Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.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 0.001367/0.001367, allocations: 100.4 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 0.001442/0.001442, allocations: 220.3 kB / 23 MB, free: 2.957 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 1.055/1.055, allocations: 230.6 MB / 256.8 MB, free: 9.59 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 1.759/1.759, allocations: 334.3 MB / 0.6323 GB, free: 8.027 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.PKOneCompartmentModel,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel")
translateModel(Pharmacolibrary.Examples.PKOneCompartmentModel,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel") [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 0.001437/0.001437, allocations: 71.89 kB / 0.867 GB, free: 8.051 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1924/0.1938, allocations: 112.8 MB / 0.9772 GB, free: 6.969 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModel): time 0.002703/0.1965, allocations: 1.958 MB / 0.9791 GB, free: 5 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.0008246/0.1973, allocations: 0.5338 MB / 0.9796 GB, free: 4.465 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.186e-05/0.1974, allocations: 0 / 0.9796 GB, free: 4.465 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001246/0.1976, allocations: 15.8 kB / 0.9796 GB, free: 4.449 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001385/0.1977, allocations: 51.61 kB / 0.9797 GB, free: 4.398 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002066/0.1979, allocations: 47.89 kB / 0.9797 GB, free: 4.352 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0002247/0.1981, allocations: 183.3 kB / 0.9799 GB, free: 4.172 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000241/0.1984, allocations: 25.91 kB / 0.9799 GB, free: 4.137 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001146/0.1985, allocations: 71.72 kB / 0.98 GB, free: 4.066 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001106/0.1986, allocations: 71.67 kB / 0.9801 GB, free: 3.996 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 2.529e-05/0.1986, allocations: 16 kB / 0.9801 GB, free: 3.98 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.417e-05/0.1986, allocations: 16 kB / 0.9801 GB, free: 3.965 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 3.708e-05/0.1987, allocations: 35.8 kB / 0.9801 GB, free: 3.93 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 7.489e-05/0.1988, allocations: 63.72 kB / 0.9802 GB, free: 3.867 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002074/0.199, allocations: 163.4 kB / 0.9804 GB, free: 3.707 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 4.418e-06/0.199, allocations: 0 / 0.9804 GB, free: 3.707 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 2.214e-06/0.199, allocations: 0 / 0.9804 GB, free: 3.707 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 6.873e-06/0.199, allocations: 0 / 0.9804 GB, free: 3.707 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 0.0006969/0.1997, allocations: 444.8 kB / 0.9808 GB, free: 3.23 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 4.325e-05/0.1997, allocations: 10.11 kB / 0.9808 GB, free: 3.223 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.814e-05/0.1998, allocations: 12.89 kB / 0.9808 GB, free: 3.211 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002769/0.2, allocations: 178.3 kB / 0.981 GB, free: 3.012 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.239e-05/0.2, allocations: 4.375 kB / 0.981 GB, free: 3.008 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.935e-05/0.2001, allocations: 24.08 kB / 0.981 GB, free: 2.984 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002366/0.2003, allocations: 155.3 kB / 0.9811 GB, free: 2.82 MB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.375e-05/0.2003, allocations: 0 / 0.9811 GB, free: 2.82 MB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.702e-05/0.2004, allocations: 15.98 kB / 0.9812 GB, free: 2.805 MB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.303e-06/0.2004, allocations: 4 kB / 0.9812 GB, free: 2.801 MB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001925/0.2006, allocations: 133.5 kB / 0.9813 GB, free: 2.664 MB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005572/0.2011, allocations: 356.2 kB / 0.9816 GB, free: 2.285 MB / 0.6824 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002551/0.2014, allocations: 164.2 kB / 0.9818 GB, free: 2.109 MB / 0.6824 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001081/0.2015, allocations: 90.67 kB / 0.9819 GB, free: 2.012 MB / 0.6824 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.321e-05/0.2015, allocations: 3.938 kB / 0.9819 GB, free: 2.008 MB / 0.6824 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002629/0.2018, allocations: 224.4 kB / 0.9821 GB, free: 1.758 MB / 0.6824 GB
Notification: Performance of pre-optimization done (n=20): time 2.044e-06/0.2018, allocations: 0 / 0.9821 GB, free: 1.758 MB / 0.6824 GB
Notification: Performance of matching and sorting (n=21): time 0.001049/0.2028, allocations: 0.6751 MB / 0.9828 GB, free: 1.023 MB / 0.6824 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.611e-05/0.2029, allocations: 144.4 kB / 0.9829 GB, free: 0.8516 MB / 0.6824 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001159/0.203, allocations: 152.2 kB / 0.983 GB, free: 0.6953 MB / 0.6824 GB
Notification: Performance of collectPreVariables (initialization): time 1.783e-05/0.203, allocations: 33.7 kB / 0.9831 GB, free: 0.6562 MB / 0.6824 GB
Notification: Performance of collectInitialEqns (initialization): time 5.733e-05/0.2031, allocations: 100.5 kB / 0.9832 GB, free: 0.5547 MB / 0.6824 GB
