Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.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 0.000888/0.000888, allocations: 91.55 kB / 20.19 MB, free: 4.348 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 0.001929/0.001929, allocations: 169 kB / 23.5 MB, free: 1.043 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 0.9204/0.9204, allocations: 177.1 MB / 203.8 MB, free: 5.219 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 1.597/1.597, allocations: 273.5 MB / 0.5213 GB, free: 14.78 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.Pharmacogenomics.Patient_PK_2C_Ibuprofen,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen")
translateModel(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.012e-06/1.012e-06, allocations: 0 / 0.6475 GB, free: 38.32 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.474e-05/1.575e-05, allocations: 3.469 kB / 0.6475 GB, free: 38.32 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen): time 0.00295/0.002966, allocations: 3.932 MB / 0.6513 GB, free: 35.74 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.00106/0.004026, allocations: 0.7925 MB / 0.6521 GB, free: 35.22 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001499/0.004175, allocations: 5.156 kB / 0.6521 GB, free: 35.22 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.000164/0.004339, allocations: 46.77 kB / 0.6521 GB, free: 35.19 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0003148/0.004654, allocations: 158 kB / 0.6523 GB, free: 35.11 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003841/0.005038, allocations: 111.1 kB / 0.6524 GB, free: 35.04 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0004338/0.005472, allocations: 498.8 kB / 0.6529 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001917/0.005664, allocations: 73.25 kB / 0.6529 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002821/0.005946, allocations: 262.8 kB / 0.6532 GB, free: 34.64 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002644/0.00621, allocations: 147.2 kB / 0.6533 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.894e-05/0.006259, allocations: 33.47 kB / 0.6534 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 4.409e-05/0.006303, allocations: 36.12 kB / 0.6534 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 4.331e-05/0.006347, allocations: 78.92 kB / 0.6535 GB, free: 34.54 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.000119/0.006466, allocations: 151 kB / 0.6536 GB, free: 34.48 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002627/0.006728, allocations: 290.3 kB / 0.6539 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.295e-06/0.006731, allocations: 0 / 0.6539 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 9.92e-07/0.006732, allocations: 0 / 0.6539 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.57e-06/0.006737, allocations: 1.5 kB / 0.6539 GB, free: 34.34 MB / 0.5262 GB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 67
 * Number of variables: 67
Notification: Performance of Generate backend data structure: time 0.0007163/0.007454, allocations: 0.7939 MB / 0.6547 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.581e-05/0.007489, allocations: 9.531 kB / 0.6547 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.297e-05/0.007572, allocations: 67.84 kB / 0.6547 GB, free: 33.63 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002109/0.007783, allocations: 236.9 kB / 0.655 GB, free: 33.43 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.79e-05/0.007801, allocations: 22.81 kB / 0.655 GB, free: 33.42 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.733e-05/0.007848, allocations: 27.56 kB / 0.655 GB, free: 33.41 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003703/0.008219, allocations: 347.6 kB / 0.6553 GB, free: 33.2 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.668e-05/0.008235, allocations: 13 kB / 0.6554 GB, free: 33.19 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.905e-05/0.008254, allocations: 10.25 kB / 0.6554 GB, free: 33.18 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.027e-06/0.008263, allocations: 8.406 kB / 0.6554 GB, free: 33.18 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002088/0.008472, allocations: 233.7 kB / 0.6556 GB, free: 33.06 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008653/0.009338, allocations: 0.8798 MB / 0.6565 GB, free: 32.42 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.000382/0.00972, allocations: 247 kB / 0.6567 GB, free: 32.26 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001575/0.009877, allocations: 163.8 kB / 0.6568 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.838e-05/0.009905, allocations: 6.531 kB / 0.6569 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003121/0.01022, allocations: 448.7 kB / 0.6573 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=46): time 1.954e-06/0.01022, allocations: 4.5 kB / 0.6573 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=49): time 0.001236/0.01146, allocations: 1.311 MB / 0.6586 GB, free: 30.88 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.649e-05/0.01151, allocations: 303.4 kB / 0.6589 GB, free: 30.53 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001868/0.0117, allocations: 318.5 kB / 0.6592 GB, free: 30.32 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.347e-05/0.01172, allocations: 