[Avida-SVN] r3268 - in development: source/analyze tests tests/collect_specification_analyze tests/collect_specification_analyze/config tests/collect_specification_analyze/expected tests/collect_specification_analyze/expected/data
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Fri May 29 08:01:17 PDT 2009
Author: blwalker
Date: 2009-05-29 11:01:17 -0400 (Fri, 29 May 2009)
New Revision: 3268
Added:
development/tests/collect_specification_analyze/
development/tests/collect_specification_analyze/config/
development/tests/collect_specification_analyze/config/analyze-spec.cfg
development/tests/collect_specification_analyze/config/avida.cfg
development/tests/collect_specification_analyze/config/default-classic.org
development/tests/collect_specification_analyze/config/detail-200000.pop
development/tests/collect_specification_analyze/config/environment.9resource
development/tests/collect_specification_analyze/config/events-collect.cfg
development/tests/collect_specification_analyze/config/instset-destroy.cfg
development/tests/collect_specification_analyze/expected/
development/tests/collect_specification_analyze/expected/data/
development/tests/collect_specification_analyze/expected/data/executed.dat
development/tests/collect_specification_analyze/test_list
Modified:
development/source/analyze/cAnalyzeGenotype.cc
development/source/analyze/cAnalyzeGenotype.h
Log:
DETAIL options for outputting collected "collect"-type nop-specification information. (Note that all specifications for all collect-type instructions used are bundled together -- this is not best used with more than one instruction of this type.) Test included, documentation to follow.
Modified: development/source/analyze/cAnalyzeGenotype.cc
===================================================================
--- development/source/analyze/cAnalyzeGenotype.cc 2009-05-28 19:04:15 UTC (rev 3267)
+++ development/source/analyze/cAnalyzeGenotype.cc 2009-05-29 15:01:17 UTC (rev 3268)
@@ -82,6 +82,7 @@
, internal_task_qualities(0)
, rbins_total(0)
, rbins_avail(0)
+ , collect_spec_counts(0)
, fitness_ratio(0.0)
, efficiency_ratio(0.0)
, comp_merit_ratio(0.0)
@@ -136,6 +137,7 @@
, internal_task_qualities(0)
, rbins_total(0)
, rbins_avail(0)
+ , collect_spec_counts(0)
, fitness_ratio(0.0)
, efficiency_ratio(0.0)
, comp_merit_ratio(0.0)
@@ -179,6 +181,7 @@
, internal_task_qualities(_gen.internal_task_qualities)
, rbins_total(_gen.rbins_total)
, rbins_avail(_gen.rbins_avail)
+ , collect_spec_counts(_gen.collect_spec_counts)
, fitness_ratio(_gen.fitness_ratio)
, efficiency_ratio(_gen.efficiency_ratio)
, comp_merit_ratio(_gen.comp_merit_ratio)
@@ -331,6 +334,8 @@
("r_avail", &cAnalyzeGenotype::DescRAvail, &cAnalyzeGenotype::GetRBinAvail));
dcm->Add("prob_task", new tDataEntryOfType<cAnalyzeGenotype, double (int)>
("prob_task", &cAnalyzeGenotype::DescTaskProb, &cAnalyzeGenotype::GetTaskProbability, 5));
+ dcm->Add("r_spec", new tDataEntryOfType<cAnalyzeGenotype, int (int)>
+ ("r_spec", &cAnalyzeGenotype::DescRSpec, &cAnalyzeGenotype::GetRSpec));
// The remaining values should actually go in a separate list called
@@ -611,6 +616,7 @@
internal_task_qualities = likely_phenotype->GetLastInternalTaskQuality();
rbins_total = likely_phenotype->GetLastRBinsTotal();
rbins_avail = likely_phenotype->GetLastRBinsAvail();
+ collect_spec_counts = likely_phenotype->GetLastCollectSpecCounts();
// Setup a new parent stats if we have a parent to work with.
