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 0.00133/0.00133, allocations: 104.3 kB / 19.71 MB, free: 440 kB / 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 0.001418/0.001418, allocations: 213.2 kB / 22.99 MB, free: 2.973 MB / 13.93 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 0.9848/0.9848, allocations: 230.6 MB / 256.8 MB, free: 9.582 MB / 202.7 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 1.824/1.824, allocations: 334.3 MB / 0.6323 GB, free: 7.906 MB / 442.7 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: Pharmacolibrary requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.001807/0.001807, allocations: 63.89 kB / 0.867 GB, free: 7.973 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1932/0.195, allocations: 112.8 MB / 0.9772 GB, free: 6.898 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate): time 0.002602/0.1976, allocations: 2.018 MB / 0.9792 GB, free: 4.867 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.0008475/0.1985, allocations: 0.5376 MB / 0.9797 GB, free: 4.328 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.305e-05/0.1986, allocations: 0 / 0.9797 GB, free: 4.328 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001087/0.1987, allocations: 27.78 kB / 0.9797 GB, free: 4.301 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001333/0.1988, allocations: 47.56 kB / 0.9798 GB, free: 4.254 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001671/0.199, allocations: 47.94 kB / 0.9798 GB, free: 4.207 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0002173/0.1992, allocations: 199.1 kB / 0.98 GB, free: 4.012 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001199/0.1993, allocations: 29.95 kB / 0.98 GB, free: 3.977 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 9.6e-05/0.1994, allocations: 67.78 kB / 0.9801 GB, free: 3.91 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.00011/0.1995, allocations: 71.67 kB / 0.9802 GB, free: 3.84 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 3.213e-05/0.1995, allocations: 16 kB / 0.9802 GB, free: 3.824 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.488e-05/0.1996, allocations: 12 kB / 0.9802 GB, free: 3.812 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 3.654e-05/0.1996, allocations: 39.8 kB / 0.9802 GB, free: 3.773 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 7.766e-05/0.1997, allocations: 59.73 kB / 0.9803 GB, free: 3.715 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001977/0.1999, allocations: 171.4 kB / 0.9804 GB, free: 3.547 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 4.037e-06/0.1999, allocations: 0 / 0.9804 GB, free: 3.547 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 1.613e-06/0.1999, allocations: 4 kB / 0.9804 GB, free: 3.543 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 5.6e-06/0.1999, allocations: 0 / 0.9804 GB, free: 3.543 MB / 0.6824 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 0.0006233/0.2005, allocations: 437 kB / 0.9809 GB, free: 3.074 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 3.612e-05/0.2006, allocations: 14.11 kB / 0.9809 GB, free: 3.062 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.392e-05/0.2006, allocations: 20.84 kB / 0.9809 GB, free: 3.043 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000175/0.2008, allocations: 158.2 kB / 0.981 GB, free: 2.863 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.317e-06/0.2008, allocations: 4.375 kB / 0.9811 GB, free: 2.859 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.701e-05/0.2008, allocations: 24.06 kB / 0.9811 GB, free: 2.836 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000253/0.2011, allocations: 166.4 kB / 0.9812 GB, free: 2.664 MB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.169e-05/0.2011, allocations: 3.938 kB / 0.9812 GB, free: 2.66 MB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.469e-05/0.2011, allocations: 4 kB / 0.9812 GB, free: 2.656 MB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.481e-06/0.2011, allocations: 4 kB / 0.9812 GB, free: 2.652 MB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002412/0.2013, allocations: 141.5 kB / 0.9814 GB, free: 2.508 MB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.000518/0.2019, allocations: 360.2 kB / 0.9817 GB, free: 2.125 MB / 0.6824 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002831/0.2021, allocations: 175.5 kB / 0.9819 GB, free: 1.941 MB / 0.6824 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001282/0.2023, allocations: 94.47 kB / 0.982 GB, free: 1.84 MB / 0.6824 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.268e-05/0.2023, allocations: 0 / 0.982 GB, free: 1.84 MB / 0.6824 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002612/0.2026, allocations: 220.5 kB / 0.9822 GB, free: 1.594 MB / 0.6824 GB
Notification: Performance of pre-optimization done (n=20): time 1.353e-06/0.2026, allocations: 4 kB / 0.9822 GB, free: 1.59 MB / 0.6824 GB
Notification: Performance of matching and sorting (n=21): time 0.001082/0.2036, allocations: 0.6872 MB / 0.9829 GB, free: 0.8398 MB / 0.6824 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.746e-05/0.2037, allocations: 136.5 kB / 0.983 GB, free: 0.6758 MB / 0.6824 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001233/0.2038, allocations: 164.4 kB / 0.9832 GB, free: 0.5078 MB / 0.6824 GB
Notification: Performance of collectPreVariables (initialization): time 1.97e-05/0.2038, allocations: 33.7 kB / 0.9832 GB, free: 480 kB / 0.6824 GB
Notification: Performance of collectInitialEqns (initialization): time 6.171e-05/0.2039, allocations: 108.5 kB / 0.9833 GB, free: 368 kB / 0.6824 GB
