[Avida-cvs] [avida-svn] r953 - in tags: . 2.4.4 2.4.4/source 2.4.4/source/support
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Wed Sep 13 18:02:44 PDT 2006
Author: brysonda
Date: 2006-09-13 21:02:44 -0400 (Wed, 13 Sep 2006)
New Revision: 953
Added:
tags/2.4.4/
tags/2.4.4/README
tags/2.4.4/source/defs.h
tags/2.4.4/source/support/genesis
Removed:
tags/2.4.4/README
tags/2.4.4/source/defs.h
tags/2.4.4/source/support/genesis
Log:
Tag 2.4.4 Release
Copied: tags/2.4.4 (from rev 951, trunk)
Deleted: tags/2.4.4/README
===================================================================
--- trunk/README 2006-09-14 00:32:37 UTC (rev 951)
+++ tags/2.4.4/README 2006-09-14 01:02:44 UTC (rev 953)
@@ -1,104 +0,0 @@
-Avida 2.3.x
-----------------------------------------------------------------------
-Digital Evolution Laboratory at Michigan State University
-
-
-REQUIREMENTS
-----------------------------------------------------------------------
-
-In order to build Avida, you must have CMake 2.x installed.
-CMake 2.x is available from http://www.cmake.org
-
-NCurses, in order to build the console viewer.
-
-OR
-
-In Mac OS X, an Xcode project has been provided for building the
-'primitive' console only version of Avida, as well as the NCurses
-viewer. Xcode 2.1 or greater is required.
-
-
-GETTING STARTED
-----------------------------------------------------------------------
-
-To compile and install Avida, all you have to do is run:
-$ ./build_avida
-
-By default, you will get an optimized version of the code, as well as
-the NCurses viewer. The installation goes into a directory called
-'work' that is created in a subdirectory named 'build' directory.
-See below how to change that.
-
-OR
-
-In Mac OS X's Xcode, click the 'Build' button on the project window.
-
-
-CMAKE CONFIGURATION OPTIONS
-----------------------------------------------------------------------
-
-Here are the main options available when configuring and building
-Avida with cmake :
-
-AVD_CONSISTENCY_TEST_PRIMITIVE
- - This is a BOOL, either ON or OFF, to enable primitive consistency
- test suites.
- OFF by default.
-
-AVD_GUI_NCURSES
- - This is a BOOL, either ON or OFF, to enable building Avida console
- interface.
- ON by default.
-
-AVD_PRIMITIVE
-This is a BOOL, either ON or OFF, to enable building interfaceless
-Avida (fastest version).
-ON by default.
-
-AVD_UNIT_TESTS
- - This is a BOOL, either ON or OFF, to enable building primitive
- unit test suites.
- OFF by default.
-
-CMAKE_BUILD_TYPE
- - This is a STRING, one of "None", "Debug", "Release",
- "RelWithDebInfo", "MinSizeRel", to vary optimization levels and
- debugging information in the build.
- "Release" by default.
-
-
-
-CONFIGURING THE CMAKE BUILD
-----------------------------------------------------------------------
-
-There are three ways by which you can set the various options.
-
-
-For a simple 'gui' like interface, from the build directory run:
-$ ccmake ../
-
-Pressing 'c' will configure
-Pressing 'g' will generate the make files and exit
-
-
-If you'd like to be prompted with questions for each option, execute
-the following from the build directory:
-$ cmake -i ../
-
-
-From the command-line option, the cmake option -D allows setting Avida
-configuration options with the following syntax:
--D<variable name>:<type>=<value>
-
-To completely specify each of the above Avida options, cd into your
-build directory and type something like :
-$ cmake -DAVD_CONSISTENCY_TEST_PRIMITIVE:BOOL=OFF \
- -DAVD_GUI_NCURSES:BOOL=ON \
- -DAVD_PRIMITIVE:BOOL=ON \
- -DAVD_UNIT_TESTS:BOOL=OFF \
