Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_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 0.001519/0.001519, allocations: 84.53 kB / 19.93 MB, free: 4.609 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 0.001475/0.001475, allocations: 173.9 kB / 23.21 MB, free: 1.328 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 0.9465/0.9465, allocations: 177.1 MB / 203.5 MB, free: 5.734 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 1.588/1.588, allocations: 273.5 MB / 0.5209 GB, free: 15.04 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.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.073e-06/2.073e-06, allocations: 0 / 0.7558 GB, free: 10.77 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.682e-05/2.889e-05, allocations: 6.281 kB / 0.7558 GB, free: 10.77 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.002565/0.002594, allocations: 2.014 MB / 0.7577 GB, free: 8.762 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.0008366/0.00343, allocations: 0.535 MB / 0.7583 GB, free: 8.23 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.807e-05/0.003518, allocations: 4 kB / 0.7583 GB, free: 8.227 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001278/0.003646, allocations: 15.8 kB / 0.7583 GB, free: 8.211 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001484/0.003794, allocations: 61.28 kB / 0.7583 GB, free: 8.168 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001775/0.003972, allocations: 41.09 kB / 0.7584 GB, free: 8.129 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0002557/0.004228, allocations: 208.9 kB / 0.7586 GB, free: 7.953 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001389/0.004367, allocations: 26.03 kB / 0.7586 GB, free: 7.922 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001364/0.004503, allocations: 111.7 kB / 0.7587 GB, free: 7.812 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001088/0.004612, allocations: 59.8 kB / 0.7588 GB, free: 7.754 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 3.246e-05/0.004644, allocations: 16 kB / 0.7588 GB, free: 7.738 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.337e-05/0.004668, allocations: 16 kB / 0.7588 GB, free: 7.723 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 3.455e-05/0.004702, allocations: 23.92 kB / 0.7588 GB, free: 7.699 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 7.065e-05/0.004773, allocations: 59.83 kB / 0.7589 GB, free: 7.641 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.000209/0.004982, allocations: 167.5 kB / 0.759 GB, free: 7.477 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 1.843e-06/0.004984, allocations: 0 / 0.759 GB, free: 7.477 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.513e-06/0.004985, allocations: 0 / 0.759 GB, free: 7.477 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 5.49e-06/0.004991, allocations: 0 / 0.759 GB, free: 7.477 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: 26
 * Number of variables: 26
Notification: Performance of Generate backend data structure: time 0.0006934/0.005684, allocations: 456.7 kB / 0.7595 GB, free: 6.988 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 4.295e-05/0.005727, allocations: 8.031 kB / 0.7595 GB, free: 6.98 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.391e-05/0.005781, allocations: 20.84 kB / 0.7595 GB, free: 6.961 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002555/0.006036, allocations: 184.7 kB / 0.7597 GB, free: 6.762 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.578e-05/0.006052, allocations: 12.38 kB / 0.7597 GB, free: 6.75 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.253e-05/0.006085, allocations: 12.38 kB / 0.7597 GB, free: 6.738 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002287/0.006313, allocations: 155.9 kB / 0.7598 GB, free: 6.574 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.284e-05/0.006326, allocations: 4 kB / 0.7599 GB, free: 6.57 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.428e-05/0.00634, allocations: 4 kB / 0.7599 GB, free: 6.566 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.005e-06/0.006348, allocations: 7.984 kB / 0.7599 GB, free: 6.559 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001882/0.006537, allocations: 129.6 kB / 0.76 GB, free: 6.426 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005175/0.007054, allocations: 356.1 kB / 0.7603 GB, free: 6.047 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002443/0.007298, allocations: 174.1 kB / 0.7605 GB, free: 5.863 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 9.707e-05/0.007395, allocations: 86.62 kB / 0.7606 GB, free: 5.77 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.045e-05/0.007406, allocations: 4 kB / 0.7606 GB, free: 5.766 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002397/0.007646, allocations: 224.4 kB / 0.7608 GB, free: 5.516 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=20): time 2.424e-06/0.007648, allocations: 0 / 0.7608 GB, free: 5.516 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=21): time 0.0009817/0.00863, allocations: 0.6825 MB / 0.7615 GB, free: 4.773 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.635e-05/0.008696, allocations: 140.5 kB / 0.7616 GB, free: 4.605 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001155/0.008812, allocations: 161.8 kB / 0.7617 GB, free: 4.441 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 1.799e-05/0.00883, allocations: 33.7 kB / 0.7618 GB, free: 4.402 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 5.928e-05/0.008889, allocations: 108.5 kB / 0.7619 GB, free: 4.293 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 4.117e-05/0.00893, allocations: 71.36 kB / 0.7619 GB, free: 4.223 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.524e-05/0.008985, allocations: 53.69 kB / 0.762 GB, free: 4.164 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 9.01e-05/0.009075, allocations: 330.8 kB / 0.7623 GB, free: 3.832 MB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001512/0.009227, allocations: 140.6 kB / 0.7625 GB, free: 3.68 MB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001601/0.009387, allocations: 204.4 kB / 0.7626 GB, free: 3.438 MB / 0.5887 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005386/0.009925, allocations: 0.4954 MB / 0.7631 GB, free: 2.879 MB / 0.5887 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.844e-06/0.009927, allocations: 0 / 0.7631 GB, free: 2.879 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0003627/0.01029, allocations: 382.7 kB / 0.7635 GB, free: 2.477 MB / 0.5887 GB
