Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.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 0.005368/0.005368, 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 0.002226/0.002226, allocations: 165.9 kB / 22.45 MB, free: 2.105 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 1.665/1.665, 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 3.473/3.473, allocations: 274 MB / 0.5207 GB, free: 14.96 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_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.703e-06/1.703e-06, allocations: 0 / 0.7563 GB, free: 10 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.038e-05/3.208e-05, allocations: 10.28 kB / 0.7563 GB, free: 9.992 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.003662/0.003694, allocations: 2.007 MB / 0.7582 GB, free: 7.992 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.001119/0.004813, allocations: 0.538 MB / 0.7588 GB, free: 7.457 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.404e-05/0.004897, allocations: 8 kB / 0.7588 GB, free: 7.449 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.000115/0.005012, allocations: 17.22 kB / 0.7588 GB, free: 7.434 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001553/0.005167, allocations: 57.41 kB / 0.7588 GB, free: 7.395 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001795/0.005347, allocations: 43.89 kB / 0.7589 GB, free: 7.352 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0003237/0.00567, allocations: 202.6 kB / 0.7591 GB, free: 7.176 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001459/0.005816, allocations: 33.95 kB / 0.7591 GB, free: 7.137 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001711/0.005987, allocations: 99.8 kB / 0.7592 GB, free: 7.039 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.00013/0.006117, allocations: 55.86 kB / 0.7593 GB, free: 6.984 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 3.806e-05/0.006155, allocations: 20 kB / 0.7593 GB, free: 6.965 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.892e-05/0.006194, allocations: 16 kB / 0.7593 GB, free: 6.949 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 5.045e-05/0.006245, allocations: 35.84 kB / 0.7593 GB, free: 6.914 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001022/0.006347, allocations: 59.83 kB / 0.7594 GB, free: 6.855 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002841/0.006631, allocations: 163.5 kB / 0.7595 GB, free: 6.695 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 3.076e-06/0.006634, allocations: 0 / 0.7595 GB, free: 6.695 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.142e-06/0.006635, allocations: 0 / 0.7595 GB, free: 6.695 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 5.079e-06/0.00664, allocations: 0 / 0.7595 GB, free: 6.695 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 0.0009211/0.007562, allocations: 448.7 kB / 0.76 GB, free: 6.215 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 3.814e-05/0.0076, allocations: 12.03 kB / 0.76 GB, free: 6.203 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.143e-05/0.007661, allocations: 20.84 kB / 0.76 GB, free: 6.184 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003669/0.008028, allocations: 186 kB / 0.7602 GB, free: 5.977 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.444e-05/0.008052, allocations: 12.38 kB / 0.7602 GB, free: 5.965 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.727e-05/0.00809, allocations: 12.38 kB / 0.7602 GB, free: 5.953 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003598/0.00845, allocations: 159.9 kB / 0.7604 GB, free: 5.785 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.58e-05/0.008465, allocations: 0 / 0.7604 GB, free: 5.785 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.451e-05/0.00848, allocations: 0 / 0.7604 GB, free: 5.785 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.114e-06/0.008487, allocations: 7.938 kB / 0.7604 GB, free: 5.777 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003488/0.008836, allocations: 141.5 kB / 0.7605 GB, free: 5.633 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007295/0.009565, allocations: 356.2 kB / 0.7608 GB, free: 5.254 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004167/0.009982, allocations: 164.2 kB / 0.761 GB, free: 5.078 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001951/0.01018, allocations: 86.69 kB / 0.7611 GB, free: 4.984 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.427e-05/0.01019, allocations: 8 kB / 0.7611 GB, free: 4.977 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0004123/0.0106, allocations: 228.3 kB / 0.7613 GB, free: 4.723 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=20): time 1.292e-06/0.0106, allocations: 0 / 0.7613 GB, free: 4.723 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=21): time 0.001729/0.01233, allocations: 0.6817 MB / 0.762 GB, free: 3.984 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001113/0.01244, allocations: 136.5 kB / 0.7621 GB, free: 3.82 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001776/0.01262, allocations: 160.4 kB / 0.7622 GB, free: 3.656 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 3.286e-05/0.01266, allocations: 33.7 kB / 0.7623 GB, free: 3.617 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 9.972e-05/0.01276, allocations: 112.5 kB / 0.7624 GB, free: 3.504 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 7.221e-05/0.01283, allocations: 71.42 kB / 0.7625 GB, free: 3.434 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.746e-05/0.01291, allocations: 45.7 kB / 0.7625 GB, free: 3.383 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 0.0001814/0.0131, allocations: 334.8 kB / 0.7628 GB, free: 3.047 MB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002546/0.01335, allocations: 128.7 kB / 0.7629 GB, free: 2.906 MB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003075/0.01366, allocations: 215.4 kB / 0.7631 GB, free: 2.656 MB / 0.5887 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0009801/0.01464, allocations: 0.5016 MB / 0.7636 GB, free: 2.098 MB / 0.5887 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.703e-06/0.01464, allocations: 0 / 0.7636 GB, free: 2.098 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0006706/0.01531, allocations: 378.5 kB / 0.764 GB, free: 1.699 MB / 0.5887 GB
