INSTALLATION INSTRUCTIONS FOR NEURALOG AND SPIKE ------------------------------------------------ (C) 1993 Lloyd Watts lloyd@pcmp.caltech.edu TABLE OF CONTENTS 1. Introduction 2. Unpacking the release tar-file 3. Compiling Spike 4. Setting your path 5. Setting up NeuraLOG 6. Trying an example 7. General installation guide for system administrators 8. If you have problems 1. INTRODUCTION ---------------- Thank you for your interest in Neuralog and Spike. Neuralog is a customization of the program Analog, by John Lazzaro and Dave Gillespie, that can be used for entering neural circuits into your computer. Spike is a fast event-driven simulator, written by Lloyd Watts, optimized for networks of spiking neurons. Spike is distributed under the GNU General Public Licence, which is included in this distribution, in the file spike/src/COPYING. This software is distributed WITHOUT ANY WARRANTY. This file contains instructions on how to install Spike and Neuralog, and how to get started with a simple example circuit. It is assumed that you already have AnaLOG running on your system, and that you are familiar with its use. If not, you may obtain them by anonymous ftp to hobiecat.pcmp.caltech.edu. They reside in the directory /usr/ftp/pub/chipmunk. Look at the file README for instructions on how to install AnaLOG and Cview. Alternately, you can avoid the use of AnaLOG/NeuraLOG altogether by specifying your schematic with a text editor such as emacs or vi. This is an alpha release of Neuralog and Spike. Thank you for your patience. 2. UNPACKING THE RELEASE TAR-FILE ---------------------------------- You should receive by email another file; the subject will be Subject: Neuralog/Spike release save that email message to a file, and give it a name (say, foo), and move it to the directory in which you would like the tools to reside (your home directory would be fine). to install the tools, execute the following commands: uudecode foo (you should now have a new file called spike.tar.Z) uncompress spike.tar.Z (you should now have a file called spike.tar) tar xvf spike.tar (you should now have a directory called spike) When the tools are installed, you will have a new directory called spike in your home directory. The spike directory will contain several subdirectories: src: contains the source code and Makefile for spike, and the GNU General Public Licence neuralog: contains the symbols for neuralog manpage: contains a manpage for the tools examples: contains several examples of small circuits 3. COMPILING SPIKE ------------------- The next step is to compile spike. Go down (cd) to spike/src; in that directory, you will find the following files: COPYING: contains the GNU General Public Licence. Please read it. spike.c: the source code for spike. Makefile: the make file. simply type make in this directory. The program should compile and produce an executable program called spike. If you have any problems, send email to lloyd@pcmp.caltech.edu. 4. SETTING YOUR PATH --------------------- Next, you need to set up your path to find spike: set path = (~/spike/src $path) (probably you will want to update your default path in your .login file) Now, if you just type spike in any directory, you should get a introductory message, something like SPIKE 1.035 A Spike-Based Neural Network Simulator Copyright (C) 1991-1993 Lloyd Watts This program is distributed under the GNU General Public License Please send comments to lloyd@pcmp.caltech.edu Usage: spike [-d ] Congratulations! Spike is now installed (for yourself). Ask your system administrator for help if you want to install the source code in a more public place. 5. SETTING UP NEURALOG ----------------------- Neuralog is simply a customization of the program AnaLOG, by John Lazzaro and Dave Gillespie. Type alias neuralog 'analog -cnlog.cnf' (and put that line in your .cshrc for later). This instruction will cause analog to look in the current directory for a configuration file called nlog.cnf. An appropriate nlog.cnf file has been included with each example directory. Congratulations! You have installed Neuralog and Spike. 6. TRYING AN EXAMPLE --------------------- There are several basic examples in the directory spike/examples. A file called README describes what they are. An introductory tutorial is in spike/examples/tonic_burster/TUTORIAL. More advanced examples demonstrate the use of buffers, hierarchy, generalized synapses, and textual input of neural circuits. Good luck! Please send comments to lloyd@pcmp.caltech.edu 7. GENERAL INSTALLATION GUIDE FOR SYSTEM ADMINISTRATORS -------------------------------------------------------- The instructions above are intended to get a new person up and running with the example files that are provided, with a minimum amount of "system administration". However, it will not be possible to edit files OTHER THAN the example files, since there are critical file dependencies lurking in critical files. The main file dependencies are built into the alias for neuralog alias neuralog 'analog -cnlog.cnf' This command instructs analog to look in the current directory for a file called nlog.cnf. A typical nlog.cnf file contains the following statements (as in the tonic_burster example) include genlog.cnf news ../../neuralog/lognews.text { load standard neuralog symbols } gates + ../../neuralog/neuralog.gate { load special gates for this design } gates + ./mygates.gate { put standard symbols into the gate catalog } get + vdd gnd from neuron synexc syninh input tonicexc tonicinh buffer { put special symbols for this design into the gate catalog } { get + your gates here } { put standard symbols into the on-screen menu } menu to from neuron synexc syninh input tonicexc tonicinh buffer vdd gnd { Tell logntk where to look for the .ntk files } logntk: LIB: ../../neuralog . Note that all of the file references use the ../../ path, which is relative to the example directory. A better solution is to replace the ../../ with the full pathname. Then you can instruct users to copy the nlog.cnf file into any design directory, and they will be up and running. There are other ways to solve this problem, but in any case, the user will have to have an nlog.cnf file in his directory, so he might as well learn about it now. 8. IF YOU HAVE PROBLEMS: ------------------------- If you have any trouble with compiling spike, please send me an email message. Tell me what machine you tried to compile it on, which compiler you used, and attach a copy of the error message. Spike is known to compile with cc on HP 300, 400, 700, and 800 series and on SUN Sparcstations. If you have any trouble running spike, i.e., you get a run-time error of some kind that is not caused by an error in one of your input files, please RERUN the program as follows: spike YOURFILE -d 10 > foo and mail me the foo file. This will set a very chatty debug mode and will help me to determine what the problem is.