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 2-3254
Executing tool marcie
Input is GPPP-PT-C0001N0000000001, examination is CTLFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r021-blw3-149440255300508
=====================================================================

--------------------
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-C0001N0000000001-CTLFireability-0
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-1
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-10
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-11
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-12
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-13
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-14
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-15
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-2
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-3
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-4
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-5
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-6
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-7
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-8
FORMULA_NAME GPPP-PT-C0001N0000000001-CTLFireability-9

=== Now, execution of the tool begins

BK_START 1494464453674

timeout --kill-after=10s --signal=SIGINT 1m for testing only

Marcie rev. 8852M (built: crohr on 2017-05-03)
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 --memory=6

parse successfull
net created successfully

Net: GPPP_PT_C0001N0000000001
(NrP: 33 NrTr: 22 NrArc: 83)

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

net check time: 0m 0.000sec

init dd package: 0m 1.142sec

parse successfull
net created successfully

Net: GPPP_PT_C0001N0000000001
(NrP: 33 NrTr: 22 NrArc: 83)

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

net check time: 0m 0.000sec

init dd package: 0m 3.783sec


RS generation: 0m 0.011sec


-> reachability set: #nodes 561 (5.6e+02) #states 10,380 (4)



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

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

-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-7 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.013sec

checking: IS_FIREABLE [TIM_forward]
normalized: IS_FIREABLE [TIM_forward]

-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-10 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: IS_FIREABLE [TIM_backward]
normalized: IS_FIREABLE [TIM_backward]

-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-14 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: EX [~ [EF [[IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Ru5P_isomerase]]]]]
normalized: EX [~ [E [true U [IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Ru5P_isomerase]]]]]

.-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-5 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.003sec

checking: EF [EF [[IS_FIREABLE [Transketolase2] & IS_FIREABLE [Transketolase1]]]]
normalized: E [true U E [true U [IS_FIREABLE [Transketolase2] & IS_FIREABLE [Transketolase1]]]]

-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-6 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: ~ [AX [EF [[IS_FIREABLE [generate] & IS_FIREABLE [Phosphoglycerate_mutase]]]]]
normalized: EX [~ [E [true U [IS_FIREABLE [generate] & IS_FIREABLE [Phosphoglycerate_mutase]]]]]

.-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-8 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: ~ [AG [EF [[IS_FIREABLE [Transketolase1] & IS_FIREABLE [TIM_forward]]]]]
normalized: E [true U ~ [E [true U [IS_FIREABLE [Transketolase1] & IS_FIREABLE [TIM_forward]]]]]

-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-9 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.006sec

checking: E [EF [~ [IS_FIREABLE [Transketolase2]]] U EX [~ [IS_FIREABLE [Hexokinase]]]]
normalized: E [E [true U ~ [IS_FIREABLE [Transketolase2]]] U EX [~ [IS_FIREABLE [Hexokinase]]]]

.-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-11 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.003sec

checking: AG [[EF [~ [IS_FIREABLE [Transaldolase]]] | A [IS_FIREABLE [G6P_dehydrogenase] U IS_FIREABLE [Hexokinase]]]]
normalized: ~ [E [true U ~ [[[~ [EG [~ [IS_FIREABLE [Hexokinase]]]] & ~ [E [~ [IS_FIREABLE [Hexokinase]] U [~ [IS_FIREABLE [Hexokinase]] & ~ [IS_FIREABLE [G6P_dehydrogenase]]]]]] | E [true U ~ [IS_FIREABLE [Transaldolase]]]]]]]

..................
EG iterations: 18
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-0 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.008sec

checking: [AG [EF [[IS_FIREABLE [TIM_forward] & IS_FIREABLE [Phosphoclucose_isomerase]]]] | IS_FIREABLE [TIM_backward]]
normalized: [~ [E [true U ~ [E [true U [IS_FIREABLE [TIM_forward] & IS_FIREABLE [Phosphoclucose_isomerase]]]]]] | IS_FIREABLE [TIM_backward]]

-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-4 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: AG [[[EG [IS_FIREABLE [Phosphoglycerate_mutase]] | EF [IS_FIREABLE [Phosphoclucose_isomerase]]] | E [IS_FIREABLE [Ru5P_isomerase] U IS_FIREABLE [Transaldolase]]]]
normalized: ~ [E [true U ~ [[E [IS_FIREABLE [Ru5P_isomerase] U IS_FIREABLE [Transaldolase]] | [E [true U IS_FIREABLE [Phosphoclucose_isomerase]] | EG [IS_FIREABLE [Phosphoglycerate_mutase]]]]]]]

