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 204K
-rw-r--r-- 1 mcc users 3.5K May 15 18:54 CTLCardinality.txt
-rw-r--r-- 1 mcc users 19K May 15 18:54 CTLCardinality.xml
-rw-r--r-- 1 mcc users 2.8K May 15 18:54 CTLFireability.txt
-rw-r--r-- 1 mcc users 14K May 15 18:54 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K May 15 18:50 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 5.7K May 15 18:50 GenericPropertiesVerdict.xml
-rw-r--r-- 1 mcc users 2.4K May 15 18:54 LTLCardinality.txt
-rw-r--r-- 1 mcc users 11K May 15 18:54 LTLCardinality.xml
-rw-r--r-- 1 mcc users 2.3K May 15 18:54 LTLFireability.txt
-rw-r--r-- 1 mcc users 9.9K May 15 18:54 LTLFireability.xml
-rw-r--r-- 1 mcc users 4.1K May 15 18:54 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 22K May 15 18:54 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 115 May 15 18:54 ReachabilityDeadlock.txt
-rw-r--r-- 1 mcc users 353 May 15 18:54 ReachabilityDeadlock.xml
-rw-r--r-- 1 mcc users 4.1K May 15 18:54 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 21K 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 18:50 equiv_col
-rw-r--r-- 1 mcc users 17 May 15 18:50 instance
-rw-r--r-- 1 mcc users 6 May 15 18:50 iscolored
-rw-r--r-- 1 mcc users 21K May 15 18:50 model.pnml
=====================================================================
Generated by BenchKit 2-3637
Executing tool itstoolsl
Input is GPPP-PT-C0100N0000010000, examination is ReachabilityDeadlock
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r093-blw7-152650005600328
=====================================================================

--------------------
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 GPPP-PT-C0100N0000010000-ReachabilityDeadlock-0

=== Now, execution of the tool begins

BK_START 1527431343985

Flatten gal took : 34 ms
Performed 4 Post agglomeration using F-continuation condition.
Iterating post reduction 0 with 4 rules applied. Total rules applied 4 place count 33 transition count 18
Constant places removed 5 places and 0 transitions.
Performed 1 Post agglomeration using F-continuation condition.
Iterating post reduction 1 with 6 rules applied. Total rules applied 10 place count 28 transition count 17
Constant places removed 2 places and 0 transitions.
Iterating post reduction 2 with 2 rules applied. Total rules applied 12 place count 26 transition count 17
Performed 1 Post agglomeration using F-continuation condition.
Constant places removed 1 places and 0 transitions.
Iterating post reduction 3 with 1 rules applied. Total rules applied 13 place count 25 transition count 16
Performed 1 Post agglomeration using F-continuation condition.
Constant places removed 1 places and 0 transitions.
Iterating post reduction 4 with 1 rules applied. Total rules applied 14 place count 24 transition count 15
Applied a total of 14 rules in 8 ms. Remains 24 /33 variables (removed 9) and now considering 15/22 (removed 7) transitions.
// Phase 1: matrix 15 rows 24 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/graph4565095785981221249.txt, -o, /tmp/graph4565095785981221249.bin, -w, /tmp/graph4565095785981221249.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/graph4565095785981221249.bin, -l, -1, -v, -w, /tmp/graph4565095785981221249.weights, -q, 0, -e, 0.001], workingDir=null]
Presburger conditions satisfied. Using coverability to approximate state space in K-Induction.
// Phase 1: matrix 15 rows 24 cols
invariant :ATP + Ru5P + Xu5P + R5P + S7P + GAP + E4P + F6P + G6P + _1_3_BPG + -1'Pyr + -1'Lac = 40000
invariant :28'Ru5P + 21'Xu5P + 1428'R5P + 1435'S7P + 14'GAP + 21'E4P + 28'F6P + 28'G6P + 16'_1_3_BPG + 16'PEP + 16'Pyr + 16'Lac + 28'Gluc + -7'a2 + 2'c2 = 11200
invariant :NADplus + _1_3_BPG + PEP + Pyr = 20000
invariant :NADH + -1'_1_3_BPG + -1'PEP + -1'Pyr = 0
invariant :Pi + _1_3_BPG + PEP + Pyr + Lac = 700
invariant :2'Ru5P + -1051'Xu5P + 210602'R5P + 209851'S7P + -300'GAP + 151'E4P + -600'F6P + 2'b2 + -1053'a2 + 300'c2 = 0
invariant :-1'Ru5P + -1'Xu5P + -1'R5P + -1'S7P + -1'GAP + -1'E4P + -1'F6P + -1'G6P + -1'_1_3_BPG + ADP + Pyr + Lac = 700
invariant :a1 + a2 = 200
invariant :c1 + c2 = 700
invariant :-2'Ru5P + 1051'Xu5P + -210602'R5P + -209851'S7P + 300'GAP + -151'E4P + 600'F6P + 2'b1 + 1053'a2 + -300'c2 = 600
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 6 ordering constraints for composite.
built 4 ordering constraints for composite.
terminate called after throwing an instance of 'char const*'
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]
Compilation finished in 499 ms.
Running link step : CommandLine [args=[gcc, -shared, -o, gal.so, model.o], workingDir=/home/mcc/execution]
Link finished in 54 ms.
Running LTSmin : CommandLine [args=[/home/mcc/BenchKit//lts_install_dir//bin/pins2lts-mc, ./gal.so, --threads=1, -p, --pins-guards, --when, -d], workingDir=/home/mcc/execution]
WARNING : LTS min runner thread failed on error :java.lang.RuntimeException: Unexpected exception when executing ltsmin :CommandLine [args=[/home/mcc/BenchKit//lts_install_dir//bin/pins2lts-mc, ./gal.so, --threads=1, -p, --pins-guards, --when, -d], workingDir=/home/mcc/execution]
255

