Execution Chart

Sorry, for this execution, no execution chart could be reported.

Trace from the execution

Formatting '/data/fkordon/mcc2025-input.r002-tall-174853728800224.qcow2', fmt=qcow2 size=4294967296 backing_file=/data/fkordon/mcc2025-input.qcow2 backing_fmt=qcow2 cluster_size=65536 lazy_refcounts=off refcount_bits=16
Waiting for the VM to be ready (probing ssh)
.....................................................................
=====================================================================
Generated by BenchKit 2-5832
Executing tool itstools
Input is Angiogenesis-PT-01, examination is StateSpace
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r002-tall-174853728800224
=====================================================================

--------------------
preparation of the directory to be used:
/home/mcc/execution
total 440K
-rw-r--r-- 1 mcc users 8.4K May 29 14:47 CTLCardinality.txt
-rw-r--r-- 1 mcc users 79K May 29 14:47 CTLCardinality.xml
-rw-r--r-- 1 mcc users 5.8K May 29 14:47 CTLFireability.txt
-rw-r--r-- 1 mcc users 54K May 29 14:47 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.2K May 29 14:32 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 4.1K May 29 14:47 LTLCardinality.txt
-rw-r--r-- 1 mcc users 27K May 29 14:47 LTLCardinality.xml
-rw-r--r-- 1 mcc users 2.2K May 29 14:47 LTLFireability.txt
-rw-r--r-- 1 mcc users 19K May 29 14:47 LTLFireability.xml
-rw-r--r-- 1 mcc users 12K May 29 14:47 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 105K May 29 14:47 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 4.5K May 29 14:47 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 30K May 29 14:47 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.7K May 29 14:47 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K May 29 14:47 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 May 29 14:32 equiv_col
-rw-r--r-- 1 mcc users 3 May 29 14:32 instance
-rw-r--r-- 1 mcc users 6 May 29 14:32 iscolored
-rw-r--r-- 1 mcc users 34K May 29 14:32 model.pnml

