Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium.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 0.001192/0.001192, allocations: 91.55 kB / 20.19 MB, free: 4.199 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 0.001154/0.001154, allocations: 173 kB / 23.5 MB, free: 0.8906 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 0.9527/0.9527, allocations: 177.1 MB / 203.8 MB, free: 5.652 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 1.617/1.617, allocations: 273.5 MB / 0.5213 GB, free: 14.87 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.Pharmacogenomics.Patient_PKPG_1C_Lithium,tolerance=1e-06,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium")
translateModel(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium,tolerance=1e-06,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.024e-06/2.024e-06, allocations: 0 / 0.647 GB, free: 38.67 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.101e-05/3.303e-05, allocations: 5.406 kB / 0.647 GB, free: 38.66 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium): time 0.004421/0.004454, allocations: 2.916 MB / 0.6499 GB, free: 36.79 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001844/0.006298, allocations: 1.043 MB / 0.6509 GB, free: 36.13 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001872/0.006485, allocations: 2.906 kB / 0.6509 GB, free: 36.13 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0005423/0.007027, allocations: 134.7 kB / 0.651 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002541/0.007282, allocations: 112.9 kB / 0.6511 GB, free: 36.03 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0006045/0.007886, allocations: 183.3 kB / 0.6513 GB, free: 35.93 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0004832/0.008369, allocations: 419.5 kB / 0.6517 GB, free: 35.72 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001855/0.008555, allocations: 67.17 kB / 0.6518 GB, free: 35.69 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003008/0.008856, allocations: 206.1 kB / 0.652 GB, free: 35.61 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002695/0.009125, allocations: 135.5 kB / 0.6521 GB, free: 35.55 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 6.424e-05/0.009189, allocations: 30.09 kB / 0.6521 GB, free: 35.55 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0003014/0.009491, allocations: 167 kB / 0.6523 GB, free: 35.51 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001206/0.009611, allocations: 92.28 kB / 0.6524 GB, free: 35.45 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.000165/0.009776, allocations: 119.2 kB / 0.6525 GB, free: 35.4 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.000596/0.01037, allocations: 410.9 kB / 0.6529 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.328e-06/0.01038, allocations: 1.312 kB / 0.6529 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.943e-06/0.01038, allocations: 1.594 kB / 0.6529 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 9.909e-06/0.01039, allocations: 0 / 0.6529 GB, free: 35.21 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: 58
 * Number of variables: 58
Notification: Performance of Generate backend data structure: time 0.00107/0.01146, allocations: 0.8169 MB / 0.6537 GB, free: 34.5 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.769e-05/0.01151, allocations: 9.312 kB / 0.6537 GB, free: 34.5 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0003541/0.01186, allocations: 129.8 kB / 0.6538 GB, free: 34.45 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003305/0.01219, allocations: 243.6 kB / 0.654 GB, free: 34.24 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.773e-05/0.01222, allocations: 21.66 kB / 0.6541 GB, free: 34.23 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.774e-05/0.01228, allocations: 25.97 kB / 0.6541 GB, free: 34.22 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004862/0.01276, allocations: 330.3 kB / 0.6544 GB, free: 34.01 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.036e-05/0.01278, allocations: 11.83 kB / 0.6544 GB, free: 34 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.729e-05/0.01281, allocations: 16.75 kB / 0.6544 GB, free: 33.99 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.329e-05/0.01282, allocations: 5.875 kB / 0.6544 GB, free: 33.99 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003223/0.01315, allocations: 244.7 kB / 0.6547 GB, free: 33.84 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001066/0.01421, allocations: 0.6303 MB / 0.6553 GB, free: 33.4 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004828/0.01469, allocations: 283.4 kB / 0.6555 GB, free: 33.2 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001858/0.01488, allocations: 198 kB / 0.6557 GB, free: 33.05 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.693e-05/0.01491, allocations: 3.781 kB / 0.6557 GB, free: 33.05 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0004358/0.01534, allocations: 424 kB / 0.6561 GB, free: 32.7 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=39): time 2.905e-06/0.01535, allocations: 0.5625 kB / 0.6561 GB, free: 32.7 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41): time 0.002141/0.01749, allocations: 1.439 MB / 0.6575 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.466e-05/0.01755, allocations: 274.1 