Execution Chart

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

Trace from the execution

Formatting '/data/fkordon/mcc2023-input.r005-oct2-167813593000357.qcow2', fmt=qcow2 cluster_size=65536 extended_l2=off compression_type=zlib size=4294967296 backing_file=/data/fkordon/mcc2023-input.qcow2 backing_fmt=qcow2 lazy_refcounts=off refcount_bits=16
Waiting for the VM to be ready (probing ssh)
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=====================================================================
Generated by BenchKit 2-5348
Executing tool itstools
Input is Angiogenesis-PT-25, examination is UpperBounds
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r005-oct2-167813593000357
=====================================================================

--------------------
preparation of the directory to be used:
/home/mcc/execution
total 500K
-rw-r--r-- 1 mcc users 7.8K Feb 26 14:50 CTLCardinality.txt
-rw-r--r-- 1 mcc users 77K Feb 26 14:50 CTLCardinality.xml
-rw-r--r-- 1 mcc users 5.5K Feb 26 14:49 CTLFireability.txt
-rw-r--r-- 1 mcc users 52K Feb 26 14:49 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.2K Jan 29 11:40 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 4.1K Feb 25 15:31 LTLCardinality.txt
-rw-r--r-- 1 mcc users 25K Feb 25 15:31 LTLCardinality.xml
-rw-r--r-- 1 mcc users 2.2K Feb 25 15:31 LTLFireability.txt
-rw-r--r-- 1 mcc users 17K Feb 25 15:31 LTLFireability.xml
-rw-r--r-- 1 mcc users 16K Feb 26 14:51 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 148K Feb 26 14:51 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 6.5K Feb 26 14:50 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 53K Feb 26 14:50 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K Feb 25 15:31 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K Feb 25 15:31 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 Mar 5 18:22 equiv_col
-rw-r--r-- 1 mcc users 3 Mar 5 18:22 instance
-rw-r--r-- 1 mcc users 6 Mar 5 18:22 iscolored
-rw-r--r-- 1 mcc users 33K Mar 5 18:22 model.pnml

--------------------
content from stdout:

=== Data for post analysis generated by BenchKit (invocation template)

The expected result is a vector of positive values
NUM_VECTOR

here is the order used to build the result vector(from text file)
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-00
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-01
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-02
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-03
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-04
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-05
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-06
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-07
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-08
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-09
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-10
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-11
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-12
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-13
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-14
FORMULA_NAME Angiogenesis-PT-25-UpperBounds-15

