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 224K
-rw-r--r-- 1 mcc users 3.7K May 30 21:19 CTLCardinality.txt
-rw-r--r-- 1 mcc users 18K May 30 21:19 CTLCardinality.xml
-rw-r--r-- 1 mcc users 3.9K May 29 15:12 CTLFireability.txt
-rw-r--r-- 1 mcc users 14K May 29 15:12 CTLFireability.xml
-rw-r--r-- 1 mcc users 2.7K May 28 09:50 LTLCardinality.txt
-rw-r--r-- 1 mcc users 11K May 28 09:50 LTLCardinality.xml
-rw-r--r-- 1 mcc users 3.4K May 28 08:05 LTLFireability.txt
-rw-r--r-- 1 mcc users 11K May 28 08:05 LTLFireability.xml
-rw-r--r-- 1 mcc users 1 May 24 11:17 NewModel
-rw-r--r-- 1 mcc users 3.7K May 28 06:22 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 17K May 28 06:22 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 104 May 26 06:29 ReachabilityDeadlock.txt
-rw-r--r-- 1 mcc users 342 May 26 06:29 ReachabilityDeadlock.xml
-rw-r--r-- 1 mcc users 7.4K May 27 03:47 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 23K May 27 03:47 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K May 28 07:31 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.7K 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 6 May 24 11:17 instance
-rw-r--r-- 1 mcc users 6 May 24 11:17 iscolored
-rw------- 1 mcc users 57K May 24 11:17 model.pnml
=====================================================================
Generated by BenchKit 2-3637
Executing tool itstoolsl
Input is EGFr-PT-02010, examination is ReachabilityDeadlock
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r285-csrt-152749176000260
=====================================================================

--------------------
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 EGFr-PT-02010-ReachabilityDeadlock-0

=== Now, execution of the tool begins

BK_START 1527990645535

Flatten gal took : 88 ms
Applied a total of 0 rules in 6 ms. Remains 40 /40 variables (removed 0) and now considering 68/68 (removed 0) transitions.
Normalized transition count is 39
// Phase 1: matrix 39 rows 40 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 39
// Phase 1: matrix 39 rows 40 cols
invariant :p27_equals_0 + p27_equals_1 = 1
invariant :pRB1_equals_0 + pRB1_equals_1 = 1
invariant :p21_equals_0 + p21_equals_1 = 1
invariant :MYC_equals_0 + MYC_equals_1 = 1
invariant :ERBB1_equals_0 + ERBB1_equals_1 = 1
invariant :ERBB2_equals_0 + ERBB2_equals_1 = 1
invariant :MEK1_equals_0 + MEK1_equals_1 = 1
invariant :IGF1R_equals_0 + IGF1R_equals_1 = 1
invariant :CyclinD1_equals_0 + CyclinD1_equals_1 = 1
invariant :CDK4_equals_0 + CDK4_equals_1 = 1
invariant :AKT1_0 + AKT1_equals_1 = 1
invariant :ERBB1_3_equals_0 + ERBB1_3_equals_1 = 1
invariant :ERalpha_equals_0 + ERalpha_equals_1 = 1
invariant :EGF_equals_0 + EGF_equals_1 = 1
invariant :ERBB3_equals_0 + ERBB3_equals_1 = 1
invariant :ERBB1_2_equals_0 + ERBB1_2_equals_1 = 1
invariant :CDK6_equals_0 + CDK6_equals_1 = 1
invariant :ERBB2_3_equals_0 + ERBB2_3_equals_1 = 1
invariant :CDK2_equals_0 + CDK2_equals_1 = 1
invariant :CyclinE1_equals_0 + CyclinE1_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/graph8612723671806501242.txt, -o, /tmp/graph8612723671806501242.bin, -w, /tmp/graph8612723671806501242.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/graph8612723671806501242.bin, -l, -1, -v, -w, /tmp/graph8612723671806501242.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 19 ordering constraints for composite.
built 5 ordering constraints for composite.
built 19 ordering constraints for composite.
built 20 ordering constraints for composite.
built 24 ordering constraints for composite.
built 23 ordering constraints for composite.
built 26 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,4200,0.056492,5624,106,6,1978,38,184,3179,12,33,0