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

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

no data necessary for post analysis


=== Now, execution of the tool begins

BK_START 1748557537647

Invoking MCC driver with
BK_TOOL=itstools
BK_EXAMINATION=StateSpace
BK_BIN_PATH=/home/mcc/BenchKit/bin/
BK_TIME_CONFINEMENT=3600
BK_INPUT=Angiogenesis-PT-01
BK_MEMORY_CONFINEMENT=16384
Not applying reductions.
Model is PT
StateSpace PT
Running Version 202505121319
[2025-05-29 22:25:38] [INFO ] Running its-tools with arguments : [-pnfolder, /home/mcc/execution, -examination, StateSpace, -its, -ltsmin, -greatspnpath, /home/mcc/BenchKit/bin//../itstools/bin//..//greatspn/, -order, META, -manyOrder, -smt, -timeout, 3600]
[2025-05-29 22:25:38] [INFO ] Parsing pnml file : /home/mcc/execution/model.pnml
[2025-05-29 22:25:38] [INFO ] Load time of PNML (sax parser for PT used): 49 ms
[2025-05-29 22:25:38] [INFO ] Transformed 39 places.
[2025-05-29 22:25:38] [INFO ] Transformed 64 transitions.
[2025-05-29 22:25:38] [INFO ] Found NUPN structural information;
[2025-05-29 22:25:38] [INFO ] Parsed PT model containing 39 places and 64 transitions and 185 arcs in 135 ms.
Starting structural reductions in STATESPACE mode, iteration 0 : 39/39 places, 64/64 transitions.
Starting Z3 with timeout 200.0 s and query timeout 20000.0 ms
[2025-05-29 22:25:39] [INFO ] Redundant transitions in 2 ms returned []
Running 61 sub problems to find dead transitions.
// Phase 1: matrix 64 rows 39 cols
[2025-05-29 22:25:39] [INFO ] Computed 8 invariants in 10 ms
Starting Z3 with timeout 30.0 s and query timeout 3000.0 ms
At refinement iteration 0 (INCLUDED_ONLY) 0/38 variables, 38/38 constraints. Problems are: Problem set: 0 solved, 61 unsolved
Problem TDEAD18 is UNSAT
Problem TDEAD19 is UNSAT
Problem TDEAD20 is UNSAT
Problem TDEAD41 is UNSAT
Problem TDEAD42 is UNSAT
Problem TDEAD43 is UNSAT
Problem TDEAD54 is UNSAT
Problem TDEAD55 is UNSAT
Problem TDEAD57 is UNSAT
At refinement iteration 1 (INCLUDED_ONLY) 0/38 variables, 7/45 constraints. Problems are: Problem set: 9 solved, 52 unsolved
Starting Z3 with timeout 120.0 s and query timeout 12000.0 ms
[2025-05-29 22:25:39] [INFO ] Deduced a trap composed of 23 places in 50 ms of which 7 ms to minimize.
Problem TDEAD23 is UNSAT
Problem TDEAD34 is UNSAT
Problem TDEAD45 is UNSAT
Problem TDEAD56 is UNSAT
Problem TDEAD61 is UNSAT
At refinement iteration 2 (INCLUDED_ONLY) 0/38 variables, 1/46 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 3 (INCLUDED_ONLY) 0/38 variables, 0/46 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 4 (OVERLAPS) 1/39 variables, 1/47 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 5 (INCLUDED_ONLY) 0/39 variables, 1/48 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 6 (INCLUDED_ONLY) 0/39 variables, 0/48 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 7 (OVERLAPS) 64/103 variables, 39/87 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 8 (INCLUDED_ONLY) 0/103 variables, 0/87 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 9 (OVERLAPS) 0/103 variables, 0/87 constraints. Problems are: Problem set: 14 solved, 47 unsolved
No progress, stopping.
After SMT solving in domain Real declared 103/103 variables, and 87 constraints, problems are : Problem set: 14 solved, 47 unsolved in 1406 ms.
Refiners :[Domain max(s): 39/39 constraints, Positive P Invariants (semi-flows): 8/8 constraints, State Equation: 39/39 constraints, PredecessorRefiner: 61/61 constraints, Known Traps: 1/1 constraints, Known Traps Along Path: 0/0 constraints]
Escalating to Integer solving :Problem set: 14 solved, 47 unsolved
Starting Z3 with timeout 30.0 s and query timeout 3000.0 ms
At refinement iteration 0 (INCLUDED_ONLY) 0/30 variables, 30/30 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 1 (INCLUDED_ONLY) 0/30 variables, 1/31 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 2 (INCLUDED_ONLY) 0/30 variables, 0/31 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 3 (OVERLAPS) 9/39 variables, 7/38 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 4 (INCLUDED_ONLY) 0/39 variables, 9/47 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 5 (INCLUDED_ONLY) 0/39 variables, 1/48 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 6 (INCLUDED_ONLY) 0/39 variables, 0/48 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 7 (OVERLAPS) 64/103 variables, 39/87 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 8 (INCLUDED_ONLY) 0/103 variables, 47/134 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 9 (INCLUDED_ONLY) 0/103 variables, 0/134 constraints. Problems are: Problem set: 14 solved, 47 unsolved
At refinement iteration 10 (OVERLAPS) 0/103 variables, 0/134 constraints. Problems are: Problem set: 14 solved, 47 unsolved
No progress, stopping.
After SMT solving in domain Int declared 103/103 variables, and 134 constraints, problems are : Problem set: 14 solved, 47 unsolved in 2442 ms.
Refiners :[Domain max(s): 39/39 constraints, Positive P Invariants (semi-flows): 8/8 constraints, State Equation: 39/39 constraints, PredecessorRefiner: 47/61 constraints, Known Traps: 1/1 constraints, Known Traps Along Path: 0/0 constraints]
After SMT, in 3921ms problems are : Problem set: 14 solved, 47 unsolved
Search for dead transitions found 14 dead transitions in 3930ms
Found 14 dead transitions using SMT.
Drop transitions (Dead Transitions using SMT only with invariants) removed 14 transitions
Dead transitions reduction (with SMT) removed 14 transitions
Starting structural reductions in STATESPACE mode, iteration 1 : 39/39 places, 50/64 transitions.
Reduce places removed 5 places and 0 transitions.
Starting structural reductions in STATESPACE mode, iteration 2 : 34/39 places, 50/64 transitions.
Finished structural reductions in STATESPACE mode , in 2 iterations and 4038 ms. Remains : 34/39 places, 50/64 transitions.
Final net has 34 places and 50 transitions.
[2025-05-29 22:25:43] [INFO ] Flatten gal took : 24 ms
[2025-05-29 22:25:43] [INFO ] Applying decomposition
[2025-05-29 22:25:43] [INFO ] Flatten gal took : 6 ms
Converted graph to binary with : '/home/mcc/BenchKit/itstools/itstools/plugins/fr.lip6.move.gal.louvain.binaries_1.0.0.202505121319/bin/convert-linux64' '-i' '/tmp/graph8924878085441697884.txt' '-o' '/tmp/graph8924878085441697884.bin' '-w' '/tmp/graph8924878085441697884.weights'
Built communities with : '/home/mcc/BenchKit/itstools/itstools/plugins/fr.lip6.move.gal.louvain.binaries_1.0.0.202505121319/bin/louvain-linux64' '/tmp/graph8924878085441697884.bin' '-l' '-1' '-v' '-w' '/tmp/graph8924878085441697884.weights' '-q' '0' '-e' '0.001'
[2025-05-29 22:25:43] [INFO ] Decomposing Gal with order
[2025-05-29 22:25:43] [INFO ] Rewriting arrays to variables to allow decomposition.
[2025-05-29 22:25:43] [INFO ] Removed a total of 28 redundant transitions.
[2025-05-29 22:25:43] [INFO ] Flatten gal took : 57 ms
[2025-05-29 22:25:43] [INFO ] Fuse similar labels procedure discarded/fused a total of 8 labels/synchronizations in 3 ms.
[2025-05-29 22:25:43] [INFO ] Time to serialize gal into /tmp/StateSpace16404249007023908888.gal : 3 ms
Invoking ITS tools like this :cd /home/mcc/execution;'/home/mcc/BenchKit/itstools/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202505121319/bin/its-reach-linux64' '--gc-threshold' '2000000' '--quiet' '-i' '/tmp/StateSpace16404249007023908888.gal' '-t' 'CGAL' '--stats'

