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)
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/home/mcc/execution
total 200K
-rw-r--r-- 1 mcc users 3.2K May 15 18:54 CTLCardinality.txt
-rw-r--r-- 1 mcc users 17K May 15 18:54 CTLCardinality.xml
-rw-r--r-- 1 mcc users 2.5K May 15 18:54 CTLFireability.txt
-rw-r--r-- 1 mcc users 14K May 15 18:54 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K May 15 18:50 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 5.6K May 15 18:50 GenericPropertiesVerdict.xml
-rw-r--r-- 1 mcc users 2.4K May 15 18:54 LTLCardinality.txt
-rw-r--r-- 1 mcc users 9.9K May 15 18:54 LTLCardinality.xml
-rw-r--r-- 1 mcc users 2.0K May 15 18:54 LTLFireability.txt
-rw-r--r-- 1 mcc users 8.8K May 15 18:54 LTLFireability.xml
-rw-r--r-- 1 mcc users 3.8K May 15 18:54 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 20K May 15 18:54 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 119 May 15 18:54 ReachabilityDeadlock.txt
-rw-r--r-- 1 mcc users 357 May 15 18:54 ReachabilityDeadlock.xml
-rw-r--r-- 1 mcc users 3.0K May 15 18:54 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 17K May 15 18:54 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.8K May 15 18:54 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K May 15 18:54 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 May 15 18:50 equiv_col
-rw-r--r-- 1 mcc users 16 May 15 18:50 instance
-rw-r--r-- 1 mcc users 6 May 15 18:50 iscolored
-rw-r--r-- 1 mcc users 36K May 15 18:50 model.pnml
=====================================================================
Generated by BenchKit 2-3637
Executing tool itstoolsl
Input is DNAwalker-PT-01track12Block1, examination is ReachabilityDeadlock
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r069-smll-152649742000230
=====================================================================

--------------------
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 DNAwalker-PT-01track12Block1-ReachabilityDeadlock-0

=== Now, execution of the tool begins

BK_START 1527367546322

Flatten gal took : 106 ms
Applied a total of 0 rules in 6 ms. Remains 13 /13 variables (removed 0) and now considering 82/82 (removed 0) transitions.
Normalized transition count is 81
// Phase 1: matrix 81 rows 13 cols
Using solver Z3 to compute partial order matrices.
Built C files in :
/home/mcc/execution
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/graph5980837730341295477.txt, -o, /tmp/graph5980837730341295477.bin, -w, /tmp/graph5980837730341295477.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/graph5980837730341295477.bin, -l, -1, -v, -w, /tmp/graph5980837730341295477.weights, -q, 0, -e, 0.001], workingDir=null]
Presburger conditions satisfied. Using coverability to approximate state space in K-Induction.
Normalized transition count is 81
// Phase 1: matrix 81 rows 13 cols
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.
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,3795,0.029714,4872,2,144,5,1806,6,0,153,1501,0


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,6,0.046883,5416,2,25,7,4992,9,1,531,2963,2

System contains 6 deadlocks (shown below if less than --print-limit option) !
FORMULA DNAwalker-PT-01track12Block1-ReachabilityDeadlock-0 TRUE TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
[ A12=1 A8=1 A2=2 ]
[ A12=1 A8=1 A3=2 ]
[ A12=1 A8=1 A4=2 ]
[ A12=1 A8=1 A7=1 A2=2 ]
[ A12=1 A11=1 A8=1 A2=2 ]
[ A12=1 A11=1 A8=1 A7=1 A2=2 ]
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 1527367553167

--------------------
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
May 26, 2018 8:45:48 PM 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]
May 26, 2018 8:45:48 PM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
May 26, 2018 8:45:48 PM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 62 ms
May 26, 2018 8:45:48 PM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 13 places.
May 26, 2018 8:45:49 PM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 82 transitions.
May 26, 2018 8:45:49 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.img.gal : 13 ms
May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 100 ms
May 26, 2018 8:45:49 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.simple.gal : 4 ms
May 26, 2018 8:45:49 PM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 82 transitions.
May 26, 2018 8:45:49 PM fr.lip6.move.gal.application.MccTranslator applyOrder
INFO: Applying decomposition
May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 25 ms
May 26, 2018 8:45:49 PM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 82 transitions.
May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 22 ms
Begin: Sat May 26 20:45:49 2018