Notification: Performance of collectInitialBindings (initialization): time 5.073e-05/0.2039, allocations: 79.36 kB / 0.9834 GB, free: 288 kB / 0.6824 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.702e-05/0.204, allocations: 49.56 kB / 0.9834 GB, free: 232 kB / 0.6824 GB
Notification: Performance of setup shared object (initialization): time 0.0001088/0.2041, allocations: 334.8 kB / 0.9837 GB, free: 15.89 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001749/0.2043, allocations: 140.6 kB / 0.9839 GB, free: 15.73 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002119/0.2045, allocations: 215.3 kB / 0.9841 GB, free: 15.48 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000682/0.2052, allocations: 0.5023 MB / 0.9846 GB, free: 14.92 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.044e-06/0.2052, allocations: 0 / 0.9846 GB, free: 14.92 MB / 0.698 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0005022/0.2057, allocations: 384.1 kB / 0.9849 GB, free: 14.52 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 5.021e-05/0.2057, allocations: 66.36 kB / 0.985 GB, free: 14.44 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.328e-06/0.2058, allocations: 3.938 kB / 0.985 GB, free: 14.44 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.882e-05/0.2058, allocations: 4 kB / 0.985 GB, free: 14.43 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001754/0.2059, allocations: 51.91 kB / 0.985 GB, free: 14.38 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.288e-06/0.206, allocations: 4 kB / 0.9851 GB, free: 14.38 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001104/0.2061, allocations: 15.98 kB / 0.9851 GB, free: 14.36 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.715e-05/0.2061, allocations: 12 kB / 0.9851 GB, free: 14.35 MB / 0.698 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 0.0002061/0.2063, allocations: 192.8 kB / 0.9853 GB, free: 14.15 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.426e-05/0.2063, allocations: 19.91 kB / 0.9853 GB, free: 14.13 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.556e-05/0.2064, allocations: 21.22 kB / 0.9853 GB, free: 14.11 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.034e-06/0.2064, allocations: 7.938 kB / 0.9853 GB, free: 14.11 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.111e-06/0.2064, allocations: 3.938 kB / 0.9853 GB, free: 14.1 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.651e-06/0.2064, allocations: 3.984 kB / 0.9853 GB, free: 14.1 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006329/0.207, allocations: 0.5187 MB / 0.9858 GB, free: 13.53 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.515e-06/0.207, allocations: 0 / 0.9858 GB, free: 13.53 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001501/0.2072, allocations: 31.97 kB / 0.9859 GB, free: 13.5 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.775e-06/0.2072, allocations: 0 / 0.9859 GB, free: 13.5 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.593e-05/0.2072, allocations: 8 kB / 0.9859 GB, free: 13.49 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.729e-06/0.2072, allocations: 15.86 kB / 0.9859 GB, free: 13.47 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.483e-06/0.2072, allocations: 4 kB / 0.9859 GB, free: 13.47 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005974/0.2078, allocations: 484.2 kB / 0.9863 GB, free: 12.96 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.742e-05/0.2078, allocations: 23.95 kB / 0.9864 GB, free: 12.94 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.034e-05/0.2078, allocations: 4 kB / 0.9864 GB, free: 12.94 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001058/0.2079, allocations: 11.98 kB / 0.9864 GB, free: 12.93 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.737e-05/0.208, allocations: 19.97 kB / 0.9864 GB, free: 12.91 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.493e-05/0.208, allocations: 8 kB / 0.9864 GB, free: 12.9 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 8.602e-05/0.2081, allocations: 125.5 kB / 0.9865 GB, free: 12.78 MB / 0.698 GB
Notification: Performance of sort global known variables: time 7e-08/0.2081, allocations: 0 / 0.9865 GB, free: 12.78 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0003108/0.2084, allocations: 48 kB / 0.9866 GB, free: 12.73 MB / 0.698 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 0.0001093/0.2086, allocations: 109.7 kB / 0.9867 GB, free: 12.62 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0004802/0.209, allocations: 375.7 kB / 0.987 GB, free: 12.21 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 3.887e-06/0.209, allocations: 8.312 kB / 0.987 GB, free: 12.2 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002004/0.2092, allocations: 165.1 kB / 0.9872 GB, free: 12.02 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003985/0.2096, allocations: 49.8 kB / 0.9872 GB, free: 11.97 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00108/0.2107, allocations: 0.6958 MB / 0.9879 GB, free: 11.23 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.271e-05/0.2108, allocations: 112.4 kB / 0.988 GB, free: 11.11 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.373e-05/0.2109, allocations: 19.44 kB / 0.9881 GB, free: 11.09 MB / 0.698 GB
Notification: Performance of SimCode: time 8.31e-07/0.2109, allocations: 0 / 0.9881 GB, free: 11.09 MB / 0.698 GB
Notification: Performance of Templates: time 0.003668/0.2145, allocations: 2.406 MB / 0.9904 GB, free: 8.688 MB / 0.698 GB
"
[Timeout remaining time 659]
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: 7.879547088872641]