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 348K
-rw-r--r-- 1 mcc users 4.4K May 30 21:45 CTLCardinality.txt
-rw-r--r-- 1 mcc users 22K May 30 21:45 CTLCardinality.xml
-rw-r--r-- 1 mcc users 6.8K May 29 15:49 CTLFireability.txt
-rw-r--r-- 1 mcc users 23K May 29 15:49 CTLFireability.xml
-rw-r--r-- 1 mcc users 2.8K May 28 09:52 LTLCardinality.txt
-rw-r--r-- 1 mcc users 12K May 28 09:52 LTLCardinality.xml
-rw-r--r-- 1 mcc users 3.4K May 28 08:07 LTLFireability.txt
-rw-r--r-- 1 mcc users 11K May 28 08:07 LTLFireability.xml
-rw-r--r-- 1 mcc users 1 May 24 11:17 NewModel
-rw-r--r-- 1 mcc users 4.3K May 28 06:38 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 20K May 28 06:38 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 106 May 26 06:29 ReachabilityDeadlock.txt
-rw-r--r-- 1 mcc users 344 May 26 06:29 ReachabilityDeadlock.xml
-rw-r--r-- 1 mcc users 4.7K May 27 04:07 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 14K May 27 04:07 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K May 28 07:31 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K May 28 07:31 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 May 24 11:17 equiv_col
-rw-r--r-- 1 mcc users 5 May 24 11:17 instance
-rw-r--r-- 1 mcc users 6 May 24 11:17 iscolored
-rw-r--r-- 1 mcc users 166K May 24 11:17 model.pnml
=====================================================================
Generated by BenchKit 2-3637
Executing tool itstoolsl
Input is MAPKbis-PT-5320, examination is ReachabilityDeadlock
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r285-csrt-152749176100305
=====================================================================

--------------------
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-ReachabilityDeadlock-0

=== Now, execution of the tool begins

BK_START 1527991652036

Flatten gal took : 136 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 15 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
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
Converted graph to binary with : CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.louvain.binaries_1.0.0.201805241334/bin/convert-linux64, -i, /tmp/graph8287989337310225553.txt, -o, /tmp/graph8287989337310225553.bin, -w, /tmp/graph8287989337310225553.weights], workingDir=null]
Built communities with : CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.louvain.binaries_1.0.0.201805241334/bin/louvain-linux64, /tmp/graph8287989337310225553.bin, -l, -1, -v, -w, /tmp/graph8287989337310225553.weights, -q, 0, -e, 0.001], workingDir=null]
Invoking ITS tools like this :CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.201805241334/bin/its-ctl-linux64, --gc-threshold, 2000000, --quiet, -i, /home/mcc/execution/ReachabilityDeadlock.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_1.0.0.201805241334/bin/its-ctl-linux64 --gc-threshold 2000000 --quiet -i /home/mcc/execution/ReachabilityDeadlock.pnml.gal -t CGAL -ctl DEADLOCK
No direction supplied, using forward translation only.
built 35 ordering constraints for composite.
built 30 ordering constraints for composite.
built 12 ordering constraints for composite.
built 53 ordering constraints for composite.
built 28 ordering constraints for composite.
built 34 ordering constraints for composite.
built 18 ordering constraints for composite.
built 28 ordering constraints for composite.
built 24 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+06,0.145953,10092,74,11,9224,100,358,21437,24,188,0


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,1,0.1541,10092,45,7,9224,100,980,21437,91,188,1622

