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)
.......
=====================================================================
Generated by BenchKit 2-3254
Executing tool itstools
Input is S_Angiogenesis-PT-25, examination is ReachabilityDeadlock
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r090-csrt-149441076500143
=====================================================================

--------------------
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-25-ReachabilityDeadlock-0

=== Now, execution of the tool begins

BK_START 1496385947488


Using solver YICES2 to compute partial order matrices.
Built C files in :
/home/mcc/execution
its-ctl command run as :

/home/mcc/BenchKit/eclipse/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.201705302212/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.
Presburger conditions satisfied. Using coverability to approximate state space in K-Induction.
// Phase 1: matrix 64 rows 39 cols
invariant : 1'GStarP3kP3 + 1'KdStarGStarP3k + 1'KdStarGStarP3kP3 + 1'KdStarGStarP3kStar + 1'KdStarGStarP3kStarP2 + 1'KdStarGStarP3kStarP3 + 1'KdStarGStarP3kStarP3P2 + 1'P3k= 25
invariant : 1'GStarPgP3 + -1'KdStar + -1'KdStarG + -1'KdStarGP3 + -1'KdStarGStar + -1'KdStarGStarP3 + -1'KdStarGStarP3k + -1'KdStarGStarP3kP3 + -1'KdStarGStarP3kStar + -1'KdStarGStarP3kStarP2 + -1'KdStarGStarP3kStarP3 + -1'KdStarGStarP3kStarP3P2 + 1'Pg= 0
invariant : -1'AktP3 + -1'DAG + -1'DAGE + 1'Gab1 + 1'KdStar + 2'KdStarG + 1'KdStarGP3 + 2'KdStarGStar + 1'KdStarGStarP3 + 2'KdStarGStarP3k + 1'KdStarGStarP3kP3 + 2'KdStarGStarP3kStar + 1'KdStarGStarP3kStarP2 + 1'KdStarGStarP3kStarP3 + 2'KdStarGStarPg + 1'KdStarGStarPgP3 + 2'KdStarGStarPgStar + 1'KdStarGStarPgStarP2 + 1'KdStarGStarPgStarP3 + 1'KdStarPg + 1'KdStarPgStar + -1'Pip2 + -1'Pip3 + 2'Pten + 1'PtP2 + 1'PtP3= 75
invariant : 1'Akt + 1'AktP3 + 1'AktStar= 25
invariant : 1'DAGE + 1'Enz= 25
invariant : -1'Gab1 + -1'GP3 + -1'GStarP3 + -1'GStarP3kP3 + -1'GStarPgP3 + 1'KdStar + 1'KdStarPg + 1'KdStarPgStar + 1'KdStarPgStarP2= 0
invariant : 1'AktP3 + 1'DAG + 1'DAGE + -1'Gab1 + -1'KdStar + -2'KdStarG + -1'KdStarGP3 + -2'KdStarGStar + -1'KdStarGStarP3 + -2'KdStarGStarP3k + -1'KdStarGStarP3kP3 + -2'KdStarGStarP3kStar + -1'KdStarGStarP3kStarP2 + -1'KdStarGStarP3kStarP3 + -2'KdStarGStarPg + -1'KdStarGStarPgP3 + -2'KdStarGStarPgStar + -1'KdStarGStarPgStarP2 + -1'KdStarGStarPgStarP3 + -1'KdStarPg + -1'KdStarPgStar + 1'Pip2 + 1'Pip3 + -1'Pten + 1'PtP3P2= -50
invariant : 1'Gab1 + 1'GP3 + 1'GStarP3 + 1'GStarP3kP3 + 1'GStarPgP3 + 1'KdStarG + 1'KdStarGP3 + 1'KdStarGStar + 1'KdStarGStarP3 + 1'KdStarGStarP3k + 1'KdStarGStarP3kP3 + 1'KdStarGStarP3kStar + 1'KdStarGStarP3kStarP2 + 1'KdStarGStarP3kStarP3 + 1'KdStarGStarP3kStarP3P2 + 1'KdStarGStarPg + 1'KdStarGStarPgP3 + 1'KdStarGStarPgStar + 1'KdStarGStarPgStarP2 + 1'KdStarGStarPgStarP3 + 1'KdStarGStarPgStarP3P2= 25
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]
Exit code :0
Running link step : CommandLine [args=[gcc, -shared, -o, gal.so, model.o], workingDir=/home/mcc/execution]
Exit code :0
Exit code :1
FORMULA Angiogenesis-PT-25-ReachabilityDeadlock-0 TRUE TECHNIQUES PARTIAL_ORDER EXPLICIT LTSMIN SAT_SMT
Detected timeout of ITS tools.

