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)
.................
/home/mcc/execution
total 196K
-rw-r--r-- 1 mcc users 3.6K May 15 18:54 CTLCardinality.txt
-rw-r--r-- 1 mcc users 20K May 15 18:54 CTLCardinality.xml
-rw-r--r-- 1 mcc users 3.1K May 15 18:54 CTLFireability.txt
-rw-r--r-- 1 mcc users 17K May 15 18:54 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K May 15 18:50 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 5.7K May 15 18:50 GenericPropertiesVerdict.xml
-rw-r--r-- 1 mcc users 2.3K May 15 18:54 LTLCardinality.txt
-rw-r--r-- 1 mcc users 9.1K May 15 18:54 LTLCardinality.xml
-rw-r--r-- 1 mcc users 2.1K May 15 18:54 LTLFireability.txt
-rw-r--r-- 1 mcc users 7.7K May 15 18:54 LTLFireability.xml
-rw-r--r-- 1 mcc users 3.4K May 15 18:54 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 17K May 15 18:54 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 115 May 15 18:54 ReachabilityDeadlock.txt
-rw-r--r-- 1 mcc users 353 May 15 18:54 ReachabilityDeadlock.xml
-rw-r--r-- 1 mcc users 4.2K May 15 18:54 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 22K May 15 18:54 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K May 15 18:54 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K May 15 18:54 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 May 15 18:50 equiv_col
-rw-r--r-- 1 mcc users 17 May 15 18:50 instance
-rw-r--r-- 1 mcc users 6 May 15 18:50 iscolored
-rw-r--r-- 1 mcc users 21K May 15 18:50 model.pnml
=====================================================================
Generated by BenchKit 2-3637
Executing tool irma4mcc-full
Input is GPPP-PT-C0100N0000001000, examination is CTLFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r090-blw7-152650001300319
=====================================================================

--------------------
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-CTLFireability-00
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-01
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-02
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-03
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-04
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-05
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-06
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-07
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-08
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-09
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-10
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-11
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-12
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-13
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-14
FORMULA_NAME GPPP-PT-C0100N0000001000-CTLFireability-15

=== Now, execution of the tool begins

BK_START 1527067406001


BK_STOP 1527067658504

--------------------
content from stderr:

Prefix is 65b80f64.
Reading known information in /usr/share/mcc4mcc/65b80f64-known.json.
Reading learned information in /usr/share/mcc4mcc/65b80f64-learned.json.
Reading value translations in /usr/share/mcc4mcc/65b80f64-values.json.
Using directory /home/mcc/execution for input, as it contains a model.pnml file.
Using GPPP-PT-C0100N0000001000 as instance name.
Using GPPP as model name.
Using algorithm or tool voting-classifier.
Model characteristics are: {'Examination': 'CTLFireability', 'Place/Transition': True, 'Colored': False, 'Relative-Time': 1, 'Relative-Memory': 1, 'Ordinary': False, 'Simple Free Choice': False, 'Extended Free Choice': False, 'State Machine': False, 'Marked Graph': False, 'Connected': True, 'Strongly Connected': True, 'Source Place': False, 'Sink Place': False, 'Source Transition': False, 'Sink Transition': False, 'Loop Free': True, 'Conservative': False, 'Sub-Conservative': False, 'Nested Units': False, 'Safe': False, 'Deadlock': None, 'Reversible': None, 'Quasi Live': True, 'Live': None}.
/usr/local/lib/python3.6/dist-packages/sklearn/preprocessing/label.py:151: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
if diff:
Known tools are: [{'Time': 1287361, 'Memory': 15936.86, 'Tool': 'marcie'}, {'Time': 2241433, 'Memory': 13620.31, 'Tool': 'lola'}, {'Time': 2247573, 'Memory': 15671.75, 'Tool': 'lola'}, {'Time': 2368727, 'Memory': 15936.83, 'Tool': 'marcie'}].
Learned tools are: [{'Tool': 'itstools'}].
CTLFireability marcie GPPP-PT-C0100N0000001000...
timeout --kill-after=10s --signal=SIGINT 1m for testing only

check for maximal unmarked siphon
Marcie rev. 8852M (built: crohr on 2017-05-03)
ok
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_C0100N0000001000
(NrP: 33 NrTr: 22 NrArc: 83)

check for constant places
ok
parse formulas
formulas created successfully
place and transition orderings generation:0m 0.000sec
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!

net check time: 0m 0.000sec

init dd package: 0m 1.354sec

parse successfull
net created successfully

Net: GPPP_PT_C0100N0000001000
(NrP: 33 NrTr: 22 NrArc: 83)

