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-C0100N0000001000, examination is ReachabilityFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r021-blw3-149440255300549
=====================================================================

--------------------
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 1494465065599

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 1.200sec

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 3.807sec


RS generation: 4m44.923sec


-> 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: 1m12.334sec

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: 3m36.460sec

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: 63469086

after gc: idd nodes used:1704912, unused:62295088; list nodes free:537463916
MC time: 3m22.392sec

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 8.031sec

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 4.718sec

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 2.342sec

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: 3m22.886sec

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 1.762sec

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]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-3 CANNOT_COMPUTE

MC time: 0m 0.025sec

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]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-13 CANNOT_COMPUTE

MC time: 0m 0.015sec

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]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-14 CANNOT_COMPUTE

MC time: 0m 0.000sec

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]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-15 CANNOT_COMPUTE

MC time: 0m 0.000sec

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]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-5 CANNOT_COMPUTE

MC time: 0m 0.000sec

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]]]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-10 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: EF [[[[[IS_FIREABLE [Ru5P_isomerase] & IS_FIREABLE [TIM_forward]] & [IS_FIREABLE [Hexokinase] | IS_FIREABLE [Phosphofructokinase]]] & [[IS_FIREABLE [TIM_backward] & IS_FIREABLE [Phosphofructokinase]] & [IS_FIREABLE [generate] & IS_FIREABLE [Ru5P_epimerase]]]] & IS_FIREABLE [Ru5P_epimerase]]]
normalized: E [true U [IS_FIREABLE [Ru5P_epimerase] & [[[IS_FIREABLE [generate] & IS_FIREABLE [Ru5P_epimerase]] & [IS_FIREABLE [TIM_backward] & IS_FIREABLE [Phosphofructokinase]]] & [[IS_FIREABLE [Hexokinase] | IS_FIREABLE [Phosphofructokinase]] & [IS_FIREABLE [Ru5P_isomerase] & IS_FIREABLE [TIM_forward]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-7 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: EF [[[[~ [IS_FIREABLE [Pyruvate_kinase]] & IS_FIREABLE [remove]] & [[IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [Phosphofructokinase]] | [IS_FIREABLE [Glutathione_reductose] | IS_FIREABLE [Glutathione_reductose]]]] & ~ [[[IS_FIREABLE [Transketolase2] & IS_FIREABLE [Phosphofructokinase]] | [IS_FIREABLE [TIM_backward] & IS_FIREABLE [Transaldolase]]]]]]
normalized: E [true U [~ [[[IS_FIREABLE [TIM_backward] & IS_FIREABLE [Transaldolase]] | [IS_FIREABLE [Transketolase2] & IS_FIREABLE [Phosphofructokinase]]]] & [[[IS_FIREABLE [Glutathione_reductose] | IS_FIREABLE [Glutathione_reductose]] | [IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [Phosphofructokinase]]] & [IS_FIREABLE [remove] & ~ [IS_FIREABLE [Pyruvate_kinase]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-6 CANNOT_COMPUTE

MC time: 0m 0.000sec

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


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-1 CANNOT_COMPUTE

MC time: 0m 0.000sec

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


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-4 CANNOT_COMPUTE

MC time: 0m 0.000sec

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]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-0 CANNOT_COMPUTE

MC time: 0m 0.000sec

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]]]]]]]


FORMULA GPPP-PT-C0100N0000001000-ReachabilityFireability-11 CANNOT_COMPUTE

MC time: 0m 0.000sec

totally nodes used: 149655982 (1.5e+08)
number of garbage collections: 2
fire ops cache: hits/miss/sum: 1356493034 397522441 1754015475
used/not used/entry size/cache size: 64702486 2406378 16 1024MB
basic ops cache: hits/miss/sum: 547409053 213557901 760966954
used/not used/entry size/cache size: 16773152 4064 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: 4311971 721170 5033141
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 32100483
1 21534695
2 8767294
3 2924460
4 1031882
5 443048
6 197813
7 74002
8 23428
9 6540
>= 10 5219

Total processing time: 19m53.525sec


BK_STOP 1494466259602

--------------------
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 201 sec


sat_reach.icc:155: Timeout: after 187 sec


sat_reach.icc:155: Timeout: after 201 sec

std::bad_alloc

std::bad_alloc

std::bad_alloc

std::bad_alloc

std::bad_alloc

std::bad_alloc

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="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/GPPP-PT-C0100N0000001000.tgz
mv 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 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 r021-blw3-149440255300549"
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 ;