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 S_GPPP-PT-C1000N0000000100, examination is CTLFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r101-blw3-149441599200580
=====================================================================

--------------------
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-C1000N0000000100-CTLFireability-0
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-1
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-10
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-11
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-12
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-13
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-14
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-15
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-2
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-3
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-4
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-5
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-6
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-7
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-8
FORMULA_NAME GPPP-PT-C1000N0000000100-CTLFireability-9

=== Now, execution of the tool begins

BK_START 1494884890606

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_C1000N0000000100
(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 1.231sec

parse successfull
net created successfully

Net: GPPP_PT_C1000N0000000100
(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 3.798sec


RS generation: 1m22.623sec


-> reachability set: #nodes 561475 (5.6e+05) #states 1,140,616,996,412,371 (15)



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

checking: EF [AX [EG [IS_FIREABLE [Enolase]]]]
normalized: E [true U ~ [EX [~ [EG [IS_FIREABLE [Enolase]]]]]]

......................................................................................................................................................................................................................MC time: 3m40.080sec

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

-> the formula is FALSE

FORMULA GPPP-PT-C1000N0000000100-CTLFireability-4 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m18.458sec

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

-> the formula is FALSE

FORMULA GPPP-PT-C1000N0000000100-CTLFireability-7 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m19.104sec

checking: AF [EX [IS_FIREABLE [TIM_forward]]]
normalized: ~ [EG [~ [EX [IS_FIREABLE [TIM_forward]]]]]

...............................................................................................................................................
FORMULA GPPP-PT-C1000N0000000100-CTLFireability-12 CANNOT_COMPUTE

MC time: 1m36.102sec

checking: [EF [IS_FIREABLE [Enolase]] | IS_FIREABLE [Phosphofructokinase]]
normalized: [IS_FIREABLE [Phosphofructokinase] | E [true U IS_FIREABLE [Enolase]]]


before gc: list nodes free: 372

after gc: idd nodes used:561586, unused:63438414; list nodes free:547351054
-> the formula is TRUE

FORMULA GPPP-PT-C1000N0000000100-CTLFireability-2 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 1m14.575sec

checking: [AX [EF [IS_FIREABLE [generate]]] | IS_FIREABLE [Phosphoclucose_isomerase]]
normalized: [IS_FIREABLE [Phosphoclucose_isomerase] | ~ [EX [~ [E [true U IS_FIREABLE [generate]]]]]]

.-> the formula is FALSE

FORMULA GPPP-PT-C1000N0000000100-CTLFireability-13 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m26.044sec

checking: [EX [~ [IS_FIREABLE [Phosphoglycerate_mutase]]] & EF [A [IS_FIREABLE [Phosphoglycerate_mutase] U IS_FIREABLE [Pyruvate_kinase]]]]
normalized: [E [true U [~ [EG [~ [IS_FIREABLE [Pyruvate_kinase]]]] & ~ [E [~ [IS_FIREABLE [Pyruvate_kinase]] U [~ [IS_FIREABLE [Phosphoglycerate_mutase]] & ~ [IS_FIREABLE [Pyruvate_kinase]]]]]]] & EX [~ [IS_FIREABLE [Phosphoglycerate_mutase]]]]

................................................................................................................................................................MC time: 4m38.510sec

checking: [EX [EF [IS_FIREABLE [Transketolase2]]] | ~ [~ [EX [[IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Transaldolase]]]]]]
normalized: [EX [[IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Transaldolase]]] | EX [E [true U IS_FIREABLE [Transketolase2]]]]

..-> the formula is TRUE

FORMULA GPPP-PT-C1000N0000000100-CTLFireability-1 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m37.671sec

checking: A [AG [IS_FIREABLE [Phosphofructokinase]] U [AX [IS_FIREABLE [Phosphoclucose_isomerase]] | EF [IS_FIREABLE [Transketolase2]]]]
normalized: [~ [EG [~ [[E [true U IS_FIREABLE [Transketolase2]] | ~ [EX [~ [IS_FIREABLE [Phosphoclucose_isomerase]]]]]]]] & ~ [E [~ [[E [true U IS_FIREABLE [Transketolase2]] | ~ [EX [~ [IS_FIREABLE [Phosphoclucose_isomerase]]]]]] U [E [true U ~ [IS_FIREABLE [Phosphofructokinase]]] & ~ [[E [true U IS_FIREABLE [Transketolase2]] | ~ [EX [~ [IS_FIREABLE [Phosphoclucose_isomerase]]]]]]]]]]

