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 0.001332/0.001332, allocations: 91.84 kB / 15.36 MB, free: 0.7383 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00911/0.00911, allocations: 169.9 kB / 16.26 MB, free: 6.613 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.402/1.402, allocations: 223.3 MB / 240.3 MB, free: 5.348 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.217/0.217, allocations: 12.25 MB / 303.7 MB, free: 1.996 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0004774/0.0004776, allocations: 8 kB / 367.5 MB, free: 9.465 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.12/0.1205, allocations: 53.08 MB / 420.6 MB, free: 4.27 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003501/0.1241, allocations: 2.487 MB / 423.1 MB, free: 1.77 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003688/0.1245, allocations: 187.2 kB / 423.3 MB, free: 1.586 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001154/0.1246, allocations: 8 kB / 423.3 MB, free: 1.578 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 6.533e-05/0.1247, allocations: 23.86 kB / 423.3 MB, free: 1.555 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001544/0.1249, allocations: 35.7 kB / 423.4 MB, free: 1.52 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002024/0.1251, allocations: 47.91 kB / 423.4 MB, free: 1.473 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002497/0.1253, allocations: 179.2 kB / 423.6 MB, free: 1.297 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002438/0.1256, allocations: 94.52 kB / 423.7 MB, free: 1.207 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001074/0.1257, allocations: 63.72 kB / 423.7 MB, free: 1.145 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000182/0.1259, allocations: 79.55 kB / 423.8 MB, free: 1.066 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.58e-05/0.1259, allocations: 12 kB / 423.8 MB, free: 1.055 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.291e-05/0.126, allocations: 8 kB / 423.8 MB, free: 1.047 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 5.076e-05/0.126, allocations: 27.84 kB / 423.9 MB, free: 1.02 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001373/0.1262, allocations: 121.1 kB / 424 MB, free: 0.8945 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.000286/0.1265, allocations: 215.4 kB / 424.2 MB, free: 0.6836 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.667e-06/0.1265, allocations: 3.984 kB / 424.2 MB, free: 0.6797 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.885e-06/0.1265, allocations: 0 / 424.2 MB, free: 0.6797 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.198e-05/0.1265, allocations: 4 kB / 424.2 MB, free: 0.6758 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 0.0008719/0.1274, allocations: 463.4 kB / 424.7 MB, free: 176 kB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.521e-05/0.1275, allocations: 12.03 kB / 424.7 MB, free: 164 kB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.804e-05/0.1276, allocations: 24.66 kB / 424.7 MB, free: 140 kB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.193/0.3206, allocations: 182.8 kB / 424.9 MB, free: 38.29 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.334e-05/0.3207, allocations: 18.88 kB / 424.9 MB, free: 38.29 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.812e-05/0.3208, allocations: 24.34 kB / 424.9 MB, free: 38.29 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004711/0.3213, allocations: 206.3 kB / 425.1 MB, free: 38.26 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.921e-05/0.3213, allocations: 5.375 kB / 425.1 MB, free: 38.26 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.106e-05/0.3213, allocations: 8.938 kB / 425.1 MB, free: 38.26 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.076e-05/0.3214, allocations: 6.188 kB / 425.1 MB, free: 38.26 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000289/0.3217, allocations: 142.9 kB / 425.3 MB, free: 38.26 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001419/0.3231, allocations: 0.7619 MB / 426 MB, free: 37.92 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001956/0.3233, allocations: 102.9 kB / 426.1 MB, free: 37.9 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002605/0.3236, allocations: 97.92 kB / 426.2 MB, free: 37.89 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.176e-05/0.3236, allocations: 6.75 kB / 426.2 MB, free: 37.89 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.873e-05/0.3236, allocations: 33.12 kB / 426.3 MB, free: 37.85 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 2.475e-06/0.3236, allocations: 0.6562 kB / 426.3 MB, free: 37.85 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001259/0.3249, allocations: 0.5737 MB / 426.8 MB, free: 37.56 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.403e-05/0.3249, allocations: 58.89 kB / 426.9 MB, free: 37.5 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001394/0.3251, allocations: 146.1 kB / 427 MB, free: 37.39 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.723e-05/0.3251, allocations: 28.33 kB / 427.1 MB, free: 37.36 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 9.126e-05/0.3252, allocations: 154.9 kB / 427.2 MB, free: 37.24 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.917e-05/0.3253, allocations: 68.98 kB / 427.3 MB, free: 