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,1,0.069227,5624,16,5,1978,38,502,3179,39,33,2148

System contains 1 deadlocks (shown below if less than --print-limit option) !
FORMULA EGFr-PT-02010-ReachabilityDeadlock-0 TRUE TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
[ i5={[ u16={[ MYC_equals_1=1 ]
} u13={[ ERalpha_equals_1=1 ]
} u5={[ CyclinE1_equals_1=1 ]
} u4={[ CyclinD1_equals_1=1 ]
} ]
} i4={[ u14={[ IGF1R_equals_0=1 ]
} u0={[ AKT1_equals_1=1 ]
} ]
} i3={[ u15={[ MEK1_equals_1=1 ]
} u9={[ ERBB1_3_equals_1=1 ]
} u8={[ ERBB1_2_equals_1=1 ]
} u7={[ ERBB1_equals_1=1 ]
} ]
} i2={[ u12={[ ERBB3_equals_1=1 ]
} u11={[ ERBB2_3_equals_1=1 ]
} u10={[ ERBB2_equals_1=1 ]
} u6={[ EGF_equals_1=1 ]
} ]
} i0={[ u18={[ p27_equals_0=1 ]
} u17={[ p21_equals_0=1 ]
} u2={[ CDK4_equals_1=1 ]
} u1={[ CDK2_equals_1=1 ]
} ]
} i1={[ u19={[ pRB1_equals_1=1 ]
} u3={[ CDK6_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 1527990649107

--------------------
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 1:50:47 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 1:50:47 AM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
Jun 03, 2018 1:50:47 AM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 44 ms
Jun 03, 2018 1:50:47 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 40 places.
Jun 03, 2018 1:50:47 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 68 transitions.
Jun 03, 2018 1:50:47 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.img.gal : 16 ms
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 84 ms
Jun 03, 2018 1:50:48 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.simple.gal : 15 ms
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 68 transitions.
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.application.MccTranslator applyOrder
INFO: Applying decomposition
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 17 ms
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 68 transitions.
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 39 ms
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver computeAndDeclareInvariants
INFO: Computed 20 place invariants in 31 ms
Begin: Sun Jun 3 01:50:48 2018

Computation of communities with the Newman-Girvan Modularity quality function

level 0:
start computation: Sun Jun 3 01:50:48 2018
network size: 40 nodes, 220 links, 136 weight
quality increased from -0.0284021 to 0.390939
end computation: Sun Jun 3 01:50:48 2018
level 1:
start computation: Sun Jun 3 01:50:48 2018
network size: 20 nodes, 108 links, 136 weight
quality increased from 0.390939 to 0.523724
end computation: Sun Jun 3 01:50:48 2018
level 2:
start computation: Sun Jun 3 01:50:48 2018
network size: 8 nodes, 40 links, 136 weight
quality increased from 0.523724 to 0.534907
end computation: Sun Jun 3 01:50:48 2018
level 3:
start computation: Sun Jun 3 01:50:48 2018
network size: 6 nodes, 24 links, 136 weight
quality increased from 0.534907 to 0.534907
end computation: Sun Jun 3 01:50:48 2018
End: Sun Jun 3 01:50:48 2018
Total duration: 0 sec
0.534907
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.instantiate.CompositeBuilder decomposeWithOrder
INFO: Decomposing Gal with order
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 22 ms
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.instantiate.CompositeBuilder rewriteArraysToAllowPartition
INFO: Rewriting arrays to variables to allow decomposition.
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.instantiate.Instantiator fuseIsomorphicEffects
INFO: Removed a total of 92 redundant transitions.
Jun 03, 2018 1:50:48 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/ReachabilityDeadlock.pnml.gal : 5 ms
Jun 03, 2018 1:50:48 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)
Jun 03, 2018 1:50:48 AM fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext transform
INFO: Built C files in 586ms 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="EGFr-PT-02010"
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/EGFr-PT-02010.tgz
mv EGFr-PT-02010 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 EGFr-PT-02010, 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-152749176000260"
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 ;