its-reach command run as :

/home/mcc/BenchKit/itstools/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.202505121319/bin/its-reach-linux64 --gc-threshold 2000000 --quiet ...220
Model ,|S| ,Time ,Mem(kb) ,fin. SDD ,fin. DDD ,peak SDD ,peak DDD ,SDD Hom ,SDD cache peak ,DDD Hom ,DDD cachepeak ,SHom cache
petri\_inst\_inst\_mod\_flat,110,0.022006,4196,82,19,422,78,173,413,43,124,0
Total reachable state count : 110

Max variable value : 1
STATE_SPACE MAX_TOKEN_IN_PLACE 1 TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
Maximum sum along a path : 8
STATE_SPACE MAX_TOKEN_PER_MARKING 8 TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
Exact state count : 110
STATE_SPACE STATES 110 TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
Total runtime 5074 ms.

BK_STOP 1748557543922

--------------------
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
+ [[ StateSpace = StateSpace ]]
+ [[ -f modelMain.xml ]]
+ /home/mcc/BenchKit/bin//../itstools/bin//..//runeclipse.sh /home/mcc/execution StateSpace -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
++ sed s/.jar//
++ perl -pe 's/.*\.//g'
++ ls /home/mcc/BenchKit/bin//../itstools/bin//..//itstools/plugins/fr.lip6.move.gal.application.pnmcc_1.0.0.202505121319.jar
+ VERSION=202505121319
+ echo 'Running Version 202505121319'
+ /home/mcc/BenchKit/bin//../itstools/bin//..//itstools/its-tools -pnfolder /home/mcc/execution -examination StateSpace -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-01"
export BK_EXAMINATION="StateSpace"
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 2-5832"
echo " Executing tool itstools"
echo " Input is Angiogenesis-PT-01, examination is StateSpace"
echo " Time confinement is $BK_TIME_CONFINEMENT seconds"
echo " Memory confinement is 16384 MBytes"
echo " Number of cores is 4"
echo " Run identifier is r002-tall-174853728800224"
echo "====================================================================="
echo
echo "--------------------"
echo "preparation of the directory to be used:"

tar xzf /home/mcc/BenchKit/INPUTS/Angiogenesis-PT-01.tgz
mv Angiogenesis-PT-01 execution
cd execution
if [ "StateSpace" = "ReachabilityDeadlock" ] || [ "StateSpace" = "UpperBounds" ] || [ "StateSpace" = "QuasiLiveness" ] || [ "StateSpace" = "StableMarking" ] || [ "StateSpace" = "Liveness" ] || [ "StateSpace" = "OneSafe" ] || [ "StateSpace" = "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 [ "StateSpace" = "UpperBounds" ] ; then
echo "The expected result is a vector of positive values"
echo NUM_VECTOR
elif [ "StateSpace" != "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 "StateSpace.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 '' StateSpace.xml | cut -d '>' -f 2 | cut -d '<' -f 1 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ "StateSpace" = "ReachabilityDeadlock" ] || [ "StateSpace" = "QuasiLiveness" ] || [ "StateSpace" = "StableMarking" ] || [ "StateSpace" = "Liveness" ] || [ "StateSpace" = "OneSafe" ] ; then
echo "FORMULA_NAME StateSpace"
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 ;