43.2 kB / 0.6592 GB, free: 30.28 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.535e-05/0.0118, allocations: 220.3 kB / 0.6594 GB, free: 30.09 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 7.561e-05/0.01187, allocations: 167.8 kB / 0.6596 GB, free: 29.95 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.658e-05/0.01197, allocations: 94.77 kB / 0.6597 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.323e-05/0.01204, allocations: 0.5179 MB / 0.6602 GB, free: 29.39 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001506/0.01219, allocations: 208.8 kB / 0.6604 GB, free: 29.23 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000181/0.01238, allocations: 383.6 kB / 0.6607 GB, free: 28.85 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0004283/0.0128, allocations: 0.7063 MB / 0.6614 GB, free: 28.21 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.348e-06/0.01281, allocations: 1.344 kB / 0.6614 GB, free: 28.21 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=73) (initialization): time 0.0004883/0.0133, allocations: 0.6425 MB / 0.662 GB, free: 27.8 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.187e-05/0.01334, allocations: 120 kB / 0.6622 GB, free: 27.67 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.923e-06/0.01334, allocations: 6.656 kB / 0.6622 GB, free: 27.67 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.551e-05/0.01336, allocations: 5.625 kB / 0.6622 GB, free: 27.67 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000244/0.0136, allocations: 114.9 kB / 0.6623 GB, free: 27.66 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.303e-05/0.01362, allocations: 18.44 kB / 0.6623 GB, free: 27.65 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001282/0.01375, allocations: 19.22 kB / 0.6623 GB, free: 27.64 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.298e-05/0.01377, allocations: 22.19 kB / 0.6623 GB, free: 27.64 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 14 variables:
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         periodicDose.absorptionLumen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         peripheral.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         peripheral.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         periodicDose.absorptionLumen.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         periodicDose.absorptionLumen.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  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
         peripheral.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         periodicDose.absorptionLumen.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 16
 * Number of states: 0 ()
 * Number of discrete variables: 29 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.Cmin,$PRE.periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.periodicDose.absorptionLumen.rising,$PRE.central.rising,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,periodicDose.absorptionLumen.rising,central.rising,$whenCondition6,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1,$whenCondition7)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (69):
 * Single equations (assignments): 65
 * Array equations: 0
 * Algorithm blocks: 4
 * 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 0.0001958/0.01396, allocations: 336.7 kB / 0.6627 GB, free: 27.34 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.985e-05/0.01401, allocations: 62.95 kB / 0.6627 GB, free: 27.32 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.061e-05/0.01405, allocations: 38.33 kB / 0.6628 GB, free: 27.29 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.789e-06/0.01406, allocations: 7.594 kB / 0.6628 GB, free: 27.29 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.413e-06/0.01406, allocations: 0 / 0.6628 GB, free: 27.29 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 8.63e-05/0.01415, allocations: 77.94 kB / 0.6628 GB, free: 27.24 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.248e-05/0.01419, allocations: 17.78 kB / 0.6629 GB, free: 27.23 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.417e-05/0.01427, allocations: 15.64 kB / 0.6629 GB, free: 27.23 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.954e-05/0.01436, allocations: 38.56 kB / 0.6629 GB, free: 27.22 MB / 0.5262 GB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.000604/0.01497, allocations: 0.6651 MB / 0.6636 GB, free: 26.8 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.0006664/0.01563, allocations: 0.9937 MB / 0.6645 GB, free: 26.09 MB / 0.5262 GB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0001634/0.0158, allocations: 213.1 kB / 0.6647 GB, free: 25.96 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001044/0.0159, allocations: 213.1 kB / 0.6649 GB, free: 25.82 MB / 0.5262 GB
Notification: Performance of Backend: time 2.31e-07/0.0159, allocations: 3.875 kB / 0.6649 GB, free: 25.82 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0005488/0.01645, allocations: 0.6132 MB / 0.6655 GB, free: 25.31 MB / 0.5262 GB
Notification: Performance of SimCode: time 0.001856/0.01831, allocations: 1.846 MB / 0.6673 GB, free: 23.79 MB / 0.5262 GB
Notification: Performance of Templates: time 0.008082/0.02639, allocations: 6.005 MB / 0.6732 GB, free: 23.3 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.827452857047319]