Notification: Performance of collectInitialBindings (initialization): time 4.401e-05/0.2031, allocations: 75.41 kB / 0.9832 GB, free: 492 kB / 0.6824 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.008e-05/0.2032, allocations: 49.7 kB / 0.9833 GB, free: 436 kB / 0.6824 GB
Notification: Performance of setup shared object (initialization): time 8.798e-05/0.2033, allocations: 330.8 kB / 0.9836 GB, free: 96 kB / 0.6824 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001555/0.2034, allocations: 132.7 kB / 0.9837 GB, free: 15.95 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001587/0.2036, allocations: 214.8 kB / 0.9839 GB, free: 15.7 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005591/0.2041, allocations: 0.4998 MB / 0.9844 GB, free: 15.13 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.355e-06/0.2041, allocations: 0 / 0.9844 GB, free: 15.13 MB / 0.698 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0003704/0.2045, allocations: 374.7 kB / 0.9848 GB, free: 14.74 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 4.463e-05/0.2045, allocations: 65.61 kB / 0.9848 GB, free: 14.66 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.333e-06/0.2046, allocations: 7.938 kB / 0.9848 GB, free: 14.66 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.734e-05/0.2046, allocations: 4 kB / 0.9848 GB, free: 14.65 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001464/0.2047, allocations: 51.91 kB / 0.9849 GB, free: 14.6 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.245e-06/0.2047, allocations: 0 / 0.9849 GB, free: 14.6 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.788e-05/0.2048, allocations: 19.98 kB / 0.9849 GB, free: 14.58 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.36e-05/0.2048, allocations: 11.94 kB / 0.9849 GB, free: 14.57 MB / 0.698 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 0.0001967/0.205, allocations: 193 kB / 0.9851 GB, free: 14.37 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 1.982e-05/0.205, allocations: 15.91 kB / 0.9851 GB, free: 14.35 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.42e-05/0.2051, allocations: 21.22 kB / 0.9851 GB, free: 14.33 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.585e-06/0.2051, allocations: 0 / 0.9851 GB, free: 14.33 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.524e-06/0.2051, allocations: 4 kB / 0.9852 GB, free: 14.33 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.739e-06/0.2051, allocations: 0 / 0.9852 GB, free: 14.33 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005174/0.2056, allocations: 0.5171 MB / 0.9857 GB, free: 13.76 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.246e-06/0.2056, allocations: 3.984 kB / 0.9857 GB, free: 13.76 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001269/0.2057, allocations: 35.98 kB / 0.9857 GB, free: 13.72 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.995e-06/0.2057, allocations: 3.938 kB / 0.9857 GB, free: 13.72 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.412e-05/0.2058, allocations: 7.984 kB / 0.9857 GB, free: 13.71 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.516e-06/0.2058, allocations: 3.938 kB / 0.9857 GB, free: 13.71 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.673e-06/0.2058, allocations: 0 / 0.9857 GB, free: 13.71 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004577/0.2062, allocations: 484.8 kB / 0.9862 GB, free: 13.2 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.99e-05/0.2062, allocations: 11.91 kB / 0.9862 GB, free: 13.19 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.569e-05/0.2063, allocations: 8.062 kB / 0.9862 GB, free: 13.18 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.416e-05/0.2063, allocations: 11.98 kB / 0.9862 GB, free: 13.17 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.752e-05/0.2064, allocations: 19.97 kB / 0.9862 GB, free: 13.15 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.252e-05/0.2064, allocations: 7.984 kB / 0.9862 GB, free: 13.14 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 5.706e-05/0.2065, allocations: 111.3 kB / 0.9863 GB, free: 13.03 MB / 0.698 GB
Notification: Performance of sort global known variables: time 6e-08/0.2065, allocations: 0 / 0.9863 GB, free: 13.03 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0001962/0.2067, allocations: 48 kB / 0.9864 GB, free: 12.98 MB / 0.698 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 9.54e-05/0.2068, allocations: 115.2 kB / 0.9865 GB, free: 12.86 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0004597/0.2072, allocations: 365.8 kB / 0.9868 GB, free: 12.46 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 1.934e-06/0.2072, allocations: 0 / 0.9868 GB, free: 12.46 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001392/0.2074, allocations: 173 kB / 0.987 GB, free: 12.28 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002816/0.2076, allocations: 44.28 kB / 0.987 GB, free: 12.23 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009065/0.2086, allocations: 0.6791 MB / 0.9877 GB, free: 11.52 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 8.347e-05/0.2086, allocations: 111.5 kB / 0.9878 GB, free: 11.38 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.546e-05/0.2087, allocations: 19.44 kB / 0.9878 GB, free: 11.37 MB / 0.698 GB
Notification: Performance of SimCode: time 8.81e-07/0.2087, allocations: 0 / 0.9878 GB, free: 11.37 MB / 0.698 GB
Notification: Performance of Templates: time 0.004403/0.2131, allocations: 2.272 MB / 0.9901 GB, free: 9.105 MB / 0.698 GB
"
[Timeout remaining time 659]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel > Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 7.358442724915221]