if (parent_genotype != NULL) {
Modified: development/source/analyze/cAnalyzeGenotype.h
===================================================================
--- development/source/analyze/cAnalyzeGenotype.h 2009-05-28 19:04:15 UTC (rev 3267)
+++ development/source/analyze/cAnalyzeGenotype.h 2009-05-29 15:01:17 UTC (rev 3268)
@@ -159,6 +159,7 @@
tArray<double> internal_task_qualities;
tArray<double> rbins_total;
tArray<double> rbins_avail;
+ tArray<int> collect_spec_counts;
tArray<int> m_env_inputs;
// Group 3 : Stats requiring parental genotype (Also from test CPUs)
@@ -458,6 +459,12 @@
return rbins_avail[resource_id];
}
cString DescRAvail(int resource_id) const { return cStringUtil::Stringf("Resource %d Available", resource_id);}
+
+ int GetRSpec(int spec_id) const {
+ if (spec_id >= collect_spec_counts.GetSize() || spec_id < 0) return -1;
+ return collect_spec_counts[spec_id];
+ }
+ cString DescRSpec(int spec_id) const { return cStringUtil::Stringf("# times specification %d used", spec_id);}
// Comparisons... Compares a genotype to the "previous" one, which is
// passed in, in one specified phenotype.
Added: development/tests/collect_specification_analyze/config/analyze-spec.cfg
===================================================================
--- development/tests/collect_specification_analyze/config/analyze-spec.cfg (rev 0)
+++ development/tests/collect_specification_analyze/config/analyze-spec.cfg 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,16 @@
+#############################################################################
+# This file is used to setup avida when it is in analysis-only mode (by
+# running "avida -a". It allows variety of methods to load organisms
+# (specifying the type of each) and analyze them once loaded.
+#
+# See the documentation in doc/analyze_mode.html for usage, or the file
+# doc/analyze_samples.html for guidelines on writing programs.
+#
+#############################################################################
+
+VERBOSE
+
+LOAD detail-200000.pop
+RECALCULATE 1
+DETAIL executed.dat inst.26 task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 sequence num_cpus length merit exe_length gest_time fitness r_spec.0 r_spec.1 r_spec.2 r_spec.3 r_spec.4 r_spec.5 r_spec.6 r_spec.7 r_spec.8 r_spec.9 r_spec.10 r_spec.11 r_spec.12
+PURGE_BATCH
Added: development/tests/collect_specification_analyze/config/avida.cfg
===================================================================
--- development/tests/collect_specification_analyze/config/avida.cfg (rev 0)
+++ development/tests/collect_specification_analyze/config/avida.cfg 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,241 @@
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.7.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 1 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 1 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+VERBOSITY 1 # Control output verbosity
+
+### ARCH_GROUP ###
+# Architecture Variables
+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 SMT CPUs
+ # 2 = Transitional SMT
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET instset-destroy.cfg # File containing instruction set
+EVENT_FILE events-collect.cfg # File containing list of events during run
+ANALYZE_FILE analyze-spec.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment.9resource # File that describes the environment
+START_CREATURE default-classic.org # Organism to seed the soup
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 0 # Which organism should be replaced on birth?
+ # 0 = Random organism in neighborhood
+ # 1 = Oldest in neighborhood
+ # 2 = Largest Age/Merit in neighborhood
+ # 3 = None (use only empty cells in neighborhood)
+ # 4 = Random from population (Mass Action)
+ # 5 = Oldest in entire population
+ # 6 = Random within deme
+ # 7 = Organism faced by parent
+ # 8 = Next grid cell (id+1)
+ # 9 = Largest energy used in entire population
+ # 10 = Largest energy used in neighborhood
+PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
+ALLOW_PARENT 1 # Allow births to replace the parent organism?
+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_GROUP ###
+# Sexual Recombination and Modularity
+RECOMBINATION_PROB 1.0 # probability of recombination in div-sex
+MAX_BIRTH_WAIT_TIME -1 # Updates incipiant orgs can wait for crossover
+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 randomly
+ # or with corresponding positions?
+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 # (Original CPU Only) Require allocate before divide?
