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 212K
-rw-r--r-- 1 mcc users 4.2K May 15 18:54 CTLCardinality.txt
-rw-r--r-- 1 mcc users 20K May 15 18:54 CTLCardinality.xml
-rw-r--r-- 1 mcc users 2.7K May 15 18:54 CTLFireability.txt
-rw-r--r-- 1 mcc users 20K May 15 18:54 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K May 15 18:49 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 6.0K May 15 18:49 GenericPropertiesVerdict.xml
-rw-r--r-- 1 mcc users 2.4K May 15 18:54 LTLCardinality.txt
-rw-r--r-- 1 mcc users 9.8K May 15 18:54 LTLCardinality.xml
-rw-r--r-- 1 mcc users 1.8K May 15 18:54 LTLFireability.txt
-rw-r--r-- 1 mcc users 8.6K May 15 18:54 LTLFireability.xml
-rw-r--r-- 1 mcc users 4.7K May 15 18:54 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 23K May 15 18:54 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 109 May 15 18:54 ReachabilityDeadlock.txt
-rw-r--r-- 1 mcc users 347 May 15 18:54 ReachabilityDeadlock.xml
-rw-r--r-- 1 mcc users 2.4K May 15 18:54 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 13K May 15 18:54 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K 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 18:49 equiv_col
-rw-r--r-- 1 mcc users 3 May 15 18:49 instance
-rw-r--r-- 1 mcc users 6 May 15 18:49 iscolored
-rw-r--r-- 1 mcc users 33K May 15 18:49 model.pnml
=====================================================================
Generated by BenchKit 2-3637
Executing tool itstoolsl
Input is Angiogenesis-PT-01, examination is ReachabilityDeadlock
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r021-qhx1-152646246200006
=====================================================================

--------------------
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 Angiogenesis-PT-01-ReachabilityDeadlock-0

=== Now, execution of the tool begins

BK_START 1527200652535

Flatten gal took : 84 ms
Constant places removed 1 places and 0 transitions.
Iterating post reduction 0 with 1 rules applied. Total rules applied 1 place count 38 transition count 64
Performed 1 Pre agglomeration using Quasi-Persistent + HF-interchangeable + Divergent Free condition.
Pre-agglomeration after 1 with 1 Pre rules applied. Total rules applied 1 place count 38 transition count 63
Constant places removed 2 places and 0 transitions.
Iterating post reduction 1 with 2 rules applied. Total rules applied 3 place count 36 transition count 63
Performed 10 Post agglomeration using F-continuation condition.
Constant places removed 10 places and 0 transitions.
Iterating post reduction 2 with 10 rules applied. Total rules applied 13 place count 26 transition count 53
Performed 5 Post agglomeration using F-continuation condition.
Constant places removed 5 places and 0 transitions.
Iterating post reduction 3 with 5 rules applied. Total rules applied 18 place count 21 transition count 59
Applied a total of 18 rules in 28 ms. Remains 21 /39 variables (removed 18) and now considering 59/64 (removed 5) transitions.
Normalized transition count is 38
// Phase 1: matrix 38 rows 21 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/graph4827784215890055812.txt, -o, /tmp/graph4827784215890055812.bin, -w, /tmp/graph4827784215890055812.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/graph4827784215890055812.bin, -l, -1, -v, -w, /tmp/graph4827784215890055812.weights, -q, 0, -e, 0.001], workingDir=null]
Presburger conditions satisfied. Using coverability to approximate state space in K-Induction.
Normalized transition count is 38
// Phase 1: matrix 38 rows 21 cols
invariant :-1'Gab1 + -1'GP3 + -1'GStarP3 + KdStar + KdStarGStarP3kStar + KdStarGStarP3kStarP3 + KdStarGStarPgStar + KdStarGStarPgStarP3 + 2'KdStarPgStar + P3k + Pg = 2
invariant :Gab1 + GP3 + GStarP3 + KdStarGStar + KdStarGStarP3 + -1'KdStarPgStar + -1'P3k + -1'Pg = -1
invariant :DAG + -1'Gab1 + -1'KdStarGStar + -1'KdStarGStarP3kStar + -1'KdStarGStarPgStar + Pip2 + Pip3 + PtP2 = 0
invariant :Pten + PtP2 = 1
invariant :GStarP3kP3 + KdStarGStarP3kStar + KdStarGStarP3kStarP3 + P3k = 1
invariant :GStarPgP3 + KdStarGStarPgStar + KdStarGStarPgStarP3 + KdStarPgStar + Pg = 1
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 8 ordering constraints for composite.
built 39 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,46,0.065821,4924,40,30,245,107,169,268,45,253,0


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,4,0.070189,4924,17,16,245,187,424,268,168,262,650

System contains 4 deadlocks (shown below if less than --print-limit option) !
FORMULA Angiogenesis-PT-01-ReachabilityDeadlock-0 TRUE TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
[ u5={[ Pg=1 ]
} i3={[ u4={[ KdStarGStarP3kStarP3=1 ]
} u3={[ ]
} ]
} u2={[ ]
} u1={[ Pten=1 ]
} u0={[ ]
[ Akt=1 ]
} ]
[ u5={[ KdStarGStarPgStarP3=1 ]
} i3={[ u4={[ P3k=1 ]
} u3={[ ]
} ]
} u2={[ ]
} u1={[ Pten=1 ]
} u0={[ ]
[ Akt=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 1527200673635