BK_STOP 1527431404691

--------------------
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 27, 2018 2:29:05 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 27, 2018 2:29:05 PM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
May 27, 2018 2:29:05 PM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 26 ms
May 27, 2018 2:29:05 PM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 33 places.
May 27, 2018 2:29:05 PM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 22 transitions.
May 27, 2018 2:29:05 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.img.gal : 5 ms
May 27, 2018 2:29:05 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 31 ms
May 27, 2018 2:29:05 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.simple.gal : 1 ms
May 27, 2018 2:29:05 PM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 22 transitions.
May 27, 2018 2:29:08 PM fr.lip6.move.gal.application.MccTranslator applyOrder
INFO: Applying decomposition
May 27, 2018 2:29:08 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 6 ms
May 27, 2018 2:29:08 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 6 ms
May 27, 2018 2:29:08 PM fr.lip6.move.gal.semantics.DeterministicNextBuilder getDeterministicNext
INFO: Input system was already deterministic with 15 transitions.
Begin: Sun May 27 14:29:08 2018

Computation of communities with the Newman-Girvan Modularity quality function

level 0:
start computation: Sun May 27 14:29:08 2018
network size: 24 nodes, 120 links, 28 weight
quality increased from -0.0501346 to 0.439466
end computation: Sun May 27 14:29:08 2018
level 1:
start computation: Sun May 27 14:29:08 2018
network size: 5 nodes, 19 links, 28 weight
quality increased from 0.439466 to 0.446358
end computation: Sun May 27 14:29:08 2018
level 2:
start computation: Sun May 27 14:29:08 2018
network size: 4 nodes, 14 links, 28 weight
quality increased from 0.446358 to 0.446358
end computation: Sun May 27 14:29:08 2018
End: Sun May 27 14:29:08 2018
Total duration: 0 sec
0.446358
May 27, 2018 2:29:08 PM fr.lip6.move.gal.instantiate.CompositeBuilder decomposeWithOrder
INFO: Decomposing Gal with order
May 27, 2018 2:29:08 PM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 9 ms
May 27, 2018 2:29:08 PM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver computeAndDeclareInvariants
INFO: Computed 10 place invariants in 5 ms
May 27, 2018 2:29:08 PM fr.lip6.move.gal.instantiate.CompositeBuilder rewriteArraysToAllowPartition
INFO: Rewriting arrays to variables to allow decomposition.
May 27, 2018 2:29:09 PM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/ReachabilityDeadlock.pnml.gal : 1 ms
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.KInductionSolver init
INFO: Proved 24 variables to be positive in 61 ms
ITS-tools command line returned an error code 134
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeAblingMatrix
INFO: Computing symmetric may disable matrix : 15 transitions.
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of disable matrix completed :0/15 took 0 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Complete disable matrix. took 0 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeAblingMatrix
INFO: Computing symmetric may enable matrix : 15 transitions.
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Complete enable matrix. took 0 ms. Total solver calls (SAT/UNSAT): 0(0/0)
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeCoEnablingMatrix
INFO: Computing symmetric co enabling matrix : 15 transitions.
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Finished co-enabling matrix. took 604 ms. Total solver calls (SAT/UNSAT): 105(91/14)
May 27, 2018 2:29:09 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver computeDoNotAccord
