Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.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 0.001439/0.001439, allocations: 92.22 kB / 19.65 MB, free: 280 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 0.001621/0.001621, allocations: 169 kB / 23.02 MB, free: 1.551 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 0.9605/0.9605, allocations: 177.1 MB / 203.4 MB, free: 5.547 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 1.595/1.595, allocations: 273.5 MB / 0.5209 GB, free: 14.73 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.PK_1C_Digoxin,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin")
translateModel(Pharmacolibrary.Examples.PK_1C_Digoxin,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.393e-06/1.393e-06, allocations: 1.203 kB / 0.647 GB, free: 38.74 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.626e-05/1.765e-05, allocations: 2.312 kB / 0.647 GB, free: 38.74 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.002169/0.002186, allocations: 2.074 MB / 0.649 GB, free: 37.39 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0007711/0.002957, allocations: 0.5464 MB / 0.6495 GB, free: 37.04 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.991e-05/0.003027, allocations: 4.688 kB / 0.6495 GB, free: 37.04 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001099/0.003137, allocations: 21.64 kB / 0.6495 GB, free: 37.02 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001323/0.003269, allocations: 52.98 kB / 0.6496 GB, free: 37 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001608/0.00343, allocations: 40.8 kB / 0.6496 GB, free: 36.98 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002098/0.00364, allocations: 193.3 kB / 0.6498 GB, free: 36.93 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001111/0.003751, allocations: 35.02 kB / 0.6499 GB, free: 36.89 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.000128/0.003879, allocations: 105.9 kB / 0.65 GB, free: 36.85 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 9.53e-05/0.003975, allocations: 56.41 kB / 0.65 GB, free: 36.84 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.722e-05/0.004002, allocations: 13.06 kB / 0.65 GB, free: 36.84 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.088e-05/0.004023, allocations: 14.38 kB / 0.65 GB, free: 36.84 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 2.913e-05/0.004052, allocations: 33.41 kB / 0.6501 GB, free: 36.81 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 5.717e-05/0.004109, allocations: 58.34 kB / 0.6501 GB, free: 36.79 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001669/0.004276, allocations: 117.6 kB / 0.6502 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 1.803e-06/0.004278, allocations: 1.344 kB / 0.6502 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 6.92e-07/0.004278, allocations: 0 / 0.6502 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.108e-06/0.004282, allocations: 0 / 0.6502 GB, free: 36.73 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 0.0005084/0.004791, allocations: 0.512 MB / 0.6507 GB, free: 36.24 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.478e-05/0.004826, allocations: 10.28 kB / 0.6507 GB, free: 36.24 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.626e-05/0.004882, allocations: 25.81 kB / 0.6508 GB, free: 36.23 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001427/0.005025, allocations: 168 kB / 0.6509 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.933e-05/0.005044, allocations: 10.25 kB / 0.6509 GB, free: 36.06 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.681e-05/0.005071, allocations: 14.84 kB / 0.651 GB, free: 36.06 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002204/0.005291, allocations: 134.4 kB / 0.6511 GB, free: 35.97 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.821e-05/0.005309, allocations: 5.781 kB / 0.6511 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.668e-05/0.005326, allocations: 10.16 kB / 0.6511 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.197e-06/0.005335, allocations: 2.219 kB / 0.6511 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001242/0.005459, allocations: 84.78 kB / 0.6512 GB, free: 35.92 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004234/0.005883, allocations: 403.3 kB / 0.6516 GB, free: 35.59 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001402/0.006023, allocations: 119.4 kB / 0.6517 GB, free: 35.51 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.021e-05/0.006073, allocations: 64.03 kB / 0.6517 GB, free: 35.46 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.257e-06/0.006082, allocations: 3.5 kB / 0.6517 GB, free: 35.46 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001607/0.006243, allocations: 201.3 kB / 0.6519 GB, free: 35.29 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.743e-06/0.006245, allocations: 0 / 0.6519 GB, free: 35.29 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.00066/0.006905, allocations: 0.5767 MB / 0.6525 GB, free: 34.88 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.544e-05/0.00695, allocations: 139.2 kB / 0.6526 GB, free: 34.71 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001031/0.007053, allocations: 201.3 kB / 0.6528 GB, free: 34.54 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.423e-05/0.007068, allocations: 33.08 kB / 0.6529 GB, free: 34.5 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 6.143e-05/0.007129, allocations: 162 kB / 0.653 