Execution Chart

We display below the execution chart for this examination (boot time has been removed).

Trace from the execution

Formatting '/data/fkordon/mcc2023-input.r225-tall-167856407900637.qcow2', fmt=qcow2 size=4294967296 backing_file=/data/fkordon/mcc2023-input.qcow2 cluster_size=65536 lazy_refcounts=off refcount_bits=16
Waiting for the VM to be ready (probing ssh)
...............
=====================================================================
Generated by BenchKit 2-5348
Executing tool marcie
Input is MAPKbis-PT-5310, examination is UpperBounds
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 1
Run identifier is r225-tall-167856407900637
=====================================================================

--------------------
preparation of the directory to be used:
/home/mcc/execution
total 628K
-rw-r--r-- 1 mcc users 6.4K Feb 25 16:17 CTLCardinality.txt
-rw-r--r-- 1 mcc users 54K Feb 25 16:17 CTLCardinality.xml
-rw-r--r-- 1 mcc users 11K Feb 25 15:59 CTLFireability.txt
-rw-r--r-- 1 mcc users 48K Feb 25 15:59 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.2K Jan 29 11:40 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 4.2K Feb 25 16:22 LTLCardinality.txt
-rw-r--r-- 1 mcc users 26K Feb 25 16:22 LTLCardinality.xml
-rw-r--r-- 1 mcc users 6.0K Feb 25 16:22 LTLFireability.txt
-rw-r--r-- 1 mcc users 21K Feb 25 16:22 LTLFireability.xml
-rw-r--r-- 1 mcc users 13K Feb 25 16:35 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 111K Feb 25 16:35 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 22K Feb 25 16:26 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 82K Feb 25 16:26 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K Feb 25 16:22 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K Feb 25 16:22 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 Mar 5 18:22 equiv_col
-rw-r--r-- 1 mcc users 5 Mar 5 18:22 instance
-rw-r--r-- 1 mcc users 6 Mar 5 18:22 iscolored
-rw-r--r-- 1 mcc users 170K Mar 5 18:22 model.pnml

--------------------
content from stdout:

=== Data for post analysis generated by BenchKit (invocation template)

The expected result is a vector of positive values
NUM_VECTOR

here is the order used to build the result vector(from text file)
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-00
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-01
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-02
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-03
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-04
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-05
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-06
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-07
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-08
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-09
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-10
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-11
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-12
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-13
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-14
FORMULA_NAME MAPKbis-PT-5310-UpperBounds-15

=== Now, execution of the tool begins

BK_START 1678641198535

bash -c /home/mcc/BenchKit/BenchKit_head.sh 2> STDERR ; echo ; echo -n "BK_STOP " ; date -u +%s%3N
Invoking MCC driver with
BK_TOOL=marcie
BK_EXAMINATION=UpperBounds
BK_BIN_PATH=/home/mcc/BenchKit/bin/
BK_TIME_CONFINEMENT=3600
BK_INPUT=MAPKbis-PT-5310
Not applying reductions.
Model is PT
UpperBounds PT
timeout --kill-after=10s --signal=SIGINT 1m for testing only

Marcie built on Linux at 2019-11-18.
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: /home/mcc/BenchKit/bin//../marcie/bin/marcie --net-file=model.pnml --mcc-file=UpperBounds.xml --memory=6 --mcc-mode

parse successfull
net created successfully

Net: MAPKbis_PT_5310
(NrP: 106 NrTr: 173 NrArc: 986)

parse formulas
formulas created successfully
place and transition orderings generation:0m 0.002sec

net check time: 0m 0.000sec

init dd package: 0m 2.874sec


RS generation: 0m 0.887sec


-> reachability set: #nodes 395 (4.0e+02) #states 3,846,411,649,024 (12)



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

checking: place_bound(BCL2_equals_1)
normalized: place_bound(BCL2_equals_1)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-00 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(ERK_equals_0)
normalized: place_bound(ERK_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-01 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(PKC_equals_0)
normalized: place_bound(PKC_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-02 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(MEK1_2_equals_0)
normalized: place_bound(MEK1_2_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-03 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(TGFBR_equals_1)
normalized: place_bound(TGFBR_equals_1)

