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 0.001095/0.001095, allocations: 105.7 kB / 16.35 MB, free: 5.824 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001085/0.001085, allocations: 189.4 kB / 17.29 MB, free: 5.48 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.334/1.334, allocations: 222.9 MB / 241 MB, free: 15.1 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06176/0.06176, allocations: 12.27 MB / 303.4 MB, free: 3.23 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001244/0.001245, allocations: 71.89 kB / 367.2 MB, free: 3.359 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.193/0.1942, allocations: 52.08 MB / 419.3 MB, free: 21.66 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003514/0.1978, allocations: 2.823 MB / 422.1 MB, free: 18.85 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.000188/0.198, allocations: 188.3 kB / 422.3 MB, free: 18.66 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 6.678e-05/0.1981, allocations: 9.219 kB / 422.3 MB, free: 18.66 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 6.246e-05/0.1981, allocations: 31.73 kB / 422.3 MB, free: 18.62 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001144/0.1983, allocations: 47.53 kB / 422.4 MB, free: 18.58 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001625/0.1984, allocations: 47.89 kB / 422.4 MB, free: 18.54 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0001485/0.1986, allocations: 191.2 kB / 422.6 MB, free: 18.35 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001904/0.1988, allocations: 103.6 kB / 422.7 MB, free: 18.24 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 5.754e-05/0.1989, allocations: 85.67 kB / 422.8 MB, free: 18.16 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001134/0.199, allocations: 95.55 kB / 422.9 MB, free: 18.07 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 2.728e-05/0.199, allocations: 20 kB / 422.9 MB, free: 18.05 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.521e-05/0.199, allocations: 20 kB / 422.9 MB, free: 18.03 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 3.388e-05/0.1991, allocations: 55.77 kB / 423 MB, free: 17.97 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 6.878e-05/0.1992, allocations: 104.9 kB / 423.1 MB, free: 17.87 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001608/0.1993, allocations: 232.8 kB / 423.3 MB, free: 17.65 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.488e-06/0.1993, allocations: 4 kB / 423.3 MB, free: 17.64 MB / 302.1 MB
Notification: Performance of FrontEnd: time 1.252e-06/0.1993, allocations: 0 / 423.3 MB, free: 17.64 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 5.55e-06/0.1994, allocations: 0.5 kB / 423.3 MB, free: 17.64 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 0.0005811/0.1999, allocations: 0.5021 MB / 423.8 MB, free: 17.09 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 2.981e-05/0.2, allocations: 8.031 kB / 423.8 MB, free: 17.09 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.551e-05/0.2, allocations: 26.75 kB / 423.8 MB, free: 17.06 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 8.534e-05/0.2001, allocations: 188 kB / 424 MB, free: 16.84 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.33e-05/0.2001, allocations: 16.94 kB / 424 MB, free: 16.82 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.144e-05/0.2002, allocations: 24.38 kB / 424.1 MB, free: 16.8 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000283/0.2005, allocations: 201.5 kB / 424.3 MB, free: 16.6 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.33e-05/0.2005, allocations: 1.531 kB / 424.3 MB, free: 16.6 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.036e-05/0.2005, allocations: 15.94 kB / 424.3 MB, free: 16.58 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.962e-06/0.2005, allocations: 4 kB / 424.3 MB, free: 16.58 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.00021/0.2007, allocations: 142.1 kB / 424.4 MB, free: 16.44 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001063/0.2018, allocations: 0.7667 MB / 425.2 MB, free: 15.61 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001447/0.202, allocations: 98.55 kB / 425.3 MB, free: 15.51 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002001/0.2022, allocations: 100.1 kB / 425.4 MB, free: 15.41 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.942e-05/0.2022, allocations: 6.688 kB / 425.4 MB, free: 15.41 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.227e-05/0.2022, allocations: 34.56 kB / 425.4 MB, free: 15.36 MB / 302.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.333e-06/0.2022, allocations: 0 / 425.4 MB, free: 15.36 MB / 302.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001065/0.2033, allocations: 0.5797 MB / 426 MB, free: 14.74 MB / 302.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 1.85e-05/0.2033, allocations: 58.16 kB / 426.1 MB, free: 14.67 MB / 302.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.83e-05/0.2034, allocations: 151.7 kB / 426.2 MB, free: 14.51 MB / 302.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.255e-05/0.2035, allocations: 29.7 kB / 426.2 MB, free: 14.47 MB / 302.1 MB
Notification: Performance of collectInitialEqns (initialization): time 4.55e-05/0.2035, allocations: 155.9 kB / 426.4 MB, free: 14.32 MB / 302.1 MB
Notification: Performance of collectInitialBindings (initialization): time 3.154e-05/0.2035, allocations: 67 kB / 426.5 MB, free: 14.25 MB / 302.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.382e-05/0.2036, allocations: 43.23 kB / 426.5 MB, free: 14.2 MB / 302.1 MB