+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.
+REQUIRED_BONUS 0 # The bonus that an organism must accumulate to divide.
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0025 # 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
+INJECT_INS_PROB 0.0 # Insertion rate (per site, applied on inject)
+INJECT_DEL_PROB 0.0 # Deletion rate (per site, applied on inject)
+INJECT_MUT_PROB 0.0 # Mutation rate (per site, applied on inject)
+META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
+META_STD_DEV 0.0 # Standard deviation of meta mutation size.
+MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
+ # 2 = Mutation rates inherited from parent.
+
+### 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 1 # Should copies that failed *not* due to mutations
+ # be eliminated?
+NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness to be considered neutral.
+NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness to be considered neutral.
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+BASE_MERIT_METHOD 4 # 0 = Constant (merit 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
+BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
+DEFAULT_BONUS 1.0 # Initial bonus before any tasks
+MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by the default bonus
+ # rather than the accumulated bonus of the parent?
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
+ # (num_threads-1) * THREAD_SLICING_METHOD + 1
+ # 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
+DONATE_SIZE 5.0 # Amount of merit donated with 'donate' command
+DONATE_MULT 10.0 # Multiple of merit given that the target receives.
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on edit distance for donate; -1=no max
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+
+### PROMOTER_GROUP ###
+# Promoters
+PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
+ # Certain instructions must also be included.
+PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating before executing each instruction.
+PROMOTER_BG_STRENGTH 0 # Probability of positions that are not promoter
+ # instructions initiating execution (promoters are 1).
+REGULATION_STRENGTH 1 # Strength added or subtracted to a promoter by regulation.
+REGULATION_DECAY_FRAC 0.1 # Fraction of regulation that decays away.
+ # (Max regulation = REGULATION_STRENGTH / REGULATION_DECAY_FRAC)
+
+### 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 #
+
+### ORGANISM_NETWORK_GROUP ###
+# Organism Network Communication
+NET_ENABLED 0 # Enable Network Communication Support
+NET_DROP_PROB 0.0 # Message drop rate
+NET_MUT_PROB 0.0 # Message corruption probability
+NET_MUT_TYPE 0 # Type of message corruption. 0 = Random Single Bit, 1 = Always Flip Last
+NET_STYLE 0 # Communication Style. 0 = Random Next, 1 = Receiver Facing
+
+### BUY_SELL_GROUP ###
+# Buying and Selling Parameters
+SAVE_RECEIVED 0 # Enable storage of all inputs bought from other orgs
+BUY_PRICE 0 # price offered by organisms attempting to buy
+SELL_PRICE 0 # price offered by organisms attempting to sell
+
+### HOARD_RESOURCE_GROUP ###
+USE_RESOURCE_BINS 1
+ABSORB_RESOURCE_FRACTION .0025
+MULTI_ABSORB_TYPE 0
+USE_STORED_FRACTION 0.0
+RETURN_STORED_ON_DEATH 1
+
+### ANALYZE_GROUP ###
+# Analysis Settings
+MT_CONCURRENCY 1 # Number of concurrent analyze threads
+ANALYZE_OPTION_1 # String variable accessible from analysis scripts
+ANALYZE_OPTION_2 # String variable accessible from analysis scripts
Added: development/tests/collect_specification_analyze/config/default-classic.org
===================================================================
--- development/tests/collect_specification_analyze/config/default-classic.org (rev 0)
+++ development/tests/collect_specification_analyze/config/default-classic.org 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+h-search # Mark the beginning of the copy loop
+h-copy # Do the copy
+if-label # If we're done copying....
