[Avida-cvs] [avida-svn] r554 - in development: . consistencytests consistencytests/Tests consistencytests/Tests/Default source source/support source/tools
kaben@myxo.css.msu.edu
kaben at myxo.css.msu.edu
Mon Apr 3 15:04:46 PDT 2006
Author: kaben
Date: 2006-04-03 18:04:39 -0400 (Mon, 03 Apr 2006)
New Revision: 554
Added:
development/source/support/avida-smt.cfg
Modified:
development/CMakeLists.txt
development/consistencytests/CMakeLists.txt
development/consistencytests/Tests/CMakeLists.txt
development/consistencytests/Tests/Default/CMakeLists.txt
development/source/CMakeLists.txt
development/source/support/avida.cfg
development/source/tools/CMakeLists.txt
development/test_avida
Log:
Changes to consistency checks for development branch:
- disabled all but Default consistency checks.
- disabled old unit-test cruft.
- avida.cfg changed to match old genesis file.
- added avida-smt.cfg.
Modified: development/CMakeLists.txt
===================================================================
--- development/CMakeLists.txt 2006-04-03 21:30:43 UTC (rev 553)
+++ development/CMakeLists.txt 2006-04-03 22:04:39 UTC (rev 554)
@@ -167,9 +167,9 @@
IF(AVD_CONSISTENCY_TEST_PRIMITIVE)
IF(EXISTS ${PROJECT_SOURCE_DIR}/consistencytests)
SET(_AvidaExePath
- "${PROJECT_BINARY_DIR}/bin/primitive"
+ "${PROJECT_BINARY_DIR}/bin/avida"
CACHE FILEPATH
- "Where can the Avida executable 'primitive' be found ?"
+ "Where can the Avida executable 'avida' be found ?"
FORCE
)
SET(BUILD_TESTING TRUE)
Modified: development/consistencytests/CMakeLists.txt
===================================================================
--- development/consistencytests/CMakeLists.txt 2006-04-03 21:30:43 UTC (rev 553)
+++ development/consistencytests/CMakeLists.txt 2006-04-03 22:04:39 UTC (rev 554)
@@ -7,9 +7,9 @@
#SET(AvidaExePath "/Users/kaben/Projects/Software/Avida/branch.kaben/current--HEAD--cvs/build.cmake.dbg/bin/primitive")
#SET(PythonExePath "/sw/bin/python")
FIND_PROGRAM(_AvidaExePath
- NAMES primitive
+ NAMES avida
PATHS ${PROJECT_BINARY_DIR}
- DOC "Where can the Avida executable 'primitive' be found ?"
+ DOC "Where can the Avida executable 'avida' be found ?"
)
IF(_AvidaExePath)
SET(AvidaExePath_FOUND TRUE)
Modified: development/consistencytests/Tests/CMakeLists.txt
===================================================================
--- development/consistencytests/Tests/CMakeLists.txt 2006-04-03 21:30:43 UTC (rev 553)
+++ development/consistencytests/Tests/CMakeLists.txt 2006-04-03 22:04:39 UTC (rev 554)
@@ -1,2 +1,2 @@
SUBDIRS(Default)
-SUBDIRS(Researchers)
+#SUBDIRS(Researchers)
Modified: development/consistencytests/Tests/Default/CMakeLists.txt
===================================================================
--- development/consistencytests/Tests/Default/CMakeLists.txt 2006-04-03 21:30:43 UTC (rev 553)
+++ development/consistencytests/Tests/Default/CMakeLists.txt 2006-04-03 22:04:39 UTC (rev 554)
@@ -23,12 +23,12 @@
# Where to find default configure files.
SET(ConfigDir "${AVIDA_SOURCE_DIR}/source/support")
# Configure files (other than the event file, generated above).
-SET(GenesisFile "${ConfigDir}/genesis")
+SET(GenesisFile "${ConfigDir}/avida.cfg")
SET(InstSetFile "${ConfigDir}/inst_set.default")
SET(EnvironmentFile "${ConfigDir}/environment.cfg")
SET(StartCreatureFile "${ConfigDir}/organism.default")
# Command-line arguments passed to Avida.
-SET(AvidaArgs "-seed %d -set WORLD-X 40 -set WORLD-Y 40 -set INST_SET ${InstSetFile} -set EVENT_FILE ${EventFile} -set ENVIRONMENT_FILE ${EnvironmentFile} -set START_CREATURE ${StartCreatureFile}")
+SET(AvidaArgs "-c ${GenesisFile} -seed %d -set WORLD_X 40 -set WORLD_Y 40 -set INST_SET ${InstSetFile} -set EVENT_FILE ${EventFile} -set ENVIRONMENT_FILE ${EnvironmentFile} -set START_CREATURE ${StartCreatureFile} -set DATA_DIR .")
