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 0.001467/0.001467, allocations: 73.97 kB / 20.66 MB, free: 3.844 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 0.001678/0.001678, allocations: 169.4 kB / 24.06 MB, free: 456 kB / 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 0.9659/0.9659, allocations: 177.1 MB / 204.5 MB, free: 5.5 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 1.584/1.584, allocations: 273.5 MB / 0.522 GB, free: 14.67 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 1.734e-06/1.734e-06, allocations: 0 / 0.6482 GB, free: 38.45 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.653e-05/2.826e-05, allocations: 2.312 kB / 0.6482 GB, free: 38.44 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.003221/0.003249, allocations: 2.06 MB / 0.6502 GB, free: 37.1 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0008903/0.004139, allocations: 0.5437 MB / 0.6507 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.643e-05/0.004225, allocations: 6.188 kB / 0.6507 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001156/0.004341, allocations: 16.64 kB / 0.6507 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001451/0.004486, allocations: 53 kB / 0.6508 GB, free: 36.71 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001664/0.004653, allocations: 46.38 kB / 0.6508 GB, free: 36.68 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002424/0.004895, allocations: 187.9 kB / 0.651 GB, free: 36.63 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001255/0.00502, allocations: 33.25 kB / 0.651 GB, free: 36.61 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001514/0.005172, allocations: 106.1 kB / 0.6511 GB, free: 36.56 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001234/0.005295, allocations: 58.31 kB / 0.6512 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.295e-05/0.005328, allocations: 17.8 kB / 0.6512 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.494e-05/0.005353, allocations: 13.88 kB / 0.6512 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 3.563e-05/0.005389, allocations: 27.53 kB / 0.6513 GB, free: 36.52 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 6.444e-05/0.005453, allocations: 54.06 kB / 0.6513 GB, free: 36.5 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001699/0.005623, allocations: 124.7 kB / 0.6514 GB, free: 36.44 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 3.596e-06/0.005627, allocations: 0 / 0.6514 GB, free: 36.44 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.323e-06/0.005628, allocations: 1.125 kB / 0.6514 GB, free: 36.44 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.188e-06/0.005632, allocations: 0 / 0.6514 GB, free: 36.44 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 0.0005625/0.006195, allocations: 0.5152 MB / 0.6519 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.332e-05/0.006238, allocations: 10.84 kB / 0.6519 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.32e-05/0.006301, allocations: 29.91 kB / 0.652 GB, free: 35.93 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001547/0.006456, allocations: 154.7 kB / 0.6521 GB, free: 35.78 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.376e-05/0.00648, allocations: 18.03 kB / 0.6521 GB, free: 35.77 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.984e-05/0.006509, allocations: 16.84 kB / 0.6521 GB, free: 35.77 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001994/0.006709, allocations: 137.1 kB / 0.6523 GB, free: 35.67 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.485e-05/0.006724, allocations: 7.172 kB / 0.6523 GB, free: 35.67 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.173e-05/0.006735, allocations: 1.938 kB / 0.6523 GB, free: 35.67 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.003e-06/0.006742, allocations: 3.656 kB / 0.6523 GB, free: 35.67 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 9.992e-05/0.006842, allocations: 75.2 kB / 0.6524 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004725/0.007315, allocations: 378.4 kB / 0.6527 GB, free: 35.32 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001359/0.007451, allocations: 117.2 kB / 0.6528 GB, free: 35.25 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 4.082e-05/0.007492, allocations: 60.66 kB / 0.6529 GB, free: 35.2 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.879e-06/0.007502, allocations: 3.906 kB / 0.6529 GB, free: 35.2 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001583/0.00766, allocations: 186.7 kB / 0.6531 GB, free: 35.04 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.864e-06/0.007662, allocations: 0 / 0.6531 GB, free: 35.04 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0005906/0.008252, allocations: 0.5404 MB / 0.6536 GB, free: 34.65 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.335e-05/0.008296, allocations: 135.9 kB / 0.6537 GB, free: 34.49 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.234e-05/0.008378, allocations: 202.8 kB / 0.6539 GB, free: 34.31 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.445e-05/0.008392, allocations: 33.23 kB / 0.654 GB, free: 34.28 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 5.418e-05/0.008447, allocations: 161.4 kB / 0.6541 GB, free: 34.12 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.297e-05/0.00848, allocations: 73.45 kB / 0.6542 GB, free: 34.07 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.556e-05/0.008535, allocations: 54.17 kB / 0.6542 GB, free: 34.03 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 9.965e-05/0.008635, allocations: 0.5013 MB / 0.6547 GB, free: 33.53 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.5e-05/0.00871, allocations: 94.31 kB / 0.6548 GB, free: 33.45 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.76e-05/0.008807, allocations: 192.1 kB / 0.655 GB, free: 33.25 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001887/0.008996, allocations: 307.6 kB / 0.6553 GB, free: 32.96 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.322e-06/0.008997, allocations: 1.469 kB / 0.6553 GB, free: 32.96 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002331/0.00923, allocations: 292.6 kB / 0.6556 GB, free: 32.77 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.87e-05/0.009269, allocations: 67.42 kB / 0.6556 GB, free: 32.7 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.582e-06/0.009276, allocations: 2.188 kB / 0.6556 GB, free: 32.7 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.258e-05/0.009288, allocations: 2.219 kB / 0.6556 GB, free: 32.7 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000132/0.00942, allocations: 51.45 kB / 0.6557 GB, free: 32.7 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.008e-06/0.009424, allocations: 1.781 kB / 0.6557 GB, free: 32.7 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.102e-05/0.009495, allocations: 16.16 kB / 0.6557 GB, free: 32.69 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.618e-05/0.009512, allocations: 14.56 kB / 0.6557 GB, free: 32.68 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 0.0001382/0.00965, allocations: 230.8 kB / 0.6559 GB, free: 32.47 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.852e-05/0.009678, allocations: 24.31 kB / 0.656 GB, free: 32.46 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 2.874e-05/0.009707, allocations: 18.86 kB / 0.656 GB, free: 32.45 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.098e-06/0.009711, allocations: 5.156 kB / 0.656 GB, free: 32.45 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.984e-06/0.009713, allocations: 0.5312 kB / 0.656 GB, free: 32.45 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.657e-06/0.009717, allocations: 0.5312 kB / 0.656 GB, free: 32.45 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003558/0.01007, allocations: 494.9 kB / 0.6565 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.694e-06/0.01007, allocations: 0 / 0.6565 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001039/0.01018, allocations: 37.42 kB / 0.6565 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 1.923e-06/0.01018, allocations: 0 / 0.6565 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.094e-05/0.01019, allocations: 10.81 kB / 0.6565 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.224e-06/0.01019, allocations: 1.688 kB / 0.6565 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.163e-06/0.01019, allocations: 0 / 0.6565 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002455/0.01044, allocations: 440.6 kB / 0.6569 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.291e-05/0.01046, allocations: 13.28 kB / 0.6569 GB, free: 31.72 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.452e-05/0.01049, allocations: 11.72 kB / 0.657 GB, free: 31.71 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.024e-05/0.01056, allocations: 15.3 kB / 0.657 GB, free: 31.71 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.115e-05/0.0106, allocations: 16.64 kB / 0.657 GB, free: 31.7 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.073e-05/0.01061, allocations: 14.2 kB / 0.657 GB, free: 31.7 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 3.521e-05/0.01064, allocations: 146.2 kB / 0.6571 GB, free: 31.58 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6e-08/0.01064, allocations: 1.781 kB / 0.6571 GB, free: 31.58 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001713/0.01082, allocations: 50.59 kB / 0.6572 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 (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 8.262e-05/0.0109, allocations: 109.1 kB / 0.6573 GB, free: 31.47 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002308/0.01113, allocations: 305.8 kB / 0.6576 GB, free: 31.22 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.723e-06/0.01113, allocations: 2.25 kB / 0.6576 GB, free: 31.22 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.000111/0.01124, allocations: 144 kB / 0.6577 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002813/0.01152, allocations: 44.34 kB / 0.6578 GB, free: 31.1 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001263/0.01279, allocations: 0.5695 MB / 0.6583 GB, free: 30.73 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.972e-05/0.01284, allocations: 86 kB / 0.6584 GB, free: 30.64 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.605e-05/0.01289, allocations: 17.92 kB / 0.6584 GB, free: 30.64 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001345/0.01303, allocations: 118.2 kB / 0.6585 GB, free: 30.57 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.12e-07/0.01303, allocations: 0.5625 kB / 0.6585 GB, free: 30.57 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004283/0.01731, allocations: 2.741 MB / 0.6612 GB, free: 30.33 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: 4.829128849785775]