More details¶
Occasionally it may happen that the system is not behaving as expected. As in generic computer programming, PeP also offers methods to analyze the execution.
In this example, the same input file as that used in An initial example will be used (input_files/input_example_3.pep)
One debugging tool is the step by step execution, that can be achieved using the --step` command line parameter.
The second debugging tool implies the -v command line parameter that increases the verbosity level.:
./pep.py input_files/input_example_3.pep -n 1 -v
With this parameter, the output of the simulator becomes:
INFO reading input file
DEBUG process_tokens (parent_type = <class 'NoneType'>, index = 0)
DEBUG token = 'num_ps'
DEBUG processing as GENERAL
DEBUG token = '='
DEBUG processing as GENERAL
INFO building NumericalPsystem
DEBUG process_tokens (parent_type = <class '__main__.NumericalPsystem'>, index = 2)
DEBUG token = '{'
DEBUG processing as NumericalPsystem
DEBUG token = 'H'
DEBUG processing as NumericalPsystem
DEBUG token = '='
DEBUG processing as NumericalPsystem
INFO building membrane list
DEBUG process_tokens (parent_type = <class 'list'>, index = 5)
DEBUG token = '{'
DEBUG processing as List
DEBUG token = 'm1'
DEBUG processing as List
DEBUG token = ','
DEBUG processing as List
DEBUG token = 'm2'
DEBUG processing as List
DEBUG token = ','
DEBUG processing as List
DEBUG token = 'm3'
DEBUG processing as List
DEBUG token = '}'
DEBUG processing as List
DEBUG token = ';'
DEBUG processing as List
DEBUG finished this block with result = ['m1', 'm2', 'm3']
DEBUG token = 'structure'
DEBUG processing as NumericalPsystem
DEBUG token = '='
DEBUG processing as NumericalPsystem
INFO building membrane structure
DEBUG process_tokens (parent_type = <class '__main__.MembraneStructure'>, index = 15)
DEBUG token = '['
DEBUG processing as MembraneStructure
DEBUG token = 'm1'
DEBUG processing as MembraneStructure
DEBUG token = '['
DEBUG processing as MembraneStructure
DEBUG token = 'm2'
DEBUG processing as MembraneStructure
DEBUG token = ']'
DEBUG processing as MembraneStructure
DEBUG token = 'm2'
DEBUG processing as MembraneStructure
DEBUG token = '['
DEBUG processing as MembraneStructure
DEBUG token = 'm3'
DEBUG processing as MembraneStructure
DEBUG token = ']'
DEBUG processing as MembraneStructure
DEBUG token = 'm3'
DEBUG processing as MembraneStructure
DEBUG token = ']'
DEBUG processing as MembraneStructure
DEBUG token = 'm1'
DEBUG processing as MembraneStructure
DEBUG token = ';'
DEBUG processing as MembraneStructure
DEBUG finished the MembraneStructure with result = [Token(type='L_BRACKET', value='[', line=5, column=16), Token(type='ID', value='m1', line=5, column=17), Token(type='L_BRACKET', value='[', line=5, column=20), Token(type='ID', value='m2', line=5, column=21), Token(type='R_BRACKET', value=']', line=5, column=24), Token(type='ID', value='m2', line=5, column=25), Token(type='L_BRACKET', value='[', line=5, column=28), Token(type='ID', value='m3', line=5, column=29), Token(type='R_BRACKET', value=']', line=5, column=32), Token(type='ID', value='m3', line=5, column=33), Token(type='R_BRACKET', value=']', line=5, column=36), Token(type='ID', value='m1', line=5, column=37)]
DEBUG token = 'm1'
DEBUG processing as NumericalPsystem
DEBUG token = '='
DEBUG processing as NumericalPsystem
INFO building Membrane
DEBUG process_tokens (parent_type = <class '__main__.Membrane'>, index = 30)
DEBUG token = '{'
DEBUG processing as Membrane
DEBUG token = 'var'
DEBUG processing as Membrane
DEBUG token = '='
DEBUG processing as Membrane
INFO building variable list