Computation of communities with the Newman-Girvan Modularity quality function

level 0:
start computation: Sat May 26 20:45:49 2018
network size: 6 nodes, 2 links, 2 weight
quality increased from -0.5 to 0
end computation: Sat May 26 20:45:49 2018
level 1:
start computation: Sat May 26 20:45:49 2018
network size: 5 nodes, 1 links, 2 weight
quality increased from 0 to 0
end computation: Sat May 26 20:45:49 2018
End: Sat May 26 20:45:49 2018
Total duration: 0 sec
0
May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder decomposeWithOrder
INFO: Decomposing Gal with order
May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 46 ms
May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder rewriteArraysToAllowPartition
INFO: Rewriting arrays to variables to allow decomposition.
May 26, 2018 8:45:49 PM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver computeAndDeclareInvariants
INFO: Computed 0 place invariants in 12 ms
May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder$Partition getIndex
INFO: Could not find partition element corresponding to A6 in partition [A1],[A2],[A3],[A4],[A5, B5],

May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder$Partition getIndex
INFO: Could not find partition element corresponding to A7 in partition [A1],[A2],[A3],[A4],[A5, B5],

May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder$Partition getIndex
INFO: Could not find partition element corresponding to A8 in partition [A1],[A2],[A3],[A4],[A5, B5],

May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder$Partition getIndex
INFO: Could not find partition element corresponding to A9 in partition [A1],[A2],[A3],[A4],[A5, B5],

May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder$Partition getIndex
INFO: Could not find partition element corresponding to A10 in partition [A1],[A2],[A3],[A4],[A5, B5],

May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder$Partition getIndex
INFO: Could not find partition element corresponding to A11 in partition [A1],[A2],[A3],[A4],[A5, B5],

May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.CompositeBuilder$Partition getIndex
INFO: Could not find partition element corresponding to A12 in partition [A1],[A2],[A3],[A4],[A5, B5],

May 26, 2018 8:45:49 PM fr.lip6.move.gal.application.MccTranslator applyOrder
WARNING: Could not apply decomposition. Using flat GAL structure.
java.lang.ArrayIndexOutOfBoundsException: -1
at org.eclipse.emf.common.util.BasicEList.get(BasicEList.java:348)
at fr.lip6.move.gal.instantiate.CompositeBuilder.galToCompositeWithPartition(CompositeBuilder.java:434)
at fr.lip6.move.gal.instantiate.CompositeBuilder.decomposeWithOrder(CompositeBuilder.java:145)
at fr.lip6.move.gal.application.MccTranslator.applyOrder(MccTranslator.java:120)
at fr.lip6.move.gal.application.MccTranslator.flattenSpec(MccTranslator.java:147)
at fr.lip6.move.gal.application.Application.start(Application.java:288)
at fr.lip6.move.gal.itscl.application.Application.start(Application.java:40)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
at org.eclipse.equinox.launcher.Main.run(Main.java:1499)
at org.eclipse.equinox.launcher.Main.main(Main.java:1472)
May 26, 2018 8:45:49 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 20 ms
May 26, 2018 8:45:49 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/ReachabilityDeadlock.pnml.gal : 15 ms
May 26, 2018 8:45:49 PM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver init
INFO: Proved 13 variables to be positive in 145 ms
May 26, 2018 8:45:49 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeAblingMatrix
INFO: Computing symmetric may disable matrix : 82 transitions.
May 26, 2018 8:45:49 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of disable matrix completed :0/82 took 0 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 26, 2018 8:45:49 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Complete disable matrix. took 5 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 26, 2018 8:45:49 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeAblingMatrix
INFO: Computing symmetric may enable matrix : 82 transitions.
May 26, 2018 8:45:49 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Complete enable matrix. took 5 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 26, 2018 8:45:49 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeCoEnablingMatrix
INFO: Computing symmetric co enabling matrix : 82 transitions.
May 26, 2018 8:45:51 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Finished co-enabling matrix. took 1992 ms. Total solver calls (SAT/UNSAT): 1081(1081/0)
Skipping mayMatrices nes/nds SMT solver raised an error on invariants :(error "Failed to assert expression: java.io.IOException: Stream closed (invariants (select s 2))")
java.lang.RuntimeException: SMT solver raised an error on invariants :(error "Failed to assert expression: java.io.IOException: Stream closed (invariants (select s 2))")
at fr.lip6.move.gal.gal2smt.bmc.KInductionSolver.addKnownInvariants(KInductionSolver.java:456)
at fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver.computeDoNotAccord(NecessaryEnablingsolver.java:572)
at fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext.printLabels(Gal2PinsTransformerNext.java:538)
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)
May 26, 2018 8:45:51 PM fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext transform
INFO: Built C files in 2367ms 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="DNAwalker-PT-01track12Block1"
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/DNAwalker-PT-01track12Block1.tgz
mv DNAwalker-PT-01track12Block1 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 DNAwalker-PT-01track12Block1, 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 r069-smll-152649742000230"
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 ;