Execution Chart

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

Trace from the execution

Formatting '/data/fkordon/mcc2019-input.r096-smll-155246587500354.qcow2', fmt=qcow2 size=4294967296 backing_file='/data/fkordon/mcc2019-input.qcow2' encryption=off cluster_size=65536 lazy_refcounts=off
Waiting for the VM to be ready (probing ssh)
......................
=====================================================================
Generated by BenchKit 2-3957
Executing tool itstools
Input is MAPKbis-PT-5320, examination is GlobalProperties
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r096-smll-155246587500354
=====================================================================

--------------------
preparation of the directory to be used:
/home/mcc/execution
total 356K
-rw-r--r-- 1 mcc users 4.5K Feb 11 22:58 CTLCardinality.txt
-rw-r--r-- 1 mcc users 22K Feb 11 22:58 CTLCardinality.xml
-rw-r--r-- 1 mcc users 6.1K Feb 7 23:51 CTLFireability.txt
-rw-r--r-- 1 mcc users 20K Feb 7 23:51 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K Mar 10 17:31 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 102 Feb 24 15:05 GlobalProperties.txt
-rw-r--r-- 1 mcc users 340 Feb 24 15:05 GlobalProperties.xml
-rw-r--r-- 1 mcc users 2.6K Feb 5 00:14 LTLCardinality.txt
-rw-r--r-- 1 mcc users 10K Feb 5 00:14 LTLCardinality.xml
-rw-r--r-- 1 mcc users 3.6K Feb 4 22:36 LTLFireability.txt
-rw-r--r-- 1 mcc users 11K Feb 4 22:36 LTLFireability.xml
-rw-r--r-- 1 mcc users 4.4K Feb 4 06:30 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 20K Feb 4 06:30 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 8.1K Feb 1 00:04 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 24K Feb 1 00:04 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K Feb 4 22:21 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K Feb 4 22:21 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 Jan 29 09:34 equiv_col
-rw-r--r-- 1 mcc users 5 Jan 29 09:34 instance
-rw-r--r-- 1 mcc users 6 Jan 29 09:34 iscolored
-rw-r--r-- 1 mcc users 0 Jan 29 09:34 model-fix.log
-rw-r--r-- 1 mcc users 166K Mar 10 17:31 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-GlobalProperties-0

=== Now, execution of the tool begins

BK_START 1552887116268

Working with output stream class java.io.PrintStream
Flatten gal took : 273 ms
Constant places removed 2 places and 9 transitions.
Iterating post reduction 0 with 2 rules applied. Total rules applied 2 place count 96 transition count 160
Constant places removed 5 places and 15 transitions.
Iterating post reduction 1 with 5 rules applied. Total rules applied 7 place count 91 transition count 145
Constant places removed 3 places and 0 transitions.
Iterating post reduction 2 with 3 rules applied. Total rules applied 10 place count 88 transition count 145
Applied a total of 10 rules in 27 ms. Remains 88 /98 variables (removed 10) and now considering 145/169 (removed 24) transitions.
Normalized transition count is 87
// Phase 1: matrix 87 rows 88 cols
Using solver Z3 to compute partial order matrices.
Built C files in :
/home/mcc/execution
Invoking ITS tools like this :CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.201903111103/bin/its-ctl-linux64, --gc-threshold, 2000000, --quiet, -i, /home/mcc/execution/GlobalProperties.pnml.gal, -t, CGAL, -ctl, DEADLOCK], workingDir=/home/mcc/execution]

its-ctl command run as :

/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.201903111103/bin/its-ctl-linux64 --gc-threshold 2000000 --quiet -i /home/mcc/execution/GlobalProperties.pnml.gal -t CGAL -ctl DEADLOCK
No direction supplied, using forward translation only.
Presburger conditions satisfied. Using coverability to approximate state space in K-Induction.
Normalized transition count is 87
// Phase 1: matrix 87 rows 88 cols
invariant :MDM2_equals_0 + MDM2_equals_1 = 1
invariant :PKC_equals_0 + PKC_equals_1 = 1
invariant :Apoptosis_equals_0 + Apoptosis_equals_1 = 1
invariant :MTK1_equals_0 + MTK1_equals_1 = 1
invariant :RAF_equals_0 + RAF_equals_1 = 1
invariant :PPP2CA_equals_0 + PPP2CA_equals_1 = 1
invariant :ATM_equals_0 + ATM_equals_1 = 1
invariant :MEK1_2_equals_0 + MEK1_2_equals_1 = 1
invariant :ERK_equals_0 + ERK_equals_1 = 1
invariant :ELK1_equals_0 + ELK1_equals_1 = 1
invariant :GAB1_equals_0 + GAB1_equals_1 = 1
invariant :MAP3K1_3_equals_0 + MAP3K1_3_equals_1 = 1
invariant :Proliferation_equals_0 + Proliferation_equals_1 = 1
invariant :ATF2_equals_0 + ATF2_equals_1 = 1
invariant :MYC_equals_0 + MYC_equals_1 = 1
invariant :DUSP1_equals_0 + DUSP1_equals_1 = 1
invariant :PLCG_equals_0 + PLCG_equals_1 = 1
invariant :p70_equals_0 + p70_equals_1 = 1
invariant :GRB2_equals_0 + GRB2_equals_1 = 1
invariant :p53_equals_0 + p53_equals_1 = 1
invariant :MSK_equals_0 + MSK_equals_1 = 1
invariant :PTEN_equals_0 + PTEN_equals_1 = 1
invariant :Growth_Arrest_equals_0 + Growth_Arrest_equals_1 = 1
invariant :AP1_equals_0 + AP1_equals_1 = 1
invariant :p14_equals_0 + p14_equals_1 = 1
invariant :PDK1_equals_0 + PDK1_equals_1 = 1
invariant :TAOK_equals_0 + TAOK_equals_1 = 1
invariant :AKT_0 + AKT_equals_1 = 1
invariant :SPRY_equals_0 + SPRY_equals_1 = 1
invariant :JUN_equals_0 + JUN_equals_1 = 1
invariant :SOS_equals_0 + SOS_equals_1 = 1
invariant :FOS_equals_0 + FOS_equals_1 = 1
invariant :FOXO3_equals_0 + FOXO3_equals_1 = 1
invariant :PI3K_equals_0 + PI3K_equals_1 = 1
invariant :EGFR_equals_0 + EGFR_equals_1 = 1
invariant :GADD45_equals_0 + GADD45_equals_1 = 1
invariant :RSK_equals_0 + RSK_equals_1 = 1
invariant :p38_equals_0 + p38_equals_1 = 1
invariant :CREB_equals_0 + CREB_equals_1 = 1
invariant :MAX_equals_0 + MAX_equals_1 = 1
invariant :p21_equals_0 + p21_equals_1 = 1
invariant :RAS_equals_0 + RAS_equals_1 = 1
invariant :BCL2_equals_0 + BCL2_equals_1 = 1
invariant :JNK_equals_0 + JNK_equals_1 = 1
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+06,0.224597,8988,2,261,5,21679,6,0,497,16084,0


Model ,|S| ,Time ,Mem(kb) ,fin. SDD ,fin. DDD ,peak SDD ,peak DDD ,SDD Hom ,SDD cache peak ,DDD Hom ,DDD cachepeak ,SHom cache
dead,1,0.26398,8988,2,89,7,21679,9,1,2050,16084,2

System contains 1 deadlocks (shown below if less than --print-limit option) !
FORMULA MAPKbis-PT-5320-GlobalProperties-0 TRUE TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL
[ Growth_Arrest_equals_1=1 Proliferation_equals_0=1 p14_equals_1=1 p21_equals_1=1 MDM2_equals_0=1 PTEN_equals_1=1 MYC_equals_1=1 ATM_equals_1=1 p53_equals_1=1 PDK1_equals_0=1 p70_equals_0=1 GADD45_equals_1=1 MAX_equals_1=1 PI3K_equals_0=1 AKT_0=1 GAB1_equals_0=1 RAS_equals_0=1 MSK_equals_1=1 SOS_equals_0=1 TAOK_equals_1=1 p38_equals_1=1 MTK1_equals_1=1 DUSP1_equals_1=1 MAP3K1_3_equals_0=1 PLCG_equals_0=1 GRB2_equals_0=1 RAF_equals_0=1 JNK_equals_1=1 PKC_equals_0=1 FOXO3_equals_1=1 PPP2CA_equals_1=1 ERK_equals_0=1 EGFR_equals_0=1 CREB_equals_1=1 BCL2_equals_0=1 RSK_equals_0=1 MEK1_2_equals_0=1 Apoptosis_equals_1=1 ELK1_equals_1=1 ATF2_equals_1=1 SPRY_equals_0=1 FOS_equals_0=1 JUN_equals_1=1 AP1_equals_1=1 ]
Running compilation step : CommandLine [args=[gcc, -c, -I/home/mcc/BenchKit//lts_install_dir//include, -I., -std=c99, -fPIC, -O2, model.c], workingDir=/home/mcc/execution]
WARNING : LTS min runner thread was asked to interrupt. Dying gracefully.

BK_STOP 1552887123215

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

+ export BINDIR=/home/mcc/BenchKit/
+ BINDIR=/home/mcc/BenchKit/
++ pwd
+ export MODEL=/home/mcc/execution
+ MODEL=/home/mcc/execution
+ [[ GlobalProperties = StateSpace ]]
+ /home/mcc/BenchKit//runeclipse.sh /home/mcc/execution GlobalProperties -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -smt
+ 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 GlobalProperties -z3path /home/mcc/BenchKit//z3/bin/z3 -yices2path /home/mcc/BenchKit//yices/bin/yices -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -smt -vmargs -Dosgi.locking=none -Declipse.stateSaveDelayInterval=-1 -Dosgi.configuration.area=/tmp/.eclipse -Xss8m -Xms40m -Xmx8192m -Dfile.encoding=UTF-8 -Dosgi.requiredJavaVersion=1.6
Mar 18, 2019 5:31:59 AM fr.lip6.move.gal.application.Application start
INFO: Running its-tools with arguments : [-pnfolder, /home/mcc/execution, -examination, GlobalProperties, -z3path, /home/mcc/BenchKit//z3/bin/z3, -yices2path, /home/mcc/BenchKit//yices/bin/yices, -its, -ltsminpath, /home/mcc/BenchKit//lts_install_dir/, -smt]
Mar 18, 2019 5:31:59 AM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
Mar 18, 2019 5:31:59 AM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 115 ms
Mar 18, 2019 5:31:59 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 106 places.
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 173 transitions.
Mar 18, 2019 5:32:00 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.img.gal : 47 ms
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.DomainAnalyzer computeVariableDomains
INFO: Found a total of 8 fixed domain variables (out of 106 variables) in GAL type MAPKbis_PT_5320
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.Simplifier printConstantVars
INFO: Found a total of 8 constant array cells/variables (out of 106 variables) in type MAPKbis_PT_5320
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.Simplifier printConstantVars
INFO: EGFR_stimulus_equals_0,TGFBR_stimulus_equals_1,TGFBR_stimulus_equals_0,FGFR3_stimulus_equals_1,DNA_damage_equals_0,DNA_damage_equals_1,EGFR_stimulus_equals_1,FGFR3_stimulus_equals_0,
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.Simplifier simplifyConstantVariables
INFO: Removed 8 constant variables :EGFR_stimulus_equals_0=1, TGFBR_stimulus_equals_1=0, TGFBR_stimulus_equals_0=1, FGFR3_stimulus_equals_1=0, DNA_damage_equals_0=0, DNA_damage_equals_1=1, EGFR_stimulus_equals_1=0, FGFR3_stimulus_equals_0=1
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.Simplifier simplifyConstantVariables
INFO: Simplified 9 expressions due to constant valuations.
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.Simplifier simplifyFalseTransitions
INFO: Removed 4 false transitions.
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.PropertySimplifier evalInInitialState
WARNING: Unexpected boolean logic operator in evalInInitialState fr.lip6.move.gal.impl.EXImpl
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.PropertySimplifier rewriteWithInitialState
INFO: Reachable property MAPKbis-PT-5320-GlobalProperties-0 is trivially true : it is verified in initial state.
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 267 ms
Mar 18, 2019 5:32:00 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.simple.gal : 8 ms
Mar 18, 2019 5:32:00 AM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 169 transitions.
Mar 18, 2019 5:32:01 AM fr.lip6.move.gal.instantiate.PropertySimplifier rewriteWithInitialState
INFO: Reachable property MAPKbis-PT-5320-GlobalProperties-0 is trivially true : it is verified in initial state.
Mar 18, 2019 5:32:01 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 82 ms
Mar 18, 2019 5:32:01 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/GlobalProperties.pnml.gal : 3 ms
Mar 18, 2019 5:32:01 AM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 145 transitions.
Mar 18, 2019 5:32:01 AM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver computeAndDeclareInvariants
INFO: Computed 44 place invariants in 19 ms
Mar 18, 2019 5:32:01 AM fr.lip6.move.gal.gal2smt.bmc.NextBMCSolver checkSat
WARNING: SMT solver unexpectedly returned 'unknown' answer, retrying.
Skipping mayMatrices nes/nds SMT solver raised an exception or timeout :(error "Failed to check-sat")
java.lang.RuntimeException: SMT solver raised an exception or timeout :(error "Failed to check-sat")
at fr.lip6.move.gal.gal2smt.bmc.NextBMCSolver.checkSat(NextBMCSolver.java:297)
at fr.lip6.move.gal.gal2smt.bmc.NextBMCSolver.checkSat(NextBMCSolver.java:305)
at fr.lip6.move.gal.gal2smt.bmc.KInductionSolver.init(KInductionSolver.java:116)
at fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver.init(NecessaryEnablingsolver.java:71)
at fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext.printLabels(Gal2PinsTransformerNext.java:471)
at fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext.printDependencyMatrix(Gal2PinsTransformerNext.java:209)
at fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext.buildBodyFile(Gal2PinsTransformerNext.java:85)
at fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext.transform(Gal2PinsTransformerNext.java:830)
at fr.lip6.move.gal.application.LTSminRunner$1.run(LTSminRunner.java:71)
at java.lang.Thread.run(Thread.java:748)
Mar 18, 2019 5:32:01 AM fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext transform
INFO: Built C files in 440ms conformant to PINS in folder :/home/mcc/execution

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="GlobalProperties"
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 2-3957"
echo " Executing tool itstools"
echo " Input is MAPKbis-PT-5320, examination is GlobalProperties"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 4"
echo " Run identifier is r096-smll-155246587500354"
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 [ "GlobalProperties" = "GlobalProperties" ] ; then
rm -f GenericPropertiesVerdict.xml
fi
if [ "GlobalProperties" = "UpperBounds" ] ; 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 [ "GlobalProperties" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "GlobalProperties" != "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 "GlobalProperties.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property GlobalProperties.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -f "GlobalProperties.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 '' GlobalProperties.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 ;