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-C0100N0000010000, examination is ReachabilityFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r021-blw3-149440255300558
=====================================================================

--------------------
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-C0100N0000010000-ReachabilityFireability-0
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-1
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-10
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-11
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-12
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-13
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-14
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-15
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-2
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-3
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-4
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-5
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-6
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-7
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-8
FORMULA_NAME GPPP-PT-C0100N0000010000-ReachabilityFireability-9

=== Now, execution of the tool begins

BK_START 1494465474747

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=ReachabilityFireability.xml --memory=6

parse successfull
net created successfully

Net: GPPP_PT_C0100N0000010000
(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 1.225sec

parse successfull
net created successfully

Net: GPPP_PT_C0100N0000010000
(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 3.540sec


RS generation: 4m51.769sec


-> reachability set: #nodes 713713 (7.1e+05) #states 20,292,531,036,711,574 (16)



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

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


FORMULA GPPP-PT-C0100N0000010000-ReachabilityFireability-2 CANNOT_COMPUTE

MC time: 1m10.901sec

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


before gc: list nodes free: 142

after gc: idd nodes used:1309047, unused:62690953; list nodes free:539723825
MC time: 3m36.273sec

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


before gc: list nodes free: 59912159

after gc: idd nodes used:1738500, unused:62261500; list nodes free:537165011
MC time: 3m21.378sec

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

MC time: 3m 8.504sec

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

MC time: 2m55.133sec

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


before gc: list nodes free: 52661971

after gc: idd nodes used:1308477, unused:62691523; list nodes free:540285038
MC time: 2m44.046sec

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

MC time: 2m33.181sec

checking: EF [[~ [IS_FIREABLE [Glutathione_reductose]] & IS_FIREABLE [Transaldolase]]]
normalized: E [true U [IS_FIREABLE [Transaldolase] & ~ [IS_FIREABLE [Glutathione_reductose]]]]

MC time: 2m23.029sec

checking: AG [~ [[[~ [IS_FIREABLE [G6P_dehydrogenase]] & IS_FIREABLE [Glutathione_reductose]] & IS_FIREABLE [Enolase]]]]
normalized: ~ [E [true U [IS_FIREABLE [Enolase] & [IS_FIREABLE [Glutathione_reductose] & ~ [IS_FIREABLE [G6P_dehydrogenase]]]]]]


FORMULA GPPP-PT-C0100N0000010000-ReachabilityFireability-11 CANNOT_COMPUTE

MC time: 0m19.788sec

checking: EF [[IS_FIREABLE [remove] & ~ [[[IS_FIREABLE [GAP_dehydrogenase] | IS_FIREABLE [Phosphoglycerate_kinase]] & [IS_FIREABLE [remove] & IS_FIREABLE [Phosphoglucose_isomerase]]]]]]
normalized: E [true U [IS_FIREABLE [remove] & ~ [[[IS_FIREABLE [remove] & IS_FIREABLE [Phosphoglucose_isomerase]] & [IS_FIREABLE [GAP_dehydrogenase] | IS_FIREABLE [Phosphoglycerate_kinase]]]]]]


before gc: list nodes free: 75

after gc: idd nodes used:713736, unused:63286264; list nodes free:546922459
-> the formula is FALSE

FORMULA GPPP-PT-C0100N0000010000-ReachabilityFireability-7 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m16.767sec

checking: EF [[~ [[[IS_FIREABLE [Phosphoglucose_isomerase] | IS_FIREABLE [Aldolase]] & ~ [IS_FIREABLE [Phosphoglucose_isomerase]]]] & ~ [[IS_FIREABLE [Lactate_dehydrogenase] | ~ [IS_FIREABLE [Aldolase]]]]]]
normalized: E [true U [~ [[IS_FIREABLE [Lactate_dehydrogenase] | ~ [IS_FIREABLE [Aldolase]]]] & ~ [[~ [IS_FIREABLE [Phosphoglucose_isomerase]] & [IS_FIREABLE [Phosphoglucose_isomerase] | IS_FIREABLE [Aldolase]]]]]]