- -DCMAKE_BUILD_TYPE:STRING=Release \
- path-to-source-directory
-
-
-
-Revised 2005-16-10 DMB
Copied: tags/2.4.4/README (from rev 952, trunk/README)
Deleted: tags/2.4.4/source/defs.h
===================================================================
--- trunk/source/defs.h 2006-09-14 00:32:37 UTC (rev 951)
+++ tags/2.4.4/source/defs.h 2006-09-14 01:02:44 UTC (rev 953)
@@ -1,185 +0,0 @@
-//////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 1993 - 2003 California Institute of Technology //
-// //
-// Read the COPYING and README files, or contact 'avida at alife.org', //
-// before continuing. SOME RESTRICTIONS MAY APPLY TO USE OF THIS FILE. //
-//////////////////////////////////////////////////////////////////////////////
-
-#ifndef DEFS_HH
-#define DEFS_HH
-
-#define VERSION "2.4.3"
-#define VERSION_TAG "Padawan"
-
-
-#define DEFAULT_DIR "../work/"
-
-/*
-FIXME: remove asap, switching to file-configureable option
-*/
-// path to html doc files
-#ifndef HTMLDIR
-#define HTMLDIR "../work/doc_html/"
-#endif
-
-
-// -= Various view modes =-
-#define VIEW_NEWVIEWER
-// #define VIEW_VISTA
-// #define VIEW_PRIMITIVE
-// #define VIEW_EXTERNAL
-// #define VIEW_CURSES
-// #define VIEW_NCURSES
-// #define VIEW_ANSI
-
-
-// -= Speedups =- (define these to allow features to be turned on)
-
-// #define BREAKPOINTS
-// #define QUICK_BASE_TEST_CPU
-// #define QUICK_HEAD_TEST_CPU
-#define INSTRUCTION_COSTS
-#define INSTRUCTION_COUNT
-
-// -= Toggles =- (define these to actually turn features on)
-
-#define SMT_FULLY_ASSOCIATIVE
-
-#define WRITE_PROTECTION
-// #define FATAL_ERRORS
-// #define FATAL_WARNINGS
-#define SINGLE_IO_BUFFER
-
-// Test to see if search approx equals size... value is +- tolerance
-// #define TEST_SEARCH_SIZE .25
-
-// #define DEBUG
-// #define DEBUG_CHECK_OK
-// #define DEBUG_MEMTRACK
-// #define INTEGRITY_CHECK
-// #define DEBUG_MEM_CHECK
-// #define TEST
-
-
-////// Compiler Compatability Stuff //////////
-
-// old compiler //
-//#define explicit
-//#define LONGINT int
-
-// snazzy compiler //
-#define LONGINT long int
-
-
-////// Don't change anything below this line. /////
-#ifdef QUICK_BASE_TEST_CPU
-#define QUICK_TEST_CPU
-#endif
-
-#ifdef QUICK_HEAD_TEST_CPU
-#define QUICK_TEST_CPU
-#endif
-
-#ifdef VIEW_primitive
-#define VIEW_PRIMITIVE
-#endif
-#ifdef VIEW_external
-#define VIEW_EXTERNAL
-#endif
-#ifdef VIEW_curses
-#define VIEW_CURSES
-#endif
-#ifdef VIEW_ncurses
-#define VIEW_NCURSES
-#endif
-#ifdef VIEW_vista
-#define VIEW_VISTA
-#define VIEW_PRIMITIVE
-#endif
-
-#ifdef VIEW_ANSI
-#define PLATFORM_WINDOWS // enable to compile for Win32 console
-#define MSVC_COMPILER // enable to compile with Microsoft VC++
-#endif
-
-// Finally, if we have turned off Assertions, define NDEBUG
-#ifndef DEBUG
-#ifndef NDEBUG
-#define NDEBUG
-#endif
-#endif
-
-#ifdef PLATFORM_WINDOWS
- #ifdef UINT // Some modules will not compile w/out this (e.g. b_struct2)
- #undef UNIT
- #endif
-
- #ifdef UCHAR
- #undef UCHAR
- #endif
-
- #include <windows.h> // Defines, prototypes, etc. for
-#endif
-
-#ifdef MSVC_COMPILER
- #ifdef _DEBUG // VC++ debug define
- #define DEBUG
- #endif
-
- #ifndef _WINDEF_
- #include <string.h>
- #endif
-#endif
-
-#define MAX_INT 4294967295
-#define MAX_INST_SET_SIZE 64
-
-// #ifndef FALSE
-// #define FALSE 0
-// #define TRUE !FALSE
-// #endif
-
-#ifndef NULL
- #define NULL 0
-#endif
-
-#ifndef _WINDEF_ // Defined by WINDOWS.H
- #define UCHAR unsigned char
- #undef UINT
- #define UINT unsigned int
-#endif
-
-#define TOOLS_DIR tools
-#define CPU_DIR cpu
-#define MAIN_DIR main
