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 360K
-rw-r--r-- 1 mcc users 4.2K May 30 21:42 CTLCardinality.txt
-rw-r--r-- 1 mcc users 21K May 30 21:42 CTLCardinality.xml
-rw-r--r-- 1 mcc users 6.4K May 29 15:41 CTLFireability.txt
-rw-r--r-- 1 mcc users 21K May 29 15:41 CTLFireability.xml
-rw-r--r-- 1 mcc users 2.8K May 28 09:52 LTLCardinality.txt
-rw-r--r-- 1 mcc users 12K May 28 09:52 LTLCardinality.xml
-rw-r--r-- 1 mcc users 3.3K May 28 08:07 LTLFireability.txt
-rw-r--r-- 1 mcc users 9.9K May 28 08:07 LTLFireability.xml
-rw-r--r-- 1 mcc users 1 May 24 11:17 NewModel
-rw-r--r-- 1 mcc users 4.5K May 28 06:35 ReachabilityCardinality.txt
-rw-r--r-- 1 mcc users 21K May 28 06:35 ReachabilityCardinality.xml
-rw-r--r-- 1 mcc users 106 May 26 06:29 ReachabilityDeadlock.txt
-rw-r--r-- 1 mcc users 344 May 26 06:29 ReachabilityDeadlock.xml
-rw-r--r-- 1 mcc users 8.0K May 27 04:04 ReachabilityFireability.txt
-rw-r--r-- 1 mcc users 24K May 27 04:04 ReachabilityFireability.xml
-rw-r--r-- 1 mcc users 1.8K May 28 07:31 UpperBounds.txt
-rw-r--r-- 1 mcc users 3.8K May 28 07:31 UpperBounds.xml
-rw-r--r-- 1 mcc users 6 May 24 11:17 equiv_col
-rw-r--r-- 1 mcc users 5 May 24 11:17 instance
-rw-r--r-- 1 mcc users 6 May 24 11:17 iscolored
-rw-r--r-- 1 mcc users 166K May 24 11:17 model.pnml
=====================================================================
Generated by BenchKit 2-3637
Executing tool itstoolsl
Input is MAPKbis-PT-5310, examination is StateSpace
Time confinement is 3600 seconds
Memory confinement is 16384 MBytes
Number of cores is 4
Run identifier is r285-csrt-152749176000289
=====================================================================

--------------------
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 1527991331138

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/graph5682049265665790956.txt, -o, /tmp/graph5682049265665790956.bin, -w, /tmp/graph5682049265665790956.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/graph5682049265665790956.bin, -l, -1, -v, -w, /tmp/graph5682049265665790956.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/StateSpace.pnml.gal, -t, CGAL, --stats], 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/StateSpace.pnml.gal -t CGAL --stats
built 43 ordering constraints for composite.
built 24 ordering constraints for composite.
built 29 ordering constraints for composite.
built 30 ordering constraints for composite.
built 26 ordering constraints for composite.
built 26 ordering constraints for composite.
built 9 ordering constraints for composite.
built 22 ordering constraints for composite.
built 63 ordering constraints for composite.
built 18 ordering constraints for composite.
built 11 ordering constraints for composite.
Model ,|S| ,Time ,Mem(kb) ,fin. SDD ,fin. DDD ,peak SDD ,peak DDD ,SDD Hom ,SDD cache peak ,DDD Hom ,DDD cachepeak ,SHom cache
MAPKbis\_PT\_5310\_flat\_flat\_flat\_mod,3.84641e+12,2.29787,65180,77,13,114614,101,398,247629,25,252,0
Total reachable state count : 3846411649024

Max variable value : 1
STATE_SPACE MAX_TOKEN_IN_PLACE 1 TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
Maximum sum along a path : 49
STATE_SPACE MAX_TOKEN_PER_MARKING 53 TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
Exact state count : 3846411649024
STATE_SPACE STATES 3846411649024 TECHNIQUES DECISION_DIAGRAMS TOPOLOGICAL USE_NUPN
ITS tools runner thread asked to quit. Dying gracefully.