kB / 0.6578 GB, free: 31.33 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003232/0.01787, allocations: 355.3 kB / 0.6581 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 3.288e-05/0.01791, allocations: 34.05 kB / 0.6582 GB, free: 31.07 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001215/0.01803, allocations: 231 kB / 0.6584 GB, free: 30.87 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 9.701e-05/0.01813, allocations: 139 kB / 0.6585 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001238/0.01825, allocations: 86.47 kB / 0.6586 GB, free: 30.71 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 9.826e-05/0.01835, allocations: 0.5282 MB / 0.6591 GB, free: 30.2 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002357/0.01858, allocations: 243.6 kB / 0.6594 GB, free: 30 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002563/0.01884, allocations: 363 kB / 0.6597 GB, free: 29.65 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0006292/0.01947, allocations: 0.7337 MB / 0.6604 GB, free: 29 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.427e-06/0.01947, allocations: 0 / 0.6604 GB, free: 29 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=57) (initialization): time 0.0008205/0.02029, allocations: 0.6994 MB / 0.6611 GB, free: 28.52 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 6.222e-05/0.02035, allocations: 147.4 kB / 0.6613 GB, free: 28.36 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.388e-06/0.02036, allocations: 2.781 kB / 0.6613 GB, free: 28.36 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.175e-05/0.02039, allocations: 4.219 kB / 0.6613 GB, free: 28.36 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003231/0.02071, allocations: 86.41 kB / 0.6613 GB, free: 28.36 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.54e-05/0.02072, allocations: 5.969 kB / 0.6613 GB, free: 28.36 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001905/0.02091, allocations: 21.34 kB / 0.6614 GB, free: 28.35 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 9.197e-05/0.02101, allocations: 55.12 kB / 0.6614 GB, free: 28.34 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 10 variables:
         dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         dose.absorptionLumen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         dose.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
         dose.absorptionLumen.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         dose.absorptionLumen.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  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
         dose.absorptionLumen.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 10
 * Number of states: 0 ()
 * Number of discrete variables: 23 ($PRE.dose.absorptionLumen.Cmin,dose.absorptionLumen.Cmin,$PRE.dose.absorptionLumen.Cmax,dose.absorptionLumen.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.dose.pulse.count,$PRE.dose.pulse.T_start,$PRE.dose.absorptionLumen.rising,CYP2C19.status,SLC22A2.status,central.rising,dose.pulse.count,dose.pulse.T_start,dose.absorptionLumen.rising,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (52):
 * Single equations (assignments): 47
 * Array equations: 0
 * Algorithm blocks: 5
 * 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 0.0002769/0.02128, allocations: 347.6 kB / 0.6618 GB, free: 28.02 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001766/0.02146, allocations: 103.8 kB / 0.6618 GB, free: 27.98 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.349e-05/0.02152, allocations: 40.22 kB / 0.6619 GB, free: 27.95 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.873e-06/0.02153, allocations: 3.703 kB / 0.6619 GB, free: 27.95 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.175e-06/0.02153, allocations: 0 / 0.6619 GB, free: 27.95 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001533/0.02169, allocations: 68.05 kB / 0.662 GB, free: 27.92 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.523e-05/0.02175, allocations: 23.88 kB / 0.662 GB, free: 27.91 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001427/0.02189, allocations: 15.81 kB / 0.662 GB, free: 27.91 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001096/0.022, allocations: 39.08 kB / 0.662 GB, free: 27.89 MB / 0.5262 GB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.0008603/0.02286, allocations: 0.6944 MB / 0.6627 GB, free: 27.41 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.001077/0.02394, allocations: 1.126 MB / 0.6638 GB, free: 26.57 MB / 0.5262 GB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0002721/0.02421, allocations: 244.3 kB / 0.664 GB, free: 26.41 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0002054/0.02442, allocations: 235.5 kB / 0.6643 GB, free: 26.26 MB / 0.5262 GB
Notification: Performance of Backend: time 5.21e-07/0.02442, allocations: 0 / 0.6643 GB, free: 26.26 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.001085/0.0255, allocations: 0.7293 MB / 0.665 GB, free: 25.65 MB / 0.5262 GB
Notification: Performance of SimCode: time 0.002662/0.02817, allocations: 1.784 MB / 0.6667 GB, free: 24.14 MB / 0.5262 GB
Notification: Performance of Templates: time 0.01271/0.04088, allocations: 6.049 MB / 0.6726 GB, free: 23.63 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.742651218082756]