=== Now, execution of the tool begins

BK_START 1678510673622

bash -c /home/mcc/BenchKit/BenchKit_head.sh 2> STDERR ; echo ; echo -n "BK_STOP " ; date -u +%s%3N
Invoking MCC driver with
BK_TOOL=itstools
BK_EXAMINATION=UpperBounds
BK_BIN_PATH=/home/mcc/BenchKit/bin/
BK_TIME_CONFINEMENT=3600
BK_INPUT=Angiogenesis-PT-25
Not applying reductions.
Model is PT
UpperBounds PT
Running Version 202303021504
[2023-03-11 04:57:56] [INFO ] Running its-tools with arguments : [-pnfolder, /home/mcc/execution, -examination, UpperBounds, -its, -ltsmin, -greatspnpath, /home/mcc/BenchKit/bin//../itstools/bin//..//greatspn/, -order, META, -manyOrder, -smt, -timeout, 3600]
[2023-03-11 04:57:56] [INFO ] Parsing pnml file : /home/mcc/execution/model.pnml
[2023-03-11 04:57:56] [INFO ] Load time of PNML (sax parser for PT used): 35 ms
[2023-03-11 04:57:56] [INFO ] Transformed 39 places.
[2023-03-11 04:57:56] [INFO ] Transformed 64 transitions.
[2023-03-11 04:57:56] [INFO ] Parsed PT model containing 39 places and 64 transitions and 185 arcs in 116 ms.
Parsed 16 properties from file /home/mcc/execution/UpperBounds.xml in 5 ms.
// Phase 1: matrix 64 rows 39 cols
[2023-03-11 04:57:56] [INFO ] Computed 8 place invariants in 5 ms
FORMULA Angiogenesis-PT-25-UpperBounds-15 25 TECHNIQUES TOPOLOGICAL INITIAL_STATE
FORMULA Angiogenesis-PT-25-UpperBounds-14 25 TECHNIQUES TOPOLOGICAL INITIAL_STATE
Incomplete random walk after 10020 steps, including 2 resets, run finished after 11 ms. (steps per millisecond=910 ) properties (out of 14) seen :250
FORMULA Angiogenesis-PT-25-UpperBounds-13 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-12 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-10 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-09 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-08 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-07 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-05 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-04 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-03 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-02 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
Incomplete Best-First random walk after 10001 steps, including 2 resets, run finished after 12 ms. (steps per millisecond=833 ) properties (out of 4) seen :4
Incomplete Best-First random walk after 10001 steps, including 2 resets, run finished after 22 ms. (steps per millisecond=454 ) properties (out of 4) seen :4
Incomplete Best-First random walk after 10001 steps, including 2 resets, run finished after 8 ms. (steps per millisecond=1250 ) properties (out of 4) seen :6
Incomplete Best-First random walk after 10001 steps, including 2 resets, run finished after 7 ms. (steps per millisecond=1428 ) properties (out of 4) seen :4
[2023-03-11 04:57:56] [INFO ] Invariant cache hit.
[2023-03-11 04:57:56] [INFO ] [Real]Absence check using 8 positive place invariants in 21 ms returned sat
[2023-03-11 04:57:56] [INFO ] [Real]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:56] [INFO ] [Real]Absence check using state equation in 96 ms returned sat
[2023-03-11 04:57:56] [INFO ] Computed and/alt/rep : 59/142/59 causal constraints (skipped 2 transitions) in 11 ms.
[2023-03-11 04:57:56] [INFO ] Solution in real domain found non-integer solution.
[2023-03-11 04:57:57] [INFO ] [Nat]Absence check using 8 positive place invariants in 10 ms returned sat
[2023-03-11 04:57:57] [INFO ] [Nat]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:57] [INFO ] [Nat]Absence check using state equation in 46 ms returned sat
[2023-03-11 04:57:57] [INFO ] Computed and/alt/rep : 59/142/59 causal constraints (skipped 2 transitions) in 6 ms.
[2023-03-11 04:57:57] [INFO ] Added : 52 causal constraints over 11 iterations in 140 ms. Result :sat
Minimization took 39 ms.
[2023-03-11 04:57:57] [INFO ] [Real]Absence check using 8 positive place invariants in 3 ms returned sat
[2023-03-11 04:57:57] [INFO ] [Real]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:57] [INFO ] [Real]Absence check using state equation in 16 ms returned sat