BK_STOP 1527991337030

--------------------
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 StateSpace -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 StateSpace -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
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.application.Application start
INFO: Running its-tools with arguments : [-pnfolder, /home/mcc/execution, -examination, StateSpace, -z3path, /home/mcc/BenchKit//z3/bin/z3, -yices2path, /home/mcc/BenchKit//yices/bin/yices, -its, -ltsminpath, /home/mcc/BenchKit//lts_install_dir/, -louvain, -smt]
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.application.MccTranslator transformPNML
INFO: Parsing pnml file : /home/mcc/execution/model.pnml
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.nupn.PTNetReader loadFromXML
INFO: Load time of PNML (sax parser for PT used): 80 ms
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 106 places.
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.pnml.togal.PTGALTransformer handlePage
INFO: Transformed 173 transitions.
Jun 03, 2018 2:02:13 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/model.pnml.img.gal : 34 ms
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.application.MccTranslator applyOrder
INFO: Applying decomposition
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.instantiate.DomainAnalyzer computeVariableDomains
INFO: Found a total of 8 fixed domain variables (out of 106 variables) in GAL type MAPKbis_PT_5310
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.instantiate.Simplifier printConstantVars
INFO: Found a total of 8 constant array cells/variables (out of 106 variables) in type MAPKbis_PT_5310
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.instantiate.Simplifier printConstantVars
INFO: DNA_damage_equals_0,TGFBR_stimulus_equals_1,DNA_damage_equals_1,FGFR3_stimulus_equals_0,TGFBR_stimulus_equals_0,EGFR_stimulus_equals_0,FGFR3_stimulus_equals_1,EGFR_stimulus_equals_1,
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.instantiate.Simplifier simplifyConstantVariables
INFO: Removed 8 constant variables :DNA_damage_equals_0=1, TGFBR_stimulus_equals_1=0, DNA_damage_equals_1=0, FGFR3_stimulus_equals_0=1, TGFBR_stimulus_equals_0=1, EGFR_stimulus_equals_0=0, FGFR3_stimulus_equals_1=0, EGFR_stimulus_equals_1=1
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.instantiate.Simplifier simplifyConstantVariables
INFO: Simplified 9 expressions due to constant valuations.
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.instantiate.Simplifier simplifyFalseTransitions
INFO: Removed 5 false transitions.
Jun 03, 2018 2:02:13 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 141 ms
Jun 03, 2018 2:02:14 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 24 ms
Begin: Sun Jun 3 02:02:14 2018

Computation of communities with the Newman-Girvan Modularity quality function

level 0:
start computation: Sun Jun 3 02:02:14 2018
network size: 98 nodes, 524 links, 336 weight
quality increased from -0.0135461 to 0.410268
end computation: Sun Jun 3 02:02:14 2018
level 1:
start computation: Sun Jun 3 02:02:14 2018
network size: 47 nodes, 231 links, 336 weight
quality increased from 0.410268 to 0.628439
end computation: Sun Jun 3 02:02:14 2018
level 2:
start computation: Sun Jun 3 02:02:14 2018
network size: 14 nodes, 86 links, 336 weight
quality increased from 0.628439 to 0.647727
end computation: Sun Jun 3 02:02:14 2018
level 3:
start computation: Sun Jun 3 02:02:14 2018
network size: 10 nodes, 60 links, 336 weight
quality increased from 0.647727 to 0.647727
end computation: Sun Jun 3 02:02:14 2018
End: Sun Jun 3 02:02:14 2018
Total duration: 0 sec
0.647727
Jun 03, 2018 2:02:14 AM fr.lip6.move.gal.instantiate.CompositeBuilder decomposeWithOrder
INFO: Decomposing Gal with order
Jun 03, 2018 2:02:14 AM fr.lip6.move.gal.instantiate.GALRewriter flatten
INFO: Flatten gal took : 26 ms
Jun 03, 2018 2:02:14 AM fr.lip6.move.gal.instantiate.CompositeBuilder rewriteArraysToAllowPartition
INFO: Rewriting arrays to variables to allow decomposition.
Jun 03, 2018 2:02:14 AM fr.lip6.move.gal.instantiate.Instantiator fuseIsomorphicEffects
INFO: Removed a total of 253 redundant transitions.
Jun 03, 2018 2:02:14 AM fr.lip6.move.serialization.SerializationUtil systemToFile
INFO: Time to serialize gal into /home/mcc/execution/StateSpace.pnml.gal : 17 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="MAPKbis-PT-5310"
export BK_EXAMINATION="StateSpace"
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/MAPKbis-PT-5310.tgz
mv MAPKbis-PT-5310 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 MAPKbis-PT-5310, 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 r285-csrt-152749176000289"
echo "====================================================================="
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.txt" ] ; then
echo "here is the order used to build the result vector(from text file)"
for x in $(grep Property StateSpace.txt | cut -d ' ' -f 2 | sort -u) ; do
echo "FORMULA_NAME $x"
done
elif [ -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
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 ;