DEBUG process_tokens (parent_type = <class 'list'>, index = 33)
DEBUG token = '{'
DEBUG processing as List
DEBUG token = 'x_1_1'
DEBUG processing as List
DEBUG token = '}'
DEBUG processing as List
DEBUG token = ';'
DEBUG processing as List
DEBUG finished this block with result = ['x_1_1']
DEBUG token = 'var0'
DEBUG processing as Membrane
DEBUG token = '='
DEBUG processing as Membrane
INFO building var0 list
DEBUG process_tokens (parent_type = <class 'list'>, index = 39)
DEBUG token = '('
DEBUG processing as List
DEBUG token = '0'
DEBUG processing as List
DEBUG token = ')'
DEBUG processing as List
DEBUG token = ';'
DEBUG processing as List
DEBUG finished this block with result = [0]
DEBUG token = '}'
DEBUG processing as Membrane
DEBUG token = ';'
DEBUG processing as Membrane
DEBUG finished this block with result = <__main__.Membrane object at 0x7f1bcecfdac8>
DEBUG token = 'm2'
DEBUG processing as NumericalPsystem
DEBUG token = '='
DEBUG processing as NumericalPsystem
INFO building Membrane
DEBUG process_tokens (parent_type = <class '__main__.Membrane'>, index = 47)
DEBUG token = '{'
DEBUG processing as Membrane
DEBUG token = 'var'
DEBUG processing as Membrane
DEBUG token = '='
DEBUG processing as Membrane
INFO building variable list
DEBUG process_tokens (parent_type = <class 'list'>, index = 50)
DEBUG token = '{'
DEBUG processing as List
DEBUG token = 'x_1_2'
DEBUG processing as List
DEBUG token = '}'
DEBUG processing as List
DEBUG token = ';'
DEBUG processing as List
DEBUG finished this block with result = ['x_1_2']
DEBUG token = 'pr'
DEBUG processing as Membrane
DEBUG token = '='
DEBUG processing as Membrane
INFO building Program
DEBUG process_tokens (parent_type = <class '__main__.Program'>, index = 56)
DEBUG token = '{'
DEBUG processing as Program
INFO building production function
DEBUG process_tokens (parent_type = <class '__main__.ProductionFunction'>, index = 57)
DEBUG token = '2'
DEBUG processing as ProductionFunction
DEBUG processing integer number
DEBUG token = '*'
DEBUG processing as ProductionFunction
DEBUG processing operator *
DEBUG token = 'x_1_2'
DEBUG processing as ProductionFunction
DEBUG processing variable
DEBUG token = '+'
DEBUG processing as ProductionFunction
DEBUG processing operator +
DEBUG token = '1'
DEBUG processing as ProductionFunction
DEBUG processing integer number
DEBUG token = '->'
DEBUG processing as ProductionFunction
DEBUG production function end; emptying stack
DEBUG finished the production function with result = [2, 'x_1_2', <OperatorType.multiply: 10>, 1, <OperatorType.add: 8>]
DEBUG token = '->'
DEBUG processing as Program
INFO building distribution rule
DEBUG process_tokens (parent_type = <class '__main__.DistributionFunction'>, index = 63)
DEBUG token = '1'
DEBUG processing as DistributionFunction
DEBUG token = '|'
DEBUG processing as DistributionFunction
DEBUG skipped '|'
DEBUG token = 'x_1_1'
DEBUG processing as DistributionFunction
DEBUG token = '}'
DEBUG processing as DistributionFunction
DEBUG finished this DistributionFunction with result = [<__main__.DistributionRule object at 0x7f1bcecfdcc0>]
DEBUG token = ';'
DEBUG processing as Program
DEBUG finished this block with result = <__main__.Program object at 0x7f1bcecfdbe0>
DEBUG token = 'var0'
DEBUG processing as Membrane
DEBUG token = '='
DEBUG processing as Membrane
INFO building var0 list
DEBUG process_tokens (parent_type = <class 'list'>, index = 70)
DEBUG token = '('
DEBUG processing as List
DEBUG token = '0'
DEBUG processing as List
DEBUG token = ')'
DEBUG processing as List
DEBUG token = ';'
DEBUG processing as List
DEBUG finished this block with result = [0]
