Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.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 0.0009442/0.0009442, allocations: 92.22 kB / 19.65 MB, free: 276 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 0.001059/0.001059, allocations: 173 kB / 23.03 MB, free: 1.539 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 0.8864/0.8864, allocations: 177.1 MB / 203.4 MB, free: 5.566 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 1.53/1.53, allocations: 273.5 MB / 0.5209 GB, free: 14.8 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_LithiumCarbonate,tolerance=1e-09,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate")
translateModel(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate,tolerance=1e-09,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.332e-06/1.332e-06, allocations: 0 / 0.647 GB, free: 38.65 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.64e-05/1.773e-05, allocations: 7.359 kB / 0.647 GB, free: 38.65 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate): time 0.002079/0.002097, allocations: 2.123 MB / 0.649 GB, free: 37.27 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0007129/0.00281, allocations: 0.5525 MB / 0.6496 GB, free: 36.91 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.765e-05/0.002878, allocations: 2.125 kB / 0.6496 GB, free: 36.91 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001059/0.002984, allocations: 23.47 kB / 0.6496 GB, free: 36.89 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001274/0.003111, allocations: 49.84 kB / 0.6496 GB, free: 36.88 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001476/0.003259, allocations: 46.22 kB / 0.6497 GB, free: 36.85 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.000198/0.003457, allocations: 210.5 kB / 0.6499 GB, free: 36.78 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001069/0.003564, allocations: 31.97 kB / 0.6499 GB, free: 36.76 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.000116/0.00368, allocations: 103.3 kB / 0.65 GB, free: 36.72 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 9.921e-05/0.003779, allocations: 62.27 kB / 0.6501 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.767e-05/0.003806, allocations: 15.12 kB / 0.6501 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.066e-05/0.003827, allocations: 16.34 kB / 0.6501 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 2.753e-05/0.003855, allocations: 29.86 kB / 0.6501 GB, free: 36.68 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 6.326e-05/0.003918, allocations: 60.55 kB / 0.6502 GB, free: 36.65 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001527/0.004071, allocations: 129.7 kB / 0.6503 GB, free: 36.59 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.064e-06/0.004073, allocations: 1.156 kB / 0.6503 GB, free: 36.59 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 8.92e-07/0.004074, allocations: 0 / 0.6503 GB, free: 36.59 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.068e-06/0.004078, allocations: 3.938 kB / 0.6503 GB, free: 36.58 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 0.0005156/0.004593, allocations: 0.5299 MB / 0.6508 GB, free: 36.09 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.32e-05/0.004626, allocations: 10.72 kB / 0.6509 GB, free: 36.09 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.561e-05/0.004682, allocations: 28.72 kB / 0.6509 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001359/0.004818, allocations: 155 kB / 0.651 GB, free: 35.92 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.073e-05/0.004839, allocations: 14.12 kB / 0.651 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.047e-05/0.004869, allocations: 13.69 kB / 0.6511 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001715/0.005041, allocations: 137.8 kB / 0.6512 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.187e-05/0.005052, allocations: 10.23 kB / 0.6512 GB, free: 35.81 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.158e-05/0.005064, allocations: 4 kB / 0.6512 GB, free: 35.81 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.753e-06/0.005071, allocations: 4.938 kB / 0.6512 GB, free: 35.81 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 9.345e-05/0.005164, allocations: 83.77 kB / 0.6513 GB, free: 35.77 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003995/0.005564, allocations: 405.6 kB / 0.6517 GB, free: 35.44 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001321/0.005696, allocations: 123.5 kB / 0.6518 GB, free: 35.36 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.127e-05/0.005747, allocations: 62.95 kB / 0.6518 GB, free: 35.3 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.668e-06/0.005757, allocations: 9.281 kB / 0.6519 GB, free: 35.3 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002623/0.006019, allocations: 203.5 kB / 0.6521 GB, free: 35.14 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 2.865e-06/0.006022, allocations: 0 / 0.6521 GB, free: 35.14 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0008989/0.006921, allocations: 0.573 MB / 0.6526 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.269e-05/0.006953, allocations: 134.4 kB / 0.6527 GB, free: 34.56 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.589e-05/0.007039, allocations: 219 kB / 0.6529 GB, free: 34.38 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.324e-05/0.007053, allocations: 33.36 kB / 0.653 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.038e-05/0.007093, allocations: 152.7 kB / 0.6531 GB, free: 34.2 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.018e-05/0.007123, allocations: 67.41 kB / 0.6532 GB, free: 34.14 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 4.942e-05/0.007173, allocations: 57.2 kB / 0.6532 GB, free: 34.11 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 4.655e-05/0.007219, allocations: 0.5017 MB / 0.6537 GB, free: 33.6 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.042e-05/0.00729, allocations: 106.1 kB / 0.6538 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.222e-05/0.007372, allocations: 193.1 kB / 0.654 GB, free: 33.31 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001782/0.00755, allocations: 322.3 kB / 0.6543 GB, free: 33.02 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.162e-06/0.007551, allocations: 0 / 0.6543 GB, free: 33.02 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002264/0.007778, allocations: 311.8 kB / 0.6546 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.416e-05/0.007802, allocations: 63.47 kB / 0.6547 GB, free: 32.75 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.909e-06/0.007807, allocations: 3.375 kB / 0.6547 GB, free: 32.75 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.194e-05/0.007819, allocations: 4.656 kB / 0.6547 GB, free: 32.75 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001513/0.00797, allocations: 52.97 kB / 0.6547 GB, free: 32.75 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.697e-06/0.007978, allocations: 7.812 kB / 0.6548 GB, free: 32.75 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.397e-05/0.008052, allocations: 12.31 kB / 0.6548 GB, free: 32.74 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.593e-05/0.008068, allocations: 14.53 kB / 0.6548 GB, free: 32.74 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 6 variables:
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" 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,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.central.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,central.rising,$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 0.0001263/0.008195, allocations: 231.6 kB / 0.655 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.253e-05/0.008227, allocations: 29.44 kB / 0.655 GB, free: 32.51 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 2.834e-05/0.008256, allocations: 19.36 kB / 0.655 GB, free: 32.5 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.587e-06/0.008259, allocations: 1.688 kB / 0.655 GB, free: 32.5 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.396e-06/0.008263, allocations: 0.5625 kB / 0.655 GB, free: 32.5 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.489e-06/0.008267, allocations: 5.875 kB / 0.6551 GB, free: 32.49 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003209/0.008588, allocations: 0.5202 MB / 0.6556 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.452e-06/0.008589, allocations: 1.5 kB / 0.6556 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001016/0.008691, allocations: 32.08 kB / 0.6556 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.024e-06/0.008693, allocations: 2.688 kB / 0.6556 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.454e-05/0.008708, allocations: 15.67 kB / 0.6556 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.142e-06/0.008709, allocations: 0 / 0.6556 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.323e-06/0.00871, allocations: 0 / 0.6556 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002717/0.008982, allocations: 451.5 kB / 0.656 GB, free: 31.74 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.873e-05/0.009001, allocations: 19.81 kB / 0.6561 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.474e-05/0.009025, allocations: 14.06 kB / 0.6561 GB, free: 31.72 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.107e-05/0.009096, allocations: 13.97 kB / 0.6561 GB, free: 31.71 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.431e-05/0.009151, allocations: 24.92 kB / 0.6561 GB, free: 31.71 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.161e-05/0.009162, allocations: 5 kB / 0.6561 GB, free: 31.71 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 5.069e-05/0.009213, allocations: 156.7 kB / 0.6563 GB, free: 31.58 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.009213, allocations: 0 / 0.6563 GB, free: 31.58 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002028/0.009416, allocations: 53.19 kB / 0.6563 GB, free: 31.57 MB / 0.5262 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (central.C,central.AUC,elim.MExc,periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass)
 * Number of discrete variables: 8 ($whenCondition1,$whenCondition2,$whenCondition3,central.Cmax,central.Cmin,central.rising,periodicDose.pulse.T_start,periodicDose.pulse.count)
 * Number of discrete states: 6 (periodicDose.pulse.count,central.Cmin,$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 6.726e-05/0.009483, allocations: 105 kB / 0.6564 GB, free: 31.48 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002667/0.00975, allocations: 330.4 kB / 0.6567 GB, free: 31.22 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.483e-06/0.009751, allocations: 0 / 0.6567 GB, free: 31.22 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001059/0.009857, allocations: 158.8 kB / 0.6569 GB, free: 31.1 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002619/0.01012, allocations: 48.64 kB / 0.6569 GB, free: 31.09 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001217/0.01134, allocations: 0.5943 MB / 0.6575 GB, free: 30.71 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 3.463e-05/0.01137, allocations: 78.78 kB / 0.6576 GB, free: 30.64 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.291e-05/0.01142, allocations: 26.03 kB / 0.6576 GB, free: 30.63 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 3.78e-05/0.01146, allocations: 18.38 kB / 0.6576 GB, free: 30.62 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.72e-07/0.01146, allocations: 0 / 0.6576 GB, free: 30.62 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004101/0.01556, allocations: 2.869 MB / 0.6604 GB, free: 30.39 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.1452692886814475]