+nop-C #
+nop-A #
+h-divide # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Added: development/tests/collect_specification_analyze/config/detail-200000.pop
===================================================================
--- development/tests/collect_specification_analyze/config/detail-200000.pop (rev 0)
+++ development/tests/collect_specification_analyze/config/detail-200000.pop 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,23 @@
+#filetype genotype_data
+#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
+
+# 1: ID
+# 2: parent ID
+# 3: parent distance
+# 4: number of organisms currently alive
+# 5: total number of organisms that ever existed
+# 6: length of genome
+# 7: merit
+# 8: gestation time
+# 9: fitness
+# 10: update born
+# 11: update deactivated
+# 12: depth in phylogentic tree
+# 13: genome of organism
+
+4335143 4333347 -1 1043 887133 106 6907.63 1518 4.55048 99642 -1 393 rhuucavczebAqrjgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab
+4322574 4321310 -1 834 480241 102 6509.31 1436 4.53295 98644 -1 394 ArpucavczmnqrhAsnndlosimuqhcmptflqtlpwwaxkzunqqcdpqpclbtncogcAqchhmdfctpaoqcgqfmocloytpyaofahofycasvab
+4333347 4325270 -1 759 916175 106 6906.83 1518 4.54995 99498 -1 392 rhuucavczebAqrbgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab
+4329568 4327105 -1 574 584475 119 10590.8 2334 4.53763 99200 -1 410 rxuczaagvcjzjkcdqeadffpmxpmomtqodpdbzitgiyshebinlzsnnygunqtppqpdlceqnccptgcqcAAacycgfckaqfigfcqdetqcfbjpbapccecfycasvab
+4334827 4328326 -1 243 209369 112 9180.82 2045 4.4894 99619 -1 416 rxucajgvcczjkcAqkridrmbpmzAmtqodndhigftsuhebazfbylulnqtppqplceqncpbtgcqcAAacycgfckaqfigfcqdetqcfbjpbpccejycasvab
+4325402 4310669 -1 147 194622 107 8886.23 1966 4.51995 98865 -1 400 rxucavcczykfctfnfjmzpsqtodfpchzbxjheyitznruulnqtppqpclceuncptgcqcAAacycefckaqigfcqAetqcfbkpkapcceaAycasvrab
Property changes on: development/tests/collect_specification_analyze/config/detail-200000.pop
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/collect_specification_analyze/config/environment.9resource
===================================================================
--- development/tests/collect_specification_analyze/config/environment.9resource (rev 0)
+++ development/tests/collect_specification_analyze/config/environment.9resource 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,33 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This environmental setup is that of a chemostat with 9 resources, each
+# with a unique task corresponding to them. All resources have a set inflow
+# of 100, and outflow rate of 0.01, setting their an equilibrium level at
+# 10,000. Given a maximum population size of 3600 and neighborhood size of
+# 9, the fraction of the resource absorbable in each reaction is simply
+# 9/3600 or 0.0025.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+RESOURCE resNOT:inflow=100:outflow=0.01 resNAND:inflow=100:outflow=0.01
+RESOURCE resAND:inflow=100:outflow=0.01 resORN:inflow=100:outflow=0.01
+RESOURCE resOR:inflow=100:outflow=0.01 resANDN:inflow=100:outflow=0.01
+RESOURCE resNOR:inflow=100:outflow=0.01 resXOR:inflow=100:outflow=0.01
+RESOURCE resEQU:inflow=100:outflow=0.01
+
+REACTION NOT not process:resource=resNOT:value=1.0:frac=0.0025:max=25
+REACTION NAND nand process:resource=resNAND:value=1.0:frac=0.0025:max=25
+REACTION AND and process:resource=resAND:value=2.0:frac=0.0025:max=25
+REACTION ORN orn process:resource=resORN:value=2.0:frac=0.0025:max=25
+REACTION OR or process:resource=resOR:value=4.0:frac=0.0025:max=25
+REACTION ANDN andn process:resource=resANDN:value=4.0:frac=0.0025:max=25
+REACTION NOR nor process:resource=resNOR:value=8.0:frac=0.0025:max=25
+REACTION XOR xor process:resource=resXOR:value=8.0:frac=0.0025:max=25
+REACTION EQU equ process:resource=resEQU:value=16.0:frac=0.0025:max=25
Added: development/tests/collect_specification_analyze/config/events-collect.cfg
===================================================================
--- development/tests/collect_specification_analyze/config/events-collect.cfg (rev 0)
+++ development/tests/collect_specification_analyze/config/events-collect.cfg 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,38 @@
+##############################################################################
+#
+# This is the setup file for the events system. From here, you can
+# configure any actions that you want to have happen during the course of
+# an experiment, including setting the times for data collection.