.
FORMULA GPPP-PT-C1000N0000000100-CTLFireability-14 CANNOT_COMPUTE

MC time: 1m27.881sec

checking: ~ [E [~ [[IS_FIREABLE [Transketolase1] & IS_FIREABLE [generate]]] U IS_FIREABLE [Pyruvate_kinase]]]
normalized: ~ [E [~ [[IS_FIREABLE [Transketolase1] & IS_FIREABLE [generate]]] U IS_FIREABLE [Pyruvate_kinase]]]


before gc: list nodes free: 164

after gc: idd nodes used:561587, unused:63438413; list nodes free:547351388
-> the formula is FALSE

FORMULA GPPP-PT-C1000N0000000100-CTLFireability-15 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 1m25.095sec

checking: EF [A [[IS_FIREABLE [Phosphoclucose_isomerase] | IS_FIREABLE [Ru5P_isomerase]] U [IS_FIREABLE [Lactate_dehydrogenase] & IS_FIREABLE [GAP_dehydrogenase]]]]
normalized: E [true U [~ [EG [~ [[IS_FIREABLE [Lactate_dehydrogenase] & IS_FIREABLE [GAP_dehydrogenase]]]]] & ~ [E [~ [[IS_FIREABLE [Lactate_dehydrogenase] & IS_FIREABLE [GAP_dehydrogenase]]] U [~ [[IS_FIREABLE [Phosphoclucose_isomerase] | IS_FIREABLE [Ru5P_isomerase]]] & ~ [[IS_FIREABLE [Lactate_dehydrogenase] & IS_FIREABLE [GAP_dehydrogenase]]]]]]]]

.
EG iterations: 1
-> the formula is TRUE

FORMULA GPPP-PT-C1000N0000000100-CTLFireability-9 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 2m30.140sec

checking: [[EF [EF [IS_FIREABLE [G6P_dehydrogenase]]] & [EF [[IS_FIREABLE [remove] & IS_FIREABLE [Phosphoglycerate_mutase]]] & ~ [EG [IS_FIREABLE [Enolase]]]]] | AX [IS_FIREABLE [Transaldolase]]]
normalized: [~ [EX [~ [IS_FIREABLE [Transaldolase]]]] | [[~ [EG [IS_FIREABLE [Enolase]]] & E [true U [IS_FIREABLE [remove] & IS_FIREABLE [Phosphoglycerate_mutase]]]] & E [true U E [true U IS_FIREABLE [G6P_dehydrogenase]]]]]

............................................................................................................................................................................MC time: 5m46.284sec

checking: AG [~ [[[[IS_FIREABLE [Phosphoglycerate_kinase] & IS_FIREABLE [GAP_dehydrogenase]] | [IS_FIREABLE [Transketolase1] | IS_FIREABLE [Glutathione_reductose]]] & EF [IS_FIREABLE [Lactate_dehydrogenase]]]]]
normalized: ~ [E [true U [E [true U IS_FIREABLE [Lactate_dehydrogenase]] & [[IS_FIREABLE [Transketolase1] | IS_FIREABLE [Glutathione_reductose]] | [IS_FIREABLE [Phosphoglycerate_kinase] & IS_FIREABLE [GAP_dehydrogenase]]]]]]


FORMULA GPPP-PT-C1000N0000000100-CTLFireability-8 CANNOT_COMPUTE

MC time: 2m39.291sec

checking: AX [[[AF [IS_FIREABLE [TIM_forward]] & ~ [IS_FIREABLE [Phosphofructokinase]]] & [[~ [IS_FIREABLE [Ru5P_epimerase]] & ~ [IS_FIREABLE [G6P_dehydrogenase]]] | ~ [IS_FIREABLE [TIM_backward]]]]]
normalized: ~ [EX [~ [[[~ [IS_FIREABLE [TIM_backward]] | [~ [IS_FIREABLE [G6P_dehydrogenase]] & ~ [IS_FIREABLE [Ru5P_epimerase]]]] & [~ [IS_FIREABLE [Phosphofructokinase]] & ~ [EG [~ [IS_FIREABLE [TIM_forward]]]]]]]]]