#
# Consistency checks configuration
Modified: development/source/CMakeLists.txt
===================================================================
--- development/source/CMakeLists.txt 2006-04-03 21:30:43 UTC (rev 553)
+++ development/source/CMakeLists.txt 2006-04-03 22:04:39 UTC (rev 554)
@@ -4,5 +4,5 @@
SUBDIRS(bindings python)
ENDIF(AVD_PY_BINDINGS)
IF(AVD_UNIT_TESTS)
- SUBDIRS(testsuites)
+ #SUBDIRS(testsuites)
ENDIF(AVD_UNIT_TESTS)
Added: development/source/support/avida-smt.cfg
===================================================================
--- development/source/support/avida-smt.cfg 2006-04-03 21:30:43 UTC (rev 553)
+++ development/source/support/avida-smt.cfg 2006-04-03 22:04:39 UTC (rev 554)
@@ -0,0 +1,183 @@
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.5.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 0 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 0 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+POPULATION_FILE - # Population file to load
+
+### ARCH_GROUP ###
+# Architecture Variables
+MAX_UPDATES -1 # Maximum updates to run experiment (-1 = no limit)
+MAX_GENERATIONS -1 # Maximum generations to run experiment (-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 Avida world
+WORLD_Y 60 # Height of the Avida world
+WORLD_GEOMETRY 2 # 1 = Bounded Grid
+ # 2 = Torus
+NUM_DEMES 0 # Number of independed groups in the population; 0=off
+RANDOM_SEED 0 # Random number seed (0 for based on time)
+HARDWARE_TYPE 2 # 0 = Original CPUs
+ # 1 = New, Stack-based CPUs
+ # 2 = Newer -- Stacks, Memory, Threading
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET inst_set.smt # 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.smt # Organism to seed the soup
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+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 population (Mass Action)
+ # 5 = Replace oldest in entire population (like Tierra)
+ # 6 = Replace random within deme
+PREFER_EMPTY 1 # Are empty cells given preference in offsping placement?
+DEATH_METHOD 2 # 0 = Never die of old age.
+ # 1 = Die when inst executed = AGE_LIMIT (+deviation)
+ # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
+AGE_LIMIT 20 # Modifies DEATH_METHOD
+AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
+ALLOC_METHOD 0 # (Orignal CPU Only)
+ # 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)
+ # 2 = Divide resets state of current thread only(does not touch possible parasite threads)
+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).
+RECOMBINATION_PROB 1.0 # probability that recombination will happen when div-sex is used
+MODULE_NUM 0 # number of modules in the genome
+CONT_REC_REGS 1 # are (modular) recombination regions continuous
+CORESPOND_REC_REGS 1 # are (modular) recombination regions swapped at random or with corresponding ones, by location
+TWO_FOLD_COST_SEX 0 # 1 = only one recombined offspring is born.
+ # 2 = both offspring are born
+SAME_LENGTH_SEX 0 # 0 = recombine with any genome
+ # 1 = only recombine w/ same length
+
+### DIVIDE_GROUP ###
+# 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 # (Origianl CPU Only) Is a an allocate required before a divide? (0/1)
+REQUIRED_TASK -1 # Task ID required for successful divide.
+IMMUNITY_TASK -1 # Task providing immunity from the required task.
+REQUIRED_REACTION -1 # Reaction ID required for successful divide.
+DIE_PROB 0.0 # probability of death when 'die' instruction is executed
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
+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
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+
+### REVERSION_GROUP ###
+# Mutation Reversion
+# These slow down avida a lot, and should be set to 0.0 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 #
+STERILIZE_NEUTRAL 0.0 #
+STERILIZE_BENEFICIAL 0.0 #
+FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
+ # be eliminated?
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 2 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+SIZE_MERIT_METHOD 0 # 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
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing -> 1 + (num_organism_threads-1) * THREAD_SLICING_METHOD.
+ # 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
+BASE_SIZE_MERIT 100 # Base merit when size is *not* used
+DEFAULT_BONUS 1.0 # The bonus an organism gets before it has completed any tasks
+MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
+MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+
+### GENEOLOGY_GROUP ###
+# Geneology
+TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
+ # 0=no, 1=yes, 2=yes,w/sexual population
+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)
+
+### LOG_GROUP ###
+# 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.
+
+### LINEAGE_GROUP ###
+# Lineage
+# NOTE: This should probably be called "Clade"
+# 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.
+# 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
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
Modified: development/source/support/avida.cfg
===================================================================
--- development/source/support/avida.cfg 2006-04-03 21:30:43 UTC (rev 553)
+++ development/source/support/avida.cfg 2006-04-03 22:04:39 UTC (rev 554)
@@ -27,7 +27,7 @@
# 2 = Torus
NUM_DEMES 0 # Number of independed groups in the population; 0=off
RANDOM_SEED 0 # Random number seed (0 for based on time)
-HARDWARE_TYPE 2 # 0 = Original CPUs
+HARDWARE_TYPE 0 # 0 = Original CPUs
# 1 = New, Stack-based CPUs
# 2 = Newer -- Stacks, Memory, Threading
@@ -119,7 +119,7 @@
SLICING_METHOD 2 # 0 = CONSTANT: all organisms get default...
# 1 = PROBABILISTIC: Run _prob_ proportional to merit.
# 2 = INTEGRATED: Perfectly integrated deterministic.
-SIZE_MERIT_METHOD 0 # 0 = off (merit is independent of size)
+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
Modified: development/source/tools/CMakeLists.txt
===================================================================
--- development/source/tools/CMakeLists.txt 2006-04-03 21:30:43 UTC (rev 553)
+++ development/source/tools/CMakeLists.txt 2006-04-03 22:04:39 UTC (rev 554)
@@ -38,6 +38,6 @@
ADD_LIBRARY(tools ${libtools_a_SOURCES})
IF(BUILD_TESTING)
- SUBDIRS(tests)
+ #SUBDIRS(tests)
ENDIF(BUILD_TESTING)
Modified: development/test_avida
===================================================================
--- development/test_avida 2006-04-03 21:30:43 UTC (rev 553)
+++ development/test_avida 2006-04-03 22:04:39 UTC (rev 554)
@@ -8,4 +8,4 @@
../
make
make install
-ctest --verbose -R Consistency
+ctest --verbose "$@"
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