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 0.001004/0.001004, allocations: 81.17 kB / 19.87 MB, free: 4.621 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 0.0009935/0.0009935, allocations: 169 kB / 23.27 MB, free: 1.223 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 0.9865/0.9865, allocations: 177.2 MB / 203.7 MB, free: 5.52 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 1.625/1.625, allocations: 273.5 MB / 0.5212 GB, free: 14.7 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 1.763e-06/1.763e-06, allocations: 0 / 0.6474 GB, free: 38.46 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.171e-05/2.347e-05, allocations: 2.312 kB / 0.6474 GB, free: 38.46 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModel): time 0.002464/0.002487, allocations: 2.052 MB / 0.6494 GB, free: 37.12 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.000703/0.00319, allocations: 0.5449 MB / 0.6499 GB, free: 36.77 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.002e-05/0.00326, allocations: 3.938 kB / 0.6499 GB, free: 36.77 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001032/0.003363, allocations: 15.44 kB / 0.6499 GB, free: 36.75 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001241/0.003487, allocations: 52 kB / 0.65 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001513/0.003639, allocations: 48.64 kB / 0.65 GB, free: 36.71 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002145/0.003853, allocations: 193.5 kB / 0.6502 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001131/0.003966, allocations: 31.23 kB / 0.6503 GB, free: 36.63 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001424/0.004109, allocations: 98.83 kB / 0.6504 GB, free: 36.59 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 9.958e-05/0.004208, allocations: 58.59 kB / 0.6504 GB, free: 36.57 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.721e-05/0.004235, allocations: 13.78 kB / 0.6504 GB, free: 36.57 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.068e-05/0.004256, allocations: 14.62 kB / 0.6504 GB, free: 36.57 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 3.287e-05/0.004289, allocations: 36.25 kB / 0.6505 GB, free: 36.55 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 5.18e-05/0.004341, allocations: 54.39 kB / 0.6505 GB, free: 36.53 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001478/0.004488, allocations: 125.4 kB / 0.6506 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.195e-06/0.004491, allocations: 2.281 kB / 0.6506 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 6.81e-07/0.004491, allocations: 1.156 kB / 0.6506 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 3.948e-06/0.004495, allocations: 0 / 0.6506 GB, free: 36.46 MB / 0.5262 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 0.0004752/0.00497, allocations: 0.5152 MB / 0.6511 GB, free: 35.97 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.954e-05/0.00501, allocations: 9.688 kB / 0.6512 GB, free: 35.97 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.005e-05/0.00505, allocations: 26.31 kB / 0.6512 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001187/0.005169, allocations: 164.7 kB / 0.6513 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.692e-05/0.005186, allocations: 7.75 kB / 0.6513 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.499e-05/0.005211, allocations: 13.91 kB / 0.6514 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001545/0.005365, allocations: 133.8 kB / 0.6515 GB, free: 35.71 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.144e-05/0.005377, allocations: 5.344 kB / 0.6515 GB, free: 35.7 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.179e-05/0.005388, allocations: 5.219 kB / 0.6515 GB, free: 35.7 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.031e-06/0.005394, allocations: 1.688 kB / 0.6515 GB, free: 35.7 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 8.022e-05/0.005475, allocations: 82.44 kB / 0.6516 GB, free: 35.66 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003508/0.005825, allocations: 376.8 kB / 0.6519 GB, free: 35.36 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001213/0.005947, allocations: 119.5 kB / 0.6521 GB, free: 35.27 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 3.995e-05/0.005987, allocations: 56.16 kB / 0.6521 GB, free: 35.23 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 8.867e-06/0.005996, allocations: 3.75 kB / 0.6521 GB, free: 35.23 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001482/0.006144, allocations: 192.4 kB / 0.6523 GB, free: 35.07 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.253e-06/0.006145, allocations: 0 / 0.6523 GB, free: 35.07 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0005585/0.006704, allocations: 0.5386 MB / 0.6528 GB, free: 34.67 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.618e-05/0.00674, allocations: 141.5 kB / 0.653 GB, free: 34.51 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 7.639e-05/0.006816, allocations: 197.4 kB / 0.6531 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.216e-05/0.006828, allocations: 33.17 kB / 0.6532 GB, free: 34.3 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.228e-05/0.006871, allocations: 160.4 kB / 0.6533 GB, free: 34.15 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.868e-05/0.006909, allocations: 72.58 kB / 0.6534 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.19e-05/0.006961, allocations: 