Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1.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 0.0009909/0.0009909, allocations: 108.3 kB / 19.71 MB, free: 436 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 0.0009885/0.0009885, allocations: 212.9 kB / 23 MB, free: 2.953 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 1.015/1.015, allocations: 230.6 MB / 256.8 MB, free: 9.594 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 1.811/1.811, allocations: 334.2 MB / 0.6323 GB, free: 7.938 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.DevModels.Palivizumab.ViralInfectionDynamics1,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1")
translateModel(Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1") [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 0.001373/0.001373, allocations: 63.89 kB / 0.867 GB, free: 8.113 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1986/0.2, allocations: 112.8 MB / 0.9772 GB, free: 7.031 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1): time 0.001283/0.2013, allocations: 0.5228 MB / 0.9777 GB, free: 6.516 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.0001499/0.2014, allocations: 23.89 kB / 0.9777 GB, free: 6.492 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 2.62e-05/0.2015, allocations: 0 / 0.9777 GB, free: 6.492 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 1.756e-05/0.2015, allocations: 3.938 kB / 0.9777 GB, free: 6.488 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 5.582e-05/0.2015, allocations: 4 kB / 0.9777 GB, free: 6.484 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001379/0.2017, allocations: 7.922 kB / 0.9777 GB, free: 6.477 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 5.592e-05/0.2017, allocations: 15.98 kB / 0.9777 GB, free: 6.461 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 4.669e-05/0.2018, allocations: 0 / 0.9777 GB, free: 6.461 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 2.013e-05/0.2018, allocations: 7.938 kB / 0.9778 GB, free: 6.453 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 6.923e-05/0.2019, allocations: 15.92 kB / 0.9778 GB, free: 6.438 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 1.377e-05/0.2019, allocations: 0 / 0.9778 GB, free: 6.438 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 1.07e-05/0.2019, allocations: 4 kB / 0.9778 GB, free: 6.434 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 1.86e-05/0.2019, allocations: 7.984 kB / 0.9778 GB, free: 6.426 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 2.28e-05/0.2019, allocations: 7.922 kB / 0.9778 GB, free: 6.418 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 7.423e-05/0.202, allocations: 7.984 kB / 0.9778 GB, free: 6.41 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 5.24e-06/0.202, allocations: 4 kB / 0.9778 GB, free: 6.406 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 1.683e-06/0.202, allocations: 0 / 0.9778 GB, free: 6.406 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 5.991e-06/0.202, allocations: 3.938 kB / 0.9778 GB, free: 6.402 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: 3
 * Number of variables: 3
Notification: Performance of Generate backend data structure: time 0.0003325/0.2024, allocations: 256.6 kB / 0.9781 GB, free: 6.121 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 4.033e-05/0.2024, allocations: 18.11 kB / 0.9781 GB, free: 6.105 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 2.887e-05/0.2024, allocations: 4.922 kB / 0.9781 GB, free: 6.102 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 7.82e-05/0.2025, allocations: 114.4 kB / 0.9782 GB, free: 5.965 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 9.237e-06/0.2025, allocations: 8.312 kB / 0.9782 GB, free: 5.957 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.205e-05/0.2025, allocations: 384 / 0.9782 GB, free: 5.957 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 9.071e-05/0.2026, allocations: 42.23 kB / 0.9782 GB, free: 5.91 MB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 6.442e-06/0.2026, allocations: 192 / 0.9782 GB, free: 5.91 MB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.026e-05/0.2026, allocations: 7.938 kB / 0.9782 GB, free: 5.902 MB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.5e-06/0.2027, allocations: 0 / 0.9782 GB, free: 5.902 MB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 2.384e-05/0.2027, allocations: 4 kB / 0.9782 GB, free: 5.898 MB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0001113/0.2028, allocations: 105.4 kB / 0.9783 GB, free: 5.766 MB / 0.6824 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002712/0.2031, allocations: 70.55 kB / 0.9784 GB, free: 5.688 MB / 0.6824 GB
