Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.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 0.002603/0.002603, allocations: 80.44 kB / 19.17 MB, free: 0.7422 MB / 13.93 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 0.003207/0.003207, allocations: 169.9 kB / 22.45 MB, free: 2.105 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 1.658/1.658, allocations: 177.1 MB / 202.8 MB, free: 5.754 MB / 186.7 MB
"
[Timeout remaining time 178]
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 3.51/3.51, allocations: 274 MB / 0.5207 GB, free: 14.91 MB / 458.7 MB
"
[Timeout remaining time 176]
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.PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.944e-06/1.944e-06, allocations: 0 / 0.7563 GB, free: 9.938 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.934e-05/3.128e-05, allocations: 4.531 kB / 0.7563 GB, free: 9.934 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.01149/0.01152, allocations: 2.371 MB / 0.7586 GB, free: 7.574 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.002378/0.0139, allocations: 0.902 MB / 0.7595 GB, free: 6.676 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001198/0.01402, allocations: 5.203 kB / 0.7595 GB, free: 6.672 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.003569/0.01759, allocations: 119.2 kB / 0.7596 GB, free: 6.559 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002374/0.01783, allocations: 81.91 kB / 0.7597 GB, free: 6.5 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0005696/0.0184, allocations: 141.1 kB / 0.7598 GB, free: 6.363 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0007196/0.01912, allocations: 282.5 kB / 0.7601 GB, free: 6.09 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000194/0.01931, allocations: 45.06 kB / 0.7601 GB, free: 6.043 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002769/0.01959, allocations: 143.7 kB / 0.7603 GB, free: 5.902 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002436/0.01983, allocations: 95.69 kB / 0.7603 GB, free: 5.809 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 6.002e-05/0.01989, allocations: 24 kB / 0.7604 GB, free: 5.785 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.001415/0.02131, allocations: 163.3 kB / 0.7605 GB, free: 5.625 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001253/0.02143, allocations: 59.77 kB / 0.7606 GB, free: 5.566 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001731/0.0216, allocations: 87.77 kB / 0.7607 GB, free: 5.48 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0007691/0.02237, allocations: 422.5 kB / 0.7611 GB, free: 5.066 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 3.367e-06/0.02238, allocations: 0 / 0.7611 GB, free: 5.066 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.262e-06/0.02238, allocations: 0 / 0.7611 GB, free: 5.066 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 5.37e-06/0.02238, allocations: 0 / 0.7611 GB, free: 5.066 MB / 0.5887 GB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 40
 * Number of variables: 40
Notification: Performance of Generate backend data structure: time 0.001163/0.02355, allocations: 0.6016 MB / 0.7617 GB, free: 4.41 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 3.876e-05/0.02359, allocations: 15.97 kB / 0.7617 GB, free: 4.395 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002261/0.02381, allocations: 44.73 kB / 0.7617 GB, free: 4.352 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004645/0.02428, allocations: 232.7 kB / 0.7619 GB, free: 4.102 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.84e-05/0.0243, allocations: 16.12 kB / 0.7619 GB, free: 4.086 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.564e-05/0.02436, allocations: 20.38 kB / 0.762 GB, free: 4.066 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0006295/0.02499, allocations: 371.8 kB / 0.7623 GB, free: 3.68 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.732e-05/0.02501, allocations: 0 / 0.7623 GB, free: 3.68 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.657e-05/0.02503, allocations: 12 kB / 0.7623 GB, free: 3.668 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.478e-06/0.02504, allocations: 7.938 kB / 0.7623 GB, free: 3.66 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005939/0.02564, allocations: 333.1 kB / 0.7627 GB, free: 3.316 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009535/0.02659, allocations: 468.2 kB / 0.7631 GB, free: 2.832 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0006627/0.02725, allocations: 363.5 kB / 0.7635 GB, free: 2.449 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004004/0.02765, allocations: 273.8 kB / 0.7637 GB, free: 2.16 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.289e-05/0.02767, allocations: 0 / 0.7637 GB, free: 2.16 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0006209/0.02829, allocations: 416.2 kB / 0.7641 GB, free: 1.711 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=26): time 1.523e-06/0.02829, allocations: 0 / 0.7641 GB, free: 1.711 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=27): time 0.002749/0.03104, allocations: 1.639 MB / 0.7657 GB, free: 15.95 MB / 0.6043 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001528/0.03119, allocations: 195.9 kB / 0.7659 GB, free: 15.71 MB / 0.6043 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003223/0.03151, allocations: 261.9 kB / 0.7661 GB, free: 15.46 MB / 0.6043 GB
Notification: Performance of collectPreVariables (initialization): time 9.619e-05/0.03161, allocations: 29.7 kB / 0.7662 GB, free: 15.42 MB / 0.6043 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001457/0.03175, allocations: 156.6 kB / 0.7663 GB, free: 15.27 MB / 0.6043 GB
Notification: Performance of collectInitialBindings (initialization): time 9.014e-05/0.03184, allocations: 83.3 kB / 0.7664 GB, free: 15.18 MB / 0.6043 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001216/0.03197, allocations: 61.92 kB / 0.7665 GB, free: 15.12 MB / 0.6043 GB
