announce.311

地球模拟器

                                TIERRA UPDATE:
   (Version 3.11 now available, FTP site reorganized, New Tools, Bug Fixes,
      Genebank Verification, Garbage Collection, New Genomes, Mneumonics
                Shortened, Virtual Extraction, DEC Grant, Sex)

This message contains:

1) Availability of Tierra V3.11 source code
   a) by ftp
   b) by snail mail on disk
2) FTP Site Reorganized
2) New Tools
3) Bug Fixes
4) Genebank Verification
5) Garbage Collection
6) New genomes distributed
7) Opcode mneumonics limited to six characters
8) Virtual Extraction
9) Grant from Digital Equipment Corporation
10) Future Sex

1) Availability of Tierra V3.11 source code

   a) by ftp

     The V3.11 source code, the source code, and DOS executables of all tools
is available now.  If you use the software, be sure to pick up new versions
soon from the ftp site.  The source in the ftp site will be replace on a
roughly monthly or bi-monthly basis.

     The complete source code and DOS executables are available by anonymous
ftp at:

tierra.slhs.udel.edu [128.175.41.34] and
  life.slhs.udel.edu [128.175.41.33]

in the directories: DOS/, almond/, beagle/, doc/, and tierra/.

To get it, ftp to tierra or life, log in as user "anonymous" and give your
email address (eg. [e-mail]) as a password.  Be sure to transfer binaries
in binary mode (it is safe to transfer everything in binary mode).
Each directory contains a compressed tar file (filename.tar.Z) and a SRC
directory that contains all the files in raw ascii format.  You can just
pick up the .tar.Z files, and they will expand into the complete directory
strucutre with the following commands:

uncompress tierra.tar.Z
tar oxvf tierra.tar

   b) by snail mail on disk

     If you do not have ftp access you may obtain everything on DOS disks
by making a check for $65 (US dollars drawn on a US bank) payable to
Virtual Life.  Specify 3.5" or 5.25" disks.  Send the check to one of the
following addresses:

Tom Ray                  (January through August)
Santa Fe Institute
1660 Old Pecos Trail
Suite A
Santa Fe, NM 87501

Virtual Life             (September through December)
P.O. Box 625
Newark, Delaware 19715

     The DOS disks contain everything but ALmond.  They include DOS
executables, source code and documentation.  The DOS disks include an easy
installation program.  This is the same source and executables available in
the ftp site.  If you have ftp access, there is no need to buy the disks.

2) New Tools

     Several new (and some old) tools, developed by Dan Pirone and Tom Ray,
are now fully documented and available in the ftp site:

rnd_inst - A tool for altering the physics of the system by randomly mapping
     opcodes to instructions, with some optional restrictions on hamming
     distances between pairs of instructions.  The output is an opcode.map
     file.

probe - A tool for surveying the genebank, with various optional selection
     criteria (a new tool, but proving very useful).

tieout - A tool for generating x,y data from the tierra.log file.  This is
     used on a regular basis to generate graphics of size of creatures over
     time during a run.

diverse - A tool that reads the birth and death records (break.X files) output
     by Tierra and transforms them into various measures of diversity, for
     graphical or other analysis.

beagle - A DOS only tool which provides a variety of graphical displays of
     the output from the Tierra simulator.  It is used after a run, and is
     highly recommended as a tool for analyzing the results of a run.

run_info - A function of the beagle program, also available as a stand-alone,
     due to its hunger for memory.

fragment - A function of the beagle program, also available as a stand-alone,
     due to its hunger for memory.

ALmond - A UNIX only tool which runs as a separate process on the same or a
     different machine.  ALmond establishes socket communications with a
     running Tierra, and provides a color display of the spatial distribution
     of the creatures in the soup, showing all births and deaths.  This tool
     has some new functions: you can view the positions of the instruction
     pointers, or the activity of the moviab instruction.

3) Bug Fixes

histograms - Version 3.1 included some obvious errors in the histogram
     display.  These have been corrected.

moviab - This instruction allows creatures to alter their own genome by
     writing on themselves.  Before V3.11, the genebanker did not watch
     for genetic changes occurring in this manner.  This created observational
     errors comparable to the ploidy bug corrected in V3.1.  The genebanker
     now catalogs genetic change by this mechanism.  It is believed that
     the genebanker is now fully reliable (see below).

chmod - The chmod function was supposed to return a value, but did not.
     This had the consequence that a flag was set every time a creature
     allocated space for a daughter, and these were recorded with the
     demography data associated with each creature.  This has been corrected.

arg r option - The arg r option (replace or add) was not working, but
     is now.

4) Genebank Verification

     Error checking code has been added which completely verifies that the
distribution of genotypes in the soup matches that reflected in the genebank,
and that various counts are internally consistent within the genebank.

5) Garbage Collection

     Routines have been added which clean-up the genebank once per million
exectued instructions.  Among other things, once a size class is extinct,
all genomes of that size are eliminated from RAM.  Permanent genomes are first
saved to disk.

6) New genomes distributed

     Many new genomes were first distributed with V3.1, but they were not
mentioned in the announcement.  These are the genomes of most of the
creatures described in the publications and videos: parasites,
hyper-parasites, social creatures, cheaters, etc.

7) Opcode mneumonics limited to six characters

     To facilitate their display by the Beagle tools, the opcode mneumonics
have been limited to six characters.  This affects push_ax, push_bx, push_cx,
push_dx, and mov_iab.  These have been changed to pushax, pushbx, pushcx,
pushdx and moviab.  This means that old ascii genome files can not be read
by the new tools.  It does not affect binary genome files.  Old binary files
will be mapped to the new names when they are converted to ascii by the new
software.  All the ascii .tie files are redistributed in the new format.

8) Virtual Extraction

     When a new genotype crosses one of the thresholds (SavThrMem or
SavThrPop) its name becomes permanent and it is ``extracted'' (written to
disk).  This event is noted in the user interface and in the tierra.log
file like: ex = 0079aaa @ 13
The new feature is that when a genotype goes extinct, then reappears and
crosses the thresholds again, it experiences a ``virtual extraction'',
which means that it is not written to disk (since it is already there),
but the extraction event is written to the interface and the tierra.log
file like: ex = 0079aaa @ 13 v
This was done to facilitate the use of the tieout tool with cumulative
genebanks, but it results in nicer extraction data in other senses as well.

9) Grant from Digital Equipment Corporation

     The Semiconductor Engineering Group of Digital Equipment Corporation has
donated two fully loaded DS5000 workstations to the Santa Fe Institute as a
part of a grant to Tom Ray titled: ``Computer Architectures for the Natural
Evolution of Machine Codes''.  These two machines will be the primary platform
for Tierra research and development in the near future.

10) Future Sex

     Walter Tackett ([e-mail] or [e-mail])
has implemented haploid sex based on cross-over (a random cross-over point
used by the moviab instruction) in his private copy of Tierra V3.0.  The
methodology used by Tackett has been implemented in the Santa Fe verison of
Tierra.  It will be released when it has undergone more testing to verify its
functions.