Fraglets: Chemical Programming with a Packet Prefix Language

Transcription

1 Fraglets: Chemical Programming with a Packet Prefix Language Thomas Meyer and Christian Tschudin Computer Science Department, University of Basel, Switzerland 15. Kolloquium Programmiersprachen und Grundlagen der Programmierung (KPS 09), Maria Taferl, Oct 13 th, 2009

2 Overview 1. Functionality of Fraglets Intro game: Random draws, yet predictable outcome Prefix programs Introductory examples: rewriting, FSM, shuttle service, active networking A duplicating Quine 2. Dynamics of Fraglets See follow up talk by Thomas Meyer Christian Tschudin KPS 09 Oct 13, 2009, 2/24

3 A Mate-And-Spread Game Given: vector of booleans, not uniform Do rounds, repeat as long as you wish: Pick two random positions; If content differs then copy randomly Question: How will the array look, on average, after some rounds? Christian Tschudin KPS 09 Oct 13, 2009, 3/24

4 A Mate-And-Spread Game Given: vector of booleans, not uniform Do rounds, repeat as long as you wish: Pick two random positions; If content differs then copy randomly #define pick(a,b) a=rand()%(len-1);b=rand()%len;if(a==b)a++ main() {char v[]=" "; int a, b, len=strlen(v), n=100; for (srand(times(0)); n>0; n--) { pick(a,b); if (v[a]!=v[b]) {pick(a,b); v[a]= 0 ; v[b]= 1 ;} printf("%s\n", v); } } Question: How will the array look, on average, after some rounds? Christian Tschudin KPS 09 Oct 13, 2009, 4/24

5 A few Mate-And-Spread Games, Results of 100 Rounds Asymptotically, all results will have an equal number of zeros and ones! Christian Tschudin KPS 09 Oct 13, 2009, 5/24

6 Mate-and-Spread : Degrees of Concurrency Single thread: sequential program with a master loop Two threads (e.g., mate and spread ), two loops What about N threads, and no loops? "mate and spread" master loop "mate" loop "spread" loop bilateral "mate" (and "spread") 1 thread 2 threads N threads Christian Tschudin KPS 09 Oct 13, 2009, 6/24

7 Fraglets = Mobile Computation Fragment Chemical metaphor: Molecules reacting with each other fraglet exchange fraglet store (multiset) fraglet exchange fraglet store (multiset) fraglet exchange Exchange of fraglets (=molecules, =packets). fraglet = word of symbols [ tag1 tag2 tag3... ] fraglet multiset (=reactor, =node) Processing rules inside a multiset: reaction (two fraglets merge) transformation (single fraglet rewriting) processing order (among molecules) is non-deterministic Christian Tschudin KPS 09 Oct 13, 2009, 7/24

8 Prefix Instructions: a Reaction and Transformations Op input output match [ match a TAIL1 ], [ a TAIL2 ] [ TAIL1 TAIL2 ] nul [ nul TAIL ] (fraglet is removed) nop [ nop a TAIL ] [ a TAIL ] fork [ fork a b TAIL ] [ a TAIL ], [ b TAIL ] split [ split PART1 * TAIL ] [ PART1 ], [ TAIL ] send A[ send b TAIL ] B[ TAIL ] (unreliably) f1 [ send B c ] B [ c ] [ a ] [ match a b ] f2 nop, pop etc [ split a * b ] [ b ] [ a c ] [ b c ] Language has similarities with (is equivalent to) Post Rewriting Systems Christian Tschudin KPS 09 Oct 13, 2009, 8/24

9 Prefix Programs (or Packets) Processing rules have a deliberate constraint: the first tag fully determines action, no loops Origin in networking: packet processing = (distributed) header rewriting A fraglet s header symbols serve as: instruction related parameters storage (the other storage is: other molecules in reactor) Christian Tschudin KPS 09 Oct 13, 2009, 9/24

10 r33/n+1 r34/n+1 r35/n+1 r36/n+1 r37/n+1 Fraglets Programs are Distributed Reaction Networks Graphical representation of a flow-control protocol step circular list t1/n+1 N/N+1 credit tokens r30/n+1/p r31/n+1/p r32/n+1/p r38/n+1 r39/n+1 N N/N+1/P N+1 r0/n/n+1/p r1/n/n+1/p r2/n/n+1/p c0/p out/ok/p out r39 t0/n c1/ok/p c2/ok/p c3/ok/p c4/ok ok out t0 t1/n producer payload next expected token s21/n s22/n N s23/n+1 s24/n+1 s25/n+1 ring/n ring s0/n s1/n s2/n ring/n+1 s20/n+1 s20/n consumer Christian Tschudin KPS 09 Oct 13, 2009, 10/24 N/N+1 N/N+1 a11/n/n+1 send/n/n+1/p a10 in/ok/p produce a11/p a0/ok/p a1/ok/p a10/ok ok send/n/n+1