-> the formula is 0

FORMULA MAPKbis-PT-5310-UpperBounds-04 0 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(TGFBR_equals_0)
normalized: place_bound(TGFBR_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-05 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(PDK1_equals_1)
normalized: place_bound(PDK1_equals_1)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-06 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(DUSP1_equals_0)
normalized: place_bound(DUSP1_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-07 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(p14_equals_1)
normalized: place_bound(p14_equals_1)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-08 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(TAOK_equals_0)
normalized: place_bound(TAOK_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-09 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(MAP3K1_3_equals_0)
normalized: place_bound(MAP3K1_3_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-10 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(p70_equals_0)
normalized: place_bound(p70_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-11 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(AKT_equals_1)
normalized: place_bound(AKT_equals_1)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-12 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(AKT_0)
normalized: place_bound(AKT_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-13 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(RSK_equals_0)
normalized: place_bound(RSK_equals_0)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-14 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

checking: place_bound(PTEN_equals_1)
normalized: place_bound(PTEN_equals_1)

-> the formula is 1

FORMULA MAPKbis-PT-5310-UpperBounds-15 1 TECHNIQUES SEQUENTIAL_PROCESSING DECISION_DIAGRAMS UNFOLDING_TO_PT

MC time: 0m 0.000sec

totally nodes used: 285856 (2.9e+05)
number of garbage collections: 0
fire ops cache: hits/miss/sum: 1096741 3487078 4583819
used/not used/entry size/cache size: 3643196 63465668 16 1024MB
basic ops cache: hits/miss/sum: 15802 48838 64640
used/not used/entry size/cache size: 81064 16696152 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: 123 395 518
used/not used/entry size/cache size: 395 8388213 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 66830567
1 271133
2 6782
3 369
4 13
5 0
6 0
7 0
8 0
9 0
>= 10 0

Total processing time: 0m 5.483sec


BK_STOP 1678641204064

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

check for maximal unmarked siphon
found
The net has a maximal unmarked siphon:
ATM_equals_1
SMAD_equals_1
TAK1_equals_1
TAOK_equals_1
TGFBR_equals_1
TGFBR_stimulus_equals_1
FGFR3_stimulus_equals_1
EGFR_stimulus_equals_0
FRS2_equals_1
DNA_damage_equals_1
FGFR3_equals_1

The net has transition(s) that can never fire:
JNK_equals_0_to_JNK_equals_1_when_DUSP1_equals_0_and_TAOK_equals_1
JNK_equals_0_to_JNK_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_0_and_MTK1_equals_0_and_TAK1_equals_1_and_TAOK_equals_1
JNK_equals_0_to_JNK_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_0_and_MTK1_equals_1_and_TAK1_equals_1
GADD45_equals_0_to_GADD45_equals_1_when_SMAD_equals_1
JNK_equals_0_to_JNK_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_0_and_MTK1_equals_1_and_TAOK_equals_1
GRB2_equals_0_to_GRB2_equals_1_when_FRS2_equals_1
GRB2_equals_0_to_GRB2_equals_1_when_TGFBR_equals_1
p53_equals_1_to_p53_equals_0_when_ATM_equals_1_and_MDM2_equals_1_and_p38_equals_0
p38_equals_0_to_p38_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_0_and_MTK1_equals_1_and_TAOK_equals_1
p38_equals_0_to_p38_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_1_and_TAK1_equals_1
p38_equals_0_to_p38_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_1_and_TAOK_equals_1
p53_equals_0_to_p53_equals_1_when_ATM_equals_1_and_MDM2_equals_0
p53_equals_0_to_p53_equals_1_when_ATM_equals_1_and_p38_equals_1
PLCG_equals_0_to_PLCG_equals_1_when_FGFR3_equals_1
TAK1_equals_0_to_TAK1_equals_1_when_TGFBR_equals_1
TAK1_equals_1_to_TAK1_equals_0_when_TGFBR_equals_0
TAOK_equals_0_to_TAOK_equals_1_when_ATM_equals_1
TAOK_equals_1_to_TAOK_equals_0_when_ATM_equals_0
TGFBR_equals_0_to_TGFBR_equals_1_when_TGFBR_stimulus_equals_1
TGFBR_equals_1_to_TGFBR_equals_0_when_TGFBR_stimulus_equals_0
p38_equals_0_to_p38_equals_1_when_DUSP1_equals_0_and_TAK1_equals_1
p38_equals_0_to_p38_equals_1_when_DUSP1_equals_0_and_TAOK_equals_1
p38_equals_0_to_p38_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_0_and_MTK1_equals_0_and_TAK1_equals_1_and_TAOK_equals_1
p38_equals_0_to_p38_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_0_and_MTK1_equals_1_and_TAK1_equals_1
JNK_equals_0_to_JNK_equals_1_when_DUSP1_equals_0_and_TAK1_equals_1
SMAD_equals_0_to_SMAD_equals_1_when_TGFBR_equals_1
SMAD_equals_1_to_SMAD_equals_0_when_TGFBR_equals_0
FGFR3_equals_0_to_FGFR3_equals_1_when_FGFR3_stimulus_equals_1_and_GRB2_equals_0_and_PKC_equals_0
FGFR3_equals_1_to_FGFR3_equals_0_when_FGFR3_stimulus_equals_0
FGFR3_equals_1_to_FGFR3_equals_0_when_GRB2_equals_1
FGFR3_equals_1_to_FGFR3_equals_0_when_PKC_equals_1
FRS2_equals_1_to_FRS2_equals_0_when_GRB2_equals_1
FRS2_equals_1_to_FRS2_equals_0_when_SPRY_equals_1
EGFR_equals_0_to_EGFR_equals_1_when_EGFR_stimulus_equals_0_and_GRB2_equals_0_and_PKC_equals_0_and_SPRY_equals_1
EGFR_equals_1_to_EGFR_equals_0_when_EGFR_stimulus_equals_0_and_SPRY_equals_0
ATM_equals_0_to_ATM_equals_1_when_DNA_damage_equals_1
JNK_equals_0_to_JNK_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_1_and_TAK1_equals_1
JNK_equals_0_to_JNK_equals_1_when_DUSP1_equals_1_and_MAP3K1_3_equals_1_and_TAOK_equals_1
FRS2_equals_0_to_FRS2_equals_1_when_FGFR3_equals_1_and_GRB2_equals_0_and_SPRY_equals_0
FRS2_equals_1_to_FRS2_equals_0_when_FGFR3_equals_0
ATM_equals_1_to_ATM_equals_0_when_DNA_damage_equals_0

check for constant places
DNA_damage_equals_0
DNA_damage_equals_1
EGFR_stimulus_equals_0
EGFR_stimulus_equals_1
FGFR3_stimulus_equals_0
FGFR3_stimulus_equals_1
TGFBR_stimulus_equals_0
TGFBR_stimulus_equals_1
found 8 constant places
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 0.003sec


iterations count:21457 (124), effective:1545 (8)

initing FirstDep: 0m 0.000sec

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="MAPKbis-PT-5310"
export BK_EXAMINATION="UpperBounds"
export BK_TOOL="marcie"
export BK_RESULT_DIR="/tmp/BK_RESULTS/OUTPUTS"
export BK_TIME_CONFINEMENT="3600"
export BK_MEMORY_CONFINEMENT="16384"
export BK_BIN_PATH="/home/mcc/BenchKit/bin/"

# 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

# this is for BenchKit: explicit launching of the test
echo "====================================================================="
echo " Generated by BenchKit 2-5348"
echo " Executing tool marcie"
echo " Input is MAPKbis-PT-5310, examination is UpperBounds"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 1"
echo " Run identifier is r225-tall-167856407900637"
echo "====================================================================="
echo
echo "--------------------"
echo "preparation of the directory to be used:"

tar xzf /home/mcc/BenchKit/INPUTS/MAPKbis-PT-5310.tgz
mv MAPKbis-PT-5310 execution
cd execution
if [ "UpperBounds" = "ReachabilityDeadlock" ] || [ "UpperBounds" = "UpperBounds" ] || [ "UpperBounds" = "QuasiLiveness" ] || [ "UpperBounds" = "StableMarking" ] || [ "UpperBounds" = "Liveness" ] || [ "UpperBounds" = "OneSafe" ] || [ "UpperBounds" = "StateSpace" ]; then
rm -f GenericPropertiesVerdict.xml
fi
pwd
ls -lh

echo
echo "--------------------"
echo "content from stdout:"
echo
echo "=== Data for post analysis generated by BenchKit (invocation template)"
echo
if [ "UpperBounds" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "UpperBounds" != "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 "UpperBounds.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property UpperBounds.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -f "UpperBounds.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 '' UpperBounds.xml | cut -d '>' -f 2 | cut -d '<' -f 1 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ "UpperBounds" = "ReachabilityDeadlock" ] || [ "UpperBounds" = "QuasiLiveness" ] || [ "UpperBounds" = "StableMarking" ] || [ "UpperBounds" = "Liveness" ] || [ "UpperBounds" = "OneSafe" ] ; then
echo "FORMULA_NAME UpperBounds"
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 ;