Execution Chart

We display below the execution chart for this examination (boot time has been removed).

Trace from the execution

Formatting '/mnt/tpsp/fkordon/mcc2020-input.r066-tajo-158922814500554.qcow2', fmt=qcow2 size=4294967296 backing_file='/mnt/tpsp/fkordon/mcc2020-input.qcow2' encryption=off cluster_size=65536 lazy_refcounts=off
Waiting for the VM to be ready (probing ssh)
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=====================================================================
Generated by BenchKit 2-4028
Executing tool itstools
Input is Diffusion2D-PT-D50N010, examination is LTLFireability
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r066-tajo-158922814500554
=====================================================================

--------------------
preparation of the directory to be used:
/home/mcc/execution
total 7.5M
-rw-r--r-- 1 mcc users 3.9K Mar 31 06:36 CTLCardinality.txt
-rw-r--r-- 1 mcc users 19K Mar 31 06:36 CTLCardinality.xml
-rw-r--r-- 1 mcc users 2.8K Mar 29 22:57 CTLFireability.txt
-rw-r--r-- 1 mcc users 14K Mar 29 22:57 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K Mar 24 05:37 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 5.8K Mar 24 05:37 GenericPropertiesVerdict.xml
-rw-r--r-- 1 mcc users 3.9K Apr 8 14:49 LTLCardinality.txt
-rw-r--r-- 1 mcc users 24K Apr 28 14:00 LTLCardinality.xml
-rw-r--r-- 1 mcc users 2.4K Apr 8 14:49 LTLFireability.txt
-rw-r--r-- 1 mcc users 15K Apr 28 14:00 LTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K Mar 28 14:32 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 18K Mar 28 14:32 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 2.6K Mar 27 07:32 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 11K Mar 27 07:32 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.8K Mar 28 14:50 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.9K Mar 28 14:50 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 Mar 24 05:37 equiv_col
-rw-r--r-- 1 mcc users 8 Mar 24 05:37 instance
-rw-r--r-- 1 mcc users 6 Mar 24 05:37 iscolored
-rw-r--r-- 1 mcc users 7.3M Mar 24 05:37 model.pnml

--------------------
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 Diffusion2D-PT-D50N010-00
FORMULA_NAME Diffusion2D-PT-D50N010-01
FORMULA_NAME Diffusion2D-PT-D50N010-02
FORMULA_NAME Diffusion2D-PT-D50N010-03
FORMULA_NAME Diffusion2D-PT-D50N010-04
FORMULA_NAME Diffusion2D-PT-D50N010-05
FORMULA_NAME Diffusion2D-PT-D50N010-06
FORMULA_NAME Diffusion2D-PT-D50N010-07
FORMULA_NAME Diffusion2D-PT-D50N010-08
FORMULA_NAME Diffusion2D-PT-D50N010-09
FORMULA_NAME Diffusion2D-PT-D50N010-10
FORMULA_NAME Diffusion2D-PT-D50N010-11
FORMULA_NAME Diffusion2D-PT-D50N010-12
FORMULA_NAME Diffusion2D-PT-D50N010-13
FORMULA_NAME Diffusion2D-PT-D50N010-14
FORMULA_NAME Diffusion2D-PT-D50N010-15

