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 0.001079/0.001079, allocations: 102.2 kB / 16.27 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 0.001128/0.001127, allocations: 191 kB / 17.2 MB, free: 5.609 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.321/1.321, allocations: 222.9 MB / 240.9 MB, free: 15.27 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.07466/0.07466, allocations: 12.28 MB / 303.3 MB, free: 3.309 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001747/0.001747, allocations: 71.88 kB / 366.4 MB, free: 4.113 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2167/0.2185, allocations: 52.07 MB / 418.5 MB, free: 21.82 MB / 302.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003707/0.2222, allocations: 2.82 MB / 421.3 MB, free: 19 MB / 302.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0002001/0.2225, allocations: 192.3 kB / 421.5 MB, free: 18.82 MB / 302.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 7.179e-05/0.2225, allocations: 8 kB / 421.5 MB, free: 18.81 MB / 302.1 MB
Notification: Performance of NFTyping.typeComponents: time 6.644e-05/0.2226, allocations: 31.73 kB / 421.6 MB, free: 18.78 MB / 302.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001182/0.2228, allocations: 47.5 kB / 421.6 MB, free: 18.73 MB / 302.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001641/0.2229, allocations: 43.94 kB / 421.6 MB, free: 18.69 MB / 302.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0001291/0.2231, allocations: 183.2 kB / 421.8 MB, free: 18.51 MB / 302.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001885/0.2233, allocations: 114.2 kB / 421.9 MB, free: 18.39 MB / 302.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 5.469e-05/0.2233, allocations: 79.72 kB / 422 MB, free: 18.32 MB / 302.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001104/0.2234, allocations: 99.53 kB / 422.1 MB, free: 18.22 MB / 302.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.174e-05/0.2235, allocations: 21.28 kB / 422.1 MB, free: 18.2 MB / 302.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.938e-05/0.2235, allocations: 20 kB / 422.1 MB, free: 18.18 MB / 302.1 MB
Notification: Performance of NFScalarize.scalarize: time 3.294e-05/0.2235, allocations: 47.84 kB / 422.2 MB, free: 18.13 MB / 302.1 MB
Notification: Performance of NFVerifyModel.verify: time 7.357e-05/0.2236, allocations: 109.7 kB / 422.3 MB, free: 18.03 MB / 302.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001695/0.2238, allocations: 233.1 kB / 422.5 MB, free: 17.8 MB / 302.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.489e-06/0.2238, allocations: 0 / 422.5 MB, free: 17.8 MB / 302.1 MB
Notification: Performance of FrontEnd: time 1.623e-06/0.2238, allocations: 0 / 422.5 MB, free: 17.8 MB / 302.1 MB
Notification: Performance of Transformations before backend: time 6.002e-06/0.2238, allocations: 0 / 422.5 MB, free: 17.8 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 0.0006032/0.2244, allocations: 0.5027 MB / 423 MB, free: 17.25 MB / 302.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.347e-05/0.2245, allocations: 12.03 kB / 423 MB, free: 17.24 MB / 302.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.867e-05/0.2245, allocations: 24.66 kB / 423.1 MB, free: 17.21 MB / 302.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 8.452e-05/0.2246, allocations: 184.1 kB / 423.2 MB, free: 17 MB / 302.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.756e-05/0.2246, allocations: 16.94 kB / 423.3 MB, free: 16.98 MB / 302.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.407e-05/0.2247, allocations: 32.83 kB / 423.3 MB, free: 16.95 MB / 302.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002859/0.225, allocations: 204.1 kB / 423.5 MB, free: 16.75 MB / 302.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.366e-05/0.225, allocations: 192 / 423.5 MB, free: 16.75 MB / 302.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.144e-05/0.225, allocations: 11.94 kB / 423.5 MB, free: 16.73 MB / 302.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.412e-06/0.225, allocations: 8 kB / 423.5 MB, free: 16.73 MB / 302.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002024/0.2253, allocations: 134.2 kB / 423.6 MB, free: 16.59 MB / 302.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001068/0.2263, allocations: 0.7729 MB / 424.4 MB, free: 15.77 MB / 302.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001519/0.2265, allocations: 106.5 kB / 424.5 MB, free: 15.66 MB / 302.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002122/0.2267, allocations: 99.02 kB / 424.6 MB, free: 15.56 MB / 302.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.579e-05/0.2267, allocations: 0.9062 kB / 424.6 MB, free: 15.56 MB / 302.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.44e-05/0.2268, allocations: 44.31 kB / 424.7 MB, free: 15.51 MB / 302.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.362e-06/0.2268, allocations: 0 / 424.7 MB, free: 15.51 MB / 302.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001102/0.2279, allocations: 0.5738 MB / 425.2 MB, free: 14.89 MB / 302.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.23e-05/0.2279, allocations: 51.41 kB / 425.3 MB, free: 14.83 MB / 302.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.046e-05/0.228, allocations: 152.7 kB / 425.4 MB, free: 14.66 MB / 302.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.286e-05/0.228, allocations: 35.36 kB / 425.5 MB, free: 14.62 MB / 302.1 MB
Notification: Performance of collectInitialEqns (initialization): time 5.029e-05/0.2281, allocations: 151.9 kB / 425.6 MB, free: 14.47 MB / 302.1 MB