MC time: 2m31.444sec

checking: AG [[~ [[IS_FIREABLE [Transketolase2] | ~ [IS_FIREABLE [TIM_backward]]]] | ~ [[[IS_FIREABLE [Transketolase1] & IS_FIREABLE [Pyruvate_kinase]] & [IS_FIREABLE [Phosphoglucose_isomerase] & IS_FIREABLE [Transketolase1]]]]]]
normalized: ~ [E [true U ~ [[~ [[[IS_FIREABLE [Phosphoglucose_isomerase] & IS_FIREABLE [Transketolase1]] & [IS_FIREABLE [Transketolase1] & IS_FIREABLE [Pyruvate_kinase]]]] | ~ [[IS_FIREABLE [Transketolase2] | ~ [IS_FIREABLE [TIM_backward]]]]]]]]

MC time: 2m19.278sec

checking: AG [[~ [~ [~ [IS_FIREABLE [Phosphoglycerate_kinase]]]] | [[IS_FIREABLE [remove] | ~ [IS_FIREABLE [remove]]] | [IS_FIREABLE [generate] & [IS_FIREABLE [remove] | IS_FIREABLE [Phosphoglucose_isomerase]]]]]]
normalized: ~ [E [true U ~ [[[[IS_FIREABLE [generate] & [IS_FIREABLE [remove] | IS_FIREABLE [Phosphoglucose_isomerase]]] | [IS_FIREABLE [remove] | ~ [IS_FIREABLE [remove]]]] | ~ [IS_FIREABLE [Phosphoglycerate_kinase]]]]]]

-> the formula is TRUE

FORMULA GPPP-PT-C0100N0000010000-ReachabilityFireability-15 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 8.960sec

checking: EF [[[[IS_FIREABLE [Ru5P_epimerase] & [IS_FIREABLE [Transketolase2] | IS_FIREABLE [Phosphoglycerate_kinase]]] & ~ [~ [IS_FIREABLE [Phosphoglycerate_mutase]]]] & [[[IS_FIREABLE [Transaldolase] & IS_FIREABLE [Phosphoglucose_isomerase]] & IS_FIREABLE [Glutathione_oxidation]] | [[IS_FIREABLE [Lactate_dehydrogenase] | IS_FIREABLE [Lactate_dehydrogenase]] & [IS_FIREABLE [remove] & IS_FIREABLE [G6P_dehydrogenase]]]]]]
normalized: E [true U [[[[IS_FIREABLE [remove] & IS_FIREABLE [G6P_dehydrogenase]] & [IS_FIREABLE [Lactate_dehydrogenase] | IS_FIREABLE [Lactate_dehydrogenase]]] | [IS_FIREABLE [Glutathione_oxidation] & [IS_FIREABLE [Transaldolase] & IS_FIREABLE [Phosphoglucose_isomerase]]]] & [IS_FIREABLE [Phosphoglycerate_mutase] & [IS_FIREABLE [Ru5P_epimerase] & [IS_FIREABLE [Transketolase2] | IS_FIREABLE [Phosphoglycerate_kinase]]]]]]

-> the formula is FALSE

FORMULA GPPP-PT-C0100N0000010000-ReachabilityFireability-13 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m10.155sec