[2023-03-11 04:57:57] [INFO ] Computed and/alt/rep : 59/142/59 causal constraints (skipped 2 transitions) in 5 ms.
[2023-03-11 04:57:57] [INFO ] Solution in real domain found non-integer solution.
[2023-03-11 04:57:57] [INFO ] [Nat]Absence check using 8 positive place invariants in 2 ms returned sat
[2023-03-11 04:57:57] [INFO ] [Nat]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:57] [INFO ] [Nat]Absence check using state equation in 15 ms returned sat
[2023-03-11 04:57:57] [INFO ] Computed and/alt/rep : 59/142/59 causal constraints (skipped 2 transitions) in 5 ms.
[2023-03-11 04:57:57] [INFO ] Added : 52 causal constraints over 11 iterations in 73 ms. Result :sat
Minimization took 45 ms.
[2023-03-11 04:57:57] [INFO ] [Real]Absence check using 8 positive place invariants in 2 ms returned sat
[2023-03-11 04:57:57] [INFO ] [Real]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:57] [INFO ] [Real]Absence check using state equation in 84 ms returned sat
[2023-03-11 04:57:57] [INFO ] Computed and/alt/rep : 59/142/59 causal constraints (skipped 2 transitions) in 4 ms.
[2023-03-11 04:57:57] [INFO ] Solution in real domain found non-integer solution.
[2023-03-11 04:57:57] [INFO ] [Nat]Absence check using 8 positive place invariants in 4 ms returned sat
[2023-03-11 04:57:57] [INFO ] [Nat]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:57] [INFO ] [Nat]Absence check using state equation in 13 ms returned sat
[2023-03-11 04:57:57] [INFO ] Computed and/alt/rep : 59/142/59 causal constraints (skipped 2 transitions) in 5 ms.
[2023-03-11 04:57:57] [INFO ] Added : 52 causal constraints over 11 iterations in 153 ms. Result :sat
Minimization took 36 ms.
[2023-03-11 04:57:57] [INFO ] [Real]Absence check using 8 positive place invariants in 2 ms returned sat
[2023-03-11 04:57:57] [INFO ] [Real]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:58] [INFO ] [Real]Absence check using state equation in 33 ms returned sat
[2023-03-11 04:57:58] [INFO ] Computed and/alt/rep : 59/142/59 causal constraints (skipped 2 transitions) in 7 ms.
[2023-03-11 04:57:58] [INFO ] Solution in real domain found non-integer solution.
[2023-03-11 04:57:58] [INFO ] [Nat]Absence check using 8 positive place invariants in 2 ms returned sat
[2023-03-11 04:57:58] [INFO ] [Nat]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:58] [INFO ] [Nat]Absence check using state equation in 25 ms returned sat
[2023-03-11 04:57:58] [INFO ] Computed and/alt/rep : 59/142/59 causal constraints (skipped 2 transitions) in 5 ms.
[2023-03-11 04:57:58] [INFO ] Added : 52 causal constraints over 11 iterations in 110 ms. Result :sat
Minimization took 38 ms.
Current structural bounds on expressions (after SMT) : [25, 25, 25, 25] Max seen :[3, 2, 4, 1]
FORMULA Angiogenesis-PT-25-UpperBounds-11 25 TECHNIQUES TOPOLOGICAL PARIKH_WALK
FORMULA Angiogenesis-PT-25-UpperBounds-00 25 TECHNIQUES TOPOLOGICAL PARIKH_WALK
Support contains 2 out of 39 places. Attempting structural reductions.
Starting structural reductions in REACHABILITY mode, iteration 0 : 39/39 places, 64/64 transitions.
Graph (complete) has 117 edges and 39 vertex of which 38 are kept as prefixes of interest. Removing 1 places using SCC suffix rule.1 ms
Discarding 1 places :
Also discarding 0 output transitions
Performed 1 Pre agglomeration using Quasi-Persistent + Divergent Free condition..
Pre-agglomeration after 0 with 1 Pre rules applied. Total rules applied 1 place count 38 transition count 63
Deduced a syphon composed of 1 places in 1 ms
Reduce places removed 2 places and 0 transitions.
Iterating global reduction 0 with 3 rules applied. Total rules applied 4 place count 36 transition count 63
Drop transitions removed 1 transitions
Reduce isomorphic transitions removed 1 transitions.
Iterating post reduction 0 with 1 rules applied. Total rules applied 5 place count 36 transition count 62
Performed 9 Post agglomeration using F-continuation condition.Transition count delta: 9
Deduced a syphon composed of 9 places in 0 ms
Reduce places removed 9 places and 0 transitions.
