SDSC "neuron" roll

Overview

This roll bundles NEURON

For more information about the various packages included in the neuron roll please visit their official web pages:

NEURON is "a flexible and powerful simulator of neurons and networks".

Requirements

To build/install this roll you must have root access to a Rocks development machine (e.g., a frontend or development appliance).

If your Rocks development machine does not have Internet access you must download the appropriate neuron source file(s) using a machine that does have Internet access and copy them into the src/<package> directories on your Rocks development machine.

Dependencies

The sdsc-roll must be installed on the build machine, since the build process depends on make include files provided by that roll.

The roll sources assume that modulefiles provided by SDSC compiler, python, and mpi rolls are available, but it will build without them as long as the environment variables they provide are otherwise defined.

The build process requires the gsl libraries and assumes that the gsl modulefile provided by the SDSC math-roll is available. It will build without the modulefile as long as the environment variables it provides are otherwise defined.

Building

To build the neuron-roll, execute this on a Rocks development machine (e.g., a frontend or development appliance):

% make 2>&1 | tee build.log

A successful build will create the file neuron-*.disk1.iso. If you built the roll on a Rocks frontend, proceed to the installation step. If you built the roll on a Rocks development appliance, you need to copy the roll to your Rocks frontend before continuing with installation.

This roll source supports building with different compilers and for different MPI flavors and python installations. The ROLLCOMPILER, ROLLMPI, and ROLLPY make variables can be used to specify the names of compiler, MPI, and python modulefiles to use for building the software, e.g.,

make ROLLCOMPILER=intel ROLLMPI=mvapich2_ib ROLLPY=opt-python 2>&1 | tee build.log

The build process recognizes "gnu", "intel" or "pgi" as the value for the ROLLCOMPILER variable; any MPI modulefile name may be used as the value of the ROLLMPI variable, and any python modulefile name for the ROLLPY variable. The default values are "gnu", "rocks-openmpi", and "python".

Installation

To install, execute these instructions on a Rocks frontend:

% rocks add roll *.iso
% rocks enable roll neuron
% cd /export/rocks/install
% rocks create distro

Subsequent installs of compute and login nodes will then include the contents of the neuron-roll. To avoid cluttering the cluster frontend with unused software, the neuron-roll is configured to install only on compute and login nodes. To force installation on your frontend, run this command after adding the neuron-roll to your distro

% rocks run roll neuron host=NAME | bash

where NAME is the DNS name of a compute or login node in your cluster.

In addition to the software itself, the roll installs neuron environment module files in:

/opt/modulefiles/applications/neuron

Testing

The neuron-roll includes a test script which can be run to verify proper installation of the roll documentation, binaries and module files. To run the test scripts execute the following command(s):

% /root/rolltests/neuron.t