checking: EF [[[[[IS_FIREABLE [Phosphoglucose_isomerase] & IS_FIREABLE [TIM_backward]] | [IS_FIREABLE [Pyruvate_kinase] & IS_FIREABLE [Transketolase2]]] & [[IS_FIREABLE [Hexokinase] | IS_FIREABLE [Hexokinase]] | [IS_FIREABLE [Hexokinase] | IS_FIREABLE [Phosphoglucose_isomerase]]]] & [[IS_FIREABLE [Phosphofructokinase] & ~ [IS_FIREABLE [Hexokinase]]] & ~ [[IS_FIREABLE [Aldolase] | IS_FIREABLE [Pyruvate_kinase]]]]]]
normalized: E [true U [[~ [[IS_FIREABLE [Aldolase] | IS_FIREABLE [Pyruvate_kinase]]] & [IS_FIREABLE [Phosphofructokinase] & ~ [IS_FIREABLE [Hexokinase]]]] & [[[IS_FIREABLE [Hexokinase] | IS_FIREABLE [Phosphoglucose_isomerase]] | [IS_FIREABLE [Hexokinase] | IS_FIREABLE [Hexokinase]]] & [[IS_FIREABLE [Pyruvate_kinase] & IS_FIREABLE [Transketolase2]] | [IS_FIREABLE [Phosphoglucose_isomerase] & IS_FIREABLE [TIM_backward]]]]]]

MC time: 2m30.013sec

checking: AG [[[[[IS_FIREABLE [Phosphofructokinase] & IS_FIREABLE [Lactate_dehydrogenase]] | [IS_FIREABLE [Phosphoglucose_isomerase] & IS_FIREABLE [Transketolase2]]] | ~ [[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [Hexokinase]]]] | [[[IS_FIREABLE [TIM_backward] & IS_FIREABLE [remove]] & [IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [Phosphoglucose_isomerase]]] & [~ [IS_FIREABLE [G6P_dehydrogenase]] & [IS_FIREABLE [Transketolase2] & IS_FIREABLE [Aldolase]]]]]]
normalized: ~ [E [true U ~ [[[[[IS_FIREABLE [Transketolase2] & IS_FIREABLE [Aldolase]] & ~ [IS_FIREABLE [G6P_dehydrogenase]]] & [[IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [Phosphoglucose_isomerase]] & [IS_FIREABLE [TIM_backward] & IS_FIREABLE [remove]]]] | [~ [[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [Hexokinase]]] | [[IS_FIREABLE [Phosphoglucose_isomerase] & IS_FIREABLE [Transketolase2]] | [IS_FIREABLE [Phosphofructokinase] & IS_FIREABLE [Lactate_dehydrogenase]]]]]]]]


FORMULA GPPP-PT-C0100N0000010000-ReachabilityFireability-0 CANNOT_COMPUTE

MC time: 1m44.029sec

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


FORMULA GPPP-PT-C0100N0000010000-ReachabilityFireability-3 CANNOT_COMPUTE


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:11921 (541), effective:2875 (130)

initing FirstDep: 0m 0.000sec

std::bad_alloc


sat_reach.icc:155: Timeout: after 215 sec


sat_reach.icc:155: Timeout: after 200 sec


sat_reach.icc:155: Timeout: after 187 sec


sat_reach.icc:155: Timeout: after 174 sec


sat_reach.icc:155: Timeout: after 163 sec


sat_reach.icc:155: Timeout: after 152 sec


sat_reach.icc:155: Timeout: after 142 sec

std::bad_alloc


sat_reach.icc:155: Timeout: after 150 sec


sat_reach.icc:155: Timeout: after 138 sec


sat_reach.icc:155: Timeout: after 149 sec

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="GPPP-PT-C0100N0000010000"
export BK_EXAMINATION="ReachabilityFireability"
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-C0100N0000010000.tgz
mv GPPP-PT-C0100N0000010000 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-C0100N0000010000, examination is ReachabilityFireability"
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-blw3-149440255300558"
echo "====================================================================="
echo
echo "--------------------"
echo "content from stdout:"
echo
echo "=== Data for post analysis generated by BenchKit (invocation template)"
echo
if [ "ReachabilityFireability" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "ReachabilityFireability" != "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 "ReachabilityFireability.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property ReachabilityFireability.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -f "ReachabilityFireability.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 '' ReachabilityFireability.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 ;