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 0.0008969/0.0008969, allocations: 92.2 kB / 20.19 MB, free: 4.363 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 0.0009153/0.0009153, allocations: 173.3 kB / 23.5 MB, free: 1.059 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 0.9595/0.9595, allocations: 177.1 MB / 203.8 MB, free: 5.637 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 1.506/1.506, allocations: 273.5 MB / 0.5213 GB, free: 14.89 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 1.653e-06/1.653e-06, allocations: 0 / 0.647 GB, free: 38.66 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.358e-05/2.524e-05, allocations: 9.844 kB / 0.647 GB, free: 38.66 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.002197/0.002222, allocations: 2.069 MB / 0.649 GB, free: 37.31 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0007191/0.002941, allocations: 0.5425 MB / 0.6495 GB, free: 36.95 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.279e-05/0.003014, allocations: 2.812 kB / 0.6495 GB, free: 36.95 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.000107/0.003121, allocations: 22.42 kB / 0.6495 GB, free: 36.94 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001237/0.003245, allocations: 53.88 kB / 0.6496 GB, free: 36.91 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001482/0.003393, allocations: 45.44 kB / 0.6496 GB, free: 36.89 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.000215/0.003608, allocations: 193.8 kB / 0.6498 GB, free: 36.84 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000119/0.003727, allocations: 33.2 kB / 0.6499 GB, free: 36.81 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001188/0.003846, allocations: 102.2 kB / 0.65 GB, free: 36.77 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001021/0.003948, allocations: 64.5 kB / 0.65 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.817e-05/0.003976, allocations: 16.38 kB / 0.65 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 1.948e-05/0.003996, allocations: 13.91 kB / 0.65 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 2.982e-05/0.004026, allocations: 25.08 kB / 0.6501 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 5.947e-05/0.004085, allocations: 62.17 kB / 0.6501 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.000167/0.004252, allocations: 118.9 kB / 0.6502 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.514e-06/0.004255, allocations: 0 / 0.6502 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.623e-06/0.004256, allocations: 2.188 kB / 0.6502 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.161e-06/0.004262, allocations: 1.25 kB / 0.6502 GB, free: 36.64 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 0.0005728/0.004835, allocations: 0.5157 MB / 0.6508 GB, free: 36.15 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.804e-05/0.004873, allocations: 9.844 kB / 0.6508 GB, free: 36.15 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.542e-05/0.004939, allocations: 28.03 kB / 0.6508 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002007/0.005139, allocations: 170.2 kB / 0.6509 GB, free: 35.98 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.223e-05/0.005152, allocations: 6.25 kB / 0.651 GB, free: 35.98 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.951e-05/0.005181, allocations: 19.22 kB / 0.651 GB, free: 35.98 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001729/0.005354, allocations: 141.3 kB / 0.6511 GB, free: 35.88 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.312e-05/0.005367, allocations: 11.48 kB / 0.6511 GB, free: 35.87 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.467e-05/0.005382, allocations: 7.375 kB / 0.6511 GB, free: 35.87 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.795e-06/0.00539, allocations: 7.469 kB / 0.6511 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001042/0.005494, allocations: 82.33 kB / 0.6512 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004273/0.005921, allocations: 400.9 kB / 0.6516 GB, free: 35.49 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001479/0.006069, allocations: 116.4 kB / 0.6517 GB, free: 35.41 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.362e-05/0.006123, allocations: 60.09 kB / 0.6518 GB, free: 35.37 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.037e-05/0.006133, allocations: 7.406 kB / 0.6518 GB, free: 35.37 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001656/0.006299, allocations: 203.7 kB / 0.652 GB, free: 35.2 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.864e-06/0.0063, allocations: 0 / 0.652 GB, free: 35.2 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0006994/0.007, allocations: 0.5758 MB / 0.6525 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.814e-05/0.007038, allocations: 139.8 kB / 0.6527 GB, free: 34.62 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.623e-05/0.007124, allocations: 200.1 kB / 0.6528 GB, free: 34.45 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.272e-05/0.007137, allocations: 32.95 kB / 0.6529 GB, free: 34.41 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.113e-05/0.007178, allocations: 156.6 kB / 0.653 GB, free: 34.26 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.204e-05/0.00721, allocations: 70.42 kB / 0.6531 