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 0.001443/0.001443, 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 0.001598/0.001598, 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 0.9599/0.9599, allocations: 177.1 MB / 203.5 MB, free: 5.746 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 1.629/1.629, allocations: 273.5 MB / 0.5209 GB, free: 15.02 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.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: Performance of FrontEnd - loaded program: time 1.513e-06/1.513e-06, allocations: 0 / 0.7558 GB, free: 10.75 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.274e-05/2.426e-05, allocations: 2.281 kB / 0.7558 GB, free: 10.75 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModel): time 0.00234/0.002364, allocations: 1.975 MB / 0.7577 GB, free: 8.777 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.0007952/0.003159, allocations: 0.5264 MB / 0.7582 GB, free: 8.254 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.49e-05/0.003234, allocations: 0 / 0.7582 GB, free: 8.254 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001175/0.003352, allocations: 21.11 kB / 0.7582 GB, free: 8.234 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001364/0.003488, allocations: 51.89 kB / 0.7583 GB, free: 8.199 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001738/0.003662, allocations: 47.88 kB / 0.7583 GB, free: 8.152 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0002365/0.003899, allocations: 193.9 kB / 0.7585 GB, free: 7.996 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001425/0.004041, allocations: 21.91 kB / 0.7585 GB, free: 7.965 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001322/0.004173, allocations: 107.7 kB / 0.7586 GB, free: 7.859 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001031/0.004276, allocations: 63.8 kB / 0.7587 GB, free: 7.797 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 3.017e-05/0.004307, allocations: 12 kB / 0.7587 GB, free: 7.785 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.036e-05/0.004327, allocations: 16 kB / 0.7587 GB, free: 7.77 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 3.437e-05/0.004361, allocations: 27.91 kB / 0.7587 GB, free: 7.742 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 6.527e-05/0.004427, allocations: 55.84 kB / 0.7588 GB, free: 7.688 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001995/0.004626, allocations: 159.5 kB / 0.7589 GB, free: 7.531 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 3.126e-06/0.004629, allocations: 4 kB / 0.7589 GB, free: 7.527 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 3.176e-06/0.004632, allocations: 4 kB / 0.7589 GB, free: 7.523 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 4.528e-06/0.004637, allocations: 4 kB / 0.759 GB, free: 7.52 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 0.0006536/0.005291, allocations: 440.8 kB / 0.7594 GB, free: 7.047 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 4.293e-05/0.005333, allocations: 8.031 kB / 0.7594 GB, free: 7.039 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.991e-05/0.005383, allocations: 16.84 kB / 0.7594 GB, free: 7.023 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002399/0.005623, allocations: 176.1 kB / 0.7596 GB, free: 6.828 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.37e-05/0.005637, allocations: 8.375 kB / 0.7596 GB, free: 6.82 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.263e-05/0.00567, allocations: 20.38 kB / 0.7596 GB, free: 6.801 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002191/0.005889, allocations: 156.5 kB / 0.7597 GB, free: 6.637 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.549e-05/0.005904, allocations: 7.891 kB / 0.7597 GB, free: 6.629 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.729e-05/0.005921, allocations: 11.98 kB / 0.7598 GB, free: 6.617 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.432e-06/0.005928, allocations: 4 kB / 0.7598 GB, free: 6.613 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001899/0.006118, allocations: 128.9 kB / 0.7599 GB, free: 6.484 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004935/0.006611, allocations: 360.1 kB / 0.7602 GB, free: 6.102 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002363/0.006848, allocations: 164.2 kB / 0.7604 GB, free: 5.926 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001087/0.006956, allocations: 93.5 kB / 0.7605 GB, free: 5.828 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.467e-06/0.006966, allocations: 144 / 0.7605 GB, free: 5.828 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002408/0.007207, allocations: 227.7 kB / 0.7607 GB, free: 5.578 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=20): time 1.433e-06/0.007208, allocations: 0 / 0.7607 GB, free: 5.578 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=21): time 0.0009689/0.008177, allocations: 0.679 MB / 0.7614 GB, free: 4.84 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.032e-05/0.008237, allocations: 140.5 kB / 0.7615 GB, free: 4.672 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001064/0.008344, allocations: 145.8 kB / 0.7616 GB, free: 4.52 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 2.016e-05/0.008364, allocations: 33.7 kB / 0.7617 GB, free: 4.48 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 6.028e-05/0.008424, allocations: 112.5 kB / 0.7618 GB, free: 4.367 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 4.079e-05/0.008465, allocations: 71.42 kB / 0.7618 GB, free: 4.297 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.193e-05/0.008517, allocations: 53.64 kB / 0.7619 GB, free: 4.238 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 8.975e-05/0.008607, allocations: 326.8 kB / 0.7622 GB, free: 3.91 MB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001334/0.00874, allocations: 136.7 kB / 0.7623 GB, free: 3.762 MB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001607/0.008901, allocations: 208.4 kB / 0.7625 GB, free: 3.516 MB / 0.5887 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005221/0.009423, allocations: 0.5018 MB / 0.763 GB, free: 2.953 MB / 0.5887 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.204e-06/0.009425, allocations: 0 / 0.763 GB, free: 2.953 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0003552/0.00978, allocations: 378.1 kB / 0.7634 GB, free: 2.555 MB / 0.5887 GB