37.2 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 4.797e-05/0.3253, allocations: 24.95 kB / 427.3 MB, free: 37.18 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 8.067e-05/0.3254, allocations: 330.1 kB / 427.6 MB, free: 36.86 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.394e-05/0.3255, allocations: 45.28 kB / 427.7 MB, free: 36.86 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.508e-05/0.3256, allocations: 96.22 kB / 427.8 MB, free: 36.81 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001418/0.327, allocations: 403.2 kB / 428.2 MB, free: 36.75 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.665e-06/0.327, allocations: 2.906 kB / 428.2 MB, free: 36.75 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.000285/0.3273, allocations: 208.8 kB / 428.4 MB, free: 36.7 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.981e-05/0.3274, allocations: 7 kB / 428.4 MB, free: 36.7 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.191e-06/0.3274, allocations: 6.344 kB / 428.4 MB, free: 36.7 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.529e-05/0.3274, allocations: 4.031 kB / 428.4 MB, free: 36.7 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001835/0.3276, allocations: 51.48 kB / 428.4 MB, free: 36.7 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.098e-05/0.3276, allocations: 8.562 kB / 428.4 MB, free: 36.69 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001046/0.3277, allocations: 13.97 kB / 428.5 MB, free: 36.69 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.536e-05/0.3277, allocations: 6.094 kB / 428.5 MB, free: 36.69 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 0.0002344/0.328, allocations: 146.2 kB / 428.6 MB, free: 36.57 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.904e-05/0.328, allocations: 16.12 kB / 428.6 MB, free: 36.56 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000286/0.3283, allocations: 174.6 kB / 428.8 MB, free: 36.53 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.109e-06/0.3283, allocations: 7 kB / 428.8 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.241e-06/0.3283, allocations: 0 / 428.8 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.458e-06/0.3283, allocations: 0 / 428.8 MB, free: 36.52 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006536/0.329, allocations: 0.5117 MB / 429.3 MB, free: 36.22 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.675e-06/0.329, allocations: 0.6562 kB / 429.3 MB, free: 36.22 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000198/0.3292, allocations: 36.8 kB / 429.4 MB, free: 36.22 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.599e-06/0.3292, allocations: 1.359 kB / 429.4 MB, free: 36.22 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.806e-05/0.3293, allocations: 4.469 kB / 429.4 MB, free: 36.22 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.525e-06/0.3293, allocations: 2.781 kB / 429.4 MB, free: 36.22 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.303e-06/0.3293, allocations: 0 / 429.4 MB, free: 36.22 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003502/0.3296, allocations: 315.8 kB / 429.7 MB, free: 36.07 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 4.291e-05/0.3297, allocations: 97.31 kB / 429.8 MB, free: 35.97 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.559e-05/0.3297, allocations: 3.312 kB / 429.8 MB, free: 35.97 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001091/0.3298, allocations: 8.031 kB / 429.8 MB, free: 35.97 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.863e-05/0.3299, allocations: 15.56 kB / 429.8 MB, free: 35.97 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.969e-06/0.3299, allocations: 3.312 kB / 429.8 MB, free: 35.97 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 6.022e-05/0.33, allocations: 112.5 kB / 429.9 MB, free: 35.89 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.3e-07/0.33, allocations: 1.219 kB / 429.9 MB, free: 35.89 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002843/0.3303, allocations: 38.69 kB / 429.9 MB, free: 35.89 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 8.744e-05/0.3303, allocations: 95.66 kB / 430 MB, free: 35.81 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002405/0.3306, allocations: 139.1 kB / 430.2 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.535e-06/0.3306, allocations: 0 / 430.2 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 8.496e-05/0.3307, allocations: 63.09 kB / 430.2 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002964/0.331, allocations: 21.2 kB / 430.3 MB, free: 35.79 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009649/0.332, allocations: 0.6507 MB / 430.9 MB, free: 35.41 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002128/0.3322, allocations: 0.7462 MB / 431.7 MB, free: 34.71 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 7.746e-05/0.3323, allocations: 13.53 kB / 431.7 MB, free: 34.71 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.458e-05/0.3323, allocations: 24.05 kB / 431.7 MB, free: 34.7 MB / 350.1 MB
Notification: Performance of SimCode: time 4.01e-07/0.3324, allocations: 0 / 431.7 MB, free: 34.7 MB / 350.1 MB
Notification: Performance of Templates: time 0.004164/0.3365, allocations: 1.302 MB / 433 MB, free: 34.64 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)