Notification: Performance of setup shared object (initialization): time 0.0001919/0.03216, allocations: 338.8 kB / 0.7668 GB, free: 14.78 MB / 0.6043 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0004451/0.0326, allocations: 328.1 kB / 0.7671 GB, free: 14.43 MB / 0.6043 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005043/0.03311, allocations: 391 kB / 0.7675 GB, free: 13.99 MB / 0.6043 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00185/0.03496, allocations: 1.262 MB / 0.7687 GB, free: 12.62 MB / 0.6043 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.508e-06/0.03496, allocations: 4 kB / 0.7687 GB, free: 12.61 MB / 0.6043 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.00117/0.03613, allocations: 0.7448 MB / 0.7694 GB, free: 11.81 MB / 0.6043 GB
Notification: Performance of prepare postOptimizeDAE: time 0.0002377/0.03637, allocations: 119 kB / 0.7696 GB, free: 11.67 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.576e-06/0.03638, allocations: 3.938 kB / 0.7696 GB, free: 11.67 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.049e-05/0.0364, allocations: 4 kB / 0.7696 GB, free: 11.66 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002446/0.03664, allocations: 59.84 kB / 0.7696 GB, free: 11.61 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.514e-06/0.03665, allocations: 0 / 0.7696 GB, free: 11.61 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001992/0.03685, allocations: 19.98 kB / 0.7696 GB, free: 11.59 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 9.432e-05/0.03694, allocations: 51.92 kB / 0.7697 GB, free: 11.54 MB / 0.6043 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: 15 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,CYP2C19.status,SLC22A2.status,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (34):
 * Single equations (assignments): 30
 * 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 0.0003347/0.03728, allocations: 274.9 kB / 0.7699 GB, free: 11.24 MB / 0.6043 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.03e-05/0.03737, allocations: 27.86 kB / 0.77 GB, free: 11.21 MB / 0.6043 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.699e-05/0.03744, allocations: 34.89 kB / 0.77 GB, free: 11.18 MB / 0.6043 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.931e-06/0.03744, allocations: 7.562 kB / 0.77 GB, free: 11.18 MB / 0.6043 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.448e-06/0.03745, allocations: 0 / 0.77 GB, free: 11.18 MB / 0.6043 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.607e-06/0.03745, allocations: 4 kB / 0.77 GB, free: 11.17 MB / 0.6043 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001454/0.0389, allocations: 0.9729 MB / 0.771 GB, free: 10.12 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.864e-06/0.03891, allocations: 0 / 0.771 GB, free: 10.12 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000218/0.03912, allocations: 39.91 kB / 0.771 GB, free: 10.09 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (simulation): time 7.094e-06/0.03913, allocations: 4 kB / 0.771 GB, free: 10.08 MB / 0.6043 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.885e-05/0.03916, allocations: 11.98 kB / 0.771 GB, free: 10.07 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.994e-06/0.03916, allocations: 0 / 0.771 GB, free: 10.07 MB / 0.6043 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.473e-06/0.03916, allocations: 0 / 0.771 GB, free: 10.07 MB / 0.6043 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00163/0.04079, allocations: 1.13 MB / 0.7721 GB, free: 8.871 MB / 0.6043 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.836e-05/0.04083, allocations: 19.86 kB / 0.7721 GB, free: 8.852 MB / 0.6043 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.711e-05/0.04088, allocations: 8.062 kB / 0.7722 GB, free: 8.844 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001788/0.04106, allocations: 15.98 kB / 0.7722 GB, free: 8.828 MB / 0.6043 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.255e-05/0.04114, allocations: 27.89 kB / 0.7722 GB, free: 8.801 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.858e-05/0.04122, allocations: 52.06 kB / 0.7722 GB, free: 8.75 MB / 0.6043 GB
Notification: Performance of sorting global known variables: time 0.000216/0.04143, allocations: 197.1 kB / 0.7724 GB, free: 8.562 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 8e-08/0.04143, allocations: 0 / 0.7724 GB, free: 8.562 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0003918/0.04183, allocations: 75.98 kB / 0.7725 GB, free: 8.488 MB / 0.6043 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: 10 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 8 (singleDose.pulse.count,SLC22A2.status,CYP2C19.status,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (22):
 * Single equations (assignments): 17
 * Array equations: 0
 * Algorithm blocks: 3
 * 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 0.0002834/0.04211, allocations: 159 kB / 0.7727 GB, free: 8.328 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.001131/0.04324, allocations: 0.8438 MB / 0.7735 GB, free: 7.395 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 2.004e-06/0.04324, allocations: 3.938 kB / 0.7735 GB, free: 7.391 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.0005712/0.04381, allocations: 474.4 kB / 0.7739 GB, free: 6.875 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004799/0.04429, allocations: 67.14 kB / 0.774 GB, free: 6.812 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001617/0.04591, allocations: 0.9128 MB / 0.7749 GB, free: 5.863 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001937/0.04611, allocations: 165.4 kB / 0.775 GB, free: 5.688 MB / 0.6043 GB
Notification: Performance of simCode: alias equations: time 8.705e-05/0.04619, allocations: 21.94 kB / 0.7751 GB, free: 5.664 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.579e-05/0.04624, allocations: 16.5 kB / 0.7751 GB, free: 5.648 MB / 0.6043 GB
Notification: Performance of SimCode: time 5.21e-07/0.04624, allocations: 0 / 0.7751 GB, free: 5.648 MB / 0.6043 GB
Notification: Performance of Templates: time 0.0102/0.05644, allocations: 4.443 MB / 0.7794 GB, free: 1.426 MB / 0.6043 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 9.326316309161484]