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 4.0K May 15 18:54 CTLCardinality.txt
-rw-r--r-- 1 mcc users 20K May 15 18:54 CTLCardinality.xml
-rw-r--r-- 1 mcc users 2.3K May 15 18:54 CTLFireability.txt
-rw-r--r-- 1 mcc users 16K May 15 18:54 CTLFireability.xml
-rw-r--r-- 1 mcc users 4.0K May 15 18:49 GenericPropertiesDefinition.xml
-rw-r--r-- 1 mcc users 6.0K May 15 18:49 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 1.8K May 15 18:54 LTLFireability.txt
-rw-r--r-- 1 mcc users 9.0K May 15 18:54 LTLFireability.xml
-rw-r--r-- 1 mcc users 4.3K May 15 18:54 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 20K May 15 18:54 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 109 May 15 18:54 ReachabilityDeadlock.txt
-rw-r--r-- 1 mcc users 347 May 15 18:54 ReachabilityDeadlock.xml
-rw-r--r-- 1 mcc users 2.7K May 15 18:54 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 17K 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 18:49 equiv_col
-rw-r--r-- 1 mcc users 3 May 15 18:49 instance
-rw-r--r-- 1 mcc users 6 May 15 18:49 iscolored
-rw-r--r-- 1 mcc users 33K May 15 18:49 model.pnml
=====================================================================
Generated by BenchKit 2-3637
Executing tool itstoolsl
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 r021-qhx1-152646246200037
=====================================================================

--------------------
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 1527211474740

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/graph4691144834654775815.txt, -o, /tmp/graph4691144834654775815.bin, -w, /tmp/graph4691144834654775815.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/graph4691144834654775815.bin, -l, -1, -v, -w, /tmp/graph4691144834654775815.weights, -q, 0, -e, 0.001], workingDir=null]
Invoking ITS tools like this :CommandLine [args=[/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.201805241334/bin/its-reach-linux64, --gc-threshold, 2000000, --quiet, -i, /home/mcc/execution/UpperBounds.pnml.gal, -t, CGAL, -reachable-file, UpperBounds.prop, --nowitness], workingDir=/home/mcc/execution]

its-reach command run as :

/home/mcc/BenchKit/itstools/plugins/fr.lip6.move.gal.itstools.binaries_1.0.0.201805241334/bin/its-reach-linux64 --gc-threshold 2000000 --quiet -i /home/mcc/execution/UpperBounds.pnml.gal -t CGAL -reachable-file UpperBounds.prop --nowitness
Loading property file UpperBounds.prop.
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-00 with value :i5.u11.PtP3
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-01 with value :i5.u12.PtP3P2
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-02 with value :i0.u8.KdStarGStarPgStarP2
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-03 with value :u3.KdStarGStarP3kP3
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-04 with value :i5.u11.PtP3
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-05 with value :i5.u0.AktP3
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-06 with value :u6.KdStarGStarP3kStar
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-07 with value :i5.u12.PtP3P2
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-08 with value :u6.KdStarGStarP3kStar
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-09 with value :u6.KdStarGStarP3k
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-10 with value :i0.u5.KdStarGStar
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-11 with value :i0.u2.GP3
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-12 with value :i1.u4.Pg
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-13 with value :i0.u8.KdStarGStarPgStar
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-14 with value :i5.u12.PtP2
Read [bounds] property : Angiogenesis-PT-25-UpperBounds-15 with value :i0.u2.Gab1
built 16 ordering constraints for composite.
built 15 ordering constraints for composite.
built 14 ordering constraints for composite.
built 8 ordering constraints for composite.
built 25 ordering constraints for composite.

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
+ /home/mcc/BenchKit//runeclipse.sh /home/mcc/execution UpperBounds -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 UpperBounds -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 25, 2018 1:24:46 AM fr.lip6.move.gal.application.Application start
INFO: Running its-tools with arguments : [-pnfolder, /home/mcc/execution, -examination, UpperBounds, -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 25, 2018 1:24:46 AM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
May 25, 2018 1:24:47 AM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 85 ms
May 25, 2018 1:24:47 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 39 places.
May 25, 2018 1:24:47 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 64 transitions.
May 25, 2018 1:24:47 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.img.gal : 15 ms
May 25, 2018 1:24:47 AM fr.lip6.move.gal.application.MccTranslator applyOrder
INFO: Applying decomposition
May 25, 2018 1:24:47 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 84 ms
May 25, 2018 1:24:47 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 30 ms
Begin: Fri May 25 01:24:47 2018

Computation of communities with the Newman-Girvan Modularity quality function

level 0:
start computation: Fri May 25 01:24:47 2018
network size: 39 nodes, 138 links, 128 weight
quality increased from -0.0310669 to 0.427765
end computation: Fri May 25 01:24:47 2018
level 1:
start computation: Fri May 25 01:24:47 2018
network size: 13 nodes, 69 links, 128 weight
quality increased from 0.427765 to 0.482574
end computation: Fri May 25 01:24:47 2018
level 2:
start computation: Fri May 25 01:24:47 2018
network size: 6 nodes, 32 links, 128 weight
quality increased from 0.482574 to 0.482574
end computation: Fri May 25 01:24:47 2018
End: Fri May 25 01:24:47 2018
Total duration: 0 sec
0.482574
May 25, 2018 1:24:47 AM fr.lip6.move.gal.instantiate.CompositeBuilder decomposeWithOrder
INFO: Decomposing Gal with order
May 25, 2018 1:24:47 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 23 ms
May 25, 2018 1:24:47 AM fr.lip6.move.gal.instantiate.CompositeBuilder rewriteArraysToAllowPartition
INFO: Rewriting arrays to variables to allow decomposition.
May 25, 2018 1:24:48 AM fr.lip6.move.gal.instantiate.Instantiator fuseIsomorphicEffects
INFO: Removed a total of 33 redundant transitions.
May 25, 2018 1:24:48 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/UpperBounds.pnml.gal : 6 ms
May 25, 2018 1:24:48 AM fr.lip6.move.serialization.SerializationUtil serializePropertiesForITSTools
INFO: Time to serialize properties into /home/mcc/execution/UpperBounds.prop : 2 ms

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="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/Angiogenesis-PT-25.tgz
mv Angiogenesis-PT-25 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 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 r021-qhx1-152646246200037"
echo "====================================================================="
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
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 ;