Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr BioChem_BioChem.Examples.CaOscillations.Cytosol.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001098/0.001098, allocations: 99.62 kB / 15.05 MB, free: 1.105 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001256/0.001256, allocations: 177.3 kB / 15.95 MB, free: 216 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.389/1.389, allocations: 223.2 MB / 239.9 MB, free: 5.441 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1888/0.1888, allocations: 12.23 MB / 303.2 MB, free: 2.016 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0004635/0.0004637, allocations: 11.98 kB / 366.8 MB, free: 9.84 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1159/0.1164, allocations: 53.08 MB / 419.9 MB, free: 4.645 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003963/0.1204, allocations: 2.332 MB / 422.2 MB, free: 2.301 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0005017/0.1209, allocations: 195.2 kB / 422.4 MB, free: 2.109 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001493/0.1211, allocations: 8 kB / 422.4 MB, free: 2.102 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.000105/0.1212, allocations: 23.86 kB / 422.5 MB, free: 2.078 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002709/0.1215, allocations: 47.84 kB / 422.5 MB, free: 2.031 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002618/0.1218, allocations: 35.94 kB / 422.5 MB, free: 1.996 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002307/0.122, allocations: 119.8 kB / 422.7 MB, free: 1.879 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002224/0.1223, allocations: 73.44 kB / 422.7 MB, free: 1.805 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 8.709e-05/0.1224, allocations: 63.7 kB / 422.8 MB, free: 1.742 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001423/0.1225, allocations: 79.62 kB / 422.9 MB, free: 1.664 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.069e-05/0.1225, allocations: 8 kB / 422.9 MB, free: 1.656 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.902e-05/0.1226, allocations: 8 kB / 422.9 MB, free: 1.648 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 3.76e-05/0.1226, allocations: 39.83 kB / 422.9 MB, free: 1.609 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 7.16e-05/0.1227, allocations: 57.58 kB / 423 MB, free: 1.547 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001759/0.1229, allocations: 171.8 kB / 423.1 MB, free: 1.379 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 2.785e-06/0.1229, allocations: 0 / 423.1 MB, free: 1.379 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.593e-06/0.1229, allocations: 0 / 423.1 MB, free: 1.379 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 9.188e-06/0.1229, allocations: 0 / 423.1 MB, free: 1.379 MB / 350.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 60
 * Number of variables: 60
Notification: Performance of Generate backend data structure: time 0.0007207/0.1236, allocations: 467.3 kB / 423.6 MB, free: 0.875 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.872e-05/0.1237, allocations: 8.031 kB / 423.6 MB, free: 0.8672 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.146e-05/0.1238, allocations: 23.72 kB / 423.6 MB, free: 0.8438 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001527/0.1239, allocations: 198.6 kB / 423.8 MB, free: 0.6094 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.357e-05/0.1239, allocations: 16.56 kB / 423.8 MB, free: 0.5938 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.936e-05/0.124, allocations: 24 kB / 423.9 MB, free: 0.5703 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000367/0.1244, allocations: 204.8 kB / 424.1 MB, free: 372 kB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.463e-05/0.1244, allocations: 4 kB / 424.1 MB, free: 368 kB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.466e-05/0.1244, allocations: 12 kB / 424.1 MB, free: 356 kB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.376e-06/0.1244, allocations: 4 kB / 424.1 MB, free: 352 kB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002542/0.1247, allocations: 134.2 kB / 424.2 MB, free: 220 kB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.227/0.3517, allocations: 0.7554 MB / 425 MB, free: 38.21 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002067/0.352, allocations: 103.8 kB / 425.1 MB, free: 38.18 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.248e-05/0.352, allocations: 2.109 kB / 425.1 MB, free: 38.18 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.106e-05/0.3521, allocations: 38.16 kB / 425.1 MB, free: 38.14 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 2.474e-06/0.3521, allocations: 0 / 425.1 MB, free: 38.14 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001247/0.3533, allocations: 0.5762 MB / 425.7 MB, free: 37.87 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.591e-05/0.3534, allocations: 61.89 kB / 425.8 MB, free: 37.8 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001527/0.3535, allocations: 151.6 kB / 425.9 MB, free: 37.7 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.883e-05/0.3536, allocations: 25.7 kB / 425.9 MB, free: 37.66 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 9.405e-05/0.3537, allocations: 159.5 kB / 426.1 MB, free: 37.55 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 5.006e-05/0.3537, allocations: 65.56 kB / 426.1 MB, free: 37.51 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.022e-05/0.3537, allocations: 4.062 kB / 426.1 MB, free: 37.51 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 7.381e-05/0.3538, allocations: 325.9 kB / 426.5 MB, free: 37.2 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.673e-05/0.3539, allocations: 45.73 kB / 426.5 MB, free: 37.2 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001082/0.354, allocations: 93.06 kB / 426.6 MB, free: 37.14 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001154/0.3541, allocations: 