Biowulf High Performance Computing at the NIH
genesis on Biowulf

GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ genesis tutorial5
Starting Genesis
==========================================================================
                               G E N E S I S
                           Release Version: 2.4


GENESIS is made available under the GNU General Public License,
GNU Library General Public License, or by the originating institution
with the permission of the authors.

Type "help" for help with GENESIS.
==========================================================================

Executable:         /usr/local/apps/genesis/2.4/genesis

--------------------------- Starting XODUS 2.0 ---------------------------

The diskio library uses the netcdf-version 3.4 library, which is provided
"as is" under the terms of distribution and usage by UCAR/Unidata.
Please see src/diskio/interface/netcdf/netcdf-3.4/copyright.html
for the full notice.

The kinetics library is copylefted under the LGPL, see kinetics/COPYRIGHT.

Startup script:     /home/susanc/.simrc
SIMPATH=. /usr/local/apps/genesis/2.4/startup /usr/local/apps/genesis/2.4/Scripts/neurokit /usr/local/apps/genesis/2.4/Scripts/neurokit/prototypes
SIMPATH=. /usr/local/apps/genesis/2.4/startup /usr/local/apps/genesis/2.4/Scripts/neurokit /usr/local/apps/genesis/2.4/Scripts/neurokit/prototypes /usr/local/apps/genesis/2.4/Scripts/X1compat
SIMNOTES=/home/susanc/.notes
GENESIS_HELP=/usr/local/apps/genesis/2.4/Doc
Simulation Script:  tutorial5
/library
/
changing clock [0] from 1 to 5e-05
reading 'cell.p'....
cell.p read: 2 compartments, 3 channels, 0 shells, 2 others
time = 0.000000 ; step = 0

genesis #0 > quit

[user@cn3144 ~]$ exit

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

To run Genesis as a batch job, you need to use nxgenesis rather than the default genesis which requires X11. Create a batch input file (e.g. genesis.sh). For example:

#!/bin/bash
set -e

module load genesis/2.4
nxgenesis myfile.g

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] genesis.sh