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
- Genesis website
- The Book of Genesis at genesis-sim.org
Important Notes
- Module Name: genesis (see the modules page for more information)
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/user/.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/user/.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 = 0genesis #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