62.38 kB / 426.7 MB, free: 37.14 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.81e-07/0.3541, allocations: 0.5625 kB / 426.7 MB, free: 37.14 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002955/0.3544, allocations: 212.2 kB / 426.9 MB, free: 37.09 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.119e-05/0.3545, allocations: 6.531 kB / 426.9 MB, free: 37.09 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.755e-06/0.3545, allocations: 2.031 kB / 426.9 MB, free: 37.09 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.846e-05/0.3545, allocations: 4.594 kB / 426.9 MB, free: 37.09 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002136/0.3547, allocations: 55.72 kB / 426.9 MB, free: 37.09 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.217e-06/0.3547, allocations: 7.047 kB / 426.9 MB, free: 37.09 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.891e-05/0.3548, allocations: 13.92 kB / 427 MB, free: 37.08 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.834e-05/0.3549, allocations: 7.438 kB / 427 MB, free: 37.08 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         p3_sbml:VARIABLE(start = 0.95 fixed = true )  type: Real
         Ca_Cyt.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         endoplasmicReticulum.CaER.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         endoplasmicReticulum.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 7
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (28):
 * Single equations (assignments): 28
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002149/0.3551, allocations: 148.1 kB / 427.1 MB, free: 36.96 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.284e-05/0.3551, allocations: 18.44 kB / 427.1 MB, free: 36.96 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002745/0.3554, allocations: 170.6 kB / 427.3 MB, free: 36.92 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.669e-06/0.3554, allocations: 5.031 kB / 427.3 MB, free: 36.92 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.212e-06/0.3554, allocations: 6.359 kB / 427.3 MB, free: 36.92 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.36e-06/0.3554, allocations: 2.062 kB / 427.3 MB, free: 36.92 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003428/0.3558, allocations: 285.5 kB / 427.6 MB, free: 36.73 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.376e-06/0.3558, allocations: 3.016 kB / 427.6 MB, free: 36.73 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001852/0.356, allocations: 33.72 kB / 427.6 MB, free: 36.73 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.284e-06/0.356, allocations: 3.719 kB / 427.6 MB, free: 36.73 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.365e-05/0.356, allocations: 1.406 kB / 427.6 MB, free: 36.73 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.226e-06/0.356, allocations: 3.344 kB / 427.6 MB, free: 36.73 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.021e-06/0.356, allocations: 0.6562 kB / 427.6 MB, free: 36.73 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003213/0.3564, allocations: 327.1 kB / 428 MB, free: 36.58 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.923e-05/0.3564, allocations: 83.98 kB / 428 MB, free: 36.48 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.465e-05/0.3564, allocations: 5.062 kB / 428 MB, free: 36.48 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001047/0.3565, allocations: 9.25 kB / 428 MB, free: 36.48 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.717e-05/0.3566, allocations: 12.98 kB / 428.1 MB, free: 36.48 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.566e-06/0.3566, allocations: 2.625 kB / 428.1 MB, free: 36.48 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.475e-05/0.3567, allocations: 114.5 kB / 428.2 MB, free: 36.41 MB / 350.1 MB
Notification: Performance of sort global known variables: time 9e-08/0.3567, allocations: 0 / 428.2 MB, free: 36.41 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002628/0.3569, allocations: 43.48 kB / 428.2 MB, free: 36.4 MB / 350.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,endoplasmicReticulum.V,endoplasmicReticulum.CaER.n,Ca_Cyt.n,p3_sbml)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (18):
 * Single equations (assignments): 18
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 8.554e-05/0.357, allocations: 97.5 kB / 428.3 MB, free: 36.32 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002421/0.3573, allocations: 142.6 kB / 428.5 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.084e-06/0.3573, allocations: 4.844 kB / 428.5 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 7.784e-05/0.3574, allocations: 65.55 kB / 428.5 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002203/0.3576, allocations: 12.31 kB / 428.5 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0008239/0.3584, allocations: 0.6265 MB / 429.2 MB, free: 35.97 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001618/0.3586, allocations: 0.7472 MB / 429.9 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 6.727e-05/0.3587, allocations: 17.91 kB / 429.9 MB, free: 35.27 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.814e-05/0.3587, allocations: 17.38 kB / 429.9 MB, free: 35.26 MB / 350.1 MB
Notification: Performance of SimCode: time 2.11e-07/0.3587, allocations: 0.5625 kB / 429.9 MB, free: 35.26 MB / 350.1 MB
Notification: Performance of Templates: time 0.00349/0.3622, allocations: 1.266 MB / 431.2 MB, free: 35.2 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile
Environment - environmentSimulation:
(rm -f BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; mkfifo BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe >> ../files/BioChem_BioChem.Examples.CaOscillations.Cytosol.sim & ./BioChem_BioChem.Examples.CaOscillations.Cytosol  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1)
Environment - environmentSimulation: