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-C1000N0000000100, examination is CTLFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r021-blw3-149440255400580
=====================================================================

--------------------
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 1494465918781

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 1.182sec

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 3.601sec


RS generation: 1m11.560sec


-> 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: 3m41.106sec

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: 0m16.779sec

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: 0m18.408sec

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

..................................................................................................................................................
before gc: list nodes free: 1571

after gc: idd nodes used:2016977, unused:61983023; list nodes free:534120981
..............................MC time: 3m54.347sec

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

-> the formula is TRUE

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

MC time: 1m 8.036sec

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: 0m22.936sec

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: 4m 6.191sec

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]]]]

.
before gc: list nodes free: 507

after gc: idd nodes used:898675, unused:63101325; list nodes free:545162278
.-> the formula is TRUE

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

MC time: 0m43.966sec

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]]]]]]]]]]

.MC time: 4m 2.396sec

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]]]

-> the formula is FALSE

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

MC time: 1m12.902sec

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: 2m38.296sec

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]]]]]


before gc: list nodes free: 67227002

after gc: idd nodes used:1465636, unused:62534364; list nodes free:532325667
....................................................................................................................MC time: 4m 2.144sec

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]]]]]]

-> the formula is FALSE

FORMULA GPPP-PT-C1000N0000000100-CTLFireability-8 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 2m45.162sec

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]]]]]]]]]

.........................................................................................................................MC time: 3m42.058sec

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: 1m27.966sec

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]]]]]]


before gc: list nodes free: 164

after gc: idd nodes used:561587, unused:63438413; list nodes free:547272065
..........................................................................
BK_TIME_CONFINEMENT_REACHED

--------------------
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:12167 (553), effective:2934 (133)

initing FirstDep: 0m 0.001sec


net_ddint.h:596: Timeout: after 220 sec


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

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

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

ctl_mc.icc:221: Timeout: after 233 sec


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

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

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

net_ddint.h:596: Timeout: after 245 sec


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

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

sat_reach.icc:155: Timeout: after 240 sec


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)

net_ddint.h:596: Timeout: after 241 sec


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

iterations count:228 (10), effective:48 (2)

net_ddint.h:596: Timeout: after 221 sec

std::bad_alloc


iterations count:223 (10), effective:42 (1)

net_ddint.h:596: Timeout: after 208 sec

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-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/GPPP-PT-C1000N0000000100.tgz
mv 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 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 r021-blw3-149440255400580"
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 ;