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 0.0008572/0.0008572, allocations: 80.88 kB / 19.94 MB, free: 4.547 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 0.0009602/0.0009602, allocations: 181 kB / 23.36 MB, free: 1.133 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 0.9669/0.9669, allocations: 177.1 MB / 203.8 MB, free: 5.457 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 1.721/1.721, allocations: 273.5 MB / 0.5213 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 1.452e-06/1.452e-06, allocations: 3.938 kB / 0.5955 GB, free: 2.707 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.756e-05/2.901e-05, allocations: 2.312 kB / 0.5955 GB, free: 2.703 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.003889/0.003918, allocations: 2.111 MB / 0.5975 GB, free: 0.5977 MB / 0.5105 GB
Notification: Performance of NFInst.instExpressions: time 0.001286/0.005203, allocations: 0.5567 MB / 0.5981 GB, free: 48 kB / 0.5105 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001017/0.005305, allocations: 4 kB / 0.5981 GB, free: 44 kB / 0.5105 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001447/0.00545, allocations: 17.11 kB / 0.5981 GB, free: 28 kB / 0.5105 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002052/0.005655, allocations: 51.78 kB / 0.5981 GB, free: 15.99 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002046/0.00586, allocations: 43.94 kB / 0.5982 GB, free: 15.95 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0002984/0.006158, allocations: 193.5 kB / 0.5984 GB, free: 15.81 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001327/0.006291, allocations: 30.5 kB / 0.5984 GB, free: 15.78 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001971/0.006488, allocations: 109 kB / 0.5985 GB, free: 15.68 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001448/0.006633, allocations: 54.28 kB / 0.5985 GB, free: 15.63 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 3.315e-05/0.006666, allocations: 16 kB / 0.5986 GB, free: 15.62 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.767e-05/0.006693, allocations: 16 kB / 0.5986 GB, free: 15.6 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 4.656e-05/0.00674, allocations: 34.73 kB / 0.5986 GB, free: 15.57 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 7.973e-05/0.00682, allocations: 55.84 kB / 0.5987 GB, free: 15.52 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002115/0.007031, allocations: 115.6 kB / 0.5988 GB, free: 15.4 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 2.134e-06/0.007033, allocations: 0 / 0.5988 GB, free: 15.4 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 8.81e-07/0.007034, allocations: 0 / 0.5988 GB, free: 15.4 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 4.609e-06/0.007039, allocations: 0 / 0.5988 GB, free: 15.4 MB / 0.5261 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 0.0006192/0.007658, allocations: 403.7 kB / 0.5992 GB, free: 14.97 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 3.738e-05/0.007696, allocations: 12.03 kB / 0.5992 GB, free: 14.96 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.137e-05/0.007747, allocations: 16.92 kB / 0.5992 GB, free: 14.95 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001943/0.007941, allocations: 141.6 kB / 0.5993 GB, free: 14.78 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.095e-05/0.007962, allocations: 8.375 kB / 0.5993 GB, free: 14.77 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.111e-05/0.007993, allocations: 12.38 kB / 0.5993 GB, free: 14.76 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002127/0.008206, allocations: 138.1 kB / 0.5995 GB, free: 14.61 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.78e-05/0.008224, allocations: 11.38 kB / 0.5995 GB, free: 14.61 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.319e-05/0.008237, allocations: 8 kB / 0.5995 GB, free: 14.6 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.945e-06/0.008245, allocations: 4 kB / 0.5995 GB, free: 14.59 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001115/0.008356, allocations: 74.23 kB / 0.5996 GB, free: 14.52 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006263/0.008983, allocations: 255.9 kB / 0.5998 GB, free: 14.25 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001604/0.009143, allocations: 104.2 kB / 0.5999 GB, free: 14.13 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.673e-05/0.0092, allocations: 50.56 kB / 0.5999 GB, free: 14.07 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.346e-05/0.009213, allocations: 7.984 kB / 0.6 GB, free: 14.07 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002138/0.009427, allocations: 184.4 kB / 0.6001 GB, free: 13.86 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=20): time 1.723e-06/0.009429, allocations: 3.938 kB / 0.6001 GB, free: 13.85 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=21): time 0.0007964/0.01023, allocations: 0.5027 MB / 0.6006 GB, free: 13.29 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.289e-05/0.01029, allocations: 136.5 kB / 0.6008 GB, free: 13.12 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001074/0.0104, allocations: 148.7 kB / 0.6009 GB, free: 12.97 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 2.228e-05/0.01042, allocations: 29.7 kB / 0.6009 GB, free: 12.93 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 5.278e-05/0.01047, allocations: 104.5 kB / 0.601 GB, free: 12.83 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 5.318e-05/0.01052, allocations: 67.42 kB / 