The version of PGENESIS installed on Lemieux is based on the GENESIS neural simulator developed at Caltech and the PGENESIS extensions developed at PSC, with modifications for MPI added at SDSC/Caltech.
This installation has been tested on a few sample scripts, but because of the large code base of GENESIS, it is strongly recommended that users confirm that their simulation results agree with the simulation results using serial GENESIS on their workstations before doing large PGENESIS runs. Due to differences in compiler optimization, floating-point arithmetic, etc., it is very likely that small numeric differences (in the last two significant digits) may occur between simulations. Large differences or other difficulties should be reported to pgenesis@psc.edu.
To use PGENESIS, simply modify your .cshrc, .tcshrc, or .bashrc
file to place /usr/local/packages/genesis/pgenesis/bin on
your PATH. A sample job for running PGENESIS in batch mode can be
found in
/usr/local/packages/genesis/pgenesis/Scripts/orient2/orient2.job.
You can run this example batch job (in the debug queue since it only
takes a few seconds) by typing:
qsub orient2.job
Files for the sample job include: