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 0.001418/0.001419, allocations: 104 kB / 15.98 MB, free: 6.359 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001261/0.001261, allocations: 199.3 kB / 16.91 MB, free: 6.191 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.611/1.611, allocations: 222.9 MB / 240.6 MB, free: 15.46 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06314/0.06314, allocations: 12.26 MB / 303 MB, free: 3.523 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.00139/0.00139, allocations: 59.89 kB / 365.9 MB, free: 4.512 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3424/0.3438, allocations: 52.07 MB / 418 MB, free: 22.05 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.006871/0.3508, allocations: 2.883 MB / 420.9 MB, free: 19.17 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0005431/0.3513, allocations: 196.5 kB / 421.1 MB, free: 18.98 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001824/0.3515, allocations: 8 kB / 421.1 MB, free: 18.97 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001263/0.3517, allocations: 15.88 kB / 421.1 MB, free: 18.96 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002341/0.352, allocations: 43.62 kB / 421.1 MB, free: 18.91 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003279/0.3523, allocations: 39.95 kB / 421.2 MB, free: 18.88 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002963/0.3526, allocations: 183.2 kB / 421.4 MB, free: 18.7 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003286/0.353, allocations: 106 kB / 421.5 MB, free: 18.59 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001405/0.3531, allocations: 77.09 kB / 421.5 MB, free: 18.52 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001871/0.3533, allocations: 107.5 kB / 421.6 MB, free: 18.41 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 5.655e-05/0.3534, allocations: 20 kB / 421.7 MB, free: 18.39 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 4.576e-05/0.3534, allocations: 27.94 kB / 421.7 MB, free: 18.36 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 6.166e-05/0.3535, allocations: 48.41 kB / 421.7 MB, free: 18.32 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001233/0.3536, allocations: 103.5 kB / 421.8 MB, free: 18.21 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002221/0.3539, allocations: 182.2 kB / 422 MB, free: 18.04 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.566e-06/0.3539, allocations: 4.672 kB / 422 MB, free: 18.04 MB / 302.1 MB
Notification: Performance of FrontEnd: time 2.675e-06/0.3539, allocations: 0 / 422 MB, free: 18.04 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 1.031e-05/0.3539, allocations: 1.594 kB / 422 MB, free: 18.04 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 0.0008865/0.3548, allocations: 0.4973 MB / 422.5 MB, free: 17.49 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.903e-05/0.3549, allocations: 12.03 kB / 422.5 MB, free: 17.48 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.531e-05/0.355, allocations: 20.66 kB / 422.5 MB, free: 17.46 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000151/0.3551, allocations: 193.4 kB / 422.7 MB, free: 17.23 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.647e-05/0.3552, allocations: 20.94 kB / 422.8 MB, free: 17.21 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.657e-05/0.3553, allocations: 24.38 kB / 422.8 MB, free: 17.19 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000438/0.3557, allocations: 202.3 kB / 423 MB, free: 16.98 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.182e-05/0.3557, allocations: 192 / 423 MB, free: 16.98 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.664e-05/0.3558, allocations: 7.938 kB / 423 MB, free: 16.98 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.415e-05/0.3558, allocations: 8.938 kB / 423 MB, free: 16.97 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002994/0.3561, allocations: 138.2 kB / 423.1 MB, free: 16.84 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001632/0.3578, allocations: 0.7648 MB / 423.9 MB, free: 16.02 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002377/0.358, allocations: 109.3 kB / 424 MB, free: 15.91 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002809/0.3583, allocations: 103.6 kB / 424.1 MB, free: 15.8 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.721e-05/0.3583, allocations: 4 kB / 424.1 MB, free: 15.8 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.301e-05/0.3584, allocations: 30.56 kB / 424.1 MB, free: 15.76 MB / 302.1 MB
Notification: Performance of pre-optimization done (n=15): time 2.234e-06/0.3584, allocations: 0 / 424.1 MB, free: 15.76 MB / 302.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001531/0.3599, allocations: 0.5687 MB / 424.7 MB, free: 15.15 MB / 302.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.394e-05/0.36, allocations: 53 kB / 424.8 MB, free: 15.09 MB / 302.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001376/0.3601, allocations: 158.3 kB / 424.9 MB, free: 14.91 MB / 302.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.9e-05/0.3601, allocations: 29.7 kB / 424.9 MB, free: 14.88 MB / 302.1 MB
Notification: Performance of collectInitialEqns (initialization): time 8.752e-05/0.3602, allocations: 156.8 kB / 425.1 MB, free: 14.72 MB / 302.1 MB
Notification: Performance of collectInitialBindings (initialization): time 5.181e-05/0.3603, allocations: 70.98 kB / 425.2 MB, free: 14.65 MB / 302.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.583e-05/0.3604, allocations: 42.3 kB / 425.2 MB, free: 14.61 MB / 302.1 MB
Notification: Performance of setup shared object (initialization): time 7.336e-05/0.3605, allocations: 324.1 kB / 425.5 MB, free: 14.28 MB / 302.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000101/0.3606, allocations: 48.22 kB / 425.6 MB, free: 14.23 MB / 302.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000128/0.3607, allocations: 100.8 kB / 425.7 MB, free: 14.12 MB / 302.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00161/0.3623, allocations: 389.4 kB / 426 MB, free: 13.73 MB / 302.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.114e-06/0.3623, allocations: 0 / 426 MB, free: 13.73 MB / 302.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003829/0.3627, allocations: 214.6 kB / 426.3 MB, free: 13.52 MB / 302.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.357e-05/0.3628, allocations: 7.938 kB / 426.3 MB, free: 13.52 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.14e-05/0.3628, allocations: 0 / 426.3 MB, free: 13.52 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.702e-05/0.3628, allocations: 7.938 kB / 426.3 MB, free: 13.51 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00025/0.3631, allocations: 59.84 kB / 426.3 MB, free: 13.45 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.175e-05/0.3631, allocations: 0 / 426.3 MB, free: 13.45 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001405/0.3633, allocations: 15.98 kB / 426.3 MB, free: 13.44 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.711e-05/0.3633, allocations: 4 kB / 426.3 MB, free: 13.43 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 0.0003155/0.3636, allocations: 155.8 kB / 426.5 MB, free: 13.27 MB / 302.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.802e-05/0.3637, allocations: 15.75 kB / 426.5 MB, free: 13.26 MB / 302.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0003582/0.364, allocations: 169.1 kB / 426.7 MB, free: 13.09 MB / 302.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.006e-06/0.364, allocations: 0 / 426.7 MB, free: 13.09 MB / 302.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.692e-06/0.3641, allocations: 4 kB / 426.7 MB, free: 13.08 MB / 302.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.07e-06/0.3641, allocations: 0 / 426.7 MB, free: 13.08 MB / 302.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008112/0.3649, allocations: 0.5178 MB / 427.2 MB, free: 12.51 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.974e-06/0.3649, allocations: 0 / 427.2 MB, free: 12.51 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002547/0.3652, allocations: 35.98 kB / 427.2 MB, free: 12.47 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.198e-06/0.3652, allocations: 0 / 427.2 MB, free: 12.47 MB / 302.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.121e-05/0.3652, allocations: 0 / 427.2 MB, free: 12.47 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.526e-06/0.3652, allocations: 3.938 kB / 427.2 MB, free: 12.47 MB / 302.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.282e-06/0.3652, allocations: 4 kB / 427.2 MB, free: 12.46 MB / 302.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004314/0.3657, allocations: 309.3 kB / 427.5 MB, free: 12.15 MB / 302.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.894e-05/0.3657, allocations: 89 kB / 427.6 MB, free: 12.04 MB / 302.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.481e-05/0.3658, allocations: 8.188 kB / 427.6 MB, free: 12.04 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001516/0.3659, allocations: 23.78 kB / 427.7 MB, free: 12.01 MB / 302.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.008e-05/0.366, allocations: 7.984 kB / 427.7 MB, free: 12 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.14e-05/0.366, allocations: 4 kB / 427.7 MB, free: 12 MB / 302.1 MB
Notification: Performance of sorting global known variables: time 6.424e-05/0.3661, allocations: 111.2 kB / 427.8 MB, free: 11.89 MB / 302.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.3661, allocations: 0 / 427.8 MB, free: 11.89 MB / 302.1 MB
Notification: Performance of remove unused functions: time 0.0003834/0.3665, allocations: 40 kB / 427.8 MB, free: 11.85 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 0.0001138/0.3666, allocations: 103.2 kB / 427.9 MB, free: 11.74 MB / 302.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003482/0.3669, allocations: 150.8 kB / 428.1 MB, free: 11.6 MB / 302.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.936e-06/0.367, allocations: 0 / 428.1 MB, free: 11.6 MB / 302.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001011/0.3671, allocations: 63.91 kB / 428.1 MB, free: 11.54 MB / 302.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000395/0.3675, allocations: 12 kB / 428.1 MB, free: 11.52 MB / 302.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001116/0.3686, allocations: 0.6279 MB / 428.8 MB, free: 10.87 MB / 302.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002181/0.3688, allocations: 0.7436 MB / 429.5 MB, free: 10.1 MB / 302.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 7.968e-05/0.3689, allocations: 19.42 kB / 429.5 MB, free: 10.08 MB / 302.1 MB
Notification: Performance of SimCode: time 2.7e-07/0.3689, allocations: 0 / 429.5 MB, free: 10.08 MB / 302.1 MB
Notification: Performance of Templates: time 0.004805/0.3737, allocations: 2.005 MB / 431.5 MB, free: 8.07 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 -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1)