmp \
--with-blas="-L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread -lm -ldl" \
--with-libxc-prefix=$HOME \
--with-fftw-prefix=$HOME \
--with-blacs="-L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread -lm -ldl" \
--with-scalapack="-L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread -lm -ldl" \
--with-gsl-prefix="/opt/gsl/2.5/intel"

make 
make install
make check

The last command make check should either pass or fail all the tests. If some tests pass and some fail, then there is something wrong with the installation. Please note that a test corresponding to the glib may fail (probably this is used when Species are read from the picture file). You may ignore it.

Run a sample calculation with more than one node. The output file should show the parallelization and anticipated resource wastage.

Your octopus is ready!

Ravindra Shinde
Ravindra Shinde
Research Scientist

I am a theoretical and computational condensed matter physicist and quantum chemist. I have around 10 years of research experience, with 6 years in scientific code development. I have authored 16 research articles, 1 book, and peer-reviewed 25 manuscripts.



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