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) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001307/0.001307, allocations: 117.8 kB / 17.13 MB, free: 5.758 MB / 14.72 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001245/0.001245, allocations: 194.1 kB / 20.08 MB, free: 2.848 MB / 14.72 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.434/1.434, allocations: 225.6 MB / 248.5 MB, free: 3.629 MB / 190.1 MB " [Timeout remaining time 178] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.09539/0.09539, allocations: 12.4 MB / 315.8 MB, free: 348 kB / 238.1 MB " [Timeout remaining time 180] 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=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol") translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol") [Timeout 660] "Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\" Notification: Performance of FrontEnd - loaded program: time 0.001978/0.001978, allocations: 63.91 kB / 440.7 MB, free: 5.676 MB / 366.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.214/0.2159, allocations: 54.92 MB / 495.6 MB, free: 23.13 MB / 366.1 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.004042/0.22, allocations: 2.815 MB / 498.4 MB, free: 21.29 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.0003422/0.2203, allocations: 205.1 kB / 498.6 MB, free: 21.13 MB / 366.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 8.218e-05/0.2204, allocations: 8.094 kB / 498.6 MB, free: 21.13 MB / 366.1 MB Notification: Performance of NFTyping.typeComponents: time 6.533e-05/0.2205, allocations: 29.48 kB / 498.7 MB, free: 21.11 MB / 366.1 MB Notification: Performance of NFTyping.typeBindings: time 0.0001363/0.2206, allocations: 42.69 kB / 498.7 MB, free: 21.08 MB / 366.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.0001761/0.2208, allocations: 62.89 kB / 498.8 MB, free: 21.04 MB / 366.1 MB Notification: Performance of NFFlatten.flatten: time 0.0001754/0.221, allocations: 183.7 kB / 499 MB, free: 20.95 MB / 366.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0001774/0.2211, allocations: 74.11 kB / 499 MB, free: 20.9 MB / 366.1 MB Notification: Performance of NFEvalConstants.evaluate: time 6.921e-05/0.2212, allocations: 78.3 kB / 499.1 MB, free: 20.86 MB / 366.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0001306/0.2213, allocations: 96.75 kB / 499.2 MB, free: 20.81 MB / 366.1 MB Notification: Performance of NFPackage.collectConstants: time 3.409e-05/0.2214, allocations: 21.12 kB / 499.2 MB, free: 20.81 MB / 366.1 MB Notification: Performance of NFFlatten.collectFunctions: time 3.421e-05/0.2214, allocations: 25.56 kB / 499.2 MB, free: 20.81 MB / 366.1 MB Notification: Performance of NFScalarize.scalarize: time 4.377e-05/0.2214, allocations: 53.19 kB / 499.3 MB, free: 20.77 MB / 366.1 MB Notification: Performance of NFVerifyModel.verify: time 9.173e-05/0.2215, allocations: 102.1 kB / 499.4 MB, free: 20.7 MB / 366.1 MB Notification: Performance of NFConvertDAE.convert: time 0.0003177/0.2219, allocations: 234 kB / 499.6 MB, free: 20.61 MB / 366.1 MB Notification: Performance of FrontEnd - DAE generated: time 4.288e-06/0.2219, allocations: 4 kB / 499.6 MB, free: 20.61 MB / 366.1 MB Notification: Performance of FrontEnd: time 1.443e-06/0.2219, allocations: 0 / 499.6 MB, free: 20.61 MB / 366.1 MB Notification: Performance of Transformations before backend: time 6.703e-06/0.2219, allocations: 1.125 kB / 499.6 MB, free: 20.61 MB / 366.1 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 0.0006726/0.2225, allocations: 0.498 MB / 0.4884 GB, free: 20.16 MB / 366.1 MB Notification: Performance of prepare preOptimizeDAE: time 2.957e-05/0.2226, allocations: 9.25 kB / 0.4884 GB, free: 20.16 MB / 366.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 5.434e-05/0.2226, allocations: 32.91 kB / 0.4884 GB, free: 20.14 MB / 366.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 8.85e-05/0.2227, allocations: 193.4 kB / 0.4886 GB, free: 19.92 MB / 366.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.881e-05/0.2227, allocations: 18.22 kB / 0.4886 GB, free: 19.91 MB / 366.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 5.543e-05/0.2228, allocations: 28.03 kB / 0.4887 GB, free: 19.9 MB / 366.