Notification: Performance of prepare postOptimizeDAE: time 4.144e-05/0.009822, allocations: 63.39 kB / 0.7634 GB, free: 2.48 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.572e-06/0.009828, allocations: 0 / 0.7634 GB, free: 2.48 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.581e-05/0.009844, allocations: 4 kB / 0.7634 GB, free: 2.477 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001337/0.009978, allocations: 51.91 kB / 0.7635 GB, free: 2.426 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.203e-06/0.009985, allocations: 3.938 kB / 0.7635 GB, free: 2.422 MB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.747e-05/0.01006, allocations: 19.98 kB / 0.7635 GB, free: 2.402 MB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.326e-05/0.01008, allocations: 8 kB / 0.7635 GB, free: 2.395 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 0.0001668/0.01024, allocations: 183.9 kB / 0.7637 GB, free: 2.203 MB / 0.5887 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 1.832e-05/0.01026, allocations: 19.89 kB / 0.7637 GB, free: 2.184 MB / 0.5887 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.25e-05/0.01029, allocations: 21.28 kB / 0.7637 GB, free: 2.168 MB / 0.5887 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.595e-06/0.0103, allocations: 0 / 0.7637 GB, free: 2.168 MB / 0.5887 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.255e-06/0.0103, allocations: 11.94 kB / 0.7638 GB, free: 2.156 MB / 0.5887 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.368e-06/0.01031, allocations: 0 / 0.7638 GB, free: 2.156 MB / 0.5887 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004741/0.01078, allocations: 0.5056 MB / 0.7642 GB, free: 1.598 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.262e-06/0.01078, allocations: 0 / 0.7642 GB, free: 1.598 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001088/0.01089, allocations: 35.97 kB / 0.7643 GB, free: 1.562 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.206e-06/0.0109, allocations: 0 / 0.7643 GB, free: 1.562 MB / 0.5887 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.362e-05/0.01091, allocations: 8 kB / 0.7643 GB, free: 1.555 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 6.713e-06/0.01092, allocations: 4 kB / 0.7643 GB, free: 1.551 MB / 0.5887 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.914e-06/0.01092, allocations: 7.922 kB / 0.7643 GB, free: 1.543 MB / 0.5887 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004374/0.01136, allocations: 492.7 kB / 0.7648 GB, free: 1.027 MB / 0.5887 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.756e-05/0.01137, allocations: 15.28 kB / 0.7648 GB, free: 1.016 MB / 0.5887 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.34e-05/0.0114, allocations: 8.062 kB / 0.7648 GB, free: 1.008 MB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.567e-05/0.01146, allocations: 7.984 kB / 0.7648 GB, free: 1 MB / 0.5887 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.391e-05/0.01153, allocations: 19.97 kB / 0.7648 GB, free: 0.9805 MB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.011e-05/0.01154, allocations: 12 kB / 0.7648 GB, free: 0.9688 MB / 0.5887 GB
Notification: Performance of sorting global known variables: time 5.829e-05/0.01159, allocations: 118 kB / 0.7649 GB, free: 0.8555 MB / 0.5887 GB
Notification: Performance of sort global known variables: time 6e-08/0.01159, allocations: 0 / 0.7649 GB, free: 0.8555 MB / 0.5887 GB
Notification: Performance of remove unused functions: time 0.000177/0.01177, allocations: 44 kB / 0.765 GB, free: 0.8125 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 9.546e-05/0.01187, allocations: 107.2 kB / 0.7651 GB, free: 0.6953 MB / 0.5887 GB
Notification: Performance of simCode: created initialization part: time 0.0003468/0.01221, allocations: 376.9 kB / 0.7654 GB, free: 296 kB / 0.5887 GB
Notification: Performance of simCode: created event and clocks part: time 1.883e-06/0.01222, allocations: 4.062 kB / 0.7654 GB, free: 292 kB / 0.5887 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001337/0.01235, allocations: 173 kB / 0.7656 GB, free: 100 kB / 0.5887 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002419/0.01259, allocations: 38.55 kB / 0.7656 GB, free: 64 kB / 0.5887 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007645/0.01336, allocations: 0.5624 MB / 0.7662 GB, free: 15.47 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.847e-05/0.01343, allocations: 111.5 kB / 0.7663 GB, free: 15.34 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.435e-05/0.01348, allocations: 20.5 kB / 0.7663 GB, free: 15.32 MB / 0.6043 GB
Notification: Performance of SimCode: time 5.91e-07/0.01348, allocations: 0 / 0.7663 GB, free: 15.32 MB / 0.6043 GB
Notification: Performance of Templates: time 0.002873/0.01635, allocations: 2.279 MB / 0.7686 GB, free: 13.09 MB / 0.6043 GB
"
[Timeout remaining time 660]
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: 6.942386286798865]