[Avida-cvs] [avida-svn] r511 - in trunk/consistencytests: . CMakeModules/Templates Tests/Researchers/dule/LocalSex Tests/Researchers/dule/LocalSex/config
kaben@myxo.css.msu.edu
kaben at myxo.css.msu.edu
Mon Mar 13 11:11:48 PST 2006
Author: kaben
Date: 2006-03-13 14:11:47 -0500 (Mon, 13 Mar 2006)
New Revision: 511
Modified:
trunk/consistencytests/CMakeLists.txt
trunk/consistencytests/CMakeModules/Templates/check_tails.py.in
trunk/consistencytests/Tests/Researchers/dule/LocalSex/CMakeLists.txt
trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/genesis
Log:
Updated genesis file for dule's LocalSex consistency tests.
Modified: trunk/consistencytests/CMakeLists.txt
===================================================================
--- trunk/consistencytests/CMakeLists.txt 2006-03-13 17:39:36 UTC (rev 510)
+++ trunk/consistencytests/CMakeLists.txt 2006-03-13 19:11:47 UTC (rev 511)
@@ -16,7 +16,7 @@
ENDIF(_AvidaExePath)
FIND_PROGRAM(_PythonExePath
- NAMES python python2.3
+ NAMES python python2.3 python2.4
DOC "Where can the Python executable be found ?"
)
IF(_PythonExePath)
@@ -34,3 +34,6 @@
SET(AvidaConsistencyChecksPythonSiteDir "${PROJECT_SOURCE_DIR}/Support/python")
SUBDIRS(Tests)
+
+# Vim modeline to tell Vim that this is a configuration script.
+# vim: set ft=config:
Modified: trunk/consistencytests/CMakeModules/Templates/check_tails.py.in
===================================================================
--- trunk/consistencytests/CMakeModules/Templates/check_tails.py.in 2006-03-13 17:39:36 UTC (rev 510)
+++ trunk/consistencytests/CMakeModules/Templates/check_tails.py.in 2006-03-13 19:11:47 UTC (rev 511)
@@ -27,8 +27,7 @@
for seed, lines in tail_checker.failures_dict.iteritems():
print 'Seed', seed, 'produced unexpected last line in file', output_file_name, ':'
- print lines[0]
- print 'Expected last line in file', expectation_file_name, ':'
+ print lines[0], 'Expected last line in file', expectation_file_name, ':'
print lines[1]
sys.exit(len(tail_checker.failures_dict))
Modified: trunk/consistencytests/Tests/Researchers/dule/LocalSex/CMakeLists.txt
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/CMakeLists.txt 2006-03-13 17:39:36 UTC (rev 510)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/CMakeLists.txt 2006-03-13 19:11:47 UTC (rev 511)
@@ -24,7 +24,7 @@
#
# This is Python list of Avida random seeds.
-# E.g., "range(100,15)" is equivalent to the Python list "[100,101,102,103,104]".
+# E.g., "range(100,105)" is equivalent to the Python list "[100,101,102,103,104]".
# I.e., SET(SeedSet "range(100,105)") is equivalent to SET(SeedSet "[100,101,102,103,104]").
SET(SeedSet "range(100,110)")
# Avida will be run in, and store output files in, ${CMAKE_CURRENT_BINARY_DIR}/Test_100, and so on.
Modified: trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/genesis
===================================================================
--- trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/genesis 2006-03-13 17:39:36 UTC (rev 510)
+++ trunk/consistencytests/Tests/Researchers/dule/LocalSex/config/genesis 2006-03-13 19:11:47 UTC (rev 511)
@@ -3,160 +3,169 @@
# For more information, see doc/genesis.html
#############################################################################
-VERSION_ID 1.99 # Do not change this value!
+# blah
+#############################################################################
+# This file includes all the basic run-time defines for avida.
+# For more information, see doc/genesis.html
+#############################################################################
+
+VERSION_ID 2.4.3 # 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.