0.6011 GB, free: 12.76 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.278e-05/0.0106, allocations: 53.66 kB / 0.6011 GB, free: 12.7 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 9.524e-05/0.01069, allocations: 326.8 kB / 0.6015 GB, free: 12.38 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.856e-05/0.01078, allocations: 92.7 kB / 0.6015 GB, free: 12.27 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001267/0.01091, allocations: 172.4 kB / 0.6017 GB, free: 12.06 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002418/0.01115, allocations: 280.1 kB / 0.602 GB, free: 11.73 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.985e-06/0.01115, allocations: 4 kB / 0.602 GB, free: 11.73 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002575/0.01141, allocations: 252.2 kB / 0.6022 GB, free: 11.45 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 4.665e-05/0.01146, allocations: 67.39 kB / 0.6023 GB, free: 11.38 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.032e-06/0.01146, allocations: 0 / 0.6023 GB, free: 11.38 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.413e-05/0.01148, allocations: 4 kB / 0.6023 GB, free: 11.37 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002286/0.0117, allocations: 55.91 kB / 0.6023 GB, free: 11.32 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.432e-06/0.01171, allocations: 7.938 kB / 0.6023 GB, free: 11.31 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001129/0.01182, allocations: 15.98 kB / 0.6024 GB, free: 11.29 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.802e-05/0.01184, allocations: 8 kB / 0.6024 GB, free: 11.29 MB / 0.5261 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 0.0001773/0.01202, allocations: 192.6 kB / 0.6026 GB, free: 11.09 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.801e-05/0.01205, allocations: 15.98 kB / 0.6026 GB, free: 11.07 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.942e-05/0.01209, allocations: 21.27 kB / 0.6026 GB, free: 11.05 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.888e-06/0.01209, allocations: 8 kB / 0.6026 GB, free: 11.04 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.264e-06/0.01209, allocations: 0 / 0.6026 GB, free: 11.04 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.167e-06/0.0121, allocations: 0 / 0.6026 GB, free: 11.04 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006591/0.01276, allocations: 358.3 kB / 0.6029 GB, free: 10.65 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.415e-06/0.01276, allocations: 0 / 0.6029 GB, free: 10.65 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001947/0.01295, allocations: 39.91 kB / 0.603 GB, free: 10.61 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.875e-06/0.01296, allocations: 0 / 0.603 GB, free: 10.61 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.801e-05/0.01297, allocations: 8 kB / 0.603 GB, free: 10.6 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.194e-06/0.01298, allocations: 0 / 0.603 GB, free: 10.6 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.082e-06/0.01298, allocations: 0 / 0.603 GB, free: 10.6 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003133/0.01329, allocations: 344.2 kB / 0.6033 GB, free: 10.23 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.281e-05/0.01331, allocations: 11.91 kB / 0.6033 GB, free: 10.22 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.952e-05/0.01334, allocations: 11.98 kB / 0.6033 GB, free: 10.21 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001152/0.01346, allocations: 12 kB / 0.6033 GB, free: 10.2 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.502e-05/0.01351, allocations: 15.97 kB / 0.6034 GB, free: 10.18 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.487e-05/0.01353, allocations: 7.984 kB / 0.6034 GB, free: 10.18 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 3.953e-05/0.01357, allocations: 31.58 kB / 0.6034 GB, free: 10.14 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 8e-08/0.01357, allocations: 0 / 0.6034 GB, free: 10.14 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0002811/0.01385, allocations: 51.94 kB / 0.6034 GB, free: 10.09 MB / 0.5261 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 0.000103/0.01395, allocations: 87.23 kB / 0.6035 GB, free: 10 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0002891/0.01424, allocations: 308.5 kB / 0.6038 GB, free: 9.652 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 4.288e-06/0.01425, allocations: 0 / 0.6038 GB, free: 9.652 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001187/0.01436, allocations: 137.9 kB / 0.604 GB, free: 9.496 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002987/0.01466, allocations: 44.28 kB / 0.604 GB, free: 9.457 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001559/0.01622, allocations: 0.5046 MB / 0.6045 GB, free: 8.926 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.448e-05/0.01628, allocations: 72 kB / 0.6046 GB, free: 8.836 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 7.611e-05/0.01635, allocations: 21.47 kB / 0.6046 GB, free: 8.816 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001541/0.01651, allocations: 95.36 kB / 0.6047 GB, free: 8.723 MB / 0.5261 GB
Notification: Performance of SimCode: time 1.052e-06/0.01651, allocations: 3.938 kB / 0.6047 GB, free: 8.719 MB / 0.5261 GB
Notification: Performance of Templates: time 0.005887/0.02239, allocations: 2.662 MB / 0.6073 GB, free: 6.211 MB / 0.5261 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.870839029084891]