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-C0100N0000001000, examination is ReachabilityFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r101-blw3-149441599100549
=====================================================================

--------------------
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-C0100N0000001000-ReachabilityFireability-0
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-1
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-10
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-11
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-12
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-13
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-14
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-15
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-2
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-3
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-4
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-5
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-6
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-7
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-8
FORMULA_NAME GPPP-PT-C0100N0000001000-ReachabilityFireability-9

=== Now, execution of the tool begins

BK_START 1494884059486

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_C0100N0000001000
(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 1.214sec

parse successfull
net created successfully

Net: GPPP_PT_C0100N0000001000
(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 3.777sec


RS generation: 4m58.620sec


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



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

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


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-12 CANNOT_COMPUTE

MC time: 1m 6.562sec

checking: EF [[IS_FIREABLE [Phosphoglycerate_kinase] & ~ [~ [IS_FIREABLE [Enolase]]]]]
normalized: E [true U [IS_FIREABLE [Phosphoglycerate_kinase] & IS_FIREABLE [Enolase]]]


before gc: list nodes free: 59

after gc: idd nodes used:1309049, unused:62690951; list nodes free:539722455
MC time: 3m36.064sec

checking: EF [[IS_FIREABLE [Ru5P_epimerase] & IS_FIREABLE [Phosphoglycerate_kinase]]]
normalized: E [true U [IS_FIREABLE [Ru5P_epimerase] & IS_FIREABLE [Phosphoglycerate_kinase]]]


before gc: list nodes free: 63475005

after gc: idd nodes used:1699900, unused:62300100; list nodes free:537502951
MC time: 3m21.064sec

checking: AG [~ [[[IS_FIREABLE [Lactate_dehydrogenase] & ~ [IS_FIREABLE [Aldolase]]] & ~ [~ [IS_FIREABLE [Phosphoclucose_isomerase]]]]]]
normalized: ~ [E [true U [IS_FIREABLE [Phosphoclucose_isomerase] & [IS_FIREABLE [Lactate_dehydrogenase] & ~ [IS_FIREABLE [Aldolase]]]]]]

MC time: 3m 8.179sec

checking: EF [~ [~ [[[IS_FIREABLE [Transketolase1] & IS_FIREABLE [Ru5P_isomerase]] & [IS_FIREABLE [TIM_backward] & IS_FIREABLE [Phosphoglycerate_mutase]]]]]]
normalized: E [true U [[IS_FIREABLE [TIM_backward] & IS_FIREABLE [Phosphoglycerate_mutase]] & [IS_FIREABLE [Transketolase1] & IS_FIREABLE [Ru5P_isomerase]]]]

-> the formula is FALSE

FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-2 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 4.958sec

checking: EF [[~ [[~ [IS_FIREABLE [Ru5P_isomerase]] | [IS_FIREABLE [remove] | IS_FIREABLE [Ru5P_isomerase]]]] & IS_FIREABLE [Ru5P_isomerase]]]
normalized: E [true U [IS_FIREABLE [Ru5P_isomerase] & ~ [[[IS_FIREABLE [remove] | IS_FIREABLE [Ru5P_isomerase]] | ~ [IS_FIREABLE [Ru5P_isomerase]]]]]]

-> the formula is FALSE

FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-9 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 2.653sec

checking: AG [[[IS_FIREABLE [Phosphoclucose_isomerase] | [IS_FIREABLE [Aldolase] | IS_FIREABLE [Hexokinase]]] | ~ [IS_FIREABLE [TIM_forward]]]]
normalized: ~ [E [true U ~ [[~ [IS_FIREABLE [TIM_forward]] | [IS_FIREABLE [Phosphoclucose_isomerase] | [IS_FIREABLE [Aldolase] | IS_FIREABLE [Hexokinase]]]]]]]

MC time: 3m22.076sec

checking: AG [[~ [[[IS_FIREABLE [Phosphofructokinase] | IS_FIREABLE [TIM_forward]] | [IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [remove]]]] | ~ [IS_FIREABLE [Pyruvate_kinase]]]]
normalized: ~ [E [true U ~ [[~ [IS_FIREABLE [Pyruvate_kinase]] | ~ [[[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [remove]] | [IS_FIREABLE [Phosphofructokinase] | IS_FIREABLE [TIM_forward]]]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-8 CANNOT_COMPUTE

MC time: 0m 8.885sec

checking: AG [[~ [~ [[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [Enolase]]]] | [[[IS_FIREABLE [Glutathione_oxidation] & IS_FIREABLE [Phosphoglycerate_mutase]] | IS_FIREABLE [Lactate_dehydrogenase]] | ~ [IS_FIREABLE [Transketolase2]]]]]
normalized: ~ [E [true U ~ [[[~ [IS_FIREABLE [Transketolase2]] | [IS_FIREABLE [Lactate_dehydrogenase] | [IS_FIREABLE [Glutathione_oxidation] & IS_FIREABLE [Phosphoglycerate_mutase]]]] | [IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [Enolase]]]]]]


before gc: list nodes free: 74

after gc: idd nodes used:713735, unused:63286265; list nodes free:546981816
-> the formula is FALSE

FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-3 FALSE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 1m34.193sec

checking: AG [~ [[[~ [IS_FIREABLE [Phosphofructokinase]] & IS_FIREABLE [generate]] & [[IS_FIREABLE [Pyruvate_kinase] | IS_FIREABLE [Aldolase]] | [IS_FIREABLE [G6P_dehydrogenase] & IS_FIREABLE [Phosphoglycerate_mutase]]]]]]
normalized: ~ [E [true U [[[IS_FIREABLE [G6P_dehydrogenase] & IS_FIREABLE [Phosphoglycerate_mutase]] | [IS_FIREABLE [Pyruvate_kinase] | IS_FIREABLE [Aldolase]]] & [IS_FIREABLE [generate] & ~ [IS_FIREABLE [Phosphofructokinase]]]]]]

-> the formula is TRUE

FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-13 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m16.150sec

checking: EF [[[IS_FIREABLE [Ru5P_epimerase] & ~ [~ [IS_FIREABLE [Lactate_dehydrogenase]]]] | [[~ [IS_FIREABLE [Aldolase]] & IS_FIREABLE [Pyruvate_kinase]] & [IS_FIREABLE [TIM_backward] & IS_FIREABLE [Glutathione_oxidation]]]]]
normalized: E [true U [[[IS_FIREABLE [TIM_backward] & IS_FIREABLE [Glutathione_oxidation]] & [IS_FIREABLE [Pyruvate_kinase] & ~ [IS_FIREABLE [Aldolase]]]] | [IS_FIREABLE [Ru5P_epimerase] & IS_FIREABLE [Lactate_dehydrogenase]]]]

MC time: 3m50.197sec

checking: EF [[IS_FIREABLE [GAP_dehydrogenase] & [[IS_FIREABLE [Pyruvate_kinase] | IS_FIREABLE [Phosphofructokinase]] & [IS_FIREABLE [Phosphoglycerate_kinase] | [IS_FIREABLE [Ru5P_isomerase] | IS_FIREABLE [Aldolase]]]]]]
normalized: E [true U [IS_FIREABLE [GAP_dehydrogenase] & [[IS_FIREABLE [Phosphoglycerate_kinase] | [IS_FIREABLE [Ru5P_isomerase] | IS_FIREABLE [Aldolase]]] & [IS_FIREABLE [Pyruvate_kinase] | IS_FIREABLE [Phosphofructokinase]]]]]


before gc: list nodes free: 48348741

after gc: idd nodes used:1921029, unused:62078971; list nodes free:534495873
MC time: 3m27.076sec

checking: AG [~ [[[[IS_FIREABLE [remove] & IS_FIREABLE [GAP_dehydrogenase]] & IS_FIREABLE [TIM_backward]] & [[IS_FIREABLE [Hexokinase] & IS_FIREABLE [generate]] | [IS_FIREABLE [Lactate_dehydrogenase] | IS_FIREABLE [TIM_backward]]]]]]
normalized: ~ [E [true U [[[IS_FIREABLE [Lactate_dehydrogenase] | IS_FIREABLE [TIM_backward]] | [IS_FIREABLE [Hexokinase] & IS_FIREABLE [generate]]] & [IS_FIREABLE [TIM_backward] & [IS_FIREABLE [remove] & IS_FIREABLE [GAP_dehydrogenase]]]]]]

-> the formula is TRUE

FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-5 TRUE TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m11.638sec

checking: AG [[[[IS_FIREABLE [Pyruvate_kinase] & [IS_FIREABLE [G6P_dehydrogenase] | IS_FIREABLE [Ru5P_isomerase]]] & [IS_FIREABLE [Phosphoglycerate_mutase] & [IS_FIREABLE [TIM_backward] | IS_FIREABLE [Lactate_dehydrogenase]]]] | ~ [IS_FIREABLE [Lactate_dehydrogenase]]]]
normalized: ~ [E [true U ~ [[~ [IS_FIREABLE [Lactate_dehydrogenase]] | [[IS_FIREABLE [Phosphoglycerate_mutase] & [IS_FIREABLE [TIM_backward] | IS_FIREABLE [Lactate_dehydrogenase]]] & [IS_FIREABLE [Pyruvate_kinase] & [IS_FIREABLE [G6P_dehydrogenase] | IS_FIREABLE [Ru5P_isomerase]]]]]]]]


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 201 sec

std::bad_alloc


iterations count:144 (6), effective:31 (1)

sat_reach.icc:155: Timeout: after 229 sec


sat_reach.icc:155: Timeout: after 206 sec


sat_reach.icc:155: Timeout: after 204 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="S_GPPP-PT-C0100N0000001000"
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/S_GPPP-PT-C0100N0000001000.tgz
mv S_GPPP-PT-C0100N0000001000 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-C0100N0000001000, 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 r101-blw3-149441599100549"
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 ;