Notification: Performance of collectInitialBindings (initialization): time 3.256e-05/0.2281, allocations: 70.98 kB / 425.7 MB, free: 14.4 MB / 302.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.766e-05/0.2282, allocations: 46.61 kB / 425.7 MB, free: 14.35 MB / 302.1 MB
Notification: Performance of setup shared object (initialization): time 4.652e-05/0.2282, allocations: 326.8 kB / 426.1 MB, free: 14.02 MB / 302.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.105e-05/0.2283, allocations: 45.41 kB / 426.1 MB, free: 13.98 MB / 302.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.421e-05/0.2284, allocations: 94.17 kB / 426.2 MB, free: 13.87 MB / 302.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001238/0.2297, allocations: 391.1 kB / 426.6 MB, free: 13.48 MB / 302.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.242e-06/0.2297, allocations: 0 / 426.6 MB, free: 13.48 MB / 302.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002547/0.2299, allocations: 208.5 kB / 426.8 MB, free: 13.28 MB / 302.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.335e-05/0.2299, allocations: 11.94 kB / 426.8 MB, free: 13.27 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.84e-06/0.23, allocations: 0 / 426.8 MB, free: 13.27 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.575e-05/0.23, allocations: 5.781 kB / 426.8 MB, free: 13.26 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001847/0.2302, allocations: 47.91 kB / 426.8 MB, free: 13.21 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.364e-06/0.2302, allocations: 7.984 kB / 426.8 MB, free: 13.21 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.359e-05/0.2303, allocations: 8 kB / 426.9 MB, free: 13.2 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.313e-05/0.2303, allocations: 19.5 kB / 426.9 MB, free: 13.18 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 0.000174/0.2305, allocations: 140.1 kB / 427 MB, free: 13.04 MB / 302.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.612e-05/0.2305, allocations: 21.94 kB / 427 MB, free: 13.02 MB / 302.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002486/0.2308, allocations: 164.9 kB / 427.2 MB, free: 12.85 MB / 302.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.926e-06/0.2308, allocations: 4 kB / 427.2 MB, free: 12.85 MB / 302.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.877e-06/0.2308, allocations: 0 / 427.2 MB, free: 12.85 MB / 302.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.018e-06/0.2308, allocations: 3.984 kB / 427.2 MB, free: 12.84 MB / 302.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005643/0.2314, allocations: 0.5179 MB / 427.7 MB, free: 12.27 MB / 302.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.474e-06/0.2314, allocations: 4 kB / 427.7 MB, free: 12.27 MB / 302.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001856/0.2316, allocations: 35.97 kB / 427.8 MB, free: 12.23 MB / 302.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.535e-06/0.2316, allocations: 0 / 427.8 MB, free: 12.23 MB / 302.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.35e-05/0.2316, allocations: 0 / 427.8 MB, free: 12.23 MB / 302.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.164e-06/0.2316, allocations: 4 kB / 427.8 MB, free: 12.23 MB / 302.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.282e-06/0.2316, allocations: 0 / 427.8 MB, free: 12.23 MB / 302.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000295/0.2319, allocations: 317.3 kB / 428.1 MB, free: 11.9 MB / 302.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.304e-05/0.2319, allocations: 85.02 kB / 428.2 MB, free: 11.8 MB / 302.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.53e-05/0.232, allocations: 8.188 kB / 428.2 MB, free: 11.79 MB / 302.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001052/0.2321, allocations: 8 kB / 428.2 MB, free: 11.79 MB / 302.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.37e-05/0.2321, allocations: 7.984 kB / 428.2 MB, free: 11.78 MB / 302.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.518e-06/0.2321, allocations: 7.984 kB / 428.2 MB, free: 11.77 MB / 302.1 MB
Notification: Performance of sorting global known variables: time 5.378e-05/0.2322, allocations: 107.3 kB / 428.3 MB, free: 11.66 MB / 302.1 MB
Notification: Performance of sort global known variables: time 6.61e-07/0.2322, allocations: 0 / 428.3 MB, free: 11.66 MB / 302.1 MB
Notification: Performance of remove unused functions: time 0.0002689/0.2325, allocations: 43.94 kB / 428.3 MB, free: 11.62 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 7.02e-05/0.2325, allocations: 103.8 kB / 428.4 MB, free: 11.51 MB / 302.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002395/0.2328, allocations: 147.7 kB / 428.6 MB, free: 11.37 MB / 302.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.164e-06/0.2328, allocations: 0 / 428.6 MB, free: 11.37 MB / 302.1 MB
Notification: Performance of simCode: created simulation system equations: time 7.616e-05/0.2329, allocations: 63.92 kB / 428.6 MB, free: 11.3 MB / 302.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002751/0.2332, allocations: 15.98 kB / 428.7 MB, free: 11.29 MB / 302.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.000685/0.2339, allocations: 0.5419 MB / 429.2 MB, free: 10.72 MB / 302.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001255/0.234, allocations: 0.7358 MB / 429.9 MB, free: 9.957 MB / 302.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.33e-05/0.2341, allocations: 19.44 kB / 430 MB, free: 9.938 MB / 302.1 MB
Notification: Performance of SimCode: time 2.3e-07/0.2341, allocations: 0 / 430 MB, free: 9.938 MB / 302.1 MB
Notification: Performance of Templates: time 0.003006/0.2371, allocations: 2.006 MB / 432 MB, free: 7.934 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)