+#
+# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
+#
+# This file is currently setup to record key information every 100 updates.
+#
+# For information on how to use this file, see: doc/events.html
+# For other sample event configurations, see: support/config/
+#
+##############################################################################
+
+# Print all of the standard data files...
+u 0:100:end PrintAverageData # Save info about they average genotypes
+u 0:100:end PrintDominantData # Save info about most abundant genotypes
+u 0:100:end PrintStatsData # Collect satistics about entire pop.
+u 0:100:end PrintCountData # Count organisms, genotypes, species, etc.
+u 0:100:end PrintTasksData # Save organisms counts for each task.
+u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
+u 0:100:end PrintResourceData # Track resource abundance.
+
+u 100:100:end PrintTasksQualData # Task quality information
+u 0:100:end PrintInternalTasksData
+u 0:100:end PrintInternalTasksQualData
+
+# Setup the full population data collection.
+u 50000:50000 SavePopulation # Save current state of population.
+u 50000:50000 SaveHistoricPopulation # Save ancestors of current population.
+
+# Start the ecological period
+u 100000 ZeroMuts # Set all mutation rates to 0, starting eco phase
+
+# Do final population data collection and exit
+u 200000 PrintDominantGenotype
+u 200000 exit # exit
Added: development/tests/collect_specification_analyze/config/instset-destroy.cfg
===================================================================
--- development/tests/collect_specification_analyze/config/instset-destroy.cfg (rev 0)
+++ development/tests/collect_specification_analyze/config/instset-destroy.cfg 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,53 @@
+nop-A 1 # a
+nop-B 1 # b
+nop-C 1 # c
+if-n-equ 1 # d
+if-less 1 # e
+pop 1 # f
+push 1 # g
+swap-stk 1 # h
+swap 1 # i
+shift-r 1 # j
+shift-l 1 # k
+inc 1 # l
+dec 1 # m
+add 1 # n
+sub 1 # o
+nand 1 # p
+IO 1 # q Puts current contents of register and gets new.
+h-alloc 1 # r Allocate as much memory as organism can use.
+h-divide 1 # s Cuts off everything between the read and write heads
+h-copy 1 # t Combine h-read and h-write
+h-search 1 # u Search for matching template, set flow head & return info
+ # # if no template, move flow-head here, set size&offset=0.
+mov-head 1 # v Move ?IP? head to flow control.
+jmp-head 1 # w Move ?IP? head by fixed amount in CX. Set old pos in CX.
+get-head 1 # x Get position of specified head in CX.
+if-label 1 # y
+set-flow 1 # z Move flow-head to address in ?CX?
+destroy 1
+
+#adv-head 1
+#jump-f 1
+#jump-b 1
+#call 1
+#return 1
+#if-bit-1 1
+#get 1
+#put 1
+#h-read 1
+#h-write 1
+#set-head 1
+#search-f 1
+#search-b 1
+
+
+# Works on multiple nops: pop push inc dec IO adv-head
+
+# What if we add a new head. Search will return the location of something,
+# and put the new head there. Then set-head will move another head to that
+# point. In the case of the copy loop, it only needs to be set once and
+# this will speed up the code quite a bit!
+
+# Search with no template returns current position (abs line number) in
+# genome.
