Execution Chart

We display below the execution chart for this examination (boot time has been removed).

Trace from the execution

Waiting for the VM to be ready (probing ssh)
.............
=====================================================================
Generated by BenchKit 2-2979
Executing tool marcie
Input is GPPP-PT-C0001N0000000100, examination is CTLFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r221su-smll-146468027600454
=====================================================================

--------------------
content from stdout:

=== Data for post analysis generated by BenchKit (invocation template)

The expected result is a vector of booleans
BOOL_VECTOR

here is the order used to build the result vector(from text file)
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-0
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-1
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-10
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-11
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-12
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-13
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-14
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-15
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-2
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-3
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-4
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-5
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-6
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-7
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-8
FORMULA_NAME GPPP-PT-C0001N0000000100-CTLFireability-9

=== Now, execution of the tool begins

BK_START 1465033911270


Marcie rev. 8535M (built: crohr on 2016-04-27)
A model checker for Generalized Stochastic Petri nets

authors: Alex Tovchigrechko (IDD package and CTL model checking)

Martin Schwarick (Symbolic numerical analysis and CSL model checking)

Christian Rohr (Simulative and approximative numerical model checking)

marcie@informatik.tu-cottbus.de

called as: marcie --net-file=model.pnml --mcc-file=CTLFireability.xml --mcc-mode --memory=6 --suppress

parse successfull
net created successfully

Net: GPPP_PT_C0001N0000000100
(NrP: 33 NrTr: 22 NrArc: 83)

net check time: 0m 0.000sec

parse formulas
formulas created successfully
place and transition orderings generation:0m 0.000sec

init dd package: 0m 3.854sec


RS generation: 0m 0.140sec


-> reachability set: #nodes 1358 (1.4e+03) #states 145,476,966 (8)



starting MCC model checker
--------------------------

checking: EF [EF [IS_FIREABLE [Pyruvate_kinase]]]
normalized: E [true U E [true U IS_FIREABLE [Pyruvate_kinase]]]

-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-0 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.042sec

checking: EG [AG [EF [IS_FIREABLE [Ru5P_isomerase]]]]
normalized: EG [~ [E [true U ~ [E [true U IS_FIREABLE [Ru5P_isomerase]]]]]]


EG iterations: 0
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-9 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.063sec

checking: ~ [[EF [AG [IS_FIREABLE [Lactate_dehydrogenase]]] | IS_FIREABLE [Pyruvate_kinase]]]
normalized: ~ [[IS_FIREABLE [Pyruvate_kinase] | E [true U ~ [E [true U ~ [IS_FIREABLE [Lactate_dehydrogenase]]]]]]]

-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-3 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.008sec

checking: [IS_FIREABLE [Transaldolase] | ~ [AG [EF [IS_FIREABLE [remove]]]]]
normalized: [IS_FIREABLE [Transaldolase] | E [true U ~ [E [true U IS_FIREABLE [remove]]]]]

-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-11 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.061sec

checking: AG [~ [AG [[IS_FIREABLE [TIM_forward] & IS_FIREABLE [Hexokinase]]]]]
normalized: ~ [E [true U ~ [E [true U ~ [[IS_FIREABLE [TIM_forward] & IS_FIREABLE [Hexokinase]]]]]]]

-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-14 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.005sec

checking: EF [AG [[[IS_FIREABLE [Hexokinase] | IS_FIREABLE [Transketolase2]] | ~ [IS_FIREABLE [Ru5P_epimerase]]]]]
normalized: E [true U ~ [E [true U ~ [[~ [IS_FIREABLE [Ru5P_epimerase]] | [IS_FIREABLE [Hexokinase] | IS_FIREABLE [Transketolase2]]]]]]]