Notification: Performance of prepare postOptimizeDAE: time 4.577e-05/0.01034, allocations: 55.41 kB / 0.7635 GB, free: 2.41 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.925e-06/0.01034, allocations: 7.984 kB / 0.7636 GB, free: 2.402 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.65e-05/0.01036, allocations: 7.938 kB / 0.7636 GB, free: 2.395 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001321/0.01049, allocations: 39.92 kB / 0.7636 GB, free: 2.355 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.718e-06/0.0105, allocations: 7.984 kB / 0.7636 GB, free: 2.348 MB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.702e-05/0.01058, allocations: 12 kB / 0.7636 GB, free: 2.336 MB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.801e-05/0.0106, allocations: 15.98 kB / 0.7636 GB, free: 2.32 MB / 0.5887 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 0.0001784/0.01078, allocations: 189.7 kB / 0.7638 GB, free: 2.129 MB / 0.5887 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.037e-05/0.0108, allocations: 19.91 kB / 0.7638 GB, free: 2.109 MB / 0.5887 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.694e-05/0.01083, allocations: 25.27 kB / 0.7639 GB, free: 2.09 MB / 0.5887 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.257e-06/0.01084, allocations: 3.938 kB / 0.7639 GB, free: 2.086 MB / 0.5887 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.234e-06/0.01084, allocations: 8 kB / 0.7639 GB, free: 2.078 MB / 0.5887 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.869e-06/0.01085, allocations: 0 / 0.7639 GB, free: 2.078 MB / 0.5887 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004982/0.01135, allocations: 0.5056 MB / 0.7644 GB, free: 1.52 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.724e-06/0.01135, allocations: 0 / 0.7644 GB, free: 1.52 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001094/0.01146, allocations: 39.91 kB / 0.7644 GB, free: 1.48 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.765e-06/0.01146, allocations: 0 / 0.7644 GB, free: 1.48 MB / 0.5887 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.347e-05/0.01147, allocations: 8 kB / 0.7644 GB, free: 1.473 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.883e-06/0.01148, allocations: 0 / 0.7644 GB, free: 1.473 MB / 0.5887 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.535e-06/0.01148, allocations: 3.938 kB / 0.7644 GB, free: 1.469 MB / 0.5887 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004356/0.01191, allocations: 499.9 kB / 0.7649 GB, free: 0.9492 MB / 0.5887 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.833e-05/0.01193, allocations: 15.84 kB / 0.7649 GB, free: 0.9336 MB / 0.5887 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.376e-05/0.01196, allocations: 8.062 kB / 0.7649 GB, free: 0.9258 MB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.381e-05/0.01203, allocations: 11.98 kB / 0.7649 GB, free: 0.9141 MB / 0.5887 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.722e-05/0.0121, allocations: 15.97 kB / 0.7649 GB, free: 0.8984 MB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.5e-05/0.01211, allocations: 12 kB / 0.765 GB, free: 0.8867 MB / 0.5887 GB
Notification: Performance of sorting global known variables: time 6.221e-05/0.01217, allocations: 115.2 kB / 0.7651 GB, free: 0.7734 MB / 0.5887 GB
Notification: Performance of sort global known variables: time 7e-08/0.01217, allocations: 4 kB / 0.7651 GB, free: 0.7695 MB / 0.5887 GB
Notification: Performance of remove unused functions: time 0.0001772/0.01235, allocations: 44 kB / 0.7651 GB, free: 0.7266 MB / 0.5887 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 9.378e-05/0.01244, allocations: 107.2 kB / 0.7652 GB, free: 0.6094 MB / 0.5887 GB
Notification: Performance of simCode: created initialization part: time 0.0003491/0.01279, allocations: 371.7 kB / 0.7656 GB, free: 208 kB / 0.5887 GB
Notification: Performance of simCode: created event and clocks part: time 2.534e-06/0.0128, allocations: 0 / 0.7656 GB, free: 208 kB / 0.5887 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001329/0.01293, allocations: 177.4 kB / 0.7657 GB, free: 12 kB / 0.5887 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002775/0.01321, allocations: 45.91 kB / 0.7658 GB, free: 15.97 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007828/0.01399, allocations: 0.5701 MB / 0.7663 GB, free: 15.38 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.64e-05/0.01407, allocations: 107.6 kB / 0.7664 GB, free: 15.25 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.712e-05/0.01411, allocations: 28.5 kB / 0.7665 GB, free: 15.22 MB / 0.6043 GB
Notification: Performance of SimCode: time 1.062e-06/0.01411, allocations: 0 / 0.7665 GB, free: 15.22 MB / 0.6043 GB
Notification: Performance of Templates: time 0.003105/0.01722, allocations: 2.375 MB / 0.7688 GB, free: 12.89 MB / 0.6043 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.553425818914548]