DEBUG token = '}'
DEBUG processing as Membrane
DEBUG token = ';'
DEBUG processing as Membrane
DEBUG finished this block with result = <__main__.Membrane object at 0x7f1bcecfdb70>
DEBUG token = 'm3'
DEBUG processing as NumericalPsystem
DEBUG token = '='
DEBUG processing as NumericalPsystem
INFO building Membrane
DEBUG process_tokens (parent_type = <class '__main__.Membrane'>, index = 78)
DEBUG token = '{'
DEBUG processing as Membrane
DEBUG token = 'var'
DEBUG processing as Membrane
DEBUG token = '='
DEBUG processing as Membrane
INFO building variable list
DEBUG process_tokens (parent_type = <class 'list'>, index = 81)
DEBUG token = '{'
DEBUG processing as List
DEBUG token = 'x_1_3'
DEBUG processing as List
DEBUG token = '}'
DEBUG processing as List
DEBUG token = ';'
DEBUG processing as List
DEBUG finished this block with result = ['x_1_3']
DEBUG token = 'pr'
DEBUG processing as Membrane
DEBUG token = '='
DEBUG processing as Membrane
INFO building Program
DEBUG process_tokens (parent_type = <class '__main__.Program'>, index = 87)
DEBUG token = '{'
DEBUG processing as Program
INFO building production function
DEBUG process_tokens (parent_type = <class '__main__.ProductionFunction'>, index = 88)
DEBUG token = '2'
DEBUG processing as ProductionFunction
DEBUG processing integer number
DEBUG token = '*'
DEBUG processing as ProductionFunction
DEBUG processing operator *
DEBUG token = '('
DEBUG processing as ProductionFunction
DEBUG processing operator (
DEBUG token = 'x_1_3'
DEBUG processing as ProductionFunction
DEBUG processing variable
DEBUG token = '+'
DEBUG processing as ProductionFunction
DEBUG processing operator +
DEBUG token = '1'
DEBUG processing as ProductionFunction
DEBUG processing integer number
DEBUG token = ')'
DEBUG processing as ProductionFunction
DEBUG processing operator )
DEBUG token = '->'
DEBUG processing as ProductionFunction
DEBUG production function end; emptying stack
DEBUG finished the production function with result = [2, 'x_1_3', 1, <OperatorType.add: 8>, <OperatorType.multiply: 10>]
DEBUG token = '->'
DEBUG processing as Program
INFO building distribution rule
DEBUG process_tokens (parent_type = <class '__main__.DistributionFunction'>, index = 96)
DEBUG token = '1'
DEBUG processing as DistributionFunction
DEBUG token = '|'
DEBUG processing as DistributionFunction
DEBUG skipped '|'
DEBUG token = 'x_1_3'
DEBUG processing as DistributionFunction
DEBUG token = '+'
DEBUG processing as DistributionFunction
DEBUG skipped '+'
DEBUG token = '1'
DEBUG processing as DistributionFunction
DEBUG token = '|'
DEBUG processing as DistributionFunction
DEBUG skipped '|'
DEBUG token = 'x_1_2'
DEBUG processing as DistributionFunction
DEBUG token = '}'
DEBUG processing as DistributionFunction
DEBUG finished this DistributionFunction with result = [<__main__.DistributionRule object at 0x7f1bcecfdda0>, <__main__.DistributionRule object at 0x7f1bcecfddd8>]
DEBUG token = ';'
DEBUG processing as Program
DEBUG finished this block with result = <__main__.Program object at 0x7f1bcecfdd30>
DEBUG token = 'var0'
DEBUG processing as Membrane
DEBUG token = '='
DEBUG processing as Membrane
INFO building var0 list
DEBUG process_tokens (parent_type = <class 'list'>, index = 107)
DEBUG token = '('
DEBUG processing as List
DEBUG token = '0'
DEBUG processing as List
DEBUG token = ')'
DEBUG processing as List
DEBUG token = ';'
DEBUG processing as List
DEBUG finished this block with result = [0]
DEBUG token = '}'
DEBUG processing as Membrane
DEBUG token = ';'
DEBUG processing as Membrane
DEBUG finished this block with result = <__main__.Membrane object at 0x7f1bcecfdcf8>