INFO: Computing Do-Not-Accords matrix : 15 transitions.
May 27, 2018 2:29:10 PM fr.lip6.move.gal.gal2smt.bmc.NecessaryEnablingsolver printStats
INFO: Computation of Completed DNA matrix. took 1191 ms. Total solver calls (SAT/UNSAT): 28(0/28)
May 27, 2018 2:29:10 PM fr.lip6.move.gal.gal2pins.Gal2PinsTransformerNext transform
INFO: Built C files in 1931ms conformant to PINS in folder :/home/mcc/execution
pins2lts-mc, 0.000: Registering PINS so language module
pins2lts-mc, 0.000: Loading model from ./gal.so
pins2lts-mc, 0.000: library has no initializer
pins2lts-mc, 0.000: loading model GAL
pins2lts-mc, 0.001: completed loading model GAL
pins2lts-mc, 0.001: Initializing POR dependencies: labels 15, guards 15
pins2lts-mc, 0.001: There are 15 state labels and 1 edge labels
pins2lts-mc, 0.001: State length is 24, there are 15 groups
pins2lts-mc, 0.001: Running bfs using 1 core (sequential)
pins2lts-mc, 0.001: Using a non-indexing tree table with 2^27 elements
pins2lts-mc, 0.001: Successor permutation: none
pins2lts-mc, 0.001: Visible groups: 0 / 15, labels: 0 / 15
pins2lts-mc, 0.001: POR cycle proviso: none
pins2lts-mc, 0.001: Global bits: 0, count bits: 0, local bits: 0
pins2lts-mc, 0.022: 28 levels 1000 states 1913 transitions
pins2lts-mc, 0.038: 33 levels 2000 states 3830 transitions
pins2lts-mc, 0.063: 38 levels 4000 states 7599 transitions
pins2lts-mc, 0.106: 44 levels 8000 states 15060 transitions
pins2lts-mc, 0.174: 51 levels 16000 states 29864 transitions
pins2lts-mc, 0.286: 62 levels 32000 states 59097 transitions
pins2lts-mc, 0.467: 77 levels 64000 states 117536 transitions
pins2lts-mc, 0.838: 98 levels 128000 states 233778 transitions
pins2lts-mc, 1.364: 127 levels 256000 states 465887 transitions
pins2lts-mc, 2.217: 168 levels 512000 states 929058 transitions
pins2lts-mc, 3.694: 226 levels 1024000 states 1854558 transitions
pins2lts-mc, 6.525: 308 levels 2048000 states 3704069 transitions
pins2lts-mc, 12.269: 424 levels 4096000 states 7400742 transitions
pins2lts-mc, 24.217: 652 levels 8192000 states 14775305 transitions
pins2lts-mc, 52.597: Error: tree leafs table full! Change -s/--ratio.
pins2lts-mc, 52.598:
pins2lts-mc, 52.598:
pins2lts-mc, 52.598: Explored 14486150 states 26108405 transitions, fanout: 1.802
pins2lts-mc, 52.598: Total exploration time 52.590 sec (52.590 sec minimum, 52.590 sec on average)
pins2lts-mc, 52.598: States per second: 275454, Transitions per second: 496452
pins2lts-mc, 52.598:
pins2lts-mc, 52.598: Queue width: 8B, total height: 20671, memory: 0.16MB
pins2lts-mc, 52.598: Tree memory: 366.6MB, 26.5 B/state, compr.: 27.1%
pins2lts-mc, 52.598: Tree fill ratio (roots/leafs): 10.0%/99.0%
pins2lts-mc, 52.598: Stored 15 string chucks using 0MB
pins2lts-mc, 52.598: Total memory used for chunk indexing: 0MB
pins2lts-mc, 52.598: Est. total memory use: 366.8MB (~1024.2MB paged-in)
java.lang.RuntimeException: Unexpected exception when executing ltsmin :CommandLine [args=[/home/mcc/BenchKit//lts_install_dir//bin/pins2lts-mc, ./gal.so, --threads=1, -p, --pins-guards, --when, -d], workingDir=/home/mcc/execution]
255
at fr.lip6.move.gal.application.LTSminRunner.checkProperty(LTSminRunner.java:167)
at fr.lip6.move.gal.application.LTSminRunner.access$9(LTSminRunner.java:122)
at fr.lip6.move.gal.application.LTSminRunner$1.run(LTSminRunner.java:91)
at java.lang.Thread.run(Thread.java:748)

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="GPPP-PT-C0100N0000010000"
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/GPPP-PT-C0100N0000010000.tgz
mv GPPP-PT-C0100N0000010000 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 GPPP-PT-C0100N0000010000, 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 r093-blw7-152650005600328"
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 ;