FORMULA GPPP-PT-C1000N0000000100-CTLFireability-10 CANNOT_COMPUTE

MC time: 0m 0.001sec

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


FORMULA GPPP-PT-C1000N0000000100-CTLFireability-6 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [EF [[[[IS_FIREABLE [Hexokinase] | IS_FIREABLE [Ru5P_epimerase]] & IS_FIREABLE [Enolase]] & ~ [[IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Phosphoglycerate_kinase]]]]] | ~ [AF [[[IS_FIREABLE [TIM_forward] | IS_FIREABLE [Transketolase2]] | [IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [Lactate_dehydrogenase]]]]]]
normalized: [EG [~ [[[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [Lactate_dehydrogenase]] | [IS_FIREABLE [TIM_forward] | IS_FIREABLE [Transketolase2]]]]] | E [true U [~ [[IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Phosphoglycerate_kinase]]] & [IS_FIREABLE [Enolase] & [IS_FIREABLE [Hexokinase] | IS_FIREABLE [Ru5P_epimerase]]]]]]


FORMULA GPPP-PT-C1000N0000000100-CTLFireability-11 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: EF [AX [EG [IS_FIREABLE [Enolase]]]]
normalized: E [true U ~ [EX [~ [EG [IS_FIREABLE [Enolase]]]]]]


FORMULA GPPP-PT-C1000N0000000100-CTLFireability-3 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [EX [~ [IS_FIREABLE [Phosphoglycerate_mutase]]] & EF [A [IS_FIREABLE [Phosphoglycerate_mutase] U IS_FIREABLE [Pyruvate_kinase]]]]
normalized: [E [true U [~ [EG [~ [IS_FIREABLE [Pyruvate_kinase]]]] & ~ [E [~ [IS_FIREABLE [Pyruvate_kinase]] U [~ [IS_FIREABLE [Phosphoglycerate_mutase]] & ~ [IS_FIREABLE [Pyruvate_kinase]]]]]]] & EX [~ [IS_FIREABLE [Phosphoglycerate_mutase]]]]


FORMULA GPPP-PT-C1000N0000000100-CTLFireability-0 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [[EF [EF [IS_FIREABLE [G6P_dehydrogenase]]] & [EF [[IS_FIREABLE [remove] & IS_FIREABLE [Phosphoglycerate_mutase]]] & ~ [EG [IS_FIREABLE [Enolase]]]]] | AX [IS_FIREABLE [Transaldolase]]]
normalized: [~ [EX [~ [IS_FIREABLE [Transaldolase]]]] | [[~ [EG [IS_FIREABLE [Enolase]]] & E [true U [IS_FIREABLE [remove] & IS_FIREABLE [Phosphoglycerate_mutase]]]] & E [true U E [true U IS_FIREABLE [G6P_dehydrogenase]]]]]


FORMULA GPPP-PT-C1000N0000000100-CTLFireability-5 CANNOT_COMPUTE

MC time: 0m 0.000sec

totally nodes used: 162835817 (1.6e+08)
number of garbage collections: 2
fire ops cache: hits/miss/sum: 1792152935 556934033 2349086968
used/not used/entry size/cache size: 65871987 1236877 16 1024MB
basic ops cache: hits/miss/sum: 375718028 113118094 488836122
used/not used/entry size/cache size: 16577723 199493 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: 3559404 567811 4127215
used/not used/entry size/cache size: 0 8388608 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 28420822
1 23949972
2 10311404
3 3056345
4 793964
5 264850
6 118558
7 97973
8 56442
9 22226
>= 10 16308

Total processing time: 28m20.179sec


BK_STOP 1494886591148

--------------------
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 0.001sec


iterations count:12167 (553), effective:2934 (133)

initing FirstDep: 0m 0.001sec


ctl_mc.icc:221: Timeout: after 219 sec


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

iterations count:26 (1), effective:1 (0)

iterations count:130 (5), effective:17 (0)
std::bad_alloc


iterations count:185 (8), effective:28 (1)

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

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

ctl_mc.icc:221: Timeout: after 277 sec


iterations count:130 (5), effective:17 (0)

iterations count:130 (5), effective:17 (0)
std::bad_alloc


iterations count:183 (8), effective:28 (1)

iterations count:37 (1), effective:2 (0)

iterations count:216 (9), effective:36 (1)

iterations count:120 (5), effective:24 (1)

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

ctl_mc.icc:221: Timeout: after 345 sec


iterations count:187 (8), effective:29 (1)
std::bad_alloc

std::bad_alloc

std::bad_alloc

std::bad_alloc

std::bad_alloc

std::bad_alloc

std::bad_alloc

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="S_GPPP-PT-C1000N0000000100"
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/S_GPPP-PT-C1000N0000000100.tgz
mv S_GPPP-PT-C1000N0000000100 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 S_GPPP-PT-C1000N0000000100, 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 r101-blw3-149441599200580"
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 ;