Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0009056/0.0009056, allocations: 80.94 kB / 19.94 MB, free: 4.547 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.001115/0.001115, allocations: 173 kB / 23.36 MB, free: 1.129 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 0.9954/0.9954, allocations: 177.2 MB / 203.8 MB, free: 5.496 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo", uses=false) [Timeout 180]
"[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/Examples/package.order:0:0-0:0:readonly] Warning: The package.order file does not list all .mo files and directories (containing package.mo) present in its directory.
Missing names are:
	Paracetamol_Experiment
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo): time 1.685/1.685, allocations: 273.5 MB / 0.5212 GB, free: 14.63 MB / 458.7 MB
"
[Timeout remaining time 178]
Using package Pharmacolibrary with version 25.09 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(Pharmacolibrary.Examples.PKOneCompartmentModel,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel")
translateModel(Pharmacolibrary.Examples.PKOneCompartmentModel,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.384e-06/2.384e-06, allocations: 0 / 0.5954 GB, free: 2.738 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 5.156e-05/5.394e-05, allocations: 6.25 kB / 0.5954 GB, free: 2.73 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModel): time 0.004609/0.004663, allocations: 2.055 MB / 0.5974 GB, free: 0.6797 MB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.001474/0.006137, allocations: 0.5504 MB / 0.5979 GB, free: 136 kB / 0.5105 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001291/0.006266, allocations: 7.938 kB / 0.5979 GB, free: 128 kB / 0.5105 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001588/0.006425, allocations: 15.84 kB / 0.598 GB, free: 112 kB / 0.5105 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002361/0.006661, allocations: 52.33 kB / 0.598 GB, free: 76 kB / 0.5105 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002693/0.00693, allocations: 51.81 kB / 0.598 GB, free: 24 kB / 0.5105 GB
Notification: Performance of NFFlatten.flatten: time 0.0003901/0.00732, allocations: 191 kB / 0.5982 GB, free: 15.89 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001773/0.007497, allocations: 34.55 kB / 0.5983 GB, free: 15.85 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002833/0.007781, allocations: 99.36 kB / 0.5984 GB, free: 15.76 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001627/0.007943, allocations: 58.59 kB / 0.5984 GB, free: 15.71 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 3.61e-05/0.00798, allocations: 12 kB / 0.5984 GB, free: 15.7 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.7e-05/0.008007, allocations: 16 kB / 0.5984 GB, free: 15.68 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 4.978e-05/0.008056, allocations: 29.77 kB / 0.5985 GB, free: 15.66 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 8.574e-05/0.008142, allocations: 56.94 kB / 0.5985 GB, free: 15.6 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002271/0.008369, allocations: 127.6 kB / 0.5986 GB, free: 15.48 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 3.797e-06/0.008373, allocations: 0 / 0.5986 GB, free: 15.48 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 1.393e-06/0.008374, allocations: 0 / 0.5986 GB, free: 15.48 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 5.35e-06/0.00838, allocations: 4 kB / 0.5987 GB, free: 15.47 MB / 0.5261 GB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 26
 * Number of variables: 26
Notification: Performance of Generate backend data structure: time 0.000829/0.009209, allocations: 395.7 kB / 0.599 GB, free: 15.05 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 6.122e-05/0.00927, allocations: 8.031 kB / 0.599 GB, free: 15.04 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.917e-05/0.009349, allocations: 20.91 kB / 0.5991 GB, free: 15.02 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002605/0.00961, allocations: 141.2 kB / 0.5992 GB, free: 14.86 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.307e-05/0.009653, allocations: 12.36 kB / 0.5992 GB, free: 14.85 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.655e-05/0.009699, allocations: 16.31 kB / 0.5992 GB, free: 14.84 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003292/0.01003, allocations: 146.7 kB / 0.5994 GB, free: 14.68 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.189e-05/0.01005, allocations: 3.938 kB / 0.5994 GB, free: 14.68 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.839e-05/0.01007, allocations: 4 kB / 0.5994 GB, free: 14.67 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.538e-06/0.01008, allocations: 4 kB / 0.5994 GB, free: 14.67 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001246/0.0102, allocations: 66.31 kB / 0.5994 GB, free: 14.6 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007591/0.01096, allocations: 259.8 kB / 0.5997 GB, free: 14.33 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001729/0.01113, allocations: 100.2 kB / 0.5998 GB, free: 14.22 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 6.193e-05/0.0112, allocations: 58.55 kB / 0.5998 GB, free: 14.15 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.186e-05/0.01121, allocations: 4 kB / 0.5998 GB, free: 14.15 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002397/0.01145, allocations: 195.2 kB / 0.6 GB, free: 13.93 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=20): time 2.635e-06/0.01145, allocations: 0 / 0.6 GB, free: 13.93 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=21): time 0.0008537/0.0123, allocations: 0.4983 MB / 0.6005 GB, free: 13.37 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.468e-05/0.01238, allocations: 136.5 kB / 0.6006 GB, free: 13.21 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001213/0.0125, allocations: 144.9 kB / 0.6008 GB, free: 13.05 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 2.431e-05/0.01253, allocations: 37.7 kB / 0.6008 GB, free: 13.01 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 5.623e-05/0.01258, allocations: 100.5 kB / 0.6009 GB, free: 12.91 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 6.114e-05/0.01264, allocations: 79.39 kB / 0.601 