Iterating global reduction 1 with 18 rules applied. Total rules applied 23 place count 27 transition count 53
Drop transitions removed 8 transitions
Reduce isomorphic transitions removed 8 transitions.
Graph (complete) has 82 edges and 27 vertex of which 26 are kept as prefixes of interest. Removing 1 places using SCC suffix rule.0 ms
Discarding 1 places :
Also discarding 0 output transitions
Iterating post reduction 1 with 9 rules applied. Total rules applied 32 place count 26 transition count 45
Drop transitions removed 1 transitions
Reduce isomorphic transitions removed 1 transitions.
Iterating post reduction 2 with 1 rules applied. Total rules applied 33 place count 26 transition count 44
Performed 4 Post agglomeration using F-continuation condition.Transition count delta: -3
Deduced a syphon composed of 4 places in 0 ms
Reduce places removed 4 places and 0 transitions.
Iterating global reduction 3 with 8 rules applied. Total rules applied 41 place count 22 transition count 47
Drop transitions removed 7 transitions
Reduce isomorphic transitions removed 7 transitions.
Iterating post reduction 3 with 7 rules applied. Total rules applied 48 place count 22 transition count 40
Drop transitions removed 5 transitions
Redundant transition composition rules discarded 5 transitions
Iterating global reduction 4 with 5 rules applied. Total rules applied 53 place count 22 transition count 35
Free-agglomeration rule (complex) applied 5 times.
Iterating global reduction 4 with 5 rules applied. Total rules applied 58 place count 22 transition count 30
Reduce places removed 5 places and 0 transitions.
Drop transitions removed 2 transitions
Reduce isomorphic transitions removed 2 transitions.
Iterating post reduction 4 with 7 rules applied. Total rules applied 65 place count 17 transition count 28
Applied a total of 65 rules in 40 ms. Remains 17 /39 variables (removed 22) and now considering 28/64 (removed 36) transitions.
Finished structural reductions in REACHABILITY mode , in 1 iterations and 40 ms. Remains : 17/39 places, 28/64 transitions.
Normalized transition count is 27 out of 28 initially.
// Phase 1: matrix 27 rows 17 cols
[2023-03-11 04:57:58] [INFO ] Computed 6 place invariants in 1 ms
Incomplete random walk after 1000000 steps, including 958 resets, run finished after 323 ms. (steps per millisecond=3095 ) properties (out of 2) seen :49
FORMULA Angiogenesis-PT-25-UpperBounds-06 25 TECHNIQUES TOPOLOGICAL RANDOM_WALK
Incomplete Best-First random walk after 1000000 steps, including 19 resets, run finished after 584 ms. (steps per millisecond=1712 ) properties (out of 1) seen :11
[2023-03-11 04:57:59] [INFO ] Flow matrix only has 27 transitions (discarded 1 similar events)
// Phase 1: matrix 27 rows 17 cols
[2023-03-11 04:57:59] [INFO ] Computed 6 place invariants in 1 ms
[2023-03-11 04:57:59] [INFO ] [Real]Absence check using 6 positive place invariants in 1 ms returned sat
[2023-03-11 04:57:59] [INFO ] [Real]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:59] [INFO ] [Real]Absence check using state equation in 25 ms returned sat
[2023-03-11 04:57:59] [INFO ] Solution in real domain found non-integer solution.
[2023-03-11 04:57:59] [INFO ] [Nat]Absence check using 6 positive place invariants in 2 ms returned sat
[2023-03-11 04:57:59] [INFO ] [Nat]Adding state equation constraints to refine reachable states.
[2023-03-11 04:57:59] [INFO ] [Nat]Absence check using state equation in 146 ms returned sat
[2023-03-11 04:57:59] [INFO ] State equation strengthened by 1 read => feed constraints.
[2023-03-11 04:57:59] [INFO ] [Nat]Added 1 Read/Feed constraints in 1 ms returned sat
[2023-03-11 04:57:59] [INFO ] Deduced a trap composed of 9 places in 56 ms of which 19 ms to minimize.
[2023-03-11 04:57:59] [INFO ] Trap strengthening procedure managed to obtain unsat after adding 1 trap constraints in 75 ms
Current structural bounds on expressions (after SMT) : [24] Max seen :[24]
FORMULA Angiogenesis-PT-25-UpperBounds-01 24 TECHNIQUES TOPOLOGICAL SAT_SMT RANDOM_WALK
All properties solved without resorting to model-checking.
Total runtime 3492 ms.

