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 0.00236/0.00236, allocations: 80.44 kB / 19.17 MB, free: 0.7422 MB / 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 0.002744/0.002744, allocations: 169.9 kB / 22.45 MB, free: 2.109 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 1.738/1.738, allocations: 177.1 MB / 202.8 MB, free: 5.746 MB / 186.7 MB
"
[Timeout remaining time 178]
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 3.619/3.619, allocations: 274 MB / 0.5207 GB, free: 14.84 MB / 458.7 MB
"
[Timeout remaining time 176]
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 4.058e-06/4.058e-06, allocations: 4 kB / 0.7563 GB, free: 9.906 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.522e-05/2.928e-05, allocations: 2.281 kB / 0.7563 GB, free: 9.902 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.003485/0.003514, allocations: 1.979 MB / 0.7582 GB, free: 7.93 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.001117/0.004631, allocations: 0.5352 MB / 0.7587 GB, free: 7.398 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.847e-05/0.00471, allocations: 0 / 0.7587 GB, free: 7.398 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001326/0.004842, allocations: 23.78 kB / 0.7587 GB, free: 7.375 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001521/0.004995, allocations: 52.55 kB / 0.7588 GB, free: 7.34 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001716/0.005166, allocations: 39.95 kB / 0.7588 GB, free: 7.301 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0002887/0.005455, allocations: 198.8 kB / 0.759 GB, free: 7.129 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001383/0.005593, allocations: 21.91 kB / 0.759 GB, free: 7.098 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001733/0.005766, allocations: 103.8 kB / 0.7591 GB, free: 6.996 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001423/0.005909, allocations: 63.8 kB / 0.7592 GB, free: 6.934 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 3.678e-05/0.005946, allocations: 12 kB / 0.7592 GB, free: 6.922 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.566e-05/0.005981, allocations: 16 kB / 0.7592 GB, free: 6.906 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 4.923e-05/0.00603, allocations: 27.91 kB / 0.7593 GB, free: 6.879 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 9.622e-05/0.006127, allocations: 59.84 kB / 0.7593 GB, free: 6.82 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002621/0.006389, allocations: 155.5 kB / 0.7595 GB, free: 6.668 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 4.989e-06/0.006394, allocations: 7.938 kB / 0.7595 GB, free: 6.66 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 7.51e-07/0.006395, allocations: 8 kB / 0.7595 GB, free: 6.652 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 4.619e-06/0.006399, allocations: 0 / 0.7595 GB, free: 6.652 MB / 0.5887 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 0.0009444/0.007344, allocations: 436.8 kB / 0.7599 GB, free: 6.184 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 4.201e-05/0.007386, allocations: 8.031 kB / 0.7599 GB, free: 6.176 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.249e-05/0.007448, allocations: 16.84 kB / 0.7599 GB, free: 6.16 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003936/0.007842, allocations: 173.5 kB / 0.7601 GB, free: 5.965 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.19e-05/0.007864, allocations: 16.3 kB / 0.7601 GB, free: 5.949 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.836e-05/0.007912, allocations: 24.31 kB / 0.7601 GB, free: 5.926 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003563/0.008268, allocations: 152.5 kB / 0.7603 GB, free: 5.766 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.484e-05/0.008293, allocations: 15.12 kB / 0.7603 GB, free: 5.754 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.745e-05/0.008311, allocations: 4 kB / 0.7603 GB, free: 5.75 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.354e-06/0.008318, allocations: 4 kB / 0.7603 GB, free: 5.746 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003398/0.008658, allocations: 125.6 kB / 0.7604 GB, free: 5.617 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007269/0.009385, allocations: 360.1 kB / 0.7608 GB, free: 5.234 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004136/0.009798, allocations: 164.3 kB / 0.7609 GB, free: 5.059 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001915/0.00999, allocations: 93.02 kB / 0.761 GB, free: 4.961 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.17e-05/0.01, allocations: 0 / 0.761 GB, free: 4.961 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003992/0.0104, allocations: 228.2 kB / 0.7612 GB, free: 4.707 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=20): time 1.413e-06/0.0104, allocations: 0 / 0.7612 GB, free: 4.707 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=21): time 0.001578/0.01198, allocations: 0.6749 MB / 0.7619 GB, free: 3.973 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001127/0.01209, allocations: 136.5 kB / 0.762 GB, free: 3.809 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001682/0.01226, allocations: 152.6 kB / 0.7621 GB, free: 3.652 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 3.523e-05/0.0123, allocations: 33.7 kB / 0.7622 GB, free: 3.613 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 9.193e-05/0.01239, allocations: 112.5 kB / 0.7623 GB, free: 3.5 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 7.135e-05/0.01246, allocations: 67.44 kB / 0.7624 GB, free: 3.434 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.191e-05/0.01254, allocations: 53.69 kB / 0.7624 GB, free: 3.375 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 0.0001911/0.01273, allocations: 326.8 kB / 0.7627 GB, free: 3.047 MB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002459/0.01298, allocations: 132.7 kB / 0.7628 GB, free: 2.902 MB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005347/0.01351, allocations: 211.4 kB / 0.763 GB, free: 2.656 MB / 0.5887 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0009721/0.01449, allocations: 0.5029 MB / 0.7635 GB, free: 2.094 MB / 0.5887 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.824e-06/0.01449, allocations: 3.938 kB / 0.7635 GB, free: 2.09 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0006576/0.01514, allocations: 380 kB / 0.7639 GB, free: 1.688 MB / 0.5887 GB