Notification: Performance of prepare postOptimizeDAE: time 5.955e-05/0.01537, allocations: 58.06 kB / 0.7641 GB, free: 1.633 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.722e-06/0.01538, allocations: 4 kB / 0.7641 GB, free: 1.629 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.3e-05/0.0154, allocations: 12.12 kB / 0.7641 GB, free: 1.617 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002261/0.01563, allocations: 51.84 kB / 0.7641 GB, free: 1.566 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.408e-06/0.01564, allocations: 4 kB / 0.7641 GB, free: 1.562 MB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001524/0.01579, allocations: 19.92 kB / 0.7641 GB, free: 1.543 MB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.104e-05/0.01581, allocations: 8 kB / 0.7641 GB, free: 1.535 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 0.0002441/0.01605, allocations: 187.8 kB / 0.7643 GB, free: 1.34 MB / 0.5887 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.507e-05/0.01609, allocations: 19.91 kB / 0.7643 GB, free: 1.32 MB / 0.5887 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.445e-05/0.01614, allocations: 17.28 kB / 0.7644 GB, free: 1.309 MB / 0.5887 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.779e-06/0.01615, allocations: 7.875 kB / 0.7644 GB, free: 1.301 MB / 0.5887 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.753e-06/0.01615, allocations: 4 kB / 0.7644 GB, free: 1.297 MB / 0.5887 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.552e-06/0.01616, allocations: 3.984 kB / 0.7644 GB, free: 1.293 MB / 0.5887 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008514/0.01701, allocations: 0.5056 MB / 0.7649 GB, free: 0.7344 MB / 0.5887 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.044e-06/0.01701, allocations: 0 / 0.7649 GB, free: 0.7344 MB / 0.5887 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002203/0.01723, allocations: 39.91 kB / 0.7649 GB, free: 0.6953 MB / 0.5887 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.245e-06/0.01724, allocations: 0 / 0.7649 GB, free: 0.6953 MB / 0.5887 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.231e-05/0.01726, allocations: 8 kB / 0.7649 GB, free: 0.6875 MB / 0.5887 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.753e-06/0.01726, allocations: 0 / 0.7649 GB, free: 0.6875 MB / 0.5887 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.129e-06/0.01727, allocations: 3.938 kB / 0.7649 GB, free: 0.6836 MB / 0.5887 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0008371/0.0181, allocations: 492 kB / 0.7654 GB, free: 176 kB / 0.5887 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.106e-05/0.01813, allocations: 15.89 kB / 0.7654 GB, free: 160 kB / 0.5887 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.759e-05/0.01817, allocations: 8.062 kB / 0.7654 GB, free: 152 kB / 0.5887 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001591/0.01833, allocations: 15.98 kB / 0.7654 GB, free: 136 kB / 0.5887 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.383e-05/0.0184, allocations: 15.97 kB / 0.7654 GB, free: 120 kB / 0.5887 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.013e-05/0.01842, allocations: 8 kB / 0.7654 GB, free: 112 kB / 0.5887 GB
Notification: Performance of sorting global known variables: time 0.0001319/0.01856, allocations: 115.3 kB / 0.7656 GB, free: 15.99 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 9e-08/0.01856, allocations: 0 / 0.7656 GB, free: 15.99 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0004427/0.019, allocations: 47.94 kB / 0.7656 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 0.0001594/0.01916, allocations: 115.1 kB / 0.7657 GB, free: 15.82 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.0006511/0.01981, allocations: 371.6 kB / 0.7661 GB, free: 15.42 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 1.492e-06/0.01981, allocations: 0 / 0.7661 GB, free: 15.42 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002889/0.0201, allocations: 169 kB / 0.7662 GB, free: 15.23 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004258/0.02053, allocations: 61.22 kB / 0.7663 GB, free: 15.18 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001173/0.0217, allocations: 0.5487 MB / 0.7668 GB, free: 14.61 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001276/0.02183, allocations: 107.6 kB / 0.7669 GB, free: 14.49 MB / 0.6043 GB
Notification: Performance of simCode: alias equations: time 8.586e-05/0.02191, allocations: 21.62 kB / 0.7669 GB, free: 14.46 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.033e-05/0.02197, allocations: 20.5 kB / 0.767 GB, free: 14.45 MB / 0.6043 GB
Notification: Performance of SimCode: time 4.51e-07/0.02197, allocations: 0 / 0.767 GB, free: 14.45 MB / 0.6043 GB
Notification: Performance of Templates: time 0.006958/0.02893, allocations: 2.588 MB / 0.7695 GB, free: 12 MB / 0.6043 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 9.328154305927455]