............
EG iterations: 12
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-1 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.014sec

checking: A [AF [[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [Phosphoclucose_isomerase]]] U E [IS_FIREABLE [Glutathione_oxidation] U IS_FIREABLE [Hexokinase]]]
normalized: [~ [EG [~ [E [IS_FIREABLE [Glutathione_oxidation] U IS_FIREABLE [Hexokinase]]]]] & ~ [E [~ [E [IS_FIREABLE [Glutathione_oxidation] U IS_FIREABLE [Hexokinase]]] U [EG [~ [[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [Phosphoclucose_isomerase]]]] & ~ [E [IS_FIREABLE [Glutathione_oxidation] U IS_FIREABLE [Hexokinase]]]]]]]


EG iterations: 0
...............
EG iterations: 15
-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-13 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.021sec

checking: E [[[~ [IS_FIREABLE [Transketolase1]] | IS_FIREABLE [Glutathione_oxidation]] | [~ [IS_FIREABLE [Glutathione_reductose]] | IS_FIREABLE [generate]]] U AX [IS_FIREABLE [Lactate_dehydrogenase]]]
normalized: E [[[~ [IS_FIREABLE [Glutathione_reductose]] | IS_FIREABLE [generate]] | [IS_FIREABLE [Glutathione_oxidation] | ~ [IS_FIREABLE [Transketolase1]]]] U ~ [EX [~ [IS_FIREABLE [Lactate_dehydrogenase]]]]]

.-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-2 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.025sec

checking: [EX [AF [[IS_FIREABLE [Transaldolase] | IS_FIREABLE [Phosphoglycerate_mutase]]]] & ~ [[EF [[IS_FIREABLE [Enolase] & IS_FIREABLE [GAP_dehydrogenase]]] | [IS_FIREABLE [Aldolase] & EF [IS_FIREABLE [generate]]]]]]
normalized: [EX [~ [EG [~ [[IS_FIREABLE [Transaldolase] | IS_FIREABLE [Phosphoglycerate_mutase]]]]]] & ~ [[[E [true U IS_FIREABLE [generate]] & IS_FIREABLE [Aldolase]] | E [true U [IS_FIREABLE [Enolase] & IS_FIREABLE [GAP_dehydrogenase]]]]]]

..........................
EG iterations: 26
.-> the formula is FALSE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-15 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.027sec

checking: ~ [[A [~ [IS_FIREABLE [Transaldolase]] U [IS_FIREABLE [Transketolase2] & IS_FIREABLE [Phosphoclucose_isomerase]]] & EG [[[IS_FIREABLE [Glutathione_oxidation] & IS_FIREABLE [Lactate_dehydrogenase]] & [IS_FIREABLE [TIM_forward] & IS_FIREABLE [GAP_dehydrogenase]]]]]]
normalized: ~ [[[~ [EG [~ [[IS_FIREABLE [Transketolase2] & IS_FIREABLE [Phosphoclucose_isomerase]]]]] & ~ [E [~ [[IS_FIREABLE [Transketolase2] & IS_FIREABLE [Phosphoclucose_isomerase]]] U [~ [[IS_FIREABLE [Transketolase2] & IS_FIREABLE [Phosphoclucose_isomerase]]] & IS_FIREABLE [Transaldolase]]]]] & EG [[[IS_FIREABLE [TIM_forward] & IS_FIREABLE [GAP_dehydrogenase]] & [IS_FIREABLE [Glutathione_oxidation] & IS_FIREABLE [Lactate_dehydrogenase]]]]]]

...
EG iterations: 3

EG iterations: 0
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-12 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.005sec

checking: [[[~ [[[IS_FIREABLE [TIM_backward] & IS_FIREABLE [generate]] | ~ [IS_FIREABLE [Phosphofructokinase]]]] | ~ [AF [IS_FIREABLE [TIM_backward]]]] & [[~ [[IS_FIREABLE [TIM_backward] | IS_FIREABLE [Phosphoglycerate_mutase]]] | IS_FIREABLE [TIM_forward]] & ~ [~ [~ [IS_FIREABLE [Hexokinase]]]]]] | [[A [IS_FIREABLE [Glutathione_reductose] U IS_FIREABLE [remove]] | EF [[IS_FIREABLE [Pyruvate_kinase] & IS_FIREABLE [Transketolase2]]]] | AG [[~ [IS_FIREABLE [Phosphoglycerate_kinase]] | [IS_FIREABLE [Enolase] | IS_FIREABLE [generate]]]]]]
normalized: [[~ [E [true U ~ [[[IS_FIREABLE [Enolase] | IS_FIREABLE [generate]] | ~ [IS_FIREABLE [Phosphoglycerate_kinase]]]]]] | [E [true U [IS_FIREABLE [Pyruvate_kinase] & IS_FIREABLE [Transketolase2]]] | [~ [EG [~ [IS_FIREABLE [remove]]]] & ~ [E [~ [IS_FIREABLE [remove]] U [~ [IS_FIREABLE [Glutathione_reductose]] & ~ [IS_FIREABLE [remove]]]]]]]] | [[~ [IS_FIREABLE [Hexokinase]] & [~ [[IS_FIREABLE [TIM_backward] | IS_FIREABLE [Phosphoglycerate_mutase]]] | IS_FIREABLE [TIM_forward]]] & [EG [~ [IS_FIREABLE [TIM_backward]]] | ~ [[~ [IS_FIREABLE [Phosphofructokinase]] | [IS_FIREABLE [TIM_backward] & IS_FIREABLE [generate]]]]]]]

..........................................
EG iterations: 42
................
EG iterations: 16
-> the formula is TRUE

FORMULA GPPP-PT-C0001N0000000001-CTLFireability-3 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.066sec

totally nodes used: 65185 (6.5e+04)
number of garbage collections: 0
fire ops cache: hits/miss/sum: 101239 194295 295534
used/not used/entry size/cache size: 251568 66857296 16 1024MB
basic ops cache: hits/miss/sum: 23159 50494 73653
used/not used/entry size/cache size: 98537 16678679 12 192MB
unary ops cache: hits/miss/sum: 0 0 0
used/not used/entry size/cache size: 0 16777216 8 128MB
abstract ops cache: hits/miss/sum: 0 0 0
used/not used/entry size/cache size: 0 16777216 12 192MB
state nr cache: hits/miss/sum: 210 561 771
used/not used/entry size/cache size: 561 8388047 32 256MB
max state cache: hits/miss/sum: 0 0 0
used/not used/entry size/cache size: 0 8388608 32 256MB
uniqueHash elements/entry size/size: 67108864 4 256MB
0 67050254
1 55915
2 2067
3 307
4 93
5 44
6 50
7 23
8 16
9 12
>= 10 83

Total processing time: 0m 6.931sec


BK_STOP 1494464460695

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

check for maximal unmarked siphon
ok
check for constant places
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

ptnet_zbdd.cc:255: Boundedness exception: net is not 1-bounded!

check for maximal unmarked siphon
ok
check for constant places
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


iterations count:446 (20), effective:99 (4)

initing FirstDep: 0m 0.000sec


iterations count:201 (9), effective:41 (1)

iterations count:465 (21), effective:111 (5)

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

iterations count:45 (2), effective:5 (0)

iterations count:25 (1), effective:1 (0)

iterations count:35 (1), effective:1 (0)

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

iterations count:391 (17), effective:97 (4)

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

iterations count:292 (13), effective:73 (3)

iterations count:292 (13), effective:73 (3)

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

iterations count:292 (13), effective:73 (3)

iterations count:324 (14), effective:69 (3)

iterations count:303 (13), effective:71 (3)

iterations count:399 (18), effective:97 (4)

iterations count:390 (17), effective:94 (4)

iterations count:24 (1), effective:1 (0)

iterations count:522 (23), effective:125 (5)

iterations count:224 (10), effective:51 (2)

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-C0001N0000000001"
export BK_EXAMINATION="CTLFireability"
export BK_TOOL="marcie"
export BK_RESULT_DIR="/tmp/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-C0001N0000000001.tgz
mv GPPP-PT-C0001N0000000001 execution

# this is for BenchKit: explicit launching of the test

cd execution
echo "====================================================================="
echo " Generated by BenchKit 2-3254"
echo " Executing tool marcie"
echo " Input is GPPP-PT-C0001N0000000001, 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 r021-blw3-149440255300508"
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 ;