56.98 kB / 0.6535 GB, free: 34.05 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 5.936e-05/0.00702, allocations: 0.4966 MB / 0.6539 GB, free: 33.55 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 5.613e-05/0.007077, allocations: 99.3 kB / 0.654 GB, free: 33.47 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 7.379e-05/0.00715, allocations: 190.3 kB / 0.6542 GB, free: 33.27 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001677/0.007318, allocations: 307.1 kB / 0.6545 GB, free: 32.99 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.673e-06/0.00732, allocations: 0 / 0.6545 GB, free: 32.99 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002057/0.007525, allocations: 297 kB / 0.6548 GB, free: 32.79 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.74e-05/0.007553, allocations: 58.97 kB / 0.6548 GB, free: 32.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.652e-06/0.00756, allocations: 2.281 kB / 0.6548 GB, free: 32.73 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.246e-05/0.007572, allocations: 2.281 kB / 0.6548 GB, free: 32.73 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000124/0.007696, allocations: 55.38 kB / 0.6549 GB, free: 32.72 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.332e-06/0.007702, allocations: 11.27 kB / 0.6549 GB, free: 32.72 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 6.625e-05/0.007769, allocations: 16.47 kB / 0.6549 GB, free: 32.71 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.303e-05/0.007782, allocations: 7.094 kB / 0.6549 GB, free: 32.71 MB / 0.5262 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 0.0001444/0.007926, allocations: 230.5 kB / 0.6552 GB, free: 32.5 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.38e-05/0.00795, allocations: 25.81 kB / 0.6552 GB, free: 32.49 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.169e-05/0.007981, allocations: 18.45 kB / 0.6552 GB, free: 32.48 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.633e-06/0.007983, allocations: 2.188 kB / 0.6552 GB, free: 32.48 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.293e-06/0.007984, allocations: 3.531 kB / 0.6552 GB, free: 32.48 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.368e-06/0.007989, allocations: 0 / 0.6552 GB, free: 32.48 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004129/0.008402, allocations: 0.4885 MB / 0.6557 GB, free: 32.08 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.693e-06/0.008403, allocations: 0 / 0.6557 GB, free: 32.08 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000107/0.00851, allocations: 41.25 kB / 0.6557 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.345e-06/0.008513, allocations: 0 / 0.6557 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.384e-05/0.008526, allocations: 11.59 kB / 0.6557 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.412e-06/0.008528, allocations: 1.5 kB / 0.6557 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.934e-06/0.00853, allocations: 0 / 0.6557 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002512/0.008781, allocations: 440.3 kB / 0.6562 GB, free: 31.75 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.557e-05/0.008797, allocations: 17.19 kB / 0.6562 GB, free: 31.74 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.035e-05/0.008817, allocations: 11.56 kB / 0.6562 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.465e-05/0.008882, allocations: 9.766 kB / 0.6562 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.442e-05/0.008926, allocations: 16.91 kB / 0.6562 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.438e-06/0.008935, allocations: 7.812 kB / 0.6562 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 3.645e-05/0.008972, allocations: 149.3 kB / 0.6564 GB, free: 31.6 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6e-08/0.008972, allocations: 1.156 kB / 0.6564 GB, free: 31.6 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001749/0.009147, allocations: 47.91 kB / 0.6564 GB, free: 31.59 MB / 0.5262 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 7.038e-05/0.009217, allocations: 115.8 kB / 0.6565 GB, free: 31.5 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002218/0.009439, allocations: 298.5 kB / 0.6568 GB, free: 31.26 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.563e-06/0.009441, allocations: 4 kB / 0.6568 GB, free: 31.25 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001139/0.009555, allocations: 149.9 kB / 0.6569 GB, free: 31.14 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002384/0.009793, allocations: 42.95 kB / 0.657 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001185/0.01098, allocations: 0.5711 MB / 0.6575 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.842e-05/0.01103, allocations: 82.84 kB / 0.6576 GB, free: 30.68 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 4.953e-05/0.01108, allocations: 23.67 kB / 0.6576 GB, free: 30.67 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001403/0.01122, allocations: 118.7 kB / 0.6578 GB, free: 30.6 MB / 0.5262 GB
Notification: Performance of SimCode: time 8.71e-07/0.01122, allocations: 0 / 0.6578 GB, free: 30.6 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004319/0.01554, allocations: 2.675 MB / 0.6604 GB, free: 30.37 MB / 0.5262 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 -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.894122747238725]