11 Example 1: Fraglet (header) rewriting In: [ i W ] Out: [ o W ] Program: [ match i o ] Execution Trace: [ match i o ] [ i W ] [ o W ] Christian Tschudin KPS 09 Oct 13, 2009, 11/24

12 Example 1b: The Temporary matchp Hack Problem: a match molecule (the program) is consumed. Quick hack: Introduce a persistent match, as a catalyst. In: [ i W ] Out: [ o W ] Program: [ matchp i o ] Execution Trace: [ matchp i o ] [ i W ] [ o W ], [ matchp i o ] Christian Tschudin KPS 09 Oct 13, 2009, 12/24

13 Example 2: (non-deterministic) Finite State Machine Transitions: [ matchp a b ] [ matchp b c ] [ matchp c d ] d [ matchp c e ] a b c [ matchp d a ] [ matchp e b ] e State token: [ a ] (initial state) Possible execution trace (visited states): [a] [b] [c] [e] [b] [c] [d] [a]... Christian Tschudin KPS 09 Oct 13, 2009, 13/24

14 Example 3: A Shuttle Service Service req: [ shuttle deliver Payload ] Shuttle srv: [ matchp shuttle send B ] data source [ matchp shuttle send B ] [ shuttle deliver Payload ] A [ deliver Payload ] B [ send B deliver Payload ] Execution Trace: A[ shuttle deliver Payload ] A [ send B deliver Payload ] B [ deliver Payload ] Christian Tschudin KPS 09 Oct 13, 2009, 14/24

15 Example 4: Active Networking (and Source Routing) Networking style called Active Networking : packets contain processing logic advantage: minimal preinstalled protocol software requirements Source routing the source node prescribes the path via H1, H2,... to some Dest Simple active networking (inband) version: [ send H1 send H2 send H3... send DEST Payload ] SRC H1 H2 DEST [ send H1 send H2...] [ send H2 send H3...] [ send H3 send...] [ Payload ] Christian Tschudin KPS 09 Oct 13, 2009, 15/24

16 Example 5: Quines Classics of informatics: Write a program that outputs its own source code. Named after Willard van Orman Quine ( ) Quines exist for every turing complete language How to write a Quine for a prefix language? Basic Quine structure: needs a blueprint active part (is using the blueprint, and is its activated form) Plus here: Our Quine duplicates (needed in second part of the talk) Christian Tschudin KPS 09 Oct 13, 2009, 16/24

17 A Duplicating Quine for Fraglets (1) [match x fork fork fork match nop x] [x fork fork fork match nop x] Christian Tschudin KPS 09 Oct 13, 2009, 17/24

18 A Duplicating Quine for Fraglets (2) [match x fork fork fork match nop x] [x fork fork fork match nop x] [fork fork fork match nop x fork fork fork match nop x] Christian Tschudin KPS 09 Oct 13, 2009, 18/24

19 A Duplicating Quine for Fraglets (3a) [match x fork fork fork match nop x] [x fork fork fork match nop x] [fork fork fork match nop x fork fork fork match nop x] [fork match nop x fork fork fork match nop x] [fork match nop x fork fork fork match nop x] Christian Tschudin KPS 09 Oct 13, 2009, 19/24

20 A Duplicating Quine for Fraglets (3b) [match x fork fork fork match nop x] [x fork fork fork match nop x] [fork fork fork match nop x fork fork fork match nop x] [fork match nop x fork fork fork match nop x] Christian Tschudin KPS 09 Oct 13, 2009, 20/24

21 A Duplicating Quine for Fraglets (4) [nop x fork fork fork match nop x] [match x fork fork fork match nop x] [x fork fork fork match nop x] [fork fork fork match nop x fork fork fork match nop x] [fork match nop x fork fork fork match nop x] Christian Tschudin KPS 09 Oct 13, 2009, 21/24

22 A Duplicating Quine for Fraglets (5) [nop x fork fork fork match nop x] [match x fork fork fork match nop x] [x fork fork fork match nop x] [fork fork fork match nop x fork fork fork match nop x] [fork match nop x fork fork fork match nop x] Christian Tschudin KPS 09 Oct 13, 2009, 22/24

23 A Duplicating Quine for Fraglets (6) [nop x fork fork fork match nop x] [match x fork fork fork match nop x] [x fork fork fork match nop x] [fork fork fork match nop x fork fork fork match nop x] [fork match nop x fork fork fork match nop x] This is an autocatalytic reaction network, no need for matchp Christian Tschudin KPS 09 Oct 13, 2009, 23/24

24 Conclusions Metaphor of chemical computations not wet-lab: string rewriting inherently parallel and non-deterministic execution We wish to exploit emergent properties of chemical systems like self-organization (see Turing s work), or robustness Active networking, prefix programs: code = data = molecule Quines also work that way: what is data and what is code is mere attributation, and not an intrinsic property. Next: Dynamics of Fraglets Remember the mate-and-spread game! Christian Tschudin KPS 09 Oct 13, 2009, 24/24