GB, free: 34.21 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 4.9e-05/0.007259, allocations: 52.44 kB / 0.6531 GB, free: 34.17 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 4.911e-05/0.007308, allocations: 0.4977 MB / 0.6536 GB, free: 33.67 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.191e-05/0.00738, allocations: 101.4 kB / 0.6537 GB, free: 33.59 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.96e-05/0.00748, allocations: 196.5 kB / 0.6539 GB, free: 33.39 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001892/0.007669, allocations: 323.7 kB / 0.6542 GB, free: 33.1 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.643e-06/0.007671, allocations: 5.344 kB / 0.6542 GB, free: 33.1 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002442/0.007915, allocations: 311.1 kB / 0.6545 GB, free: 32.89 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.906e-05/0.007944, allocations: 66.03 kB / 0.6546 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.651e-06/0.007949, allocations: 4.219 kB / 0.6546 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.544e-05/0.007965, allocations: 3.938 kB / 0.6546 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001448/0.00811, allocations: 51.53 kB / 0.6546 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.833e-06/0.008116, allocations: 6.812 kB / 0.6547 GB, free: 32.81 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.972e-05/0.008196, allocations: 14.55 kB / 0.6547 GB, free: 32.81 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.31e-05/0.008209, allocations: 13.38 kB / 0.6547 GB, free: 32.8 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 0.0001443/0.008353, allocations: 228.4 kB / 0.6549 GB, free: 32.59 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.71e-05/0.008381, allocations: 30.38 kB / 0.6549 GB, free: 32.58 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.53e-05/0.008416, allocations: 18.5 kB / 0.6549 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.285e-06/0.008418, allocations: 0 / 0.6549 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.078e-06/0.008422, allocations: 1.281 kB / 0.6549 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.769e-06/0.008427, allocations: 7.125 kB / 0.655 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003452/0.008772, allocations: 0.517 MB / 0.6555 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.783e-06/0.008774, allocations: 0.5 kB / 0.6555 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000115/0.008889, allocations: 30.53 kB / 0.6555 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.876e-06/0.008892, allocations: 3.938 kB / 0.6555 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.344e-05/0.008905, allocations: 8.406 kB / 0.6555 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.363e-06/0.008907, allocations: 0 / 0.6555 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.62e-07/0.008908, allocations: 0 / 0.6555 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002744/0.009182, allocations: 463.1 kB / 0.6559 GB, free: 31.8 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.656e-05/0.009199, allocations: 18.95 kB / 0.656 GB, free: 31.79 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.379e-05/0.009222, allocations: 8.312 kB / 0.656 GB, free: 31.79 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.336e-05/0.009296, allocations: 16.28 kB / 0.656 GB, free: 31.79 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.027e-05/0.009356, allocations: 16.86 kB / 0.656 GB, free: 31.79 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.125e-05/0.009367, allocations: 9.875 kB / 0.656 GB, free: 31.78 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 4.329e-05/0.009411, allocations: 148.8 kB / 0.6562 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6.1e-08/0.009411, allocations: 0 / 0.6562 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002068/0.009617, allocations: 48.28 kB / 0.6562 GB, free: 31.65 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 9.009e-05/0.009708, allocations: 109.2 kB / 0.6563 GB, free: 31.56 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002334/0.009941, allocations: 323.2 kB / 0.6566 GB, free: 31.3 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.222e-06/0.009942, allocations: 0 / 0.6566 GB, free: 31.3 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 7.946e-05/0.01002, allocations: 149.4 kB / 0.6568 GB, free: 31.19 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002577/0.01028, allocations: 48.92 kB / 0.6568 GB, free: 31.17 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001264/0.01154, allocations: 0.5825 MB / 0.6574 GB, free: 30.81 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.567e-05/0.01159, allocations: 81.83 kB / 0.6574 GB, free: 30.73 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 6.051e-05/0.01165, allocations: 17.83 kB / 0.6575 GB, free: 30.72 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.758e-05/0.0117, allocations: 22.12 kB / 0.6575 GB, free: 30.71 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.91e-07/0.0117, allocations: 0 / 0.6575 GB, free: 30.71 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004158/0.01586, allocations: 2.439 MB / 0.6599 GB, free: 30.52 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: 4.676267000148073]