GB, free: 12.83 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.101e-05/0.01271, allocations: 41.69 kB / 0.601 GB, free: 12.79 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 0.0001067/0.01282, allocations: 326.8 kB / 0.6013 GB, free: 12.46 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 9.471e-05/0.01291, allocations: 100.7 kB / 0.6014 GB, free: 12.34 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001186/0.01303, allocations: 164.3 kB / 0.6016 GB, free: 12.14 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000262/0.0133, allocations: 292.1 kB / 0.6019 GB, free: 11.8 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.954e-06/0.0133, allocations: 0 / 0.6019 GB, free: 11.8 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002675/0.01356, allocations: 244.2 kB / 0.6021 GB, free: 11.54 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 6.294e-05/0.01363, allocations: 71.33 kB / 0.6022 GB, free: 11.45 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.746e-06/0.01364, allocations: 4 kB / 0.6022 GB, free: 11.45 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.544e-05/0.01365, allocations: 192 / 0.6022 GB, free: 11.45 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001826/0.01383, allocations: 55.91 kB / 0.6022 GB, free: 11.39 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.143e-06/0.01384, allocations: 4 kB / 0.6022 GB, free: 11.39 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001031/0.01394, allocations: 12 kB / 0.6022 GB, free: 11.38 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.555e-05/0.01396, allocations: 8 kB / 0.6022 GB, free: 11.37 MB / 0.5261 GB
Warning: Assuming fixed start value for the following 6 variables:
         singleDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         singleDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 7
 * Number of states: 0 ()
 * Number of discrete variables: 13 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (30):
 * Single equations (assignments): 28
 * Array equations: 0
 * Algorithm blocks: 2
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002247/0.01419, allocations: 188.4 kB / 0.6024 GB, free: 11.17 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.409e-05/0.01422, allocations: 15.98 kB / 0.6024 GB, free: 11.16 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.306e-05/0.01426, allocations: 21.28 kB / 0.6025 GB, free: 11.13 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.466e-06/0.01427, allocations: 0 / 0.6025 GB, free: 11.13 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.336e-06/0.01427, allocations: 4 kB / 0.6025 GB, free: 11.13 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.581e-06/0.01427, allocations: 3.984 kB / 0.6025 GB, free: 11.12 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004221/0.0147, allocations: 353.8 kB / 0.6028 GB, free: 10.74 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.294e-06/0.0147, allocations: 0 / 0.6028 GB, free: 10.74 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001452/0.01484, allocations: 31.98 kB / 0.6028 GB, free: 10.71 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 6.422e-06/0.01485, allocations: 7.922 kB / 0.6028 GB, free: 10.7 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.719e-05/0.01487, allocations: 8 kB / 0.6029 GB, free: 10.7 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.535e-06/0.01487, allocations: 0 / 0.6029 GB, free: 10.7 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.966e-06/0.01487, allocations: 3.938 kB / 0.6029 GB, free: 10.69 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005867/0.01546, allocations: 338.9 kB / 0.6032 GB, free: 10.33 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.563e-05/0.01549, allocations: 11.91 kB / 0.6032 GB, free: 10.32 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.238e-05/0.01553, allocations: 11.98 kB / 0.6032 GB, free: 10.31 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001106/0.01564, allocations: 8 kB / 0.6032 GB, free: 10.3 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.224e-05/0.0157, allocations: 23.97 kB / 0.6032 GB, free: 10.28 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.419e-05/0.01572, allocations: 7.984 kB / 0.6032 GB, free: 10.27 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 4.254e-05/0.01576, allocations: 30.89 kB / 0.6033 GB, free: 10.24 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 5e-08/0.01576, allocations: 0 / 0.6033 GB, free: 10.24 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0002841/0.01604, allocations: 48 kB / 0.6033 GB, free: 10.19 MB / 0.5261 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 8 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising)
 * Number of discrete states: 6 (singleDose.pulse.count,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (18):
 * Single equations (assignments): 15
 * Array equations: 0
 * Algorithm blocks: 1
 * Record equations: 0
 * When equations: 2
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0001325/0.01617, allocations: 86.08 kB / 0.6034 GB, free: 10.1 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0003044/0.01648, allocations: 312.4 kB / 0.6037 GB, free: 9.746 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 7.334e-06/0.01649, allocations: 384 / 0.6037 GB, free: 9.746 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001221/0.01661, allocations: 141.9 kB / 0.6038 GB, free: 9.586 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003078/0.01692, allocations: 43.2 kB / 0.6039 GB, free: 9.547 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001515/0.01843, allocations: 0.5156 MB / 0.6044 GB, free: 9.008 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.508e-05/0.01851, allocations: 72 kB / 0.6044 GB, free: 8.918 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 7.575e-05/0.01858, allocations: 13.48 kB / 0.6045 GB, free: 8.906 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001453/0.01873, allocations: 99.33 kB / 0.6046 GB, free: 8.809 MB / 0.5261 GB
Notification: Performance of SimCode: time 1.193e-06/0.01873, allocations: 0 / 0.6046 GB, free: 8.809 MB / 0.5261 GB
Notification: Performance of Templates: time 0.005278/0.02401, allocations: 2.593 MB / 0.6071 GB, free: 6.352 MB / 0.5261 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.861603470053524]