December 2013

More basis testing

Here is a more complete set of basis testing using different basis sets.

Note: Whenever there is a zero in the NRLMOL results, it means that the basis for that atom was not available at the time.

Click here.

How to run a job with less processors than a full node in Hopper

The Hopper system at NERSC has 24 processors per node, usually we just submit jobs using full node usage for example:

#PBS -q regular
#PBS -l mppwidth=256
#PBS -l walltime=24:00:00
#PBS -N 256_job
#PBS -e $PBS_JOBID.err
#PBS -o $PBS_JOBID.out
echo "Changing to workdir $PBS_O_WORKDIR"
echo "listing workdir contents"
ls -ltr
aprun -n 256 ./cluster > log.txt

Sparsity of Hamiltonian and overlap matrices

We are currently running tests to implement Scalapack, and are jotting down the percentage of zeros in the test system (a zero is considered when its < 1e-8), the test system is Sc3N@C80-Phtalocyanine.
For the Hamiltonian matrix: out of 11,117,970 upper triangular elements, 5,009,259 correspond to zeros (45%)
For the overlap matrix 5,384,683 are zeros (48%)