BK_STOP 1496386550440

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

+ export BINDIR=/home/mcc/BenchKit/
+ BINDIR=/home/mcc/BenchKit/
++ pwd
+ export MODEL=/home/mcc/execution
+ MODEL=/home/mcc/execution
+ [[ ReachabilityDeadlock = StateSpace ]]
+ /home/mcc/BenchKit//runeclipse.sh /home/mcc/execution ReachabilityDeadlock -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -smt
+ ulimit -s 65536
+ java -Dosgi.requiredJavaVersion=1.6 -Xss8m -Xms40m -Xmx8192m -Declipse.pde.launch=true -Dfile.encoding=UTF-8 -classpath /home/mcc/BenchKit//eclipse/plugins/org.eclipse.equinox.launcher_1.3.201.v20161025-1711.jar org.eclipse.equinox.launcher.Main -application fr.lip6.move.gal.application.pnmcc -data /home/mcc/BenchKit//workspace -os linux -ws gtk -arch x86_64 -nl en_US -consoleLog -pnfolder /home/mcc/execution -examination ReachabilityDeadlock -yices2path /home/mcc/BenchKit//yices/bin/yices -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -smt
Jun 02, 2017 6:45:48 AM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 43 ms
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 39 places.
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 64 transitions.
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.logic.togal.ToGalTransformer toGal
WARNING: Unknown predicate type in boolean expression fr.lip6.move.gal.logic.impl.DeadlockImpl
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.instantiate.PropertySimplifier rewriteWithInitialState
INFO: Reachable property Angiogenesis-PT-25-ReachabilityDeadlock-0 is trivially true : it is verified in initial state.
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 43 ms
Jun 02, 2017 6:45:49 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/ReachabilityDeadlock.pnml.gal : 9 ms
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver computeAndDeclareInvariants
INFO: Computed 8 place invariants in 21 ms
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver init
INFO: Proved 39 variables to be positive in 101 ms
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeAblingMatrix
INFO: Computing symmetric may disable matrix : 64 transitions.
Jun 02, 2017 6:45:49 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Completed :0/64 took 11 ms. Total solver calls (SAT/UNSAT): 16(8/8)
Jun 02, 2017 6:45:50 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Complete disable matrix. took 292 ms. Total solver calls (SAT/UNSAT): 506(230/276)
Jun 02, 2017 6:45:50 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeAblingMatrix
INFO: Computing symmetric may enable matrix : 64 transitions.
Jun 02, 2017 6:45:50 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Complete enable matrix. took 237 ms. Total solver calls (SAT/UNSAT): 506(258/248)
Jun 02, 2017 6:45:50 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeCoEnablingMatrix
INFO: Computing symmetric co enabling matrix : 64 transitions.
Jun 02, 2017 6:45:51 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Finished enabling matrix. took 797 ms. Total solver calls (SAT/UNSAT): 2080(2080/0)
Jun 02, 2017 6:45:51 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeDoNotAccord
INFO: Computing Do-Not-Accords matrix : 64 transitions.
Jun 02, 2017 6:46:01 AM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Completed DNA matrix. took 10407 ms. Total solver calls (SAT/UNSAT): 375(0/375)
Jun 02, 2017 6:46:01 AM fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext transform
INFO: Built C files in 12162ms conformant to PINS in folder :/home/mcc/execution
Jun 02, 2017 6:55:50 AM fr.lip6.move.gal.itstools.Runner runTool
INFO: Standard error output from running tool CommandLine [args=[/home/mcc/BenchKit//lts_install_dir//bin/pins2lts-seq, ./gal.so, -p, --pins-guards, --when, -d], workingDir=/home/mcc/execution]
pins2lts-seq, 0.001: Registering PINS so language module
pins2lts-seq, 0.001: Loading model from ./gal.so
pins2lts-seq, 0.001: library has no initializer
pins2lts-seq, 0.001: loading model GAL
pins2lts-seq, 0.002: completed loading model GAL
pins2lts-seq, 0.002: Initializing POR dependencies: labels 65, guards 64
pins2lts-seq, 0.005: There are 65 state labels and 1 edge labels
pins2lts-seq, 0.005: State length is 39, there are 64 groups
pins2lts-seq, 0.005: Running dfs search strategy
pins2lts-seq, 0.005: Using a tree for state storage
pins2lts-seq, 0.005: Visible groups: 0 / 64, labels: 0 / 65
pins2lts-seq, 0.005: POR cycle proviso: none
pins2lts-seq, 0.173: explored 8832 levels ~10000 states ~46482 transitions
pins2lts-seq, 0.350: explored 17312 levels ~20000 states ~97878 transitions
pins2lts-seq, 0.702: explored 30678 levels ~40000 states ~192761 transitions
pins2lts-seq, 1.411: explored 58590 levels ~80000 states ~378048 transitions
pins2lts-seq, 2.872: explored 109092 levels ~160000 states ~754939 transitions
pins2lts-seq, 6.165: explored 209713 levels ~320000 states ~1509964 transitions
pins2lts-seq, 12.608: explored 407593 levels ~640000 states ~3070937 transitions
pins2lts-seq, 26.327: explored 790878 levels ~1280000 states ~6300463 transitions
pins2lts-seq, 56.354: explored 1548609 levels ~2560000 states ~12898354 transitions
pins2lts-seq, 119.950: explored 3033575 levels ~5120000 states ~26417896 transitions
pins2lts-seq, 249.342: explored 5918395 levels ~10240000 states ~54047746 transitions
pins2lts-seq, 528.966: explored 11653955 levels ~20480000 states ~111006271 transitions
pins2lts-seq, 586.961:
pins2lts-seq, 586.961: deadlock () found at depth 12779205!
pins2lts-seq, 586.961:
pins2lts-seq, 586.961: exiting now

Jun 02, 2017 6:55:50 AM fr.lip6.move.gal.itstools.ProcessController$1 run
WARNING: null
Jun 02, 2017 6:55:50 AM fr.lip6.move.gal.itstools.ProcessController forwardStream
WARNING: Stream closed
Jun 02, 2017 6:55:50 AM fr.lip6.move.gal.itstools.ProcessController forwardStream
WARNING: Stream closed

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="S_Angiogenesis-PT-25"
export BK_EXAMINATION="ReachabilityDeadlock"
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

tar xzf /home/mcc/BenchKit/INPUTS/S_Angiogenesis-PT-25.tgz
mv S_Angiogenesis-PT-25 execution

# this is for BenchKit: explicit launching of the test

cd execution
echo "====================================================================="
echo " Generated by BenchKit 2-3254"
echo " Executing tool itstools"
echo " Input is S_Angiogenesis-PT-25, 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 r090-csrt-149441076500143"
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 ;