December 2013

More basis testing

lbasurto's picture
Submitted by lbasurto on Mon, 12/02/2013 - 12:16

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

lbasurto's picture
Submitted by lbasurto on Tue, 12/03/2013 - 11:59

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
#PBS -V
cd $PBS_O_WORKDIR
echo "Changing to workdir $PBS_O_WORKDIR"
echo "listing workdir contents"
ls -ltr
aprun -n 256 ./cluster > log.txt

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Sparsity of Hamiltonian and overlap matrices

lbasurto's picture
Submitted by lbasurto on Mon, 12/16/2013 - 17:44

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%)