\ No newline at end of file
Added: development/tests/collect_specification_analyze/expected/data/executed.dat
===================================================================
--- development/tests/collect_specification_analyze/expected/data/executed.dat (rev 0)
+++ development/tests/collect_specification_analyze/expected/data/executed.dat 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,41 @@
+#filetype genotype_data
+#format inst task task task task task task task task task sequence num_cpus length merit exe_length gest_time fitness r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec
+
+# Legend:
+# 1: # Times destroy Executed
+# 2: Not
+# 3: Nand
+# 4: And
+# 5: OrNot
+# 6: Or
+# 7: AndNot
+# 8: Nor
+# 9: Xor
+# 10: Equals
+# 11: Genome Sequence
+# 12: Number of CPUs
+# 13: Genome Length
+# 14: Merit
+# 15: Executed Length
+# 16: Gestation Time
+# 17: Fitness
+# 18: # times specification 0 used
+# 19: # times specification 1 used
+# 20: # times specification 2 used
+# 21: # times specification 3 used
+# 22: # times specification 4 used
+# 23: # times specification 5 used
+# 24: # times specification 6 used
+# 25: # times specification 7 used
+# 26: # times specification 8 used
+# 27: # times specification 9 used
+# 28: # times specification 10 used
+# 29: # times specification 11 used
+# 30: # times specification 12 used
+
+112 0 0 0 37 0 74 0 36 36 rhuucavczebAqrjgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab 1043 106 102 102 1518 0.0671937 75 0 37 0 0 0 0 0 0 0 0 0 0
+37 0 35 0 0 0 70 0 0 68 ArpucavczmnqrhAsnndlosimuqhcmptflqtlpwwaxkzunqqcdpqpclbtncogcAqchhmdfctpaoqcgqfmocloytpyaofahofycasvab 834 102 99 99 1436 0.0689415 37 0 0 0 0 0 0 0 0 0 0 0 0
+112 0 0 0 37 0 74 0 36 36 rhuucavczebAqrbgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab 759 106 102 102 1518 0.0671937 75 0 37 0 0 0 0 0 0 0 0 0 0
+114 56 0 0 0 116 0 164 0 0 rxuczaagvcjzjkcdqeadffpmxpmomtqodpdbzitgiyshebinlzsnnygunqtppqpdlceqnccptgcqcAAacycgfckaqfigfcqdetqcfbjpbapccecfycasvab 574 119 116 116 2334 0.0497001 57 0 0 0 0 0 57 0 0 0 0 0 0
+110 54 0 0 0 108 0 157 0 0 rxucajgvcczjkcAqkridrmbpmzAmtqodndhigftsuhebazfbylulnqtppqplceqncpbtgcqcAAacycgfckaqfigfcqdetqcfbjpbpccejycasvab 243 112 106 106 2045 0.0518337 56 0 0 0 0 0 54 0 0 0 0 0 0
+159 52 51 153 0 51 0 0 0 0 rxucavcczykfctfnfjmzpsqtodfpchzbxjheyitznruulnqtppqpclceuncptgcqcAAacycefckaqigfcqAetqcfbkpkapcceaAycasvrab 147 107 99 99 1966 0.0503561 107 0 0 0 0 0 52 0 0 0 0 0 0
Added: development/tests/collect_specification_analyze/test_list
===================================================================
--- development/tests/collect_specification_analyze/test_list (rev 0)
+++ development/tests/collect_specification_analyze/test_list 2009-05-29 15:01:17 UTC (rev 3268)
@@ -0,0 +1,37 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+; Command line arguments to pass to the application
+args = -s 4927 -a
+
+app = %(default_app)s ; Application path to test
+nonzeroexit = disallow ; Exit code handling (disallow, allow, or require)
+ ; disallow - treat non-zero exit codes as failures
+ ; allow - all exit codes are acceptable
+ ; require - treat zero exit codes as failures, useful
+ ; for creating tests for app error checking
+createdby = blw ; Who created the test
+email = blwalker at egr.msu.edu ; Email address for the test's creator
+
+[consistency]
+enabled = yes ; Is this test a consistency test?
+long = no ; Is this test a long test?
+
+[performance]
+enabled = no ; Is this test a performance test?
+long = no ; Is this test a long test?
+
+; The following variables can be used in constructing setting values by calling
+; them with %(variable_name)s. For example see 'app' above.
+;
+; builddir
+; cpus
+; default_app
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
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