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003368/0.2231, allocations: 200.1 kB / 0.4889 GB, free: 19.81 MB / 366.1 MB Notification: Performance of preOpt findStateOrder (simulation): time 1.583e-05/0.2231, allocations: 192 / 0.4889 GB, free: 19.81 MB / 366.1 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.21e-05/0.2232, allocations: 14.91 kB / 0.4889 GB, free: 19.8 MB / 366.1 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.773e-06/0.2232, allocations: 6.062 kB / 0.4889 GB, free: 19.8 MB / 366.1 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002661/0.2234, allocations: 139.3 kB / 0.489 GB, free: 19.75 MB / 366.1 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001208/0.2246, allocations: 0.7604 MB / 0.4898 GB, free: 19.23 MB / 366.1 MB Notification: Performance of preOpt comSubExp (simulation): time 0.0001717/0.2248, allocations: 93.52 kB / 0.4898 GB, free: 19.18 MB / 366.1 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0002534/0.2251, allocations: 99.27 kB / 0.4899 GB, free: 19.15 MB / 366.1 MB Notification: Performance of preOpt evalFunc (simulation): time 2.205e-05/0.2251, allocations: 1.5 kB / 0.4899 GB, free: 19.15 MB / 366.1 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.137e-05/0.2251, allocations: 35.84 kB / 0.49 GB, free: 19.11 MB / 366.1 MB Notification: Performance of pre-optimization done (n=15): time 1.142e-06/0.2251, allocations: 0 / 0.49 GB, free: 19.11 MB / 366.1 MB Notification: Performance of matching and sorting (n=17): time 0.001165/0.2263, allocations: 0.5846 MB / 0.4905 GB, free: 18.7 MB / 366.1 MB Notification: Performance of inlineWhenForInitialization (initialization): time 1.78e-05/0.2263, allocations: 54.48 kB / 0.4906 GB, free: 18.64 MB / 366.1 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.576e-05/0.2264, allocations: 154.6 kB / 0.4907 GB, free: 18.51 MB / 366.1 MB Notification: Performance of collectPreVariables (initialization): time 1.223e-05/0.2264, allocations: 31.48 kB / 0.4908 GB, free: 18.48 MB / 366.1 MB Notification: Performance of collectInitialEqns (initialization): time 5.056e-05/0.2264, allocations: 152.6 kB / 0.4909 GB, free: 18.34 MB / 366.1 MB Notification: Performance of collectInitialBindings (initialization): time 3.407e-05/0.2265, allocations: 65.3 kB / 0.491 GB, free: 18.29 MB / 366.1 MB Notification: Performance of simplifyInitialFunctions (initialization): time 5.84e-05/0.2265, allocations: 48.55 kB / 0.491 GB, free: 18.26 MB / 366.1 MB Notification: Performance of setup shared object (initialization): time 3.933e-05/0.2266, allocations: 324.8 kB / 0.4913 GB, free: 17.94 MB / 366.1 MB Notification: Performance of preBalanceInitialSystem (initialization): time 8.09e-05/0.2267, allocations: 43.05 kB / 0.4914 GB, free: 17.93 MB / 366.1 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001116/0.2268, allocations: 96.8 kB / 0.4915 GB, free: 17.85 MB / 366.1 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.001345/0.2281, allocations: 385.6 kB / 0.4918 GB, free: 17.7 MB / 366.1 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.292e-06/0.2281, allocations: 0.9688 kB / 0.4918 GB, free: 17.7 MB / 366.1 MB Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002883/0.2284, allocations: 211.1 kB / 0.492 GB, free: 17.59 MB / 366.1 MB Notification: Performance of prepare postOptimizeDAE: time 1.398e-05/0.2284, allocations: 7.031 kB / 0.4921 GB, free: 17.59 MB / 366.1 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.949e-06/0.2284, allocations: 1.062 kB / 0.4921 GB, free: 17.59 MB / 366.1 MB Notification: Performance of postOpt tearingSystem (initialization): time 4.703e-05/0.2285, allocations: 11.59 kB / 0.4921 GB, free: 17.58 MB / 366.1 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002048/0.2287, allocations: 50.03 kB / 0.4921 GB, free: 17.58 MB / 366.