--------------------
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 24, 2018 10:24:30 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 24, 2018 10:24:30 PM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
May 24, 2018 10:24:30 PM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 58 ms
May 24, 2018 10:24:30 PM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 39 places.
May 24, 2018 10:24:31 PM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 64 transitions.
May 24, 2018 10:24:31 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.img.gal : 12 ms
May 24, 2018 10:24:31 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 78 ms
May 24, 2018 10:24:31 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.simple.gal : 4 ms
May 24, 2018 10:24:31 PM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 64 transitions.
May 24, 2018 10:24:31 PM fr.lip6.move.gal.application.MccTranslator applyOrder
INFO: Applying decomposition
May 24, 2018 10:24:31 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 27 ms
May 24, 2018 10:24:31 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 17 ms
May 24, 2018 10:24:31 PM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 59 transitions.
Begin: Thu May 24 22:24:31 2018

Computation of communities with the Newman-Girvan Modularity quality function

level 0:
start computation: Thu May 24 22:24:31 2018
network size: 21 nodes, 96 links, 80 weight
quality increased from -0.0657552 to 0.320964
end computation: Thu May 24 22:24:31 2018
level 1:
start computation: Thu May 24 22:24:31 2018
network size: 6 nodes, 21 links, 80 weight
quality increased from 0.320964 to 0.326797
end computation: Thu May 24 22:24:31 2018
level 2:
start computation: Thu May 24 22:24:31 2018
network size: 5 nodes, 14 links, 80 weight
quality increased from 0.326797 to 0.326797
end computation: Thu May 24 22:24:31 2018
End: Thu May 24 22:24:31 2018
Total duration: 0 sec
0.326797
May 24, 2018 10:24:31 PM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver computeAndDeclareInvariants
INFO: Computed 6 place invariants in 9 ms
May 24, 2018 10:24:31 PM fr.lip6.move.gal.instantiate.CompositeBuilder decomposeWithOrder
INFO: Decomposing Gal with order
May 24, 2018 10:24:31 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 35 ms
May 24, 2018 10:24:31 PM fr.lip6.move.gal.instantiate.CompositeBuilder rewriteArraysToAllowPartition
INFO: Rewriting arrays to variables to allow decomposition.
May 24, 2018 10:24:31 PM fr.lip6.move.gal.instantiate.Instantiator fuseIsomorphicEffects
INFO: Removed a total of 48 redundant transitions.
May 24, 2018 10:24:31 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/ReachabilityDeadlock.pnml.gal : 20 ms
May 24, 2018 10:24:32 PM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver init
INFO: Proved 21 variables to be positive in 238 ms
May 24, 2018 10:24:32 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeAblingMatrix
INFO: Computing symmetric may disable matrix : 59 transitions.
May 24, 2018 10:24:32 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of disable matrix completed :0/59 took 4 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 24, 2018 10:24:32 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Complete disable matrix. took 9 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 24, 2018 10:24:32 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeAblingMatrix
INFO: Computing symmetric may enable matrix : 59 transitions.
May 24, 2018 10:24:32 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Complete enable matrix. took 2 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 24, 2018 10:24:32 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeCoEnablingMatrix
INFO: Computing symmetric co enabling matrix : 59 transitions.
May 24, 2018 10:24:32 PM org.smtlib.impl.Script execute
WARNING: Script execution failed on command (assert (>= (select s0 9) 0)) with error
May 24, 2018 10:24:32 PM org.smtlib.impl.Script execute
WARNING: Script execution failed on command (assert (>= (select s0 10) 0)) with error (error "Failed to assert expression: java.io.IOException: Broken pipe (>= (select s0 10) 0)")
[(declare-fun s0 () (Array Int Int)), (assert (= (+ (select s0 14) (select s0 17) (select s0 18) -1) (+ (select s0 2) (select s0 3) (select s0 4) (select s0 8) (select s0 9)))), (assert (= (+ (select s0 2) (select s0 8) (select s0 10) (select s0 12) 0) (+ (select s0 1) (select s0 15) (select s0 16) (select s0 20)))), (assert (and (>= (select s0 8) 1) (>= (select s0 16) 1))), (assert (>= (select s0 1) 0)), (assert (>= (select s0 2) 0)), (assert (>= (select s0 3) 0)), (assert (>= (select s0 4) 0)), (assert (>= (select s0 8) 0)), (assert (>= (select s0 9) 0)), (assert (>= (select s0 10) 0)), (assert (>= (select s0 12) 0)), (assert (>= (select s0 14) 0)), (assert (>= (select s0 15) 0)), (assert (>= (select s0 16) 0)), (assert (>= (select s0 17) 0)), (assert (>= (select s0 18) 0)), (assert (>= (select s0 20) 0))]
Skipping mayMatrices nes/nds SMT solver raised an exception or timeout when executing script :
org.smtlib.impl.Script@5f07eb0c
java.lang.RuntimeException: SMT solver raised an exception or timeout when executing script :
org.smtlib.impl.Script@5f07eb0c
at fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver.computeCoEnablingMatrix(NecessaryEnablingsolver.java:448)
at fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext.printLabels(Gal2PinsTransformerNext.java:530)
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 24, 2018 10:24:32 PM fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext transform
INFO: Built C files in 602ms 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="Angiogenesis-PT-01"
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/Angiogenesis-PT-01.tgz
mv Angiogenesis-PT-01 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 Angiogenesis-PT-01, 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 r021-qhx1-152646246200006"
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 ;