Notification: Performance of preOpt resolveLoops (simulation): time 2.19e-05/0.2031, allocations: 12.86 kB / 0.9784 GB, free: 5.672 MB / 0.6824 GB
Notification: Performance of preOpt evalFunc (simulation): time 7.454e-06/0.2031, allocations: 0 / 0.9784 GB, free: 5.672 MB / 0.6824 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.698e-05/0.2031, allocations: 34.56 kB / 0.9785 GB, free: 5.629 MB / 0.6824 GB
Notification: Performance of pre-optimization done (n=3): time 8.11e-07/0.2031, allocations: 0 / 0.9785 GB, free: 5.629 MB / 0.6824 GB
Notification: Performance of matching and sorting (n=3): time 0.0001408/0.2032, allocations: 61.66 kB / 0.9785 GB, free: 5.562 MB / 0.6824 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.716e-05/0.2033, allocations: 51.41 kB / 0.9786 GB, free: 5.5 MB / 0.6824 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 5.512e-05/0.2033, allocations: 105.8 kB / 0.9787 GB, free: 5.387 MB / 0.6824 GB
Notification: Performance of collectPreVariables (initialization): time 1.124e-05/0.2033, allocations: 25.7 kB / 0.9787 GB, free: 5.355 MB / 0.6824 GB
Notification: Performance of collectInitialEqns (initialization): time 2.7e-05/0.2034, allocations: 88.14 kB / 0.9788 GB, free: 5.266 MB / 0.6824 GB
Notification: Performance of collectInitialBindings (initialization): time 2.679e-05/0.2034, allocations: 19.83 kB / 0.9788 GB, free: 5.246 MB / 0.6824 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 2.797e-05/0.2034, allocations: 21.7 kB / 0.9788 GB, free: 5.219 MB / 0.6824 GB
Notification: Performance of setup shared object (initialization): time 7.321e-05/0.2035, allocations: 310.8 kB / 0.9791 GB, free: 4.906 MB / 0.6824 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 1.65e-05/0.2035, allocations: 8 kB / 0.9791 GB, free: 4.898 MB / 0.6824 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 1.37e-05/0.2035, allocations: 7.984 kB / 0.9791 GB, free: 4.891 MB / 0.6824 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001956/0.2037, allocations: 65.14 kB / 0.9792 GB, free: 4.824 MB / 0.6824 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.866e-06/0.2037, allocations: 4 kB / 0.9792 GB, free: 4.82 MB / 0.6824 GB
Notification: Performance of matching and sorting (n=6) (initialization): time 7.233e-05/0.2038, allocations: 73.58 kB / 0.9793 GB, free: 4.742 MB / 0.6824 GB
Notification: Performance of prepare postOptimizeDAE: time 1.236e-05/0.2038, allocations: 4 kB / 0.9793 GB, free: 4.738 MB / 0.6824 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.29e-06/0.2038, allocations: 4 kB / 0.9793 GB, free: 4.734 MB / 0.6824 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.308e-05/0.2038, allocations: 3.938 kB / 0.9793 GB, free: 4.73 MB / 0.6824 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 3.54e-05/0.2039, allocations: 11.98 kB / 0.9793 GB, free: 4.719 MB / 0.6824 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.442e-06/0.2039, allocations: 0 / 0.9793 GB, free: 4.719 MB / 0.6824 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 2.069e-05/0.2039, allocations: 3.938 kB / 0.9793 GB, free: 4.715 MB / 0.6824 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.744e-06/0.2039, allocations: 0 / 0.9793 GB, free: 4.715 MB / 0.6824 GB
Warning: Assuming fixed start value for the following 3 variables:
         V:VARIABLE(start = 10.0 fixed = true )  \"count of viral particles\" type: Real
         I:VARIABLE(start = 0.0 fixed = true )  \"count of infectious cells\" type: Real
         T:VARIABLE(start = 1e6 fixed = true )  \"count of target(susceptible) cells\" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 1
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (6):
 * Single equations (assignments): 6
 * Array equations: 0
 * Algorithm blocks: 0