-MAX_CPU_THREADS 1 # Number of Threads CPU's can spawn
-RANDOM_SEED 0 # Random number seed. (0 for based on time)
+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 0 # 0 = Original CPUs
+ # 1 = New, Stack-based CPUs
### Configuration Files ###
DEFAULT_DIR ../work/ # Directory in which config files are found
-INST_SET inst_set.asex # File containing instruction set
+INST_SET inst_set.asex # 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.100.asex # Organism to seed the soup
+START_CREATURE organism.100.asex # Organism to seed the soup
-### Reproduction ###
-BIRTH_METHOD 0 # 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)
-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)
+### Birth and Death ###
+BIRTH_METHOD 0 # 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 # 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 # 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
-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 0.95 # Code fraction which must be copied before divide.
+MIN_EXE_LINES 0.05 # Code fraction which must be executed before divide.
+REQUIRE_ALLOCATE 1 # 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 # probability of death when 'die' instruction is executed
-### Divide Restrictions ####
-CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
-MIN_COPIED_LINES 0.95 # Code fraction which must be copied before divide.
-MIN_EXE_LINES 0.05 # 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 ###
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0 # Mutation rate (per copy)
+INS_MUT_PROB 0.0005 # Insertion rate (per site, applied on divide)
+DEL_MUT_PROB 0.0005 # Deletion rate (per site, applied on divide)
+DIV_MUT_PROB 0.002 # Mutation rate (per site, applied on divide)
+DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
+DIVIDE_INS_PROB 0.0 # Insertion rate (per divide)
+DIVIDE_DEL_PROB 0.0 # 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
-# mutations that occur during execution..
-POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
-COPY_MUT_PROB 0.0 # Mutation rate (per copy).
-
-# mutations that occur on divide...
-INS_MUT_PROB 0.0005 # Insertion rate (per site, applied on divide).
-DEL_MUT_PROB 0.0005 # Deletion rate (per site, applied on divide).
-DIV_MUT_PROB 0.002 # Mutation rate (per site, applied on divide).
-DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide).
-DIVIDE_INS_PROB 0.0 # Insertion rate (per divide).
-DIVIDE_DEL_PROB 0.0 # 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
-
-MUT_RATE_SOURCE 0 # 0 = Organisms get mut rates from the environment
- # 1 = ... from their parents
-MUT_RATE_INC 0.0 # Probability of mutation rates increasing... (at birth)
-MUT_RATE_DEC 0.0 # Probability of mutation rates decreasing... (at birth)
-MUT_CHANGE_FACTOR 1.0 # Factor by which mutation rates change (must be >= 1.0)
-
-MUT_RATE_FLOOR 0.0 # Lowest possible mutation rate (for MUT_RATE_SOURCE=1)
-MUT_RATE_CEILING 1.0 # Highest possible mutation rate (for MUT_RATE_SOURCE=1)
-
-### 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?
+### 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 # 0.0 to 1.0; Probability of reset.
-STERILIZE_NEUTRAL 0.0
-STERILIZE_BENEFICIAL 0.0
+STERILIZE_NEUTRAL 0.0 #
+STERILIZE_BENEFICIAL 0.0 #
+FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
+ # be eliminated?
-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.
+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 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
+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 # The bonus an organism gets before it has completed any tasks
+MERIT_TIME 1 # 0 = Merit Calculated when task completed
+ # 1 = Merit Calculated on Divide
+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.
-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
+### 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)
-### 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_GENEOLOGY 0 # 0 = off, 1 = all, 2 = parents only.
-LOG_LANDSCAPE 0 # 0/1 (off/on) toggle to print file.
+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
+### Viewer Settings ###
+VIEW_MODE 0 # Initial viewer screen
+
+### 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.
-# 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)
+# *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)
+# (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.
@@ -164,10 +173,5 @@
# currently in the same lineage.
# 7 = when a child's (potential) fitness is higher than that of any
# organism in its line of descent
-
-### Debug ###
-DEBUG_LEVEL 2 # 0 = ERRORS ONLY, 1 = WARNINGS, 2 = COMMENTS
-
-### END ###
-
-
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
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