Notification: Performance of prepare postOptimizeDAE: time 5.821e-05/0.0152, allocations: 59.41 kB / 0.764 GB, free: 1.617 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.35e-06/0.01521, allocations: 0 / 0.764 GB, free: 1.617 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.425e-05/0.01523, allocations: 7.984 kB / 0.764 GB, free: 1.609 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002174/0.01545, allocations: 47.92 kB / 0.764 GB, free: 1.562 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.317e-05/0.01546, allocations: 7.922 kB / 0.764 GB, free: 1.555 MB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001591/0.01562, allocations: 20 kB / 0.764 GB, free: 1.535 MB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.182e-05/0.01564, allocations: 12.17 kB / 0.764 GB, free: 1.523 MB / 0.5887 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 0.0002405/0.01588, allocations: 188.7 kB / 0.7642 GB, free: 1.332 MB / 0.5887 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.164e-05/0.01592, allocations: 15.91 kB / 0.7642 GB, free: 1.316 MB / 0.5887 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.545e-05/0.01596, allocations: 21.28 kB / 0.7643 GB, free: 1.301 MB / 0.5887 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.779e-06/0.01597, allocations: 3.984 kB / 0.7643 GB, free: 1.297 MB / 0.5887 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.267e-06/0.01598, allocations: 7.938 kB / 0.7643 GB, free: 1.289 MB / 0.5887 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.307e-06/0.01598, allocations: 0 / 0.7643 GB, free: 1.289 MB / 0.5887 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008353/0.01681, allocations: 0.5056 MB / 0.7648 GB, free: 0.7305 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.663e-06/0.01682, allocations: 0 / 0.7648 GB, free: 0.7305 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002021/0.01702, allocations: 35.97 kB / 0.7648 GB, free: 0.6953 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.004e-06/0.01702, allocations: 0 / 0.7648 GB, free: 0.6953 MB / 0.5887 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.182e-05/0.01704, allocations: 12 kB / 0.7648 GB, free: 0.6836 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.533e-06/0.01704, allocations: 0 / 0.7648 GB, free: 0.6836 MB / 0.5887 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.433e-06/0.01704, allocations: 0 / 0.7648 GB, free: 0.6836 MB / 0.5887 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0008293/0.01787, allocations: 488.7 kB / 0.7653 GB, free: 176 kB / 0.5887 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.862e-05/0.0179, allocations: 15.89 kB / 0.7653 GB, free: 160 kB / 0.5887 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.472e-05/0.01794, allocations: 8.062 kB / 0.7653 GB, free: 152 kB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001454/0.01808, allocations: 7.984 kB / 0.7653 GB, free: 144 kB / 0.5887 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.765e-05/0.01816, allocations: 19.97 kB / 0.7653 GB, free: 124 kB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.916e-05/0.01818, allocations: 12 kB / 0.7653 GB, free: 112 kB / 0.5887 GB
Notification: Performance of sorting global known variables: time 0.0001259/0.01831, allocations: 115.3 kB / 0.7655 GB, free: 15.99 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 8.1e-08/0.01831, allocations: 0 / 0.7655 GB, free: 15.99 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0002925/0.0186, allocations: 47.88 kB / 0.7655 GB, free: 15.95 MB / 0.6043 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 0.0001463/0.01874, allocations: 105.3 kB / 0.7656 GB, free: 15.84 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.0006484/0.01939, allocations: 378.9 kB / 0.766 GB, free: 15.43 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 1.623e-06/0.01939, allocations: 4.125 kB / 0.766 GB, free: 15.42 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002807/0.01968, allocations: 173 kB / 0.7661 GB, free: 15.23 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003864/0.02006, allocations: 46.59 kB / 0.7662 GB, free: 15.19 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001153/0.02122, allocations: 0.5324 MB / 0.7667 GB, free: 14.64 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001412/0.02136, allocations: 119.5 kB / 0.7668 GB, free: 14.5 MB / 0.6043 GB
Notification: Performance of simCode: alias equations: time 7.286e-05/0.02143, allocations: 13.48 kB / 0.7668 GB, free: 14.49 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.598e-05/0.02149, allocations: 20.5 kB / 0.7668 GB, free: 14.47 MB / 0.6043 GB
Notification: Performance of SimCode: time 4.51e-07/0.02149, allocations: 0 / 0.7668 GB, free: 14.47 MB / 0.6043 GB
Notification: Performance of Templates: time 0.006543/0.02803, allocations: 2.406 MB / 0.7692 GB, free: 12.19 MB / 0.6043 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: 9.134532184805721]