Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.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 0.001666/0.001666, allocations: 84.53 kB / 19.93 MB, free: 4.605 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 0.001124/0.001124, 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 0.9642/0.9642, allocations: 177.1 MB / 203.5 MB, free: 5.738 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 1.521/1.521, allocations: 273.5 MB / 0.5209 GB, free: 14.99 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_LithiumCarbonate,tolerance=1e-09,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate")
translateModel(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate,tolerance=1e-09,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.756e-06/2.756e-06, allocations: 4 kB / 0.7558 GB, free: 10.69 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.99e-05/3.265e-05, allocations: 2.281 kB / 0.7558 GB, free: 10.68 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate): time 0.002733/0.002765, allocations: 2.02 MB / 0.7577 GB, free: 8.672 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.0008879/0.003653, allocations: 0.5413 MB / 0.7583 GB, free: 8.137 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.639e-05/0.00375, allocations: 0 / 0.7583 GB, free: 8.137 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001413/0.003891, allocations: 21.09 kB / 0.7583 GB, free: 8.117 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001608/0.004052, allocations: 57.3 kB / 0.7583 GB, free: 8.078 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002015/0.004253, allocations: 53.52 kB / 0.7584 GB, free: 8.027 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0002779/0.004531, allocations: 201.7 kB / 0.7586 GB, free: 7.855 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001556/0.004687, allocations: 22.03 kB / 0.7586 GB, free: 7.828 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.00015/0.004837, allocations: 107.8 kB / 0.7587 GB, free: 7.723 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001141/0.004951, allocations: 63.8 kB / 0.7588 GB, free: 7.66 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 3.396e-05/0.004985, allocations: 16 kB / 0.7588 GB, free: 7.645 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.294e-05/0.005008, allocations: 12 kB / 0.7588 GB, free: 7.633 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 3.79e-05/0.005046, allocations: 27.92 kB / 0.7588 GB, free: 7.605 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 7.761e-05/0.005123, allocations: 59.83 kB / 0.7589 GB, free: 7.547 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002104/0.005334, allocations: 171.5 kB / 0.759 GB, free: 7.379 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 2.885e-06/0.005336, allocations: 0 / 0.759 GB, free: 7.379 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.624e-06/0.005338, allocations: 3.938 kB / 0.7591 GB, free: 7.375 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 4.628e-06/0.005343, allocations: 0 / 0.7591 GB, free: 7.375 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 0.000703/0.006046, allocations: 449 kB / 0.7595 GB, free: 6.895 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 4.576e-05/0.006091, allocations: 8.031 kB / 0.7595 GB, free: 6.887 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.983e-05/0.006141, allocations: 20.84 kB / 0.7595 GB, free: 6.867 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001949/0.006336, allocations: 155.4 kB / 0.7597 GB, free: 6.691 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.669e-05/0.006353, allocations: 12.38 kB / 0.7597 GB, free: 6.68 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.148e-05/0.006384, allocations: 16.31 kB / 0.7597 GB, free: 6.664 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002656/0.00665, allocations: 155.9 kB / 0.7598 GB, free: 6.5 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.481e-05/0.006665, allocations: 7.891 kB / 0.7598 GB, free: 6.492 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.131e-05/0.006686, allocations: 8 kB / 0.7598 GB, free: 6.484 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.602e-06/0.006693, allocations: 4 kB / 0.7599 GB, free: 6.48 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002111/0.006904, allocations: 142.3 kB / 0.76 GB, free: 6.336 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005657/0.007469, allocations: 364.1 kB / 0.7603 GB, free: 5.949 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.000267/0.007736, allocations: 164.2 kB / 0.7605 GB, free: 5.773 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001111/0.007848, allocations: 90.67 kB / 0.7606 GB, free: 5.676 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.093e-05/0.007859, allocations: 4 kB / 0.7606 GB, free: 5.672 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002687/0.008127, allocations: 230.7 kB / 0.7608 GB, free: 5.418 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=20): time 2.515e-06/0.00813, allocations: 0 / 0.7608 GB, free: 5.418 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=21): time 0.00137/0.0095, allocations: 0.6916 MB / 0.7615 GB, free: 4.664 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.13e-05/0.009571, allocations: 132.5 kB / 0.7616 GB, free: 4.504 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000116/0.009687, allocations: 164.7 kB / 0.7618 GB, free: 4.336 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 1.707e-05/0.009704, allocations: 29.7 kB / 0.7618 GB, free: 4.301 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 5.899e-05/0.009763, allocations: 116.5 kB / 0.7619 GB, free: 4.184 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 4.054e-05/0.009803, allocations: 71.42 kB / 0.762 GB, free: 4.113 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.418e-05/0.009858, allocations: 57.59 kB / 0.762 GB, free: 4.051 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 8.685e-05/0.009944, allocations: 326.8 kB / 0.7623 GB, free: 3.723 MB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001368/0.01008, allocations: 132.7 kB / 0.7625 GB, free: 3.578 MB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001631/0.01024, allocations: 220.3 kB / 0.7627 GB, free: 3.32 MB / 0.5887 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005481/0.01079, allocations: 0.5053 MB / 0.7632 GB, free: 2.754 MB / 0.5887 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.414e-06/0.01079, allocations: 4 kB / 0.7632 GB, free: 2.75 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0003642/0.01116, allocations: 376.1 kB / 0.7635 GB, free: 2.352 MB / 0.5887 GB