-#define VIEW_DIR viewers
-
-#define MIN_CREATURE_SIZE 8
-#define MAX_CREATURE_SIZE 2048
-
-#define MIN_INJECT_SIZE 8
-
-// Number of distinct input and outputs stored in the IOBufs (to test tasks)
-#define INPUT_BUF_SIZE 3
-#define OUTPUT_BUF_SIZE 3
-#define SEND_BUF_SIZE 3
-#define RECEIVE_BUF_SIZE 3
-
-// Task Merit Method //
-#define TASK_MERIT_NONE 0
-#define TASK_MERIT_NORMAL 1 // Bonus just equals the task bonus
-
-#define MERIT_TIME_AT_TASK 0
-#define MERIT_TIME_AT_DIVIDE 1
-
-#define FILE_TYPE_TEXT 0
-#define FILE_TYPE_HTML 1
-
-enum tHARDWARE_TYPE
-{
- HARDWARE_TYPE_CPU_ORIGINAL = 0,
- HARDWARE_TYPE_CPU_4STACK,
- HARDWARE_TYPE_CPU_SMT
-};
-
-#endif
Copied: tags/2.4.4/source/defs.h (from rev 952, trunk/source/defs.h)
Deleted: tags/2.4.4/source/support/genesis
===================================================================
--- trunk/source/support/genesis 2006-09-14 00:32:37 UTC (rev 951)
+++ tags/2.4.4/source/support/genesis 2006-09-14 01:02:44 UTC (rev 953)
@@ -1,166 +0,0 @@
-#############################################################################
-# This file includes all the basic run-time defines for avida.
-# For more information, see doc/genesis.html
-#############################################################################
-
-VERSION_ID 2.3.1 # Do not change this value!
-
-### Architecture Variables ###
-MAX_UPDATES -1 # Maximum updates to run simulation (-1 = no limit)
-MAX_GENERATIONS -1 # Maximum generations to run simulation (-1 = no limit)
-END_CONDITION_MODE 0 # End run when ...
- # 0 = MAX_UPDATES _OR_ MAX_GENERATIONS is reached
- # 1 = MAX_UPDATES _AND_ MAX_GENERATIONS is reached
-WORLD-X 60 # Width of the world in Avida mode.
-WORLD-Y 60 # Height of the world in Avida mode.
-WORLD_GEOMETRY 2 # 1 = Bounded Grid
- # 2 = Torus (Default)
-RANDOM_SEED 0 # Random number seed. (0 for based on time)
-HARDWARE_TYPE 0 # 0 = Original CPUs
- # 1 = New, Stack-based CPUs
-MAX_CPU_THREADS 1 # Number of Threads CPUs can spawn
-
-### Configuration Files ###
-DEFAULT_DIR ../work/ # Directory in which config files are found
-INST_SET inst_set.default # File containing instruction set
-EVENT_FILE events.cfg # File containing list of events during run
-ANALYZE_FILE analyze.cfg # File used for analysis mode
-ENVIRONMENT_FILE environment.cfg # File that describes the environment
-START_CREATURE organism.default # Organism to seed the soup
-
-### Reproduction ###
-BIRTH_METHOD 4 # 0 = Replace random organism in neighborhood
- # 1 = Replace oldest organism in neighborhood
- # 2 = Replace largest Age/Merit in neighborhood
- # 3 = Place only in empty cells in neighborhood
- # 4 = Replace random from entire population (Mass Action)
- # 5 = Replace oldest in entire population (like Tierra)
-PREFER_EMPTY 1 # Are empty cells given preference in offspring placement?
-DEATH_METHOD 2 # 0 = Never die of old age.
- # 1 = Die when inst executed = AGE_LIMIT (with deviation)
- # 2 = Die when inst executed = length * AGE_LIMIT (+ dev.)
-AGE_LIMIT 20 # Modifies DEATH_METHOD
-AGE_DEVIATION 0 # Modified DEATH_METHOD
-ALLOC_METHOD 0 # 0 = Allocated space is set to default instruction.
- # 1 = Set to section of dead genome (Necrophilia)
- # 2 = Allocated space is set to random instruction.
-DIVIDE_METHOD 1 # 0 = Divide leaves state of mother untouched.
- # 1 = Divide resets state of mother
- # (after the divide, we have 2 children)
-
-GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
- # increased on divide.
- # 1 = Both the generation of the mother and child are
- # increased on divide (good with DIVIDE_METHOD 1).