DEBUG token = '}'
DEBUG processing as NumericalPsystem
DEBUG constructing a global list of variables used in the entire P system
DEBUG constructing a global list of enzymes used in the entire P system
DEBUG cross-referencing string identifiers of VARIABLES to the corresponding Pobject instance
DEBUG processing membrane m1
DEBUG processing membrane m2
DEBUG replacing 'x_1_1' in distribution function
DEBUG processing membrane m3
DEBUG processing membrane m1
DEBUG processing membrane m2
DEBUG replacing 'x_1_2' in production function
DEBUG processing membrane m3
DEBUG replacing 'x_1_2' in distribution function
DEBUG processing membrane m1
DEBUG processing membrane m2
DEBUG processing membrane m3
DEBUG replacing 'x_1_3' in production function
DEBUG replacing 'x_1_3' in distribution function
DEBUG cross-referencing string identifiers of ENZYMES to the corresponding Pobject instance
DEBUG Constructing the internal membrane structure of the P system
num_ps = {
m1:
var = { x_1_1: 0.00, }
E = {}
m2:
var = { x_1_2: 0.00, }
E = {}
pr_0 = { 2 * x_1_2 + 1 -> 1|x_1_1 }
m3:
var = { x_1_3: 0.00, }
E = {}
pr_0 = { 2 * ( x_1_3 + 1 ) -> 1|x_1_3 + 1|x_1_2 }
}
INFO Starting simulation step 1
DEBUG Production for membrane m2
DEBUG postfixStack = [2]
DEBUG postfixStack = [2, 0]
DEBUG postfixStack = [0]
DEBUG postfixStack = [0, 1]
DEBUG postfixStack = [1]
DEBUG Production for membrane m3
DEBUG postfixStack = [2]
DEBUG postfixStack = [2, 0]
DEBUG postfixStack = [2, 0, 1]
DEBUG postfixStack = [2, 1]
DEBUG postfixStack = [2]
DEBUG Resetting all variables that are part of production functions to 0
DEBUG Resetting all enzymes that are part of production functions to 0
DEBUG Distribution for membrane m2 of unitary value 1.00
DEBUG Distribution for membrane m3 of unitary value 1.00
INFO Simulation step finished succesfully
num_ps = {
m1:
var = { x_1_1: 1.00, }
E = {}
m2:
var = { x_1_2: 1.00, }
E = {}
m3:
var = { x_1_3: 1.00, }
E = {}
}
INFO Starting simulation step 2
DEBUG Production for membrane m2
DEBUG postfixStack = [2]
DEBUG postfixStack = [2, 1.0]
DEBUG postfixStack = [2.0]
DEBUG postfixStack = [2.0, 1]
DEBUG postfixStack = [3.0]
DEBUG Production for membrane m3
DEBUG postfixStack = [2]
DEBUG postfixStack = [2, 1.0]
DEBUG postfixStack = [2, 1.0, 1]
DEBUG postfixStack = [2, 2.0]
DEBUG postfixStack = [4.0]
DEBUG Resetting all variables that are part of production functions to 0
DEBUG Resetting all enzymes that are part of production functions to 0
DEBUG Distribution for membrane m2 of unitary value 3.00
DEBUG Distribution for membrane m3 of unitary value 2.00
INFO Simulation step finished succesfully
num_ps = {
m1:
var = { x_1_1: 4.00, }
E = {}
m2:
var = { x_1_2: 2.00, }
E = {}
m3:
var = { x_1_3: 2.00, }
E = {}
}
The output now includes DEBUG messages that offer usefull information regarding:
- Input file parsing.
- Any input file error will be easy to spot by tracing back the previous messages that show the context of the parsing
- Production function expresion.
- The expression is evaluated as a postfix notation (Reverse Polish, RPN) and by watching the postfixStack messages, it is easy to evaluate the correctness of the calculations.
DEBUG postfixStack = [2, 0]
- Distribution function expression
- There are messages that show the unitary value that will be distributed from each membrane:
DEBUG Distribution for membrane m2 of unitary value 1.00- [Enzymatic] Numerical P Systems also show a special DEBUG message,
DEBUG Program 0 activated by enzyme e_1_1,that helps in observing which program was activated by an enzyme at each simulation step.