Notification: Performance of prepare postOptimizeDAE: time 4.602e-05/0.01121, allocations: 59.41 kB / 0.7636 GB, free: 2.281 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.005e-06/0.01121, allocations: 4.188 kB / 0.7636 GB, free: 2.277 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.066e-05/0.01123, allocations: 7.984 kB / 0.7636 GB, free: 2.27 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001426/0.01138, allocations: 51.91 kB / 0.7636 GB, free: 2.219 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.298e-06/0.01139, allocations: 3.938 kB / 0.7636 GB, free: 2.215 MB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.474e-05/0.01147, allocations: 19.98 kB / 0.7637 GB, free: 2.195 MB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.771e-05/0.01149, allocations: 8 kB / 0.7637 GB, free: 2.188 MB / 0.5887 GB
Warning: Assuming fixed start value for the following 6 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.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" 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,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.central.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,central.rising,$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 0.0001813/0.01167, allocations: 191.2 kB / 0.7639 GB, free: 1.992 MB / 0.5887 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 1.882e-05/0.01169, allocations: 19.91 kB / 0.7639 GB, free: 1.973 MB / 0.5887 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.541e-05/0.01172, allocations: 17.27 kB / 0.7639 GB, free: 1.961 MB / 0.5887 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.307e-06/0.01173, allocations: 4 kB / 0.7639 GB, free: 1.957 MB / 0.5887 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.112e-06/0.01173, allocations: 3.938 kB / 0.7639 GB, free: 1.953 MB / 0.5887 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.05e-06/0.01174, allocations: 4 kB / 0.7639 GB, free: 1.949 MB / 0.5887 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004972/0.01224, allocations: 0.5202 MB / 0.7644 GB, free: 1.379 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.833e-06/0.01224, allocations: 0 / 0.7644 GB, free: 1.379 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001066/0.01234, allocations: 35.92 kB / 0.7644 GB, free: 1.344 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.9e-06/0.01235, allocations: 3.984 kB / 0.7644 GB, free: 1.34 MB / 0.5887 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.451e-05/0.01236, allocations: 8 kB / 0.7645 GB, free: 1.332 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.515e-06/0.01237, allocations: 3.938 kB / 0.7645 GB, free: 1.328 MB / 0.5887 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.673e-06/0.01237, allocations: 0 / 0.7645 GB, free: 1.328 MB / 0.5887 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000526/0.01289, allocations: 499.6 kB / 0.7649 GB, free: 0.8086 MB / 0.5887 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.103e-05/0.01291, allocations: 19.91 kB / 0.765 GB, free: 0.7891 MB / 0.5887 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.72e-05/0.01294, allocations: 11.94 kB / 0.765 GB, free: 0.7773 MB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.053e-05/0.01302, allocations: 11.98 kB / 0.765 GB, free: 0.7656 MB / 0.5887 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.151e-05/0.01309, allocations: 19.97 kB / 0.765 GB, free: 0.7461 MB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.226e-05/0.01311, allocations: 11.98 kB / 0.765 GB, free: 0.7344 MB / 0.5887 GB
Notification: Performance of sorting global known variables: time 6.762e-05/0.01317, allocations: 120.3 kB / 0.7651 GB, free: 0.6172 MB / 0.5887 GB
Notification: Performance of sort global known variables: time 6e-08/0.01317, allocations: 0 / 0.7651 GB, free: 0.6172 MB / 0.5887 GB
Notification: Performance of remove unused functions: time 0.0001878/0.01336, allocations: 44 kB / 0.7652 GB, free: 0.5742 MB / 0.5887 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (central.C,central.AUC,elim.MExc,periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass)
 * Number of discrete variables: 8 ($whenCondition1,$whenCondition2,$whenCondition3,central.Cmax,central.Cmin,central.rising,periodicDose.pulse.T_start,periodicDose.pulse.count)
 * Number of discrete states: 6 (periodicDose.pulse.count,central.Cmin,$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 0.0001097/0.01347, allocations: 107.2 kB / 0.7653 GB, free: 468 kB / 0.5887 GB
Notification: Performance of simCode: created initialization part: time 0.0003687/0.01384, allocations: 383.6 kB / 0.7656 GB, free: 40 kB / 0.5887 GB
Notification: Performance of simCode: created event and clocks part: time 1.984e-06/0.01384, allocations: 0 / 0.7656 GB, free: 40 kB / 0.5887 GB
Notification: Performance of simCode: created simulation system equations: time 0.000164/0.01401, allocations: 179.3 kB / 0.7658 GB, free: 15.85 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002808/0.01429, allocations: 48.47 kB / 0.7659 GB, free: 15.8 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0008279/0.01511, allocations: 0.5667 MB / 0.7664 GB, free: 15.21 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.656e-05/0.01519, allocations: 112.2 kB / 0.7665 GB, free: 15.08 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.925e-05/0.01524, allocations: 28.11 kB / 0.7665 GB, free: 15.05 MB / 0.6043 GB
Notification: Performance of SimCode: time 1.212e-06/0.01524, allocations: 4 kB / 0.7665 GB, free: 15.05 MB / 0.6043 GB
Notification: Performance of Templates: time 0.003678/0.01892, allocations: 2.421 MB / 0.7689 GB, free: 12.68 MB / 0.6043 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 7.290689117042348]