Update on 5/26/2017: Parameter search using this tool is now implemented on the Neuroscience Gateway (NSG) neural simulation platform. To use it, select "Parameter Search in Singularity on Comet" from the tools list. So far it's only limited to calling GENESIS 2.4, but potentially it could call any simulator or any other program.
param-search-neuro is a collection of scripts to simulate a neuron
model for each of the entries in a parameter set, but in practice it
could run any simulator. Evaluating the model at different places in
its parameter space allows mapping its output and also
creating
neuronal model databases.
It provides a simple method to run a set of parameters locally or on high-performance computing (HPC) platforms by defining the concept of a parameter file. This is a text file that contains a matrix of numbers, where columns represent different parameters and rows represent different model runs or trials with different parameter configurations.
Here's an example parameter file 5rows9pars.par with 5 rows of
different parameter configurations and 9 columns of parameters:
5 9 # Rows and columns
1 1 2.1 9 2 0.6 50 48 0
1 1 2.15 9 2 0.6 50 48 0
1 1 2.2 9 2 0.6 50 48 0
1 1 2.25 9 2 0.6 50 48 0
1 1 2.3 9 2 0.6 50 48 0The trials can then be simulated serially or in parallel through the use of the provided scripts. Scripts here allow constructing the parameter file in a variety of ways, including but not limited to selecting all combinations of discrete values of each parameter. Parameter files can also be easily imported from other sources.
Using these scripts is efficient because, before running simulation sets, text parameter files are compiled into binary objects (using Perl). These hashtable objects reach parameters of requested trials in constant time (i.e. O(1)) and allows direct addressing of trials. Therefore they can be executed in arbitrary order, which is necessary in parallel environments because it eliminates the need to prevent race conditions.
HPC platforms supported:
- Sun/Oracle Grid Engine (SGE)
- PBS/MOAB
- SLURM
Running parameter sets on parallel environments is demonstrated using the GENESIS simulator here, but in principle it is very easy to run any other simulator. Parameters are passed to individual GENESIS processes using environmental variables, but they can also be passed on the command line.
To use these scripts, either add the paths param_file/ and your
cluster-specific script directory (e.g., pbs_scripts) in your search
PATH, or refer to these scripts with full paths.
See the tutorial below and the examples in the relevant subdirectories for up-to-date usage.
param_file/: Common scripts for running simulations and for maintaining parameter files.pbs_scripts/: Scripts specific to PBS/Moab.slurm_scripts/: Scripts specific to SLURM.sge_scripts/: Scripts specific to the Sun/Oracle Grid Engine (SGE).maintenance/: Miscellaneous cluster and file maintenance scripts.
Subdirectories contain additional documentation. Start with the parameter file documentation.
Full examples for several simulation programs are provided under the SGE subfolder.
Documentation credits: Cengiz Gunay (cengique AT users.sf.net) and Anca Doloc-Mihu (adolocm AT emory.edu).