GB, free: 34.35 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.015e-05/0.007169, allocations: 70.23 kB / 0.6531 GB, free: 34.3 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.234e-05/0.007232, allocations: 53.89 kB / 0.6531 GB, free: 34.26 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.713e-05/0.007299, allocations: 0.4953 MB / 0.6536 GB, free: 33.76 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.501e-05/0.007384, allocations: 108.1 kB / 0.6537 GB, free: 33.68 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000104/0.007488, allocations: 189.6 kB / 0.6539 GB, free: 33.48 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00024/0.007728, allocations: 322.5 kB / 0.6542 GB, free: 33.19 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.823e-06/0.007729, allocations: 0 / 0.6542 GB, free: 33.19 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002798/0.008009, allocations: 317.7 kB / 0.6545 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.311e-05/0.008042, allocations: 62.12 kB / 0.6546 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.222e-06/0.008049, allocations: 2.375 kB / 0.6546 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.747e-05/0.008066, allocations: 3.375 kB / 0.6546 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001605/0.008227, allocations: 54.02 kB / 0.6546 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.335e-06/0.008235, allocations: 6.719 kB / 0.6546 GB, free: 32.9 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.768e-05/0.008313, allocations: 15.11 kB / 0.6546 GB, free: 32.9 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.826e-05/0.008331, allocations: 14.12 kB / 0.6547 GB, free: 32.9 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 0.0001297/0.00846, allocations: 217.5 kB / 0.6549 GB, free: 32.69 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.145e-05/0.008492, allocations: 21.25 kB / 0.6549 GB, free: 32.68 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 2.748e-05/0.008519, allocations: 22.41 kB / 0.6549 GB, free: 32.67 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.198e-06/0.008524, allocations: 3.281 kB / 0.6549 GB, free: 32.67 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.54e-06/0.008529, allocations: 0.5625 kB / 0.6549 GB, free: 32.67 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.027e-06/0.008533, allocations: 3.938 kB / 0.6549 GB, free: 32.67 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003391/0.008872, allocations: 0.5269 MB / 0.6554 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.643e-06/0.008874, allocations: 0 / 0.6554 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000103/0.008977, allocations: 31.31 kB / 0.6555 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.324e-06/0.008979, allocations: 2.156 kB / 0.6555 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.211e-05/0.008991, allocations: 6.219 kB / 0.6555 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.743e-06/0.008993, allocations: 1.469 kB / 0.6555 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.62e-07/0.008994, allocations: 0 / 0.6555 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002815/0.009276, allocations: 462.5 kB / 0.6559 GB, free: 31.91 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.621e-05/0.009292, allocations: 17.22 kB / 0.6559 GB, free: 31.89 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.396e-05/0.009316, allocations: 6.219 kB / 0.6559 GB, free: 31.89 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.082e-05/0.009387, allocations: 13.97 kB / 0.6559 GB, free: 31.89 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.663e-05/0.009443, allocations: 16.09 kB / 0.656 GB, free: 31.88 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.32e-05/0.009456, allocations: 8.719 kB / 0.656 GB, free: 31.88 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 5.951e-05/0.009516, allocations: 149.2 kB / 0.6561 GB, free: 31.76 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5.1e-08/0.009516, allocations: 0.5312 kB / 0.6561 GB, free: 31.76 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.000215/0.009731, allocations: 47.66 kB / 0.6562 GB, free: 31.75 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 9.982e-05/0.009831, allocations: 109.9 kB / 0.6563 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003673/0.0102, allocations: 323.4 kB / 0.6566 GB, free: 31.4 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 2.174e-06/0.0102, allocations: 0.5625 kB / 0.6566 GB, free: 31.4 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001458/0.01035, allocations: 151 kB / 0.6567 GB, free: 31.29 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002971/0.01064, allocations: 48.38 kB / 0.6568 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001314/0.01196, allocations: 0.5845 MB / 0.6573 GB, free: 30.9 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.17e-05/0.01201, allocations: 86.72 kB / 0.6574 GB, free: 30.82 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.884e-05/0.01207, allocations: 13.11 kB / 0.6574 GB, free: 30.82 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.501e-05/0.01211, allocations: 19.78 kB / 0.6574 GB, free: 30.81 MB / 0.5262 GB
Notification: Performance of SimCode: time 8.41e-07/0.01211, allocations: 0 / 0.6574 GB, free: 30.81 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004221/0.01633, allocations: 2.572 MB / 0.66 GB, free: 30.61 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.640456020832062]