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 0.001458/0.001458, allocations: 108.6 kB / 16.37 MB, free: 6 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001407/0.001407, allocations: 197.6 kB / 17.31 MB, free: 5.613 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.411/1.411, allocations: 222.9 MB / 241 MB, free: 15.17 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06217/0.06217, allocations: 12.27 MB / 303.4 MB, free: 3.238 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001313/0.001313, allocations: 71.89 kB / 367.2 MB, free: 3.371 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.253/0.2544, allocations: 52.07 MB / 419.3 MB, free: 21.83 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.004153/0.2585, allocations: 2.82 MB / 422.1 MB, free: 19.02 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003479/0.2589, allocations: 191.8 kB / 422.3 MB, free: 18.83 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001393/0.2591, allocations: 10.78 kB / 422.3 MB, free: 18.82 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001079/0.2592, allocations: 23.75 kB / 422.3 MB, free: 18.8 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001908/0.2594, allocations: 51.5 kB / 422.4 MB, free: 18.75 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002441/0.2597, allocations: 43.94 kB / 422.4 MB, free: 18.7 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002301/0.2599, allocations: 183.2 kB / 422.6 MB, free: 18.52 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002557/0.2602, allocations: 106.8 kB / 422.7 MB, free: 18.42 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001221/0.2603, allocations: 79.66 kB / 422.8 MB, free: 18.34 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000153/0.2605, allocations: 99.55 kB / 422.9 MB, free: 18.24 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.445e-05/0.2605, allocations: 25 kB / 422.9 MB, free: 18.22 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.246e-05/0.2606, allocations: 24 kB / 422.9 MB, free: 18.2 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.27e-05/0.2606, allocations: 47.83 kB / 423 MB, free: 18.15 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 9.22e-05/0.2607, allocations: 105.5 kB / 423.1 MB, free: 18.05 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002197/0.2609, allocations: 237 kB / 423.3 MB, free: 17.82 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.511e-06/0.261, allocations: 3.938 kB / 423.3 MB, free: 17.81 MB / 302.1 MB
Notification: Performance of FrontEnd: time 2.084e-06/0.261, allocations: 0 / 423.3 MB, free: 17.81 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 1.088e-05/0.261, allocations: 0 / 423.3 MB, free: 17.81 MB / 302.1 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 0.0007199/0.2617, allocations: 0.5054 MB / 423.8 MB, free: 17.26 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.52e-05/0.2618, allocations: 12.75 kB / 423.8 MB, free: 17.25 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.664e-05/0.2618, allocations: 24.66 kB / 423.9 MB, free: 17.22 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001201/0.262, allocations: 180.6 kB / 424 MB, free: 17.01 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.824e-05/0.262, allocations: 25.92 kB / 424.1 MB, free: 16.98 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.206e-05/0.262, allocations: 24.38 kB / 424.1 MB, free: 16.96 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003273/0.2624, allocations: 201.5 kB / 424.3 MB, free: 16.76 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.85e-05/0.2624, allocations: 2.281 kB / 424.3 MB, free: 16.76 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.322e-05/0.2624, allocations: 15.88 kB / 424.3 MB, free: 16.74 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.356e-06/0.2625, allocations: 8 kB / 424.3 MB, free: 16.73 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002181/0.2627, allocations: 134.2 kB / 424.4 MB, free: 16.6 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001252/0.2639, allocations: 0.7658 MB / 425.2 MB, free: 15.78 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001591/0.2641, allocations: 103.5 kB / 425.3 MB, free: 15.67 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002043/0.2643, allocations: 99.56 kB / 425.4 MB, free: 15.57 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.932e-05/0.2643, allocations: 0.7812 kB / 425.4 MB, free: 15.57 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.592e-05/0.2644, allocations: 36.3 kB / 425.4 MB, free: 15.53 MB / 302.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.633e-06/0.2644, allocations: 0 / 425.4 MB, free: 15.53 MB / 302.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001169/0.2655, allocations: 0.571 MB / 426 MB, free: 14.91 MB / 302.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.447e-05/0.2656, allocations: 56.03 kB / 426.1 MB, free: 14.84 MB / 302.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.747e-05/0.2657, allocations: 152.5 kB / 426.2 MB, free: 14.68 MB / 302.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.317e-05/0.2657, allocations: 27.33 kB / 426.2 MB, free: 14.64 MB / 302.1 MB
Notification: Performance of collectInitialEqns (initialization): time 7.369e-05/0.2658, allocations: 159.9 kB / 426.4 MB, free: 14.48 MB / 302.1 MB
Notification: Performance of collectInitialBindings (initialization): time 3.373e-05/0.2658, allocations: 70.98 kB / 426.5 MB, free: 14.41 MB / 302.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.627e-05/0.2659, allocations: 41.7 kB / 426.5 MB, free: 14.37 MB / 302.1 MB
