Execution Chart

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

Trace from the execution

Formatting '/local/x2003239/mcc2020-input.r111-csrt-158961257100099.qcow2', fmt=qcow2 size=4294967296 backing_file=/local/x2003239/mcc2020-input.qcow2 encryption=off cluster_size=65536 lazy_refcounts=off refcount_bits=16
Waiting for the VM to be ready (probing ssh)
...........................................................................................................................................................................................................................
=====================================================================
Generated by BenchKit 2-4028
Executing tool itstools
Input is MAPKbis-PT-5320, examination is CTLCardinality
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r111-csrt-158961257100099
=====================================================================

--------------------
preparation of the directory to be used:
/home/mcc/execution
total 376K
-rw-r--r-- 1 mcc users 4.6K Apr 27 15:14 CTLCardinality.txt
-rw-r--r-- 1 mcc users 23K Apr 27 15:14 CTLCardinality.xml
-rw-r--r-- 1 mcc users 6.8K Apr 27 15:14 CTLFireability.txt
-rw-r--r-- 1 mcc users 23K Apr 27 15:14 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K Apr 27 15:14 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 6.5K Apr 27 15:14 GenericPropertiesVerdict.xml
-rw-r--r-- 1 mcc users 4.0K Apr 27 15:14 LTLCardinality.txt
-rw-r--r-- 1 mcc users 24K Apr 28 14:01 LTLCardinality.xml
-rw-r--r-- 1 mcc users 5.0K Apr 27 15:14 LTLFireability.txt
-rw-r--r-- 1 mcc users 19K Apr 28 14:01 LTLFireability.xml
-rw-r--r-- 1 mcc users 4.2K Apr 27 15:14 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 18K Apr 27 15:14 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 5.2K Apr 27 15:14 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 15K Apr 27 15:14 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K Apr 27 15:14 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K Apr 27 15:14 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 Apr 27 15:14 equiv_col
-rw-r--r-- 1 mcc users 5 Apr 27 15:14 instance
-rw-r--r-- 1 mcc users 6 Apr 27 15:14 iscolored
-rw-r--r-- 1 mcc users 170K Apr 27 15:14 model.pnml

--------------------
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 MAPKbis-PT-5320-CTLCardinality-00
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-01
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-02
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-03
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-04
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-05
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-06
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-07
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-08
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-09
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-10
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-11
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-12
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-13
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-14
FORMULA_NAME MAPKbis-PT-5320-CTLCardinality-15

