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 0.001071/0.001071, allocations: 111.3 kB / 15.23 MB, free: 0.6602 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001113/0.001113, allocations: 194.2 kB / 16.13 MB, free: 6.66 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.306/1.306, allocations: 222.9 MB / 239.8 MB, free: 4.582 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1687/0.1687, allocations: 12.26 MB / 302.2 MB, free: 1.32 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001189/0.001189, allocations: 60.03 kB / 365.1 MB, free: 10.24 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09193/0.09313, allocations: 52.08 MB / 417.2 MB, free: 6.051 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.004394/0.09756, allocations: 2.864 MB / 420 MB, free: 3.168 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003055/0.0979, allocations: 191.2 kB / 420.2 MB, free: 2.98 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.757e-05/0.09802, allocations: 8 kB / 420.2 MB, free: 2.973 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 8.268e-05/0.09811, allocations: 23.86 kB / 420.3 MB, free: 2.949 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001281/0.09826, allocations: 35.7 kB / 420.3 MB, free: 2.914 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001926/0.09846, allocations: 51.88 kB / 420.3 MB, free: 2.863 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0001679/0.09864, allocations: 175.2 kB / 420.5 MB, free: 2.691 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001862/0.09883, allocations: 86.58 kB / 420.6 MB, free: 2.609 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 8.618e-05/0.09892, allocations: 75.66 kB / 420.7 MB, free: 2.535 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001256/0.09905, allocations: 95.55 kB / 420.8 MB, free: 2.441 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.296e-05/0.09909, allocations: 16 kB / 420.8 MB, free: 2.426 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.996e-05/0.09913, allocations: 12 kB / 420.8 MB, free: 2.414 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 3.955e-05/0.09917, allocations: 39.84 kB / 420.8 MB, free: 2.375 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 9.987e-05/0.09928, allocations: 107.4 kB / 420.9 MB, free: 2.27 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002103/0.09949, allocations: 219.5 kB / 421.1 MB, free: 2.055 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.789e-06/0.09951, allocations: 0 / 421.1 MB, free: 2.055 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.072e-06/0.09952, allocations: 0 / 421.1 MB, free: 2.055 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 7.344e-06/0.09953, allocations: 0 / 421.1 MB, free: 2.055 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 0.0007233/0.1003, allocations: 0.5033 MB / 421.6 MB, free: 1.5 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.207e-05/0.1003, allocations: 11.97 kB / 421.7 MB, free: 1.488 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.768e-05/0.1004, allocations: 24.66 kB / 421.7 MB, free: 1.465 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001279/0.1005, allocations: 196 kB / 421.9 MB, free: 1.234 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.236e-05/0.1006, allocations: 16.94 kB / 421.9 MB, free: 1.219 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.835e-05/0.1006, allocations: 24.38 kB / 421.9 MB, free: 1.195 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003664/0.101, allocations: 205.4 kB / 422.1 MB, free: 0.9922 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.552e-05/0.101, allocations: 4.188 kB / 422.1 MB, free: 0.9883 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.771e-05/0.101, allocations: 15.94 kB / 422.1 MB, free: 0.9727 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.434e-06/0.1011, allocations: 7.938 kB / 422.1 MB, free: 0.9648 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002534/0.1013, allocations: 142.2 kB / 422.3 MB, free: 0.8281 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001351/0.1027, allocations: 0.7631 MB / 423 MB, free: 4 kB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.1678/0.2705, allocations: 99.47 kB / 423.1 MB, free: 40.77 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002346/0.2707, allocations: 93.92 kB / 423.2 MB, free: 40.76 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.2e-05/0.2708, allocations: 3.375 kB / 423.2 MB, free: 40.76 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.648e-05/0.2708, allocations: 35 kB / 423.3 MB, free: 40.72 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.693e-06/0.2708, allocations: 0 / 423.3 MB, free: 40.72 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001361/0.2722, allocations: 0.5744 MB / 423.8 MB, free: 40.48 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.481e-05/0.2722, allocations: 57.59 kB / 423.9 MB, free: 40.41 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001549/0.2724, allocations: 152.4 kB / 424.1 MB, free: 40.31 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.278e-05/0.2724, allocations: 31.23 kB / 424.1 MB, free: 40.28 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 8.835e-05/0.2725, allocations: 156.9 kB / 424.2 MB, free: 40.16 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.405e-05/0.2726, allocations: 65.06 kB / 424.3 MB, free: 40.12 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.417e-05/0.2727, allocations: 40.72 kB / 424.3 MB, free: 40.1 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 9.26e-05/0.2728, allocations: 322.5 kB / 424.7 MB, free: 39.79 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001039/0.2729, allocations: 45.59 kB / 424.7 MB, free: 39.79 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001357/0.273, allocations: 93.81 kB / 424.8 MB, free: 39.73 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001431/0.2745, allocations: 393.4 kB / 425.2 MB, free: 39.68 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.395e-06/0.2745, allocations: 1.781 kB / 425.2 MB, free: 39.68 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003136/0.2748, allocations: 210.6 kB / 425.4 MB, free: 39.63 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.497e-05/0.2748, allocations: 10.95 kB / 425.4 MB, free: 39.63 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.033e-06/0.2748, allocations: 1.75 kB / 425.4 MB, free: 39.63 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.828e-05/0.2749, allocations: 3.5 kB / 425.4 MB, free: 39.63 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002069/0.2751, allocations: 51.2 kB / 425.4 MB, free: 39.63 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.147e-05/0.2751, allocations: 7.438 kB / 425.5 MB, free: 39.63 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001064/0.2752, allocations: 16.34 kB / 425.5 MB, free: 39.62 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.688e-05/0.2752, allocations: 7.656 kB / 425.5 MB, free: 39.62 MB / 350.1 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 0.0003223/0.2756, allocations: 146.2 kB / 425.6 MB, free: 39.51 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.518e-05/0.2756, allocations: 18.28 kB / 425.6 MB, free: 39.5 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0003341/0.2759, allocations: 166.6 kB / 425.8 MB, free: 39.46 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.97e-06/0.276, allocations: 4.875 kB / 425.8 MB, free: 39.46 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.231e-06/0.276, allocations: 1.875 kB / 425.8 MB, free: 39.46 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.42e-06/0.276, allocations: 1.078 kB / 425.8 MB, free: 39.46 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008077/0.2768, allocations: 0.5196 MB / 426.3 MB, free: 39.16 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.405e-06/0.2768, allocations: 3.094 kB / 426.3 MB, free: 39.16 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001819/0.277, allocations: 37.16 kB / 426.4 MB, free: 39.16 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.797e-06/0.277, allocations: 4.219 kB / 426.4 MB, free: 39.16 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.491e-05/0.277, allocations: 0 / 426.4 MB, free: 39.16 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.725e-06/0.277, allocations: 3.141 kB / 426.4 MB, free: 39.16 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.645e-06/0.277, allocations: 3.406 kB / 426.4 MB, free: 39.16 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003417/0.2774, allocations: 308.5 kB / 426.7 MB, free: 39.02 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.336e-05/0.2774, allocations: 91.06 kB / 426.8 MB, free: 38.92 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.755e-05/0.2775, allocations: 3.688 kB / 426.8 MB, free: 38.92 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001178/0.2776, allocations: 6.188 kB / 426.8 MB, free: 38.92 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.567e-05/0.2776, allocations: 11.75 kB / 426.8 MB, free: 38.92 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.13e-05/0.2776, allocations: 9.938 kB / 426.8 MB, free: 38.92 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.34e-05/0.2777, allocations: 111 kB / 426.9 MB, free: 38.84 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.11e-07/0.2777, allocations: 0 / 426.9 MB, free: 38.84 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002756/0.278, allocations: 40.62 kB / 426.9 MB, free: 38.84 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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 9.508e-05/0.2781, allocations: 101.6 kB / 427 MB, free: 38.75 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002496/0.2783, allocations: 137.3 kB / 427.2 MB, free: 38.75 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.677e-06/0.2784, allocations: 2.688 kB / 427.2 MB, free: 38.75 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 8.98e-05/0.2784, allocations: 71.41 kB / 427.3 MB, free: 38.75 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000288/0.2787, allocations: 16.2 kB / 427.3 MB, free: 38.75 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007933/0.2795, allocations: 0.5901 MB / 427.9 MB, free: 38.43 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00013/0.2797, allocations: 0.741 MB / 428.6 MB, free: 37.73 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 7.207e-05/0.2798, allocations: 18.69 kB / 428.6 MB, free: 37.72 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.833e-05/0.2798, allocations: 16.94 kB / 428.6 MB, free: 37.72 MB / 350.1 MB
Notification: Performance of SimCode: time 2.2e-07/0.2798, allocations: 0 / 428.6 MB, free: 37.72 MB / 350.1 MB
Notification: Performance of Templates: time 0.003363/0.2832, allocations: 1.332 MB / 430 MB, free: 37.66 MB / 350.1 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 -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1)