-
-### Divide Restrictions ####
-CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
-MIN_COPIED_LINES 0.5 # Code fraction which must be copied before divide.
-MIN_EXE_LINES 0.5 # Code fraction which must be executed before divide.
-REQUIRE_ALLOCATE 1 # Is a an allocate required before a divide? (0/1)
-REQUIRED_TASK -1 # Number of task required for successful divide.
-
-### Mutations ###
-
-# mutations that occur during execution..
-POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
-COPY_MUT_PROB 0.0075 # Mutation rate (per copy).
-
-# mutations that occur on divide...
-INS_MUT_PROB 0.0 # Insertion rate (per site, applied on divide).
-DEL_MUT_PROB 0.0 # Deletion rate (per site, applied on divide).
-DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide).
-DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide).
-DIVIDE_INS_PROB 0.05 # Insertion rate (per divide).
-DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide).
-PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
-
-# heads based mutations
-# READ_SHIFT_PROB 0.0
-# READ INS_PROB 0.0
-# READ_DEL_PROB 0.0
-# WRITE_SHIFT_PROB 0.0
-# WRITE_INS_PROB 0.0
-# WRITE_DEL_PROB 0.0
-
-
-### Mutation reversions ###
-# these slow down avida a lot, and should be set to 0 normally.
-REVERT_FATAL 0.0 # Should any mutations be reverted on birth?
-REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
-REVERT_NEUTRAL 0.0
-REVERT_BENEFICIAL 0.0
-
-STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
-STERILIZE_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reset.
-STERILIZE_NEUTRAL 0.0
-STERILIZE_BENEFICIAL 0.0
-
-FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
- # be eliminated?
-
-### Time Slicing ###
-AVE_TIME_SLICE 30
-SLICING_METHOD 2 # 0 = CONSTANT: all organisms get default...
- # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
- # 2 = INTEGRATED: Perfectly integrated deterministic.
-SIZE_MERIT_METHOD 4 # 0 = off (merit is independent of size)
- # 1 = Merit proportional to copied size
- # 2 = Merit prop. to executed size
- # 3 = Merit prop. to full size
- # 4 = Merit prop. to min of executed or copied size
- # 5 = Merit prop. to sqrt of the minimum size
-TASK_MERIT_METHOD 1 # 0 = No task bonuses
- # 1 = Bonus just equals the task bonus
-THREAD_SLICING_METHOD 0 # 0 = One thread executed per time slice.
- # 1 = All threads executed each time slice.
-
-MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
-MERIT_TIME 1 # 0 = Merit Calculated when task completed
- # 1 = Merit Calculated on Divide
-MAX_NUM_TASKS_REWARDED -1 # -1 = Unlimited
-
-### Genotype Info ###
-THRESHOLD 3 # Number of organisms in a genotype needed for it
- # to be considered viable.
-GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
-GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
- # this many updates. (0 = off)
-SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
-SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
-SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
-TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
-TRACK_MAIN_LINEAGE 1 # Track primary lineage leading to final population?
-
-### Log Files ###
-LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
-LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
-LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
-LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
-LOG_LANDSCAPE 0 # 0/1 (off/on) toggle to print file.
-
-LOG_LINEAGES 0 # 0/1 (off/on) to log advantageous mutations
-# This one can slow down avida a lot. It is used to get an idea of how
-# often an advantageous mutation arises, and where it goes afterwards.
-# See also LINEAGE_CREATION_METHOD.
-
-LINEAGE_CREATION_METHOD 0
-# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
-# 0 = manual creation (on inject, use successive integers as lineage labels).
-# 1 = when a child's (potential) fitness is higher than that of its parent.
-# 2 = when a child's (potential) fitness is higher than max in population.
-# 3 = when a child's (potential) fitness is higher than max in dom. lineage
-# *and* the child is in the dominant lineage, or (2)
-# 4 = when a child's (potential) fitness is higher than max in dom. lineage
-# (and that of its own lineage)
-# 5 = same as child's (potential) fitness is higher than that of the
-# currently dominant organism, and also than that of any organism
-# currently in the same lineage.
-# 6 = when a child's (potential) fitness is higher than any organism
-# currently in the same lineage.
-# 7 = when a child's (potential) fitness is higher than that of any
-# organism in its line of descent
-
-### END ###
-
-
Copied: tags/2.4.4/source/support/genesis (from rev 952, trunk/source/support/genesis)
More information about the Avida-cvs
mailing list