=== Now, execution of the tool begins

BK_START 1589827366819

[2020-05-18 18:42:49] [INFO ] Running its-tools with arguments : [-pnfolder, /home/mcc/execution, -examination, CTLCardinality, -z3path, /home/mcc/BenchKit//z3/bin/z3, -yices2path, /home/mcc/BenchKit//yices/bin/yices, -its, -ltsminpath, /home/mcc/BenchKit//lts_install_dir/, -greatspnpath, /home/mcc/BenchKit//greatspn/, -order, META, -manyOrder, -smt, -timeout, 3600]
[2020-05-18 18:42:49] [INFO ] Parsing pnml file : /home/mcc/execution/model.pnml
[2020-05-18 18:42:49] [INFO ] Load time of PNML (sax parser for PT used): 75 ms
[2020-05-18 18:42:49] [INFO ] Transformed 106 places.
[2020-05-18 18:42:49] [INFO ] Transformed 173 transitions.
[2020-05-18 18:42:49] [INFO ] Found NUPN structural information;
[2020-05-18 18:42:49] [INFO ] Parsed PT model containing 106 places and 173 transitions in 124 ms.
Deduced a syphon composed of 29 places in 2 ms
Reduce places removed 33 places and 106 transitions.
Parsed 16 properties from file /home/mcc/execution/CTLCardinality.xml in 23 ms.
Incomplete random walk after 100000 steps, including 2982 resets, run finished after 373 ms. (steps per millisecond=268 ) properties seen :[1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1]
[2020-05-18 18:42:49] [INFO ] Flow matrix only has 47 transitions (discarded 20 similar events)
// Phase 1: matrix 47 rows 73 cols
[2020-05-18 18:42:49] [INFO ] Computed 49 place invariants in 4 ms
[2020-05-18 18:42:49] [INFO ] [Real]Absence check using 49 positive place invariants in 51 ms returned sat
[2020-05-18 18:42:49] [INFO ] [Real]Adding state equation constraints to refine reachable states.
[2020-05-18 18:42:49] [INFO ] [Real]Absence check using state equation in 50 ms returned sat
[2020-05-18 18:42:49] [INFO ] Solution in real domain found non-integer solution.
[2020-05-18 18:42:50] [INFO ] [Nat]Absence check using 49 positive place invariants in 11 ms returned unsat
[2020-05-18 18:42:50] [INFO ] [Real]Absence check using 49 positive place invariants in 10 ms returned unsat
[2020-05-18 18:42:50] [INFO ] [Real]Absence check using 49 positive place invariants in 8 ms returned unsat
[2020-05-18 18:42:50] [INFO ] [Real]Absence check using 49 positive place invariants in 8 ms returned unsat
[2020-05-18 18:42:50] [INFO ] [Real]Absence check using 49 positive place invariants in 4 ms returned unsat
[2020-05-18 18:42:50] [INFO ] [Real]Absence check using 49 positive place invariants in 14 ms returned sat
[2020-05-18 18:42:50] [INFO ] [Real]Adding state equation constraints to refine reachable states.
[2020-05-18 18:42:50] [INFO ] [Real]Absence check using state equation in 66 ms returned sat
[2020-05-18 18:42:50] [INFO ] Solution in real domain found non-integer solution.
[2020-05-18 18:42:50] [INFO ] [Nat]Absence check using 49 positive place invariants in 12 ms returned unsat
[2020-05-18 18:42:50] [INFO ] [Real]Absence check using 49 positive place invariants in 17 ms returned unsat
Successfully simplified 7 atomic propositions for a total of 7 simplifications.
[2020-05-18 18:42:50] [INFO ] Found a total of 25 fixed domain variables (out of 73 variables) in GAL type petri
[2020-05-18 18:42:50] [INFO ] Found a total of 25 constant array cells/variables (out of 73 variables) in type petri
[2020-05-18 18:42:50] [INFO ] PI3K_equals_0,FGFR3_equals_0,MAP3K1_3_equals_0,SPRY_equals_0,RAF_equals_0,SMAD_equals_0,Proliferation_equals_0,EGFR_equals_0,GRB2_equals_0,FOS_equals_0,p70_equals_0,SOS_equals_0,AKT_0,ERK_equals_0,TAK1_equals_0,PDK1_equals_0,RSK_equals_0,RAS_equals_0,PLCG_equals_0,GAB1_equals_0,TGFBR_equals_0,PKC_equals_0,BCL2_equals_0,FRS2_equals_0,MEK1_2_equals_0,
[2020-05-18 18:42:50] [INFO ] Removed 25 constant variables :PI3K_equals_0=1, FGFR3_equals_0=1, MAP3K1_3_equals_0=1, SPRY_equals_0=1, RAF_equals_0=1, SMAD_equals_0=1, Proliferation_equals_0=1, EGFR_equals_0=1, GRB2_equals_0=1, FOS_equals_0=1, p70_equals_0=1, SOS_equals_0=1, AKT_0=1, ERK_equals_0=1, TAK1_equals_0=1, PDK1_equals_0=1, RSK_equals_0=1, RAS_equals_0=1, PLCG_equals_0=1, GAB1_equals_0=1, TGFBR_equals_0=1, PKC_equals_0=1, BCL2_equals_0=1, FRS2_equals_0=1, MEK1_2_equals_0=1
[2020-05-18 18:42:50] [INFO ] Simplified 30 expressions due to constant valuations.
[2020-05-18 18:42:50] [INFO ] Initial state reduction rules for CTL removed 15 formulas.
[2020-05-18 18:42:50] [INFO ] Flatten gal took : 61 ms
[2020-05-18 18:42:50] [INFO ] Initial state reduction rules for CTL removed 15 formulas.
[2020-05-18 18:42:50] [INFO ] Flatten gal took : 11 ms
FORMULA MAPKbis-PT-5320-CTLCardinality-15 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-14 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-13 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-12 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-11 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-09 TRUE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-08 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-07 TRUE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-06 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-05 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-04 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-03 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-02 TRUE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-01 TRUE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA MAPKbis-PT-5320-CTLCardinality-00 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
[2020-05-18 18:42:50] [INFO ] Applying decomposition
[2020-05-18 18:42:50] [INFO ] Flatten gal took : 8 ms
Converted graph to binary with : CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.louvain.binaries_1.0.0.202005100927/bin/convert-linux64, -i, /tmp/graph13485072514639387386.txt, -o, /tmp/graph13485072514639387386.bin, -w, /tmp/graph13485072514639387386.weights], workingDir=null]
Built communities with : CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.louvain.binaries_1.0.0.202005100927/bin/louvain-linux64, /tmp/graph13485072514639387386.bin, -l, -1, -v, -w, /tmp/graph13485072514639387386.weights, -q, 0, -e, 0.001], workingDir=null]
[2020-05-18 18:42:50] [INFO ] Decomposing Gal with order
[2020-05-18 18:42:50] [INFO ] Rewriting arrays to variables to allow decomposition.
[2020-05-18 18:42:50] [INFO ] Removed a total of 86 redundant transitions.
[2020-05-18 18:42:50] [INFO ] Flatten gal took : 82 ms
[2020-05-18 18:42:50] [INFO ] Fuse similar labels procedure discarded/fused a total of 0 labels/synchronizations in 2 ms.
[2020-05-18 18:42:50] [INFO ] Time to serialize gal into /home/mcc/execution/CTLCardinality.pnml.gal : 9 ms
[2020-05-18 18:42:50] [INFO ] Time to serialize properties into /home/mcc/execution/CTLCardinality.ctl : 1 ms
Invoking ITS tools like this :CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202005100927/bin/its-ctl-linux64, --gc-threshold, 2000000, --quiet, -i, /home/mcc/execution/CTLCardinality.pnml.gal, -t, CGAL, -ctl, /home/mcc/execution/CTLCardinality.ctl], workingDir=/home/mcc/execution]

its-ctl command run as :

/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202005100927/bin/its-ctl-linux64 --gc-threshold 2000000 --quiet -i /home/mcc/execution/CTLCardinality.pnml.gal -t CGAL -ctl /home/mcc/execution/CTLCardinality.ctl
No direction supplied, using forward translation only.
Parsed 1 CTL formulae.
built 13 ordering constraints for composite.
built 6 ordering constraints for composite.
built 12 ordering constraints for composite.
built 7 ordering constraints for composite.
built 13 ordering constraints for composite.
built 3 ordering constraints for composite.
built 14 ordering constraints for composite.
built 9 ordering constraints for composite.
built 7 ordering constraints for composite.
Model ,|S| ,Time ,Mem(kb) ,fin. SDD ,fin. DDD ,peak SDD ,peak DDD ,SDD Hom ,SDD cache peak ,DDD Hom ,DDD cachepeak ,SHom cache
reachable,8.12646e+06,0.069371,6388,47,6,3541,36,192,8425,12,34,0


Converting to forward existential form...Done !
original formula: AG(!(AX(FALSE)))
=> equivalent forward existential formula: [(FwdU(Init,TRUE) * !(EX(!(FALSE))))] = FALSE
Reverse transition relation is NOT exact ! Due to transitions ATF2_equals_1_to_ATF2_equals_0_when_JNK_equals_0_and_p38_equals_0, Apoptosis_equals_1_to_Apoptosis_equals_0_when_p53_equals_0, DUSP1_equals_1_to_DUSP1_equals_0_when_CREB_equals_0, ELK1_equals_1_to_ELK1_equals_0_when_ERK_equals_0_and_JNK_equals_0_and_p38_equals_0, FOXO3_equals_1_to_FOXO3_equals_0_when_JNK_equals_0, GADD45_equals_1_to_GADD45_equals_0_when_SMAD_equals_0_and_p53_equals_0, JNK_equals_1_to_JNK_equals_0_when_DUSP1_equals_0_and_MAP3K1_3_equals_0_and_MTK1_equals_0_and_TAK1_equals_0_and_TAOK_equals_0, JUN_equals_1_to_JUN_equals_0_when_JNK_equals_0, MAX_equals_1_to_MAX_equals_0_when_p38_equals_0, MSK_equals_1_to_MSK_equals_0_when_ERK_equals_0_and_p38_equals_0, MYC_equals_1_to_MYC_equals_0_when_MSK_equals_0, TAOK_equals_0_to_TAOK_equals_1_when_ATM_equals_1, p21_equals_1_to_p21_equals_0_when_p53_equals_0, p38_equals_1_to_p38_equals_0_when_DUSP1_equals_0_and_MAP3K1_3_equals_0_and_MTK1_equals_0_and_TAK1_equals_0_and_TAOK_equals_0, p38_equals_1_to_p38_equals_0_when_DUSP1_equals_1_and_MAP3K1_3_equals_0_and_MTK1_equals_0_and_TAK1_equals_0, p38_equals_1_to_p38_equals_0_when_DUSP1_equals_1_and_MAP3K1_3_equals_0_and_MTK1_equals_0_and_TAOK_equals_0, p53_equals_0_to_p53_equals_1_when_ATM_equals_1_and_p38_equals_1, i0.Apoptosis_equals_1_to_Apoptosis_equals_0_when_FOXO3_equals_0, i1.MTK1_equals_1_to_MTK1_equals_0_when_GADD45_equals_0, i1.MTK1_equals_0_to_MTK1_equals_1_when_GADD45_equals_1, i2.AP1_equals_1_to_AP1_equals_0_when_JUN_equals_0, i2.AP1_equals_1_to_AP1_equals_0_when_ATF2_equals_0_and_FOS_equals_0, i3.p53_equals_0_to_p53_equals_1_when_ATM_equals_1_and_MDM2_equals_0, i3.PTEN_equals_1_to_PTEN_equals_0_when_p53_equals_0, i3.MDM2_equals_1_to_MDM2_equals_0_when_AKT_equals_0_and_p53_equals_0, i3.u2.ATM_equals_0_to_ATM_equals_1_when_DNA_damage_equals_1, i4.CREB_equals_1_to_CREB_equals_0_when_MSK_equals_0, i5.p14_equals_1_to_p14_equals_0_when_MYC_equals_0, i5.MYC_equals_1_to_MYC_equals_0_when_AKT_equals_0_and_MAX_equals_0, i6.Growth_Arrest_equals_1_to_Growth_Arrest_equals_0_when_p21_equals_0, i7.PPP2CA_equals_1_to_PPP2CA_equals_0_when_p38_equals_0, Intersection with reachable at each step enabled. (destroyed/reverse/intersect/total) :4/32/31/67
(forward)formula 0,0,0.082479,6388,1,0,3541,36,763,8425,43,34,2764
FORMULA MAPKbis-PT-5320-CTLCardinality-10 FALSE TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
Formula is FALSE !

***************************************


BK_STOP 1589827371370

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

+ export BINDIR=/home/mcc/BenchKit/
+ BINDIR=/home/mcc/BenchKit/
++ pwd
+ export MODEL=/home/mcc/execution
+ MODEL=/home/mcc/execution
+ [[ CTLCardinality = StateSpace ]]
+ /home/mcc/BenchKit//runeclipse.sh /home/mcc/execution CTLCardinality -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -greatspnpath /home/mcc/BenchKit//greatspn/ -order META -manyOrder -smt -timeout 3600
+ ulimit -s 65536
+ [[ -z '' ]]
+ export LTSMIN_MEM_SIZE=8589934592
+ LTSMIN_MEM_SIZE=8589934592
+ /home/mcc/BenchKit//itstools/its-tools -data /home/mcc/execution/workspace -pnfolder /home/mcc/execution -examination CTLCardinality -z3path /home/mcc/BenchKit//z3/bin/z3 -yices2path /home/mcc/BenchKit//yices/bin/yices -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -greatspnpath /home/mcc/BenchKit//greatspn/ -order META -manyOrder -smt -timeout 3600 -vmargs -Dosgi.locking=none -Declipse.stateSaveDelayInterval=-1 -Dosgi.configuration.area=/tmp/.eclipse -Xss128m -Xms40m -Xmx16000m -Dfile.encoding=UTF-8 -Dosgi.requiredJavaVersion=1.6

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-5320"
export BK_EXAMINATION="CTLCardinality"
export BK_TOOL="itstools"
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

# this is for BenchKit: explicit launching of the test
echo "====================================================================="
echo " Generated by BenchKit 2-4028"
echo " Executing tool itstools"
echo " Input is MAPKbis-PT-5320, examination is CTLCardinality"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 4"
echo " Run identifier is r111-csrt-158961257100099"
echo "====================================================================="
echo
echo "--------------------"
echo "preparation of the directory to be used:"

tar xzf /home/mcc/BenchKit/INPUTS/MAPKbis-PT-5320.tgz
mv MAPKbis-PT-5320 execution
cd execution
if [ "CTLCardinality" = "ReachabilityDeadlock" ] || [ "CTLCardinality" = "UpperBounds" ] || [ "CTLCardinality" = "QuasiLiveness" ] || [ "CTLCardinality" = "StableMarking" ] || [ "CTLCardinality" = "Liveness" ] || [ "CTLCardinality" = "OneSafe" ] || [ "CTLCardinality" = "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 [ "CTLCardinality" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "CTLCardinality" != "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 "CTLCardinality.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property CTLCardinality.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -f "CTLCardinality.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 '' CTLCardinality.xml | cut -d '>' -f 2 | cut -d '<' -f 1 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ "CTLCardinality" = "ReachabilityDeadlock" ] || [ "CTLCardinality" = "QuasiLiveness" ] || [ "CTLCardinality" = "StableMarking" ] || [ "CTLCardinality" = "Liveness" ] || [ "CTLCardinality" = "OneSafe" ] ; then
echo "FORMULA_NAME CTLCardinality"
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 ;