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-C0100N0000100000, examination is CTLFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r021-blw3-149440255300562
=====================================================================

--------------------
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-C0100N0000100000-CTLFireability-0
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-1
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-10
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-11
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-12
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-13
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-14
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-15
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-2
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-3
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-4
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-5
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-6
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-7
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-8
FORMULA_NAME GPPP-PT-C0100N0000100000-CTLFireability-9

=== Now, execution of the tool begins

BK_START 1494465635852

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_C0100N0000100000
(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 1.204sec

parse successfull
net created successfully

Net: GPPP_PT_C0100N0000100000
(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 3.937sec


RS generation: 5m17.239sec


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



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

checking: EF [AX [AG [IS_FIREABLE [GAP_dehydrogenase]]]]
normalized: E [true U ~ [EX [E [true U ~ [IS_FIREABLE [GAP_dehydrogenase]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-6 CANNOT_COMPUTE

MC time: 1m24.326sec

checking: AF [IS_FIREABLE [TIM_backward]]
normalized: ~ [EG [~ [IS_FIREABLE [TIM_backward]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-7 CANNOT_COMPUTE

MC time: 0m 0.001sec

checking: ~ [E [~ [~ [IS_FIREABLE [G6P_dehydrogenase]]] U AF [IS_FIREABLE [TIM_backward]]]]
normalized: ~ [E [IS_FIREABLE [G6P_dehydrogenase] U ~ [EG [~ [IS_FIREABLE [TIM_backward]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-9 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: AF [[IS_FIREABLE [Ru5P_isomerase] | EG [~ [IS_FIREABLE [TIM_backward]]]]]
normalized: ~ [EG [~ [[IS_FIREABLE [Ru5P_isomerase] | EG [~ [IS_FIREABLE [TIM_backward]]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-12 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: AG [EX [[~ [IS_FIREABLE [Transaldolase]] | IS_FIREABLE [TIM_backward]]]]
normalized: ~ [E [true U ~ [EX [[IS_FIREABLE [TIM_backward] | ~ [IS_FIREABLE [Transaldolase]]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-13 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: AG [[AX [[IS_FIREABLE [Phosphoglucose_isomerase] | IS_FIREABLE [Hexokinase]]] | ~ [AG [IS_FIREABLE [Glutathione_reductose]]]]]
normalized: ~ [E [true U ~ [[E [true U ~ [IS_FIREABLE [Glutathione_reductose]]] | ~ [EX [~ [[IS_FIREABLE [Phosphoglucose_isomerase] | IS_FIREABLE [Hexokinase]]]]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-0 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: AF [A [~ [IS_FIREABLE [Transketolase2]] U [IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [TIM_backward]]]]
normalized: ~ [EG [~ [[~ [EG [~ [[IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [TIM_backward]]]]] & ~ [E [~ [[IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [TIM_backward]]] U [IS_FIREABLE [Transketolase2] & ~ [[IS_FIREABLE [Ru5P_epimerase] | IS_FIREABLE [TIM_backward]]]]]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-14 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: ~ [[IS_FIREABLE [Ru5P_epimerase] | A [~ [IS_FIREABLE [Transketolase2]] U [IS_FIREABLE [Phosphofructokinase] | IS_FIREABLE [Phosphoglycerate_kinase]]]]]
normalized: ~ [[IS_FIREABLE [Ru5P_epimerase] | [~ [EG [~ [[IS_FIREABLE [Phosphofructokinase] | IS_FIREABLE [Phosphoglycerate_kinase]]]]] & ~ [E [~ [[IS_FIREABLE [Phosphofructokinase] | IS_FIREABLE [Phosphoglycerate_kinase]]] U [IS_FIREABLE [Transketolase2] & ~ [[IS_FIREABLE [Phosphofructokinase] | IS_FIREABLE [Phosphoglycerate_kinase]]]]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-2 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [EF [AG [IS_FIREABLE [Phosphoglucose_isomerase]]] | E [[IS_FIREABLE [Phosphoglycerate_mutase] & ~ [IS_FIREABLE [Hexokinase]]] U AG [IS_FIREABLE [TIM_forward]]]]
normalized: [E [[IS_FIREABLE [Phosphoglycerate_mutase] & ~ [IS_FIREABLE [Hexokinase]]] U ~ [E [true U ~ [IS_FIREABLE [TIM_forward]]]]] | E [true U ~ [E [true U ~ [IS_FIREABLE [Phosphoglucose_isomerase]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-5 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [~ [EG [[[IS_FIREABLE [Transaldolase] | IS_FIREABLE [GAP_dehydrogenase]] & ~ [IS_FIREABLE [Ru5P_isomerase]]]]] & [IS_FIREABLE [Transaldolase] | EF [AG [IS_FIREABLE [Enolase]]]]]
normalized: [[IS_FIREABLE [Transaldolase] | E [true U ~ [E [true U ~ [IS_FIREABLE [Enolase]]]]]] & ~ [EG [[~ [IS_FIREABLE [Ru5P_isomerase]] & [IS_FIREABLE [Transaldolase] | IS_FIREABLE [GAP_dehydrogenase]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-3 CANNOT_COMPUTE