BK_STOP 1678510680078

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

+ export BINDIR=/home/mcc/BenchKit/bin//../itstools/bin//../
+ BINDIR=/home/mcc/BenchKit/bin//../itstools/bin//../
++ pwd
+ export MODEL=/home/mcc/execution
+ MODEL=/home/mcc/execution
+ [[ UpperBounds = StateSpace ]]
+ /home/mcc/BenchKit/bin//../itstools/bin//..//runeclipse.sh /home/mcc/execution UpperBounds -its -ltsmin -greatspnpath /home/mcc/BenchKit/bin//../itstools/bin//..//greatspn/ -order META -manyOrder -smt -timeout 3600
+ ulimit -s 65536
+ [[ -z '' ]]
+ export LTSMIN_MEM_SIZE=8589934592
+ LTSMIN_MEM_SIZE=8589934592
+ export PYTHONPATH=/home/mcc/BenchKit/itstools/pylibs
+ PYTHONPATH=/home/mcc/BenchKit/itstools/pylibs
+ export LD_LIBRARY_PATH=/home/mcc/BenchKit/itstools/pylibs:
+ LD_LIBRARY_PATH=/home/mcc/BenchKit/itstools/pylibs:
++ sed s/.jar//
++ perl -pe 's/.*\.//g'
++ ls /home/mcc/BenchKit/bin//../itstools/bin//..//itstools/plugins/fr.lip6.move.gal.application.pnmcc_1.0.0.202303021504.jar
+ VERSION=202303021504
+ echo 'Running Version 202303021504'
+ /home/mcc/BenchKit/bin//../itstools/bin//..//itstools/its-tools -pnfolder /home/mcc/execution -examination UpperBounds -its -ltsmin -greatspnpath /home/mcc/BenchKit/bin//../itstools/bin//..//greatspn/ -order META -manyOrder -smt -timeout 3600

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-25"
export BK_EXAMINATION="UpperBounds"
export BK_TOOL="itstools"
export BK_RESULT_DIR="/tmp/BK_RESULTS/OUTPUTS"
export BK_TIME_CONFINEMENT="3600"
export BK_MEMORY_CONFINEMENT="16384"
export BK_BIN_PATH="/home/mcc/BenchKit/bin/"

# 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 2-5348"
echo " Executing tool itstools"
echo " Input is Angiogenesis-PT-25, examination is UpperBounds"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 4"
echo " Run identifier is r005-oct2-167813593000357"
echo "====================================================================="
echo
echo "--------------------"
echo "preparation of the directory to be used:"

tar xzf /home/mcc/BenchKit/INPUTS/Angiogenesis-PT-25.tgz
mv Angiogenesis-PT-25 execution
cd execution
if [ "UpperBounds" = "ReachabilityDeadlock" ] || [ "UpperBounds" = "UpperBounds" ] || [ "UpperBounds" = "QuasiLiveness" ] || [ "UpperBounds" = "StableMarking" ] || [ "UpperBounds" = "Liveness" ] || [ "UpperBounds" = "OneSafe" ] || [ "UpperBounds" = "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 [ "UpperBounds" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "UpperBounds" != "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 "UpperBounds.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property UpperBounds.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -f "UpperBounds.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 '' UpperBounds.xml | cut -d '>' -f 2 | cut -d '<' -f 1 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ "UpperBounds" = "ReachabilityDeadlock" ] || [ "UpperBounds" = "QuasiLiveness" ] || [ "UpperBounds" = "StableMarking" ] || [ "UpperBounds" = "Liveness" ] || [ "UpperBounds" = "OneSafe" ] ; then
echo "FORMULA_NAME UpperBounds"
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 ;