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.323e-06/0.2287, allocations: 3.281 kB / 0.4921 GB, free: 17.58 MB / 366.1 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.756e-05/0.2288, allocations: 7.344 kB / 0.4921 GB, free: 17.57 MB / 366.1 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.64e-05/0.2288, allocations: 14.56 kB / 0.4921 GB, free: 17.57 MB / 366.1 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 0.000162/0.2289, allocations: 164.9 kB / 0.4923 GB, free: 17.41 MB / 366.1 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.849e-05/0.229, allocations: 16.91 kB / 0.4923 GB, free: 17.41 MB / 366.1 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002777/0.2293, allocations: 173.8 kB / 0.4925 GB, free: 17.31 MB / 366.1 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.555e-06/0.2293, allocations: 1.406 kB / 0.4925 GB, free: 17.31 MB / 366.1 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 8.356e-06/0.2293, allocations: 1.922 kB / 0.4925 GB, free: 17.31 MB / 366.1 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.798e-06/0.2293, allocations: 0.7969 kB / 0.4925 GB, free: 17.31 MB / 366.1 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000641/0.2299, allocations: 0.5169 MB / 0.493 GB, free: 16.89 MB / 366.1 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.342e-06/0.2299, allocations: 1.062 kB / 0.493 GB, free: 16.89 MB / 366.1 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002141/0.2301, allocations: 41.09 kB / 0.493 GB, free: 16.88 MB / 366.1 MB Notification: Performance of postOpt tearingSystem (simulation): time 2.826e-06/0.2301, allocations: 0.9375 kB / 0.493 GB, free: 16.88 MB / 366.1 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.566e-05/0.2302, allocations: 1 kB / 0.493 GB, free: 16.88 MB / 366.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.204e-06/0.2302, allocations: 0.9375 kB / 0.493 GB, free: 16.88 MB / 366.1 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.362e-06/0.2302, allocations: 1.031 kB / 0.493 GB, free: 16.88 MB / 366.1 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003239/0.2305, allocations: 307.4 kB / 0.4933 GB, free: 16.66 MB / 366.1 MB Notification: Performance of postOpt removeConstants (simulation): time 2.462e-05/0.2305, allocations: 92.45 kB / 0.4934 GB, free: 16.55 MB / 366.1 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.326e-05/0.2305, allocations: 6.312 kB / 0.4934 GB, free: 16.55 MB / 366.1 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001074/0.2306, allocations: 5.25 kB / 0.4934 GB, free: 16.54 MB / 366.1 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 3.11e-05/0.2307, allocations: 16.91 kB / 0.4934 GB, free: 16.53 MB / 366.1 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.033e-05/0.2307, allocations: 3.375 kB / 0.4934 GB, free: 16.53 MB / 366.1 MB Notification: Performance of sorting global known variables: time 5.294e-05/0.2307, allocations: 113.6 kB / 0.4935 GB, free: 16.44 MB / 366.1 MB Notification: Performance of sort global known variables: time 8e-08/0.2307, allocations: 0 / 0.4935 GB, free: 16.44 MB / 366.1 MB Notification: Performance of remove unused functions: time 0.0003208/0.2311, allocations: 37.53 kB / 0.4936 GB, free: 16.44 MB / 366.1 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 6.3e-05/0.2311, allocations: 108.2 kB / 0.4937 GB, free: 16.34 MB / 366.1 MB Notification: Performance of simCode: created initialization part: time 0.0002401/0.2314, allocations: 133.9 kB / 0.4938 GB, free: 16.29 MB / 366.1 MB Notification: Performance of simCode: created event and clocks part: time 1.633e-06/0.2314, allocations: 0 / 0.4938 GB, free: 16.29 MB / 366.1 MB Notification: Performance of simCode: created simulation system equations: time 8.499e-05/0.2314, allocations: 58.23 kB / 0.4939 GB, free: 16.26 MB / 366.1 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002614/0.2317, allocations: 17.64 kB / 0.4939 GB, free: 16.25 MB / 366.1 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007398/0.2324, allocations: 0.547 MB / 0.4944 GB, free: 15.82 MB / 366.1 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001312/0.2326, allocations: 0.7424 MB / 0.4951 GB, free: 15.1 MB / 366.1 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 9.194e-05/0.2327, allocations: 17.81 kB / 0.4952 GB, free: 15.09 MB / 366.1 MB Notification: Performance of SimCode: time 3.41e-07/0.2327, allocations: 0 / 0.4952 GB, free: 15.09 MB / 366.1 MB Notification: Performance of Templates: time 0.003427/0.2361, allocations: 2.025 MB / 0.4971 GB, free: 14.03 MB / 366.1 MB " [Timeout remaining time 660] make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile [Timeout 660] (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) [Timeout 480] [Calling sys.exit(0), Time elapsed: 6.676882076077163] Failed to read output from testmodel.py, exit status != 0: 0.24346688692457974 0.25268638599999993 0.02872489999999994 Calling exit ...