Notification: Performance of setup shared object (initialization): time 3.758e-05/0.2036, allocations: 322.8 kB / 426.8 MB, free: 13.88 MB / 302.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.417e-05/0.2037, allocations: 44.22 kB / 426.9 MB, free: 13.84 MB / 302.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001017/0.2038, allocations: 96.14 kB / 427 MB, free: 13.72 MB / 302.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001344/0.2052, allocations: 389.3 kB / 427.3 MB, free: 13.33 MB / 302.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.423e-06/0.2052, allocations: 0 / 427.3 MB, free: 13.33 MB / 302.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002618/0.2055, allocations: 213.4 kB / 427.5 MB, free: 13.12 MB / 302.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.207e-05/0.2055, allocations: 7.938 kB / 427.5 MB, free: 13.11 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.611e-06/0.2055, allocations: 4 kB / 427.6 MB, free: 13.11 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.454e-05/0.2055, allocations: 3.938 kB / 427.6 MB, free: 13.11 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001942/0.2057, allocations: 47.92 kB / 427.6 MB, free: 13.06 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.955e-06/0.2057, allocations: 7.984 kB / 427.6 MB, free: 13.05 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.803e-05/0.2058, allocations: 4 kB / 427.6 MB, free: 13.05 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.462e-05/0.2058, allocations: 15.98 kB / 427.6 MB, free: 13.03 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 0.0001624/0.206, allocations: 142.2 kB / 427.8 MB, free: 12.89 MB / 302.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.583e-05/0.2061, allocations: 23.8 kB / 427.8 MB, free: 12.87 MB / 302.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002536/0.2063, allocations: 176.2 kB / 428 MB, free: 12.69 MB / 302.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.605e-06/0.2063, allocations: 0 / 428 MB, free: 12.69 MB / 302.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.208e-06/0.2063, allocations: 0 / 428 MB, free: 12.69 MB / 302.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.688e-06/0.2063, allocations: 3.984 kB / 428 MB, free: 12.69 MB / 302.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006034/0.207, allocations: 0.5142 MB / 428.5 MB, free: 12.12 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.683e-06/0.207, allocations: 3.938 kB / 428.5 MB, free: 12.11 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001967/0.2072, allocations: 35.91 kB / 428.5 MB, free: 12.08 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.056e-06/0.2072, allocations: 3.812 kB / 428.5 MB, free: 12.08 MB / 302.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.668e-05/0.2072, allocations: 8 kB / 428.5 MB, free: 12.07 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.884e-06/0.2072, allocations: 0 / 428.5 MB, free: 12.07 MB / 302.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.81e-07/0.2072, allocations: 0 / 428.5 MB, free: 12.07 MB / 302.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003127/0.2075, allocations: 310.1 kB / 428.8 MB, free: 11.75 MB / 302.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.882e-05/0.2076, allocations: 85.02 kB / 428.9 MB, free: 11.65 MB / 302.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.879e-05/0.2076, allocations: 8.062 kB / 428.9 MB, free: 11.64 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001095/0.2077, allocations: 4.109 kB / 428.9 MB, free: 11.64 MB / 302.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.377e-05/0.2078, allocations: 20.11 kB / 429 MB, free: 11.62 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.194e-05/0.2078, allocations: 11.98 kB / 429 MB, free: 11.61 MB / 302.1 MB
Notification: Performance of sorting global known variables: time 5.293e-05/0.2079, allocations: 107.3 kB / 429.1 MB, free: 11.5 MB / 302.1 MB
Notification: Performance of sort global known variables: time 2.71e-07/0.2079, allocations: 0 / 429.1 MB, free: 11.5 MB / 302.1 MB
Notification: Performance of remove unused functions: time 0.000279/0.2081, allocations: 40 kB / 429.1 MB, free: 11.46 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 7.51e-05/0.2082, allocations: 95.78 kB / 429.2 MB, free: 11.36 MB / 302.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002336/0.2085, allocations: 148 kB / 429.3 MB, free: 11.22 MB / 302.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.635e-06/0.2085, allocations: 4.062 kB / 429.3 MB, free: 11.21 MB / 302.1 MB
Notification: Performance of simCode: created simulation system equations: time 7.861e-05/0.2086, allocations: 59.92 kB / 429.4 MB, free: 11.16 MB / 302.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002812/0.2088, allocations: 15.94 kB / 429.4 MB, free: 11.14 MB / 302.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.000705/0.2096, allocations: 0.5009 MB / 429.9 MB, free: 10.62 MB / 302.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001353/0.2097, allocations: 0.7475 MB / 430.7 MB, free: 9.844 MB / 302.1 MB
Notification: Performance of simCode: alias equations: time 6.355e-05/0.2098, allocations: 17.42 kB / 430.7 MB, free: 9.828 MB / 302.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.986e-05/0.2098, allocations: 15.44 kB / 430.7 MB, free: 9.812 MB / 302.1 MB
Notification: Performance of SimCode: time 2.31e-07/0.2098, allocations: 0 / 430.7 MB, free: 9.812 MB / 302.1 MB
Notification: Performance of Templates: time 0.003613/0.2135, allocations: 1.382 MB / 432.1 MB, free: 8.445 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 gbode -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1)