System contains 1 deadlocks (shown below if less than --print-limit option) !
FORMULA MAPKbis-PT-5320-ReachabilityDeadlock-0 TRUE TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
[ i7={[ u30={[ PTEN_equals_1=1 ]
} u41={[ p53_equals_1=1 ]
} u20={[ MDM2_equals_0=1 ]
} u3={[ ATM_equals_1=1 ]
} u13={[ GADD45_equals_1=1 ]
} ]
} i6={[ u32={[ RAF_equals_0=1 ]
} u11={[ FOXO3_equals_1=1 ]
} u4={[ Apoptosis_equals_1=1 ]
} u0={[ AKT_0=1 ]
} ]
} i5={[ u29={[ PPP2CA_equals_1=1 ]
} u21={[ MEK1_2_equals_0=1 ]
} u1={[ AP1_equals_1=1 ]
} u17={[ JUN_equals_1=1 ]
} u2={[ ATF2_equals_1=1 ]
} ]
} i4={[ u33={[ RAS_equals_0=1 ]
} u35={[ SOS_equals_0=1 ]
} u28={[ PLCG_equals_0=1 ]
} u27={[ PKC_equals_0=1 ]
} u26={[ PI3K_equals_0=1 ]
} u25={[ PDK1_equals_0=1 ]
} u12={[ GAB1_equals_0=1 ]
} u14={[ GRB2_equals_0=1 ]
} u7={[ EGFR_equals_0=1 ]
} ]
} i3={[ u38={[ p14_equals_1=1 ]
} u24={[ MYC_equals_1=1 ]
} u22={[ MSK_equals_1=1 ]
} u19={[ MAX_equals_1=1 ]
} u6={[ CREB_equals_1=1 ]
} u5={[ BCL2_equals_0=1 ]
} ]
} i2={[ u40={[ p38_equals_1=1 ]
} u37={[ TAOK_equals_1=1 ]
} u23={[ MTK1_equals_1=1 ]
} u16={[ JNK_equals_1=1 DUSP1_equals_1=1 ]
} u18={[ MAP3K1_3_equals_0=1 ]
} ]
} i1={[ u42={[ p70_equals_0=1 ]
} u39={[ p21_equals_1=1 ]
} u31={[ Proliferation_equals_0=1 ]
} u15={[ Growth_Arrest_equals_1=1 ]
} ]
} i0={[ u36={[ SPRY_equals_0=1 ]
} u34={[ RSK_equals_0=1 ]
} u10={[ FOS_equals_0=1 ]
} u9={[ ERK_equals_0=1 ]
} u8={[ ELK1_equals_1=1 ]
} ]
} ]
Running compilation step : CommandLine [args=[gcc, -c, -I/home/mcc/BenchKit//lts_install_dir//include, -I., -std=c99, -fPIC, -O3, model.c], workingDir=/home/mcc/execution]
WARNING : LTS min runner thread was asked to interrupt. Dying gracefully.

BK_STOP 1527991655944

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

+ export BINDIR=/home/mcc/BenchKit/
+ BINDIR=/home/mcc/BenchKit/
++ pwd
+ export MODEL=/home/mcc/execution
+ MODEL=/home/mcc/execution
+ /home/mcc/BenchKit//runeclipse.sh /home/mcc/execution ReachabilityDeadlock -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -louvain -smt
+ ulimit -s 65536
+ [[ -z '' ]]
+ export LTSMIN_MEM_SIZE=8589934592
+ LTSMIN_MEM_SIZE=8589934592
+ /home/mcc/BenchKit//itstools/its-tools -consoleLog -data /home/mcc/execution/workspace -pnfolder /home/mcc/execution -examination ReachabilityDeadlock -z3path /home/mcc/BenchKit//z3/bin/z3 -yices2path /home/mcc/BenchKit//yices/bin/yices -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -louvain -smt -vmargs -Dosgi.locking=none -Declipse.stateSaveDelayInterval=-1 -Dosgi.configuration.area=/tmp/.eclipse -Xss8m -Xms40m -Xmx8192m -Dfile.encoding=UTF-8 -Dosgi.requiredJavaVersion=1.6
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.application.Application start
INFO: Running its-tools with arguments : [-pnfolder, /home/mcc/execution, -examination, ReachabilityDeadlock, -z3path, /home/mcc/BenchKit//z3/bin/z3, -yices2path, /home/mcc/BenchKit//yices/bin/yices, -its, -ltsminpath, /home/mcc/BenchKit//lts_install_dir/, -louvain, -smt]
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 70 ms
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 106 places.
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 173 transitions.
Jun 03, 2018 2:07:34 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.img.gal : 21 ms
Jun 03, 2018 2:07:34 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
Jun 03, 2018 2:07:34 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
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.instantiate.Simplifier printConstantVars
INFO: DNA_damage_equals_0,TGFBR_stimulus_equals_1,DNA_damage_equals_1,FGFR3_stimulus_equals_0,TGFBR_stimulus_equals_0,EGFR_stimulus_equals_0,FGFR3_stimulus_equals_1,EGFR_stimulus_equals_1,
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.instantiate.Simplifier simplifyConstantVariables
INFO: Removed 8 constant variables :DNA_damage_equals_0=0, TGFBR_stimulus_equals_1=0, DNA_damage_equals_1=1, FGFR3_stimulus_equals_0=1, TGFBR_stimulus_equals_0=1, EGFR_stimulus_equals_0=1, FGFR3_stimulus_equals_1=0, EGFR_stimulus_equals_1=0
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.instantiate.Simplifier simplifyConstantVariables
INFO: Simplified 9 expressions due to constant valuations.
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.instantiate.Simplifier simplifyFalseTransitions
INFO: Removed 4 false transitions.
Jun 03, 2018 2:07:34 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 132 ms
Jun 03, 2018 2:07:34 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.simple.gal : 7 ms
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 169 transitions.
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.application.MccTranslator applyOrder
INFO: Applying decomposition
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 27 ms
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 40 ms
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 145 transitions.
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver computeAndDeclareInvariants
INFO: Computed 44 place invariants in 9 ms
Begin: Sun Jun 3 02:07:35 2018

Computation of communities with the Newman-Girvan Modularity quality function

level 0:
start computation: Sun Jun 3 02:07:35 2018
network size: 88 nodes, 466 links, 290 weight
quality increased from -0.013976 to 0.396371
end computation: Sun Jun 3 02:07:35 2018
level 1:
start computation: Sun Jun 3 02:07:35 2018
network size: 43 nodes, 209 links, 290 weight
quality increased from 0.396371 to 0.607699
end computation: Sun Jun 3 02:07:35 2018
level 2:
start computation: Sun Jun 3 02:07:35 2018
network size: 15 nodes, 93 links, 290 weight
quality increased from 0.607699 to 0.629523
end computation: Sun Jun 3 02:07:35 2018
level 3:
start computation: Sun Jun 3 02:07:35 2018
network size: 8 nodes, 48 links, 290 weight
quality increased from 0.629523 to 0.629523
end computation: Sun Jun 3 02:07:35 2018
End: Sun Jun 3 02:07:35 2018
Total duration: 0 sec
0.629523
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.instantiate.CompositeBuilder decomposeWithOrder
INFO: Decomposing Gal with order
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 24 ms
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.instantiate.CompositeBuilder rewriteArraysToAllowPartition
INFO: Rewriting arrays to variables to allow decomposition.
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.instantiate.Instantiator fuseIsomorphicEffects
INFO: Removed a total of 214 redundant transitions.
Jun 03, 2018 2:07:35 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/ReachabilityDeadlock.pnml.gal : 13 ms
Jun 03, 2018 2:07:35 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 error :unknown
java.lang.RuntimeException: SMT solver raised an error :unknown
at fr.lip6.move.gal.gal2smt.bmc.NextBMCSolver.checkSat(NextBMCSolver.java:318)
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)
Jun 03, 2018 2:07:35 AM fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext transform
INFO: Built C files in 475ms 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="ReachabilityDeadlock"
export BK_TOOL="itstoolsl"
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/MAPKbis-PT-5320.tgz
mv MAPKbis-PT-5320 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 itstoolsl"
echo " Input is MAPKbis-PT-5320, examination is ReachabilityDeadlock"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 4"
echo " Run identifier is r285-csrt-152749176100305"
echo "====================================================================="
echo
echo "--------------------"
echo "content from stdout:"
echo
echo "=== Data for post analysis generated by BenchKit (invocation template)"
echo
if [ "ReachabilityDeadlock" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "ReachabilityDeadlock" != "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 "ReachabilityDeadlock.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property ReachabilityDeadlock.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -f "ReachabilityDeadlock.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 '' ReachabilityDeadlock.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 ;