MC time: 0m 0.000sec

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


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-15 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: EF [[AG [IS_FIREABLE [Aldolase]] & [IS_FIREABLE [Transketolase1] | [[IS_FIREABLE [TIM_backward] & IS_FIREABLE [Phosphoglucose_isomerase]] | [IS_FIREABLE [Transaldolase] | IS_FIREABLE [Aldolase]]]]]]
normalized: E [true U [[IS_FIREABLE [Transketolase1] | [[IS_FIREABLE [Transaldolase] | IS_FIREABLE [Aldolase]] | [IS_FIREABLE [TIM_backward] & IS_FIREABLE [Phosphoglucose_isomerase]]]] & ~ [E [true U ~ [IS_FIREABLE [Aldolase]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-10 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: ~ [[[[AG [IS_FIREABLE [Ru5P_isomerase]] & ~ [[IS_FIREABLE [Aldolase] & IS_FIREABLE [Phosphoglucose_isomerase]]]] | EG [~ [IS_FIREABLE [TIM_backward]]]] & EF [[~ [IS_FIREABLE [Enolase]] | [IS_FIREABLE [remove] & IS_FIREABLE [GAP_dehydrogenase]]]]]]
normalized: ~ [[E [true U [[IS_FIREABLE [remove] & IS_FIREABLE [GAP_dehydrogenase]] | ~ [IS_FIREABLE [Enolase]]]] & [EG [~ [IS_FIREABLE [TIM_backward]]] | [~ [[IS_FIREABLE [Aldolase] & IS_FIREABLE [Phosphoglucose_isomerase]]] & ~ [E [true U ~ [IS_FIREABLE [Ru5P_isomerase]]]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-4 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: ~ [[[~ [AX [IS_FIREABLE [TIM_forward]]] | [AG [IS_FIREABLE [Lactate_dehydrogenase]] & ~ [[IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Transaldolase]]]]] & AF [[IS_FIREABLE [TIM_backward] | [IS_FIREABLE [Lactate_dehydrogenase] & IS_FIREABLE [Phosphoglycerate_kinase]]]]]]
normalized: ~ [[~ [EG [~ [[IS_FIREABLE [TIM_backward] | [IS_FIREABLE [Lactate_dehydrogenase] & IS_FIREABLE [Phosphoglycerate_kinase]]]]]] & [[~ [[IS_FIREABLE [GAP_dehydrogenase] & IS_FIREABLE [Transaldolase]]] & ~ [E [true U ~ [IS_FIREABLE [Lactate_dehydrogenase]]]]] | EX [~ [IS_FIREABLE [TIM_forward]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-8 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [~ [A [~ [IS_FIREABLE [G6P_dehydrogenase]] U ~ [IS_FIREABLE [Lactate_dehydrogenase]]]] | ~ [[[[IS_FIREABLE [Transketolase1] & [IS_FIREABLE [Phosphoglycerate_mutase] | IS_FIREABLE [Phosphoglucose_isomerase]]] & EG [IS_FIREABLE [Ru5P_isomerase]]] | [AF [IS_FIREABLE [TIM_forward]] | IS_FIREABLE [G6P_dehydrogenase]]]]]
normalized: [~ [[[IS_FIREABLE [G6P_dehydrogenase] | ~ [EG [~ [IS_FIREABLE [TIM_forward]]]]] | [EG [IS_FIREABLE [Ru5P_isomerase]] & [IS_FIREABLE [Transketolase1] & [IS_FIREABLE [Phosphoglycerate_mutase] | IS_FIREABLE [Phosphoglucose_isomerase]]]]]] | ~ [[~ [EG [IS_FIREABLE [Lactate_dehydrogenase]]] & ~ [E [IS_FIREABLE [Lactate_dehydrogenase] U [IS_FIREABLE [G6P_dehydrogenase] & IS_FIREABLE [Lactate_dehydrogenase]]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-11 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [[[[[[IS_FIREABLE [TIM_forward] & IS_FIREABLE [Aldolase]] & [IS_FIREABLE [Glutathione_oxidation] & IS_FIREABLE [Transketolase1]]] & [~ [IS_FIREABLE [Transketolase1]] & ~ [IS_FIREABLE [Transketolase2]]]] & IS_FIREABLE [Lactate_dehydrogenase]] & AX [~ [[IS_FIREABLE [Phosphoglucose_isomerase] & IS_FIREABLE [Hexokinase]]]]] | [IS_FIREABLE [generate] & AG [EF [IS_FIREABLE [Ru5P_isomerase]]]]]
normalized: [[IS_FIREABLE [generate] & ~ [E [true U ~ [E [true U IS_FIREABLE [Ru5P_isomerase]]]]]] | [~ [EX [[IS_FIREABLE [Phosphoglucose_isomerase] & IS_FIREABLE [Hexokinase]]]] & [IS_FIREABLE [Lactate_dehydrogenase] & [[~ [IS_FIREABLE [Transketolase2]] & ~ [IS_FIREABLE [Transketolase1]]] & [[IS_FIREABLE [Glutathione_oxidation] & IS_FIREABLE [Transketolase1]] & [IS_FIREABLE [TIM_forward] & IS_FIREABLE [Aldolase]]]]]]]


FORMULA GPPP-PT-C0100N0000100000-CTLFireability-1 CANNOT_COMPUTE

MC time: 0m 0.000sec

totally nodes used: 31295330 (3.1e+07)
number of garbage collections: 0
fire ops cache: hits/miss/sum: 322397821 82158759 404556580
used/not used/entry size/cache size: 49266233 17842631 16 1024MB
basic ops cache: hits/miss/sum: 116167960 29320648 145488608
used/not used/entry size/cache size: 16391252 385964 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: 686270 7702338 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 51581339
1 8453695
2 3211781
3 1399776
4 1339010
5 590916
6 342300
7 96655
8 46078
9 22377
>= 10 24937

Total processing time: 6m55.529sec


BK_STOP 1494466051798

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


iterations count:102 (4), effective:10 (0)
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

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-C0100N0000100000"
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-C0100N0000100000.tgz
mv GPPP-PT-C0100N0000100000 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-C0100N0000100000, 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-blw3-149440255300562"
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 ;