-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-2 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.056sec

checking: [EX [EF [IS_FIREABLE [Lactate_dehydrogenase]]] & ~ [AF [[[IS_FIREABLE [G6P_dehydrogenase] & IS_FIREABLE [Pyruvate_kinase]] & ~ [IS_FIREABLE [Transketolase1]]]]]]
normalized: [EG [~ [[~ [IS_FIREABLE [Transketolase1]] & [IS_FIREABLE [G6P_dehydrogenase] & IS_FIREABLE [Pyruvate_kinase]]]]] & EX [E [true U IS_FIREABLE [Lactate_dehydrogenase]]]]

..
EG iterations: 1
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-6 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.102sec

checking: [AF [IS_FIREABLE [TIM_backward]] & ~ [AX [[IS_FIREABLE [GAP_dehydrogenase] & [IS_FIREABLE [Phosphofructokinase] | IS_FIREABLE [generate]]]]]]
normalized: [EX [~ [[IS_FIREABLE [GAP_dehydrogenase] & [IS_FIREABLE [Phosphofructokinase] | IS_FIREABLE [generate]]]]] & ~ [EG [~ [IS_FIREABLE [TIM_backward]]]]]

...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 563
.-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-7 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 1.306sec

checking: [[~ [E [IS_FIREABLE [Pyruvate_kinase] U IS_FIREABLE [Ru5P_epimerase]]] | IS_FIREABLE [generate]] & AG [EF [IS_FIREABLE [Aldolase]]]]
normalized: [~ [E [true U ~ [E [true U IS_FIREABLE [Aldolase]]]]] & [IS_FIREABLE [generate] | ~ [E [IS_FIREABLE [Pyruvate_kinase] U IS_FIREABLE [Ru5P_epimerase]]]]]

-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-10 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.071sec

checking: [[AG [AF [IS_FIREABLE [TIM_forward]]] & EF [~ [[IS_FIREABLE [Aldolase] | IS_FIREABLE [Pyruvate_kinase]]]]] | IS_FIREABLE [Lactate_dehydrogenase]]
normalized: [IS_FIREABLE [Lactate_dehydrogenase] | [E [true U ~ [[IS_FIREABLE [Aldolase] | IS_FIREABLE [Pyruvate_kinase]]]] & ~ [E [true U EG [~ [IS_FIREABLE [TIM_forward]]]]]]]

.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 581
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-12 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 1.687sec

checking: [~ [EG [~ [[IS_FIREABLE [Aldolase] | IS_FIREABLE [Ru5P_epimerase]]]]] | ~ [AX [[~ [IS_FIREABLE [Glutathione_reductose]] | [IS_FIREABLE [GAP_dehydrogenase] | IS_FIREABLE [Pyruvate_kinase]]]]]]
normalized: [EX [~ [[[IS_FIREABLE [GAP_dehydrogenase] | IS_FIREABLE [Pyruvate_kinase]] | ~ [IS_FIREABLE [Glutathione_reductose]]]]] | ~ [EG [~ [[IS_FIREABLE [Aldolase] | IS_FIREABLE [Ru5P_epimerase]]]]]]

...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 559
.-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-1 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 3.888sec

checking: [[IS_FIREABLE [GAP_dehydrogenase] | [IS_FIREABLE [Phosphofructokinase] | AF [[IS_FIREABLE [GAP_dehydrogenase] | IS_FIREABLE [TIM_backward]]]]] | ~ [EF [EX [IS_FIREABLE [Glutathione_oxidation]]]]]
normalized: [~ [E [true U EX [IS_FIREABLE [Glutathione_oxidation]]]] | [IS_FIREABLE [GAP_dehydrogenase] | [IS_FIREABLE [Phosphofructokinase] | ~ [EG [~ [[IS_FIREABLE [GAP_dehydrogenase] | IS_FIREABLE [TIM_backward]]]]]]]]

...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 563
.-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-4 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.099sec

checking: EF [[[~ [[IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [Ru5P_epimerase]]] & IS_FIREABLE [Ru5P_epimerase]] | A [IS_FIREABLE [Ru5P_epimerase] U IS_FIREABLE [Pyruvate_kinase]]]]
normalized: E [true U [[~ [EG [~ [IS_FIREABLE [Pyruvate_kinase]]]] & ~ [E [~ [IS_FIREABLE [Pyruvate_kinase]] U [~ [IS_FIREABLE [Pyruvate_kinase]] & ~ [IS_FIREABLE [Ru5P_epimerase]]]]]] | [IS_FIREABLE [Ru5P_epimerase] & ~ [[IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [Ru5P_epimerase]]]]]]

....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 516
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-8 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 3.290sec

checking: [~ [[[~ [~ [IS_FIREABLE [Glutathione_reductose]]] & ~ [IS_FIREABLE [G6P_dehydrogenase]]] | EF [[IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Ru5P_isomerase]]]]] | EG [[AF [IS_FIREABLE [Phosphoglycerate_mutase]] | EG [IS_FIREABLE [Hexokinase]]]]]
normalized: [EG [[EG [IS_FIREABLE [Hexokinase]] | ~ [EG [~ [IS_FIREABLE [Phosphoglycerate_mutase]]]]]] | ~ [[E [true U [IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Ru5P_isomerase]]] | [IS_FIREABLE [Glutathione_reductose] & ~ [IS_FIREABLE [G6P_dehydrogenase]]]]]]

........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 520
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 522
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 533
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-5 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m10.186sec

checking: [~ [IS_FIREABLE [Glutathione_oxidation]] & [~ [[AG [IS_FIREABLE [Transketolase2]] | [[IS_FIREABLE [TIM_forward] & IS_FIREABLE [Glutathione_oxidation]] & [IS_FIREABLE [Phosphoclucose_isomerase] & IS_FIREABLE [Phosphofructokinase]]]]] & AF [AF [IS_FIREABLE [TIM_forward]]]]]
normalized: [[~ [EG [EG [~ [IS_FIREABLE [TIM_forward]]]]] & ~ [[[[IS_FIREABLE [Phosphoclucose_isomerase] & IS_FIREABLE [Phosphofructokinase]] & [IS_FIREABLE [TIM_forward] & IS_FIREABLE [Glutathione_oxidation]]] | ~ [E [true U ~ [IS_FIREABLE [Transketolase2]]]]]]] & ~ [IS_FIREABLE [Glutathione_oxidation]]]

.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 581
.
EG iterations: 1
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-13 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.189sec

checking: [[AG [[~ [IS_FIREABLE [Ru5P_isomerase]] & IS_FIREABLE [TIM_forward]]] | [[[IS_FIREABLE [Phosphoglycerate_mutase] & [IS_FIREABLE [Transaldolase] & IS_FIREABLE [Phosphoglycerate_kinase]]] | AF [IS_FIREABLE [Enolase]]] & [AG [IS_FIREABLE [G6P_dehydrogenase]] | AF [IS_FIREABLE [G6P_dehydrogenase]]]]] & EX [[[[IS_FIREABLE [GAP_dehydrogenase] | IS_FIREABLE [Transketolase2]] | IS_FIREABLE [Pyruvate_kinase]] & IS_FIREABLE [generate]]]]
normalized: [EX [[IS_FIREABLE [generate] & [IS_FIREABLE [Pyruvate_kinase] | [IS_FIREABLE [GAP_dehydrogenase] | IS_FIREABLE [Transketolase2]]]]] & [[[~ [EG [~ [IS_FIREABLE [G6P_dehydrogenase]]]] | ~ [E [true U ~ [IS_FIREABLE [G6P_dehydrogenase]]]]] & [~ [EG [~ [IS_FIREABLE [Enolase]]]] | [IS_FIREABLE [Phosphoglycerate_mutase] & [IS_FIREABLE [Transaldolase] & IS_FIREABLE [Phosphoglycerate_kinase]]]]] | ~ [E [true U ~ [[IS_FIREABLE [TIM_forward] & ~ [IS_FIREABLE [Ru5P_isomerase]]]]]]]]

...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 515
..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
EG iterations: 522
.-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000100-CTLFireability-15 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 6.471sec


Total processing time: 0m33.275sec


BK_STOP 1465033944623

--------------------
content from stderr:

check for maximal unmarked siphon
ok
check if there are places and transitions
ok
check if there are transitions without pre-places
ok
check if at least one transition is enabled in m0
ok
check if there are transitions that can never fire
ok


initing FirstDep: 0m 0.000sec

1092 1181 1384 1145 1128 1217 1330 1177 1171 1200 1709 1811 1769 1769 1783
iterations count:15790 (717), effective:3705 (168)

initing FirstDep: 0m 0.000sec


iterations count:171 (7), effective:38 (1)

iterations count:22 (1), effective:0 (0)

iterations count:360 (16), effective:85 (3)

iterations count:29 (1), effective:7 (0)

iterations count:359 (16), effective:85 (3)

iterations count:37 (1), effective:3 (0)

iterations count:336 (15), effective:79 (3)

iterations count:168 (7), effective:32 (1)

iterations count:48 (2), effective:6 (0)

iterations count:300 (13), effective:72 (3)

iterations count:62 (2), effective:10 (0)

iterations count:303 (13), effective:70 (3)

iterations count:28 (1), effective:2 (0)

iterations count:171 (7), effective:38 (1)

iterations count:29 (1), effective:1 (0)

iterations count:50 (2), effective:7 (0)

iterations count:61 (2), effective:3 (0)

Sequence of Actions to be Executed by the VM

This is useful if one wants to reexecute the tool in the VM from the submitted image disk.

set -x
# this is for BenchKit: configuration of major elements for the test
export BK_INPUT="GPPP-PT-C0001N0000000100"
export BK_EXAMINATION="CTLFireability"
export BK_TOOL="marcie"
export BK_RESULT_DIR="/root/BK_RESULTS/OUTPUTS"
export BK_TIME_CONFINEMENT="3600"
export BK_MEMORY_CONFINEMENT="16384"

# this is specific to your benchmark or test

export BIN_DIR="$HOME/BenchKit/bin"

# remove the execution directoty if it exists (to avoid increse of .vmdk images)
if [ -d execution ] ; then
rm -rf execution
fi

tar xzf /home/mcc/BenchKit/INPUTS/GPPP-PT-C0001N0000000100.tgz
mv GPPP-PT-C0001N0000000100 execution

# this is for BenchKit: explicit launching of the test

cd execution
echo "====================================================================="
echo " Generated by BenchKit 2-2979"
echo " Executing tool marcie"
echo " Input is GPPP-PT-C0001N0000000100, examination is CTLFireability"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 1"
echo " Run identifier is r221su-smll-146468027600454"
echo "====================================================================="
echo
echo "--------------------"
echo "content from stdout:"
echo
echo "=== Data for post analysis generated by BenchKit (invocation template)"
echo
if [ "CTLFireability" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "CTLFireability" != "StateSpace" ] ; then
echo "The expected result is a vector of booleans"
echo BOOL_VECTOR
else
echo "no data necessary for post analysis"
fi
echo
if [ -f "CTLFireability.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property CTLFireability.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -f "CTLFireability.xml" ] ; then # for cunf (txt files deleted;-)
echo echo "here is the order used to build the result vector(from xml file)"
for x in $(grep '' CTLFireability.xml | cut -d '>' -f 2 | cut -d '<' -f 1 | sort -u) ; do
echo "FORMULA_NAME $x"
done
fi
echo
echo "=== Now, execution of the tool begins"
echo
echo -n "BK_START "
date -u +%s%3N
echo
timeout -s 9 $BK_TIME_CONFINEMENT bash -c "/home/mcc/BenchKit/BenchKit_head.sh 2> STDERR ; echo ; echo -n \"BK_STOP \" ; date -u +%s%3N"
if [ $? -eq 137 ] ; then
echo
echo "BK_TIME_CONFINEMENT_REACHED"
fi
echo
echo "--------------------"
echo "content from stderr:"
echo
cat STDERR ;