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

parse formulas
formulas created successfully
place and transition orderings generation:0m 0.000sec

net check time: 0m 0.000sec


init dd package: 0m 3.980sec

initing FirstDep: 0m 0.000sec


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

initing FirstDep: 0m 0.000sec


RS generation: 3m44.438sec


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



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

std::bad_alloc

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


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-09 CANNOT_COMPUTE

MC time: 0m11.651sec

checking: IS_FIREABLE [Phosphofructokinase]
normalized: IS_FIREABLE [Phosphofructokinase]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-15 CANNOT_COMPUTE

MC time: 0m 0.098sec

checking: [~ [~ [EF [~ [IS_FIREABLE [TIM_forward]]]]] & EF [IS_FIREABLE [Pyruvate_kinase]]]
normalized: [E [true U IS_FIREABLE [Pyruvate_kinase]] & E [true U ~ [IS_FIREABLE [TIM_forward]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-00 CANNOT_COMPUTE

MC time: 0m 0.019sec

checking: [EF [IS_FIREABLE [Lactate_dehydrogenase]] & ~ [IS_FIREABLE [GAP_dehydrogenase]]]
normalized: [~ [IS_FIREABLE [GAP_dehydrogenase]] & E [true U IS_FIREABLE [Lactate_dehydrogenase]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-03 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: EF [[AG [IS_FIREABLE [Phosphoglycerate_kinase]] & AG [~ [IS_FIREABLE [generate]]]]]
normalized: E [true U [~ [E [true U IS_FIREABLE [generate]]] & ~ [E [true U ~ [IS_FIREABLE [Phosphoglycerate_kinase]]]]]]
std::bad_alloc



std::bad_alloc
FORMULA GPPP-PT-C0100N0000001000-CTLFireability-10 CANNOT_COMPUTE


MC time: 0m 0.000sec

checking: EF [AF [[IS_FIREABLE [TIM_forward] & [IS_FIREABLE [Pyruvate_kinase] | IS_FIREABLE [Enolase]]]]]
std::bad_alloc
normalized: E [true U ~ [EG [~ [[IS_FIREABLE [TIM_forward] & [IS_FIREABLE [Pyruvate_kinase] | IS_FIREABLE [Enolase]]]]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-01 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [~ [IS_FIREABLE [Transketolase2]] & A [EF [IS_FIREABLE [Aldolase]] U IS_FIREABLE [TIM_forward]]]
normalized: [[~ [EG [~ [IS_FIREABLE [TIM_forward]]]] & ~ [E [~ [IS_FIREABLE [TIM_forward]] U [~ [E [true U IS_FIREABLE [Aldolase]]] & ~ [IS_FIREABLE [TIM_forward]]]]]] & ~ [IS_FIREABLE [Transketolase2]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-02 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: EF [[IS_FIREABLE [Ru5P_isomerase] & AG [[IS_FIREABLE [Phosphoglycerate_mutase] | IS_FIREABLE [Transketolase1]]]]]

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

normalized: E [true U [IS_FIREABLE [Ru5P_isomerase] & ~ [E [true U ~ [[IS_FIREABLE [Phosphoglycerate_mutase] | IS_FIREABLE [Transketolase1]]]]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-07 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [AG [AX [IS_FIREABLE [Hexokinase]]] & EX [[EF [IS_FIREABLE [remove]] & [~ [IS_FIREABLE [generate]] | ~ [IS_FIREABLE [Phosphoglycerate_kinase]]]]]]
normalized: [EX [[[~ [IS_FIREABLE [Phosphoglycerate_kinase]] | ~ [IS_FIREABLE [generate]]] & E [true U IS_FIREABLE [remove]]]] & ~ [E [true U EX [~ [IS_FIREABLE [Hexokinase]]]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-05 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [EF [EX [[IS_FIREABLE [generate] & IS_FIREABLE [Glutathione_oxidation]]]] & ~ [[IS_FIREABLE [Enolase] | IS_FIREABLE [Phosphoglycerate_mutase]]]]
normalized: [~ [[IS_FIREABLE [Enolase] | IS_FIREABLE [Phosphoglycerate_mutase]]] & E [true U EX [[IS_FIREABLE [generate] & IS_FIREABLE [Glutathione_oxidation]]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-06 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [EX [EX [IS_FIREABLE [TIM_forward]]] | AG [~ [[[IS_FIREABLE [Transketolase2] & IS_FIREABLE [TIM_backward]] & ~ [IS_FIREABLE [Transketolase2]]]]]]
normalized: [~ [E [true U [~ [IS_FIREABLE [Transketolase2]] & [IS_FIREABLE [Transketolase2] & IS_FIREABLE [TIM_backward]]]]] | EX [EX [IS_FIREABLE [TIM_forward]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-11 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: ~ [E [EF [IS_FIREABLE [Phosphoglycerate_kinase]] U [[IS_FIREABLE [remove] & IS_FIREABLE [Glutathione_oxidation]] & IS_FIREABLE [generate]]]]
normalized: ~ [E [E [true U IS_FIREABLE [Phosphoglycerate_kinase]] U [IS_FIREABLE [generate] & [IS_FIREABLE [remove] & IS_FIREABLE [Glutathione_oxidation]]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-13 CANNOT_COMPUTE

