Toolset

The toolset consist of the following:

Hierarchy of instruction sets with projections/embeddings.

Instruction sets:

PGLA, PGLB, PGLC, PGLD, PGLDg, PGLE, PGLEc, PGLEcw, PGLEcr, PGLEcm, PGLAu, PGLBu, PGLBg

Basic instruction sets:

Generic
MPP - Molecular Programming Primitives
MPPV - MPP with Values
HMPPV - Highlevel MPPV
FMN - Focus Method Notation
MSP - Molecular Scripting Primitives (extends HMPPV with instructions on values)
MSPea - extension of MSP with eval/apply
MSPio - extension of MSP with simple I/O
HMPPVis - HMPPV with inverse selection
MSPfunc - extension of MSPea with functions

Projections/embeddings:

pglb2pgla, pglc2pglb, pgld2pglc, pgldg2pgld, pgle2pgldg, pglec2pgle, pglecw2pglec, pglecr2pglec, pglecm2pglecr, pglau2pglbu, pglbu2pglbg, pglbg2pglb

Tools:

genparser - generic parser
gensim - generic simulator
prog2lts - program to labelled transition system translator
bisim - bisimulator of labelled transition systems
parsim - parallel simulator
pgla-jumpopt - pgla jump optimizer
gencompiler - generic compiler (available modules for compiling PGLEc.MSPio to PIR (Parrot Intermediate code Representation; Parrot is the virtual machine for Perl 6 that is currently being developed), and PGLEc.MSPio to CIL (Common Intermediate Language; the intermediate language voor the MS .NET Framework).
threadsim - thread simulator

Statemachines (to be used with basic instruction set FMN):

smbr - boolean register
smnnr - natural number register
smnnc - natural number counter
smnns - natural number stack
Console

Requirements

A machine running Unix or Linux with the following installed:

Perl version 5.x
Tcl/Tk version 8.x
Tcldot - part of Graphviz from AT&T Bell Laboratories
Most Linux distributions have packages for graphviz available. Look for the packages graphviz and graphviz-tcl (ubuntu: libgv-tcl).
Note: There is a bug in the tcldot part of all versions (latest version 2.38) of graphviz higher than 2.28. This bug is reported to the graphviz organisation, but there is no fix yet. It is best to install from the sources of version 2.28.
ToolBus - this is only needed for the parallel simulator and the thread simulator
(locally available - see Download)
It depends on some standard software (yacc/bison, (f)lex).

Tested on

Linux - Fedora 31, CentOS 6.6, Ubuntu 18.04

Copyright

This toolset is copyrighted by Bob Diertens, 2001-2020. It may be used free of charge for educational purposes only.

This toolset comes with absolutely no warranty. It may not be sold and only be distributed in the form as found here.

Download

Sources

You have to download the following gzipped tar-files:

pga-1.8.tar.gz (June 29, 2017)
toolbus-bundle-0.1.1.tar.gz

Install

PGA Toolset
Execute the commands
```
    tar zxf pga-1.8.tar.gz
    cd pga-1.8
```
And follow the instructions in the file INSTALL.

ToolBus
Execute the commands

    tar zxf toolbus-bundle-0.1.1.tar.gz
    cd toolbus-bundle-0.1.1
    ./configure --prefix=<install-directory>
    make
    make install

Use the same install-directory as with the PGA Toolset.

Packages

The packages include the Toolbus bundle and the older version of graphviz. They will install in /usr/local/PGA.

Note that these packages are experimental at the moment. Please report any problems with them.

Linux system version package

Fedora 31 pga-1.8-1.fc31.x86_64.rpm

Ubuntu 18 LTS pga_1.8-1_amd64.deb

Ubuntu 19 pga_1.8-1-ub19fix_amd64.deb *

Ubuntu 20 LTS pga_1.8-2-ub20fix_amd64.deb **

* altered version of pga_1.8-1_amd64.deb by changing dependency on libperl5.26 to libperl5.28
** altered version of pga_1.8-1_amd64.deb by changing dependency on libperl5.26 to libperl5.30

Linux system	version	package
Fedora	31	pga-1.8-1.fc31.x86_64.rpm
Ubuntu	18 LTS	pga_1.8-1_amd64.deb
Ubuntu	19	pga_1.8-1-ub19fix_amd64.deb *
Ubuntu	20 LTS	pga_1.8-2-ub20fix_amd64.deb **

Usage

Information on how to use the various tools can be found in the files in the directory doc in the distribution and after installation in the directory doc in the installation directory. Here, you can find the user manual in various formats, which can also be viewed online.