Notification: Performance of setup shared object (initialization): time 4.956e-05/0.2659, allocations: 327.8 kB / 426.8 MB, free: 14.04 MB / 302.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.363e-05/0.266, allocations: 45.19 kB / 426.9 MB, free: 14 MB / 302.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.769e-05/0.2661, allocations: 95.23 kB / 427 MB, free: 13.88 MB / 302.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001271/0.2674, allocations: 393.3 kB / 427.3 MB, free: 13.49 MB / 302.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.204e-06/0.2674, allocations: 0 / 427.3 MB, free: 13.49 MB / 302.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002802/0.2677, allocations: 209.2 kB / 427.5 MB, free: 13.28 MB / 302.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.757e-05/0.2677, allocations: 7.188 kB / 427.6 MB, free: 13.28 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.741e-06/0.2677, allocations: 4 kB / 427.6 MB, free: 13.27 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.426e-05/0.2678, allocations: 11.5 kB / 427.6 MB, free: 13.27 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001939/0.268, allocations: 47.91 kB / 427.6 MB, free: 13.22 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.236e-06/0.268, allocations: 4 kB / 427.6 MB, free: 13.21 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.027e-05/0.2681, allocations: 8 kB / 427.6 MB, free: 13.21 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.596e-05/0.2681, allocations: 8 kB / 427.6 MB, free: 13.2 MB / 302.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         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
         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
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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001753/0.2683, allocations: 160.9 kB / 427.8 MB, free: 13.05 MB / 302.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.58e-05/0.2683, allocations: 11.81 kB / 427.8 MB, free: 13.04 MB / 302.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002636/0.2686, allocations: 174.6 kB / 428 MB, free: 12.86 MB / 302.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.497e-06/0.2686, allocations: 4 kB / 428 MB, free: 12.85 MB / 302.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.488e-06/0.2686, allocations: 0 / 428 MB, free: 12.85 MB / 302.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.988e-06/0.2686, allocations: 6.859 kB / 428 MB, free: 12.85 MB / 302.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000581/0.2692, allocations: 0.509 MB / 428.5 MB, free: 12.29 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.805e-06/0.2692, allocations: 0 / 428.5 MB, free: 12.29 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001914/0.2694, allocations: 39.91 kB / 428.5 MB, free: 12.25 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.356e-06/0.2694, allocations: 0 / 428.5 MB, free: 12.25 MB / 302.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.693e-05/0.2695, allocations: 4 kB / 428.5 MB, free: 12.24 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.564e-06/0.2695, allocations: 192 / 428.5 MB, free: 12.24 MB / 302.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.193e-06/0.2695, allocations: 8 kB / 428.5 MB, free: 12.23 MB / 302.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000325/0.2698, allocations: 309.3 kB / 428.8 MB, free: 11.92 MB / 302.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.844e-05/0.2699, allocations: 88.95 kB / 428.9 MB, free: 11.81 MB / 302.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.358e-05/0.2699, allocations: 0 / 428.9 MB, free: 11.81 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001158/0.27, allocations: 4.188 kB / 428.9 MB, free: 11.81 MB / 302.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.379e-05/0.2701, allocations: 23.95 kB / 429 MB, free: 11.79 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.035e-05/0.2701, allocations: 4 kB / 429 MB, free: 11.78 MB / 302.1 MB
Notification: Performance of sorting global known variables: time 5.203e-05/0.2701, allocations: 111.3 kB / 429.1 MB, free: 11.67 MB / 302.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.2701, allocations: 0 / 429.1 MB, free: 11.67 MB / 302.1 MB
Notification: Performance of remove unused functions: time 0.0002788/0.2704, allocations: 36 kB / 429.1 MB, free: 11.64 MB / 302.1 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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 8.747e-05/0.2705, allocations: 107.7 kB / 429.2 MB, free: 11.52 MB / 302.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002385/0.2708, allocations: 143.7 kB / 429.4 MB, free: 11.38 MB / 302.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.344e-06/0.2708, allocations: 0 / 429.4 MB, free: 11.38 MB / 302.1 MB
Notification: Performance of simCode: created simulation system equations: time 7.908e-05/0.2709, allocations: 59.92 kB / 429.4 MB, free: 11.32 MB / 302.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003216/0.2712, allocations: 24.36 kB / 429.4 MB, free: 11.3 MB / 302.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007642/0.272, allocations: 0.5071 MB / 429.9 MB, free: 10.77 MB / 302.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001922/0.2722, allocations: 0.7358 MB / 430.7 MB, free: 10.01 MB / 302.1 MB
Notification: Performance of simCode: alias equations: time 7.112e-05/0.2722, allocations: 13.42 kB / 430.7 MB, free: 10 MB / 302.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.896e-05/0.2723, allocations: 19.44 kB / 430.7 MB, free: 9.98 MB / 302.1 MB
Notification: Performance of SimCode: time 2e-07/0.2723, allocations: 7.938 kB / 430.7 MB, free: 9.973 MB / 302.1 MB
Notification: Performance of Templates: time 0.003983/0.2763, allocations: 1.373 MB / 432.1 MB, free: 8.609 MB / 302.1 MB
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile
(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 -s cvode -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1)