=== Now, execution of the tool begins

BK_START 1590126300198

[2020-05-22 05:45:01] [INFO ] Running its-tools with arguments : [-pnfolder, /home/mcc/execution, -examination, LTLFireability, -z3path, /home/mcc/BenchKit//z3/bin/z3, -yices2path, /home/mcc/BenchKit//yices/bin/yices, -its, -ltsminpath, /home/mcc/BenchKit//lts_install_dir/, -greatspnpath, /home/mcc/BenchKit//greatspn/, -order, META, -manyOrder, -smt, -timeout, 3600]
[2020-05-22 05:45:01] [INFO ] Parsing pnml file : /home/mcc/execution/model.pnml
[2020-05-22 05:45:02] [INFO ] Load time of PNML (sax parser for PT used): 348 ms
[2020-05-22 05:45:02] [INFO ] Transformed 2500 places.
[2020-05-22 05:45:02] [INFO ] Transformed 19404 transitions.
[2020-05-22 05:45:02] [INFO ] Parsed PT model containing 2500 places and 19404 transitions in 438 ms.
Parsed 16 properties from file /home/mcc/execution/LTLFireability.xml in 105 ms.
Working with output stream class java.io.PrintStream
Incomplete random walk after 100000 steps, including 0 resets, run finished after 1039 ms. (steps per millisecond=96 ) properties seen :[1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
// Phase 1: matrix 19404 rows 2500 cols
[2020-05-22 05:45:03] [INFO ] Computed 1 place invariants in 175 ms
[2020-05-22 05:45:03] [INFO ] [Real]Absence check using 1 positive place invariants in 45 ms returned sat
[2020-05-22 05:45:03] [INFO ] [Real]Adding state equation constraints to refine reachable states.
[2020-05-22 05:45:23] [INFO ] SMT solver returned unknown. Retrying;
[2020-05-22 05:45:23] [INFO ] [Real]Absence check using state equation in 19705 ms returned (error "Failed to check-sat")
[2020-05-22 05:45:24] [INFO ] Initial state reduction rules for CTL removed 3 formulas.
[2020-05-22 05:45:24] [INFO ] Flatten gal took : 629 ms
FORMULA Diffusion2D-PT-D50N010-11 TRUE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA Diffusion2D-PT-D50N010-10 TRUE TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA Diffusion2D-PT-D50N010-00 FALSE TECHNIQUES TOPOLOGICAL INITIAL_STATE
[2020-05-22 05:45:24] [INFO ] Flatten gal took : 330 ms
Using solver Z3 to compute partial order matrices.
Built C files in :
/home/mcc/execution
[2020-05-22 05:45:25] [INFO ] Applying decomposition
[2020-05-22 05:45:26] [INFO ] Flatten gal took : 582 ms
[2020-05-22 05:45:26] [INFO ] Input system was already deterministic with 19404 transitions.
[2020-05-22 05:45:26] [INFO ] Too many transitions (19404) to apply POR reductions. Disabling POR matrices.
[2020-05-22 05:45:27] [INFO ] Built C files in 1603ms conformant to PINS in folder :/home/mcc/execution
Running compilation step : CommandLine [args=[gcc, -c, -I/home/mcc/BenchKit//lts_install_dir//include, -I., -std=c99, -fPIC, -O2, model.c], workingDir=/home/mcc/execution]
Converted graph to binary with : CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.louvain.binaries_1.0.0.202005100927/bin/convert-linux64, -i, /tmp/graph6748241123439330055.txt, -o, /tmp/graph6748241123439330055.bin, -w, /tmp/graph6748241123439330055.weights], workingDir=null]
Built communities with : CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.louvain.binaries_1.0.0.202005100927/bin/louvain-linux64, /tmp/graph6748241123439330055.bin, -l, -1, -v, -w, /tmp/graph6748241123439330055.weights, -q, 0, -e, 0.001], workingDir=null]
[2020-05-22 05:45:27] [INFO ] Decomposing Gal with order
[2020-05-22 05:45:27] [INFO ] Rewriting arrays to variables to allow decomposition.
[2020-05-22 05:45:28] [INFO ] Removed a total of 13418 redundant transitions.
[2020-05-22 05:45:29] [INFO ] Flatten gal took : 968 ms
[2020-05-22 05:45:29] [INFO ] Fuse similar labels procedure discarded/fused a total of 68 labels/synchronizations in 115 ms.
[2020-05-22 05:45:29] [INFO ] Time to serialize gal into /home/mcc/execution/LTLFireability.pnml.gal : 116 ms
[2020-05-22 05:45:29] [INFO ] Time to serialize properties into /home/mcc/execution/LTLFireability.ltl : 2 ms
Invoking ITS tools like this :CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202005100927/bin/its-ltl-linux64, --gc-threshold, 2000000, -i, /home/mcc/execution/LTLFireability.pnml.gal, -t, CGAL, -LTL, /home/mcc/execution/LTLFireability.ltl, -c, -stutter-deadlock], workingDir=/home/mcc/execution]

its-ltl command run as :

/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202005100927/bin/its-ltl-linux64 --gc-threshold 2000000 -i /home/mcc/execution/LTLFireability.pnml.gal -t CGAL -LTL /home/mcc/execution/LTLFireability.ltl -c -stutter-deadlock
Read 13 LTL properties
Checking formula 0 : !((X((X(G((((X("(i3.u240.cAMP__5_5_>=1)"))||(X("(i10.u201.cAMP__36_33_>=1)")))||("(i11.u213.cAMP__37_8_>=1)"))||("(i16.u328.cAMP__4_16_>=1)"))))||(F("(i10.u201.cAMP__36_33_>=1)")))))
Formula 0 simplified : !X(XG("(i11.u213.cAMP__37_8_>=1)" | "(i16.u328.cAMP__4_16_>=1)" | X"(i3.u240.cAMP__5_5_>=1)" | X"(i10.u201.cAMP__36_33_>=1)") | F"(i10.u201.cAMP__36_33_>=1)")
built 37 ordering constraints for composite.
built 109 ordering constraints for composite.
built 99 ordering constraints for composite.
built 76 ordering constraints for composite.
built 51 ordering constraints for composite.
built 35 ordering constraints for composite.
built 69 ordering constraints for composite.
built 43 ordering constraints for composite.
built 51 ordering constraints for composite.
built 47 ordering constraints for composite.
built 131 ordering constraints for composite.
built 145 ordering constraints for composite.
built 126 ordering constraints for composite.
built 104 ordering constraints for composite.
built 132 ordering constraints for composite.
built 102 ordering constraints for composite.
built 158 ordering constraints for composite.
built 186 ordering constraints for composite.
built 181 ordering constraints for composite.
built 109 ordering constraints for composite.
built 115 ordering constraints for composite.
built 196 ordering constraints for composite.
built 109 ordering constraints for composite.
built 108 ordering constraints for composite.
built 154 ordering constraints for composite.
built 68 ordering constraints for composite.
Reverse transition relation is exact ! Faster fixpoint algorithm enabled.
WARNING : LTS min runner thread failed on error :java.lang.RuntimeException: Compilation or link of executable timed out.java.util.concurrent.TimeoutException: Subprocess running CommandLine [args=[gcc, -c, -I/home/mcc/BenchKit//lts_install_dir//include, -I., -std=c99, -fPIC, -O2, model.c], workingDir=/home/mcc/execution] killed by timeout after 400 SECONDS
java.lang.RuntimeException: Compilation or link of executable timed out.java.util.concurrent.TimeoutException: Subprocess running CommandLine [args=[gcc, -c, -I/home/mcc/BenchKit//lts_install_dir//include, -I., -std=c99, -fPIC, -O2, model.c], workingDir=/home/mcc/execution] killed by timeout after 400 SECONDS
at fr.lip6.move.gal.application.LTSminRunner$1.run(LTSminRunner.java:80)
at java.base/java.lang.Thread.run(Thread.java:834)
Detected timeout of ITS tools.
[2020-05-22 06:05:37] [INFO ] Flatten gal took : 407 ms
[2020-05-22 06:05:38] [INFO ] Time to serialize gal into /home/mcc/execution/LTLFireability.pnml.gal : 102 ms
[2020-05-22 06:05:38] [INFO ] Time to serialize properties into /home/mcc/execution/LTLFireability.ltl : 8 ms
Invoking ITS tools like this :CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202005100927/bin/its-ltl-linux64, --gc-threshold, 2000000, -i, /home/mcc/execution/LTLFireability.pnml.gal, -t, CGAL, -LTL, /home/mcc/execution/LTLFireability.ltl, -c, -stutter-deadlock, --gen-order, FOLLOW], workingDir=/home/mcc/execution]

its-ltl command run as :

/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202005100927/bin/its-ltl-linux64 --gc-threshold 2000000 -i /home/mcc/execution/LTLFireability.pnml.gal -t CGAL -LTL /home/mcc/execution/LTLFireability.ltl -c -stutter-deadlock --gen-order FOLLOW
Read 13 LTL properties
Checking formula 0 : !((X((X(G((((X("(cAMP__5_5_>=1)"))||(X("(cAMP__36_33_>=1)")))||("(cAMP__37_8_>=1)"))||("(cAMP__4_16_>=1)"))))||(F("(cAMP__36_33_>=1)")))))
Formula 0 simplified : !X(XG("(cAMP__4_16_>=1)" | "(cAMP__37_8_>=1)" | X"(cAMP__5_5_>=1)" | X"(cAMP__36_33_>=1)") | F"(cAMP__36_33_>=1)")
Reverse transition relation is exact ! Faster fixpoint algorithm enabled.
Detected timeout of ITS tools.
[2020-05-22 06:25:46] [INFO ] Flatten gal took : 723 ms
[2020-05-22 06:25:48] [INFO ] Input system was already deterministic with 19404 transitions.
[2020-05-22 06:25:48] [INFO ] Transformed 2500 places.
[2020-05-22 06:25:48] [INFO ] Transformed 19404 transitions.
Running greatSPN : CommandLine [args=[/home/mcc/BenchKit//greatspn//bin/pinvar, /home/mcc/execution/gspn], workingDir=/home/mcc/execution]
Run of greatSPN captured in /home/mcc/execution/outPut.txt
Running greatSPN : CommandLine [args=[/home/mcc/BenchKit//greatspn//bin/RGMEDD2, /home/mcc/execution/gspn, -META, -varord-only], workingDir=/home/mcc/execution]
Run of greatSPN captured in /home/mcc/execution/outPut.txt
Using order generated by GreatSPN with heuristic : META
[2020-05-22 06:25:50] [INFO ] Time to serialize gal into /home/mcc/execution/LTLFireability.pnml.gal : 54 ms
[2020-05-22 06:25:50] [INFO ] Time to serialize properties into /home/mcc/execution/LTLFireability.ltl : 1 ms
Invoking ITS tools like this :CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202005100927/bin/its-ltl-linux64, --gc-threshold, 2000000, -i, /home/mcc/execution/LTLFireability.pnml.gal, -t, CGAL, -LTL, /home/mcc/execution/LTLFireability.ltl, -c, -stutter-deadlock, --load-order, /home/mcc/execution/model.ord, --gen-order, FOLLOW], workingDir=/home/mcc/execution]

its-ltl command run as :

/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202005100927/bin/its-ltl-linux64 --gc-threshold 2000000 -i /home/mcc/execution/LTLFireability.pnml.gal -t CGAL -LTL /home/mcc/execution/LTLFireability.ltl -c -stutter-deadlock --load-order /home/mcc/execution/model.ord --gen-order FOLLOW
Read 13 LTL properties
Successfully loaded order from file /home/mcc/execution/model.ord
Checking formula 0 : !((X((X(G((((X("(cAMP__5_5_>=1)"))||(X("(cAMP__36_33_>=1)")))||("(cAMP__37_8_>=1)"))||("(cAMP__4_16_>=1)"))))||(F("(cAMP__36_33_>=1)")))))
Formula 0 simplified : !X(XG("(cAMP__4_16_>=1)" | "(cAMP__37_8_>=1)" | X"(cAMP__5_5_>=1)" | X"(cAMP__36_33_>=1)") | F"(cAMP__36_33_>=1)")
Reverse transition relation is exact ! Faster fixpoint algorithm enabled.

BK_TIME_CONFINEMENT_REACHED

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

+ export BINDIR=/home/mcc/BenchKit/
+ BINDIR=/home/mcc/BenchKit/
++ pwd
+ export MODEL=/home/mcc/execution
+ MODEL=/home/mcc/execution
+ [[ LTLFireability = StateSpace ]]
+ /home/mcc/BenchKit//runeclipse.sh /home/mcc/execution LTLFireability -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -greatspnpath /home/mcc/BenchKit//greatspn/ -order META -manyOrder -smt -timeout 3600
+ ulimit -s 65536
+ [[ -z '' ]]
+ export LTSMIN_MEM_SIZE=8589934592
+ LTSMIN_MEM_SIZE=8589934592
+ /home/mcc/BenchKit//itstools/its-tools -data /home/mcc/execution/workspace -pnfolder /home/mcc/execution -examination LTLFireability -z3path /home/mcc/BenchKit//z3/bin/z3 -yices2path /home/mcc/BenchKit//yices/bin/yices -its -ltsminpath /home/mcc/BenchKit//lts_install_dir/ -greatspnpath /home/mcc/BenchKit//greatspn/ -order META -manyOrder -smt -timeout 3600 -vmargs -Dosgi.locking=none -Declipse.stateSaveDelayInterval=-1 -Dosgi.configuration.area=/tmp/.eclipse -Xss128m -Xms40m -Xmx16000m -Dfile.encoding=UTF-8 -Dosgi.requiredJavaVersion=1.6

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="Diffusion2D-PT-D50N010"
export BK_EXAMINATION="LTLFireability"
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

# this is for BenchKit: explicit launching of the test
echo "====================================================================="
echo " Generated by BenchKit 2-4028"
echo " Executing tool itstools"
echo " Input is Diffusion2D-PT-D50N010, examination is LTLFireability"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 4"
echo " Run identifier is r066-tajo-158922814500554"
echo "====================================================================="
echo
echo "--------------------"
echo "preparation of the directory to be used:"

tar xzf /home/mcc/BenchKit/INPUTS/Diffusion2D-PT-D50N010.tgz
mv Diffusion2D-PT-D50N010 execution
cd execution
if [ "LTLFireability" = "ReachabilityDeadlock" ] || [ "LTLFireability" = "UpperBounds" ] || [ "LTLFireability" = "QuasiLiveness" ] || [ "LTLFireability" = "StableMarking" ] || [ "LTLFireability" = "Liveness" ] || [ "LTLFireability" = "OneSafe" ] || [ "LTLFireability" = "StateSpace" ]; then
rm -f GenericPropertiesVerdict.xml
fi
pwd
ls -lh

echo
echo "--------------------"
echo "content from stdout:"
echo
echo "=== Data for post analysis generated by BenchKit (invocation template)"
echo
if [ "LTLFireability" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "LTLFireability" != "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 "LTLFireability.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property LTLFireability.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -f "LTLFireability.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 '' LTLFireability.xml | cut -d '>' -f 2 | cut -d '<' -f 1 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ "LTLFireability" = "ReachabilityDeadlock" ] || [ "LTLFireability" = "QuasiLiveness" ] || [ "LTLFireability" = "StableMarking" ] || [ "LTLFireability" = "Liveness" ] || [ "LTLFireability" = "OneSafe" ] ; then
echo "FORMULA_NAME LTLFireability"
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 ;