 * 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 0.0001112/0.204, allocations: 123.3 kB / 0.9794 GB, free: 4.59 MB / 0.6824 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.695e-06/0.204, allocations: 7.953 kB / 0.9794 GB, free: 4.582 MB / 0.6824 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 1.885e-05/0.204, allocations: 11.62 kB / 0.9794 GB, free: 4.566 MB / 0.6824 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.487e-06/0.204, allocations: 3.938 kB / 0.9794 GB, free: 4.562 MB / 0.6824 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.238e-06/0.204, allocations: 0 / 0.9794 GB, free: 4.562 MB / 0.6824 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.717e-06/0.204, allocations: 3.984 kB / 0.9794 GB, free: 4.559 MB / 0.6824 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 6.272e-05/0.2041, allocations: 105.3 kB / 0.9795 GB, free: 4.426 MB / 0.6824 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.183e-06/0.2041, allocations: 4.172 kB / 0.9795 GB, free: 4.422 MB / 0.6824 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 4.207e-05/0.2042, allocations: 4 kB / 0.9795 GB, free: 4.418 MB / 0.6824 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.188e-06/0.2042, allocations: 4 kB / 0.9795 GB, free: 4.414 MB / 0.6824 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.684e-06/0.2042, allocations: 0 / 0.9795 GB, free: 4.414 MB / 0.6824 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.696e-06/0.2042, allocations: 7.984 kB / 0.9796 GB, free: 4.406 MB / 0.6824 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.055e-06/0.2042, allocations: 7.922 kB / 0.9796 GB, free: 4.398 MB / 0.6824 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0001173/0.2043, allocations: 89.12 kB / 0.9796 GB, free: 4.293 MB / 0.6824 GB
Notification: Performance of postOpt removeConstants (simulation): time 6.052e-06/0.2043, allocations: 3.953 kB / 0.9796 GB, free: 4.289 MB / 0.6824 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 9.137e-06/0.2043, allocations: 0 / 0.9796 GB, free: 4.289 MB / 0.6824 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 1.308e-05/0.2043, allocations: 4.062 kB / 0.9797 GB, free: 4.285 MB / 0.6824 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.102e-05/0.2043, allocations: 11.97 kB / 0.9797 GB, free: 4.273 MB / 0.6824 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.633e-06/0.2043, allocations: 0 / 0.9797 GB, free: 4.273 MB / 0.6824 GB
Notification: Performance of sorting global known variables: time 2.691e-05/0.2044, allocations: 83.28 kB / 0.9797 GB, free: 4.191 MB / 0.6824 GB
Notification: Performance of sort global known variables: time 5e-08/0.2044, allocations: 7.938 kB / 0.9797 GB, free: 4.184 MB / 0.6824 GB
Notification: Performance of remove unused functions: time 0.0001113/0.2045, allocations: 4 kB / 0.9798 GB, free: 4.18 MB / 0.6824 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 3 (V,I,T)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (3):
 * Single equations (assignments): 3
 * Array equations: 0
 * Algorithm blocks: 0
 * 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 Backend phase and start with SimCode phase: time 7.208e-05/0.2045, allocations: 99.19 kB / 0.9798 GB, free: 4.07 MB / 0.6824 GB
Notification: Performance of simCode: created initialization part: time 8.591e-05/0.2046, allocations: 27.98 kB / 0.9799 GB, free: 4.043 MB / 0.6824 GB
Notification: Performance of simCode: created event and clocks part: time 1.352e-06/0.2046, allocations: 0 / 0.9799 GB, free: 4.043 MB / 0.6824 GB
Notification: Performance of simCode: created simulation system equations: time 1.327e-05/0.2046, allocations: 11.98 kB / 0.9799 GB, free: 4.031 MB / 0.6824 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0001063/0.2048, allocations: 4 kB / 0.9799 GB, free: 4.027 MB / 0.6824 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0002637/0.205, allocations: 172.5 kB / 0.9801 GB, free: 3.828 MB / 0.6824 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 3.88e-05/0.2051, allocations: 71.33 kB / 0.9801 GB, free: 3.738 MB / 0.6824 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 2.362e-05/0.2051, allocations: 7.438 kB / 0.9801 GB, free: 3.73 MB / 0.6824 GB
Notification: Performance of SimCode: time 7.61e-07/0.2051, allocations: 4 kB / 0.9801 GB, free: 3.727 MB / 0.6824 GB
Notification: Performance of Templates: time 0.001459/0.2065, allocations: 0.5906 MB / 0.9807 GB, free: 3.137 MB / 0.6824 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1 > Pharmacolibrary_Pharmacolibrary.DevModels.Palivizumab.ViralInfectionDynamics1.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 7.351500096032396]