MC time: 0m 0.000sec

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


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-04 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: E [EF [[IS_FIREABLE [TIM_backward] & IS_FIREABLE [generate]]] U [IS_FIREABLE [Enolase] & ~ [[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [generate]]]]]
normalized: E [E [true U [IS_FIREABLE [TIM_backward] & IS_FIREABLE [generate]]] U [IS_FIREABLE [Enolase] & ~ [[IS_FIREABLE [Phosphoglycerate_mutase] & IS_FIREABLE [generate]]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-12 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [[IS_FIREABLE [Phosphoglycerate_mutase] & ~ [[[[IS_FIREABLE [Transketolase2] & IS_FIREABLE [Lactate_dehydrogenase]] | IS_FIREABLE [Aldolase]] & AF [IS_FIREABLE [GAP_dehydrogenase]]]]] & A [AX [IS_FIREABLE [Glutathione_reductose]] U ~ [~ [IS_FIREABLE [Glutathione_oxidation]]]]]
normalized: [[~ [EG [~ [IS_FIREABLE [Glutathione_oxidation]]]] & ~ [E [~ [IS_FIREABLE [Glutathione_oxidation]] U [EX [~ [IS_FIREABLE [Glutathione_reductose]]] & ~ [IS_FIREABLE [Glutathione_oxidation]]]]]] & [IS_FIREABLE [Phosphoglycerate_mutase] & ~ [[~ [EG [~ [IS_FIREABLE [GAP_dehydrogenase]]]] & [IS_FIREABLE [Aldolase] | [IS_FIREABLE [Transketolase2] & IS_FIREABLE [Lactate_dehydrogenase]]]]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-14 CANNOT_COMPUTE

MC time: 0m 0.000sec

checking: [A [AF [IS_FIREABLE [Pyruvate_kinase]] U EF [IS_FIREABLE [Enolase]]] | [E [[IS_FIREABLE [G6P_dehydrogenase] | IS_FIREABLE [Enolase]] U [IS_FIREABLE [G6P_dehydrogenase] | IS_FIREABLE [Phosphoclucose_isomerase]]] & EG [[IS_FIREABLE [Enolase] & ~ [IS_FIREABLE [Glutathione_oxidation]]]]]]
normalized: [[EG [[IS_FIREABLE [Enolase] & ~ [IS_FIREABLE [Glutathione_oxidation]]]] & E [[IS_FIREABLE [G6P_dehydrogenase] | IS_FIREABLE [Enolase]] U [IS_FIREABLE [G6P_dehydrogenase] | IS_FIREABLE [Phosphoclucose_isomerase]]]] | [~ [EG [~ [E [true U IS_FIREABLE [Enolase]]]]] & ~ [E [~ [E [true U IS_FIREABLE [Enolase]]] U [EG [~ [IS_FIREABLE [Pyruvate_kinase]]] & ~ [E [true U IS_FIREABLE [Enolase]]]]]]]]


FORMULA GPPP-PT-C0100N0000001000-CTLFireability-08 CANNOT_COMPUTE

MC time: 0m 0.000sec

totally nodes used: 30673877 (3.1e+07)
number of garbage collections: 0
fire ops cache: hits/miss/sum: 218899669 41627131 260526800
used/not used/entry size/cache size: 34428580 32680284 16 1024MB
basic ops cache: hits/miss/sum: 109522499 23349380 132871879
used/not used/entry size/cache size: 16212337 564879 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 52024476
1 8107151
2 3159085
3 1370489
4 1336476
5 584734
6 339973
7 94075
8 45741
9 21750
>= 10 24914

Total processing time: 4m 8.319sec

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="CTLFireability"
export BK_TOOL="irma4mcc-full"
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
cd execution
pwd
ls -lh

# this is for BenchKit: explicit launching of the test
echo "====================================================================="
echo " Generated by BenchKit 2-3637"
echo " Executing tool irma4mcc-full"
echo " Input is GPPP-PT-C0100N0000001000, examination is CTLFireability"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 4"
echo " Run identifier is r090-blw7-152650001300319"
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 ;