Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.GMO.cell.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 0.001677/0.001677, allocations: 120.3 kB / 17.13 MB, free: 5.918 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 0.001815/0.001815, allocations: 193.2 kB / 20.08 MB, free: 2.988 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 1.492/1.492, allocations: 225.6 MB / 248.5 MB, free: 3.645 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 0.1398/0.1398, allocations: 12.41 MB / 315.8 MB, free: 400 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.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell") translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell") [Timeout 660] "Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\" Notification: Performance of FrontEnd - loaded program: time 0.001975/0.001975, allocations: 60.09 kB / 440.7 MB, free: 36.66 MB / 350.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.07805/0.08003, allocations: 54.93 MB / 495.6 MB, free: 7.762 MB / 350.1 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005221/0.08525, allocations: 4.33 MB / 499.9 MB, free: 4.551 MB / 350.1 MB Notification: Performance of NFInst.instExpressions: time 0.0002979/0.08555, allocations: 305.3 kB / 0.4885 GB, free: 4.289 MB / 350.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001664/0.08571, allocations: 14.84 kB / 0.4885 GB, free: 4.289 MB / 350.1 MB Notification: Performance of NFTyping.typeComponents: time 8.737e-05/0.0858, allocations: 53.08 kB / 0.4886 GB, free: 4.242 MB / 350.1 MB Notification: Performance of NFTyping.typeBindings: time 0.0001556/0.08596, allocations: 75.28 kB / 0.4887 GB, free: 4.176 MB / 350.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.0001635/0.08612, allocations: 70.7 kB / 0.4887 GB, free: 4.113 MB / 350.1 MB Notification: Performance of NFFlatten.flatten: time 0.0002241/0.08634, allocations: 294.9 kB / 0.489 GB, free: 3.941 MB / 350.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0002537/0.0866, allocations: 121.5 kB / 0.4891 GB, free: 3.859 MB / 350.1 MB Notification: Performance of NFEvalConstants.evaluate: time 9.352e-05/0.08669, allocations: 125.5 kB / 0.4892 GB, free: 3.785 MB / 350.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0001393/0.08683, allocations: 159.4 kB / 0.4894 GB, free: 3.633 MB / 350.1 MB Notification: Performance of NFPackage.collectConstants: time 3.738e-05/0.08687, allocations: 32 kB / 0.4894 GB, free: 3.602 MB / 350.1 MB Notification: Performance of NFFlatten.collectFunctions: time 3.772e-05/0.08691, allocations: 36 kB / 0.4895 GB, free: 3.566 MB / 350.1 MB Notification: Performance of NFScalarize.scalarize: time 3.968e-05/0.08695, allocations: 83.69 kB / 0.4895 GB, free: 3.484 MB / 350.1 MB Notification: Performance of NFVerifyModel.verify: time 9.21e-05/0.08704, allocations: 163.1 kB / 0.4897 GB, free: 3.324 MB / 350.1 MB Notification: Performance of NFConvertDAE.convert: time 0.0002462/0.08728, allocations: 362.5 kB / 0.49 GB, free: 2.969 MB / 350.1 MB Notification: Performance of FrontEnd - DAE generated: time 3.466e-06/0.08729, allocations: 0 / 0.49 GB, free: 2.969 MB / 350.1 MB Notification: Performance of FrontEnd: time 1.172e-06/0.08729, allocations: 0 / 0.49 GB, free: 2.969 MB / 350.1 MB Notification: Performance of Transformations before backend: time 5.971e-06/0.08729, allocations: 0 / 0.49 GB, free: 2.969 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: 96 * Number of variables: 96 Notification: Performance of Generate backend data structure: time 0.0007932/0.08809, allocations: 0.6083 MB / 0.4906 GB, free: 2.309 MB / 350.1 MB Notification: Performance of prepare preOptimizeDAE: time 2.838e-05/0.08812, allocations: 8.031 kB / 0.4906 GB, free: 2.301 MB / 350.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.005e-05/0.08818, allocations: 40.69 kB / 0.4907 GB, free: 2.262 MB / 350.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001378/0.08831, allocations: 204 kB / 0.4909 GB, free: 2.023 MB / 350.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.734e-05/0.08833, allocations: 29.38 kB / 0.4909 GB, free: 1.996 MB / 350.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 5.148e-05/0.08838, allocations: 40.38 kB / 0.4909 GB, free: 1.957 MB / 350.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003803/0.08876, allocations: 311 kB / 0.4912 GB, free: 1.648 MB / 350.1 MB Notification: Performance of preOpt findStateOrder (simulation): time 1.809e-05/0.08878, allocations: 4.172 kB / 0.4912 GB, free: 1.645 MB / 350.1 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.55e-05/0.08881, allocations: 19.94 kB / 0.4913 GB, free: 1.625 MB / 350.1 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.424e-06/0.08881, allocations: 8 kB / 0.4913 GB, free: 1.617 MB / 350.1 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003099/0.08912, allocations: 239.9 kB / 0.4915 GB, free: 1.379 MB / 350.1 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001437/0.09056, allocations: 1.036 MB / 0.4925 GB, free: 300 kB / 350.1 MB Notification: Performance of preOpt comSubExp (simulation): time 0.0002628/0.09082, allocations: 174.5 kB / 0.4927 GB, free: 116 kB / 350.1 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001522/0.09098, allocations: 104.8 kB / 0.4928 GB, free: 8 kB / 350.1 MB Notification: Performance of preOpt evalFunc (simulation): time 1.382e-05/0.09099, allocations: 0 / 0.4928 GB, free: 8 kB / 350.1 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.261e-05/0.09103, allocations: 34.94 kB / 0.4928 GB, free: 15.96 MB / 366.1 MB Notification: Performance of pre-optimization done (n=22): time 1.142e-06/0.09103, allocations: 0 / 0.4928 GB, free: 15.96 MB / 366.1 MB Notification: Performance of matching and sorting (n=26): time 0.002081/0.09311, allocations: 0.9006 MB / 0.4937 GB, free: 15.02 MB / 366.1 MB Notification: Performance of inlineWhenForInitialization (initialization): time 4.224e-05/0.09316, allocations: 63.39 kB / 0.4938 GB, free: 14.94 MB / 366.1 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001529/0.09331, allocations: 164.5 kB / 0.4939 GB, free: 14.77 MB / 366.1 MB Notification: Performance of collectPreVariables (initialization): time 2.988e-05/0.09334, allocations: 29.7 kB / 0.4939 GB, free: 14.73 MB / 366.1 MB Notification: Performance of collectInitialEqns (initialization): time 0.0001267/0.09347, allocations: 208.1 kB / 0.4941 GB, free: 14.52 MB / 366.1 MB Notification: Performance of collectInitialBindings (initialization): time 0.0001103/0.09358, allocations: 107.1 kB / 0.4942 GB, free: 14.42 MB / 366.1 MB Notification: Performance of simplifyInitialFunctions (initialization): time 9.074e-05/0.09367, allocations: 61.7 kB / 0.4943 GB, free: 14.35 MB / 366.1 MB Notification: Performance of setup shared object (initialization): time 0.0001445/0.09381, allocations: 338.7 kB / 0.4946 GB, free: 14.01 MB / 366.1 MB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001415/0.09395, allocations: 84.34 kB / 0.4947 GB, free: 13.93 MB / 366.1 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002283/0.09418, allocations: 192.2 kB / 0.4949 GB, free: 13.69 MB / 366.1 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.003334/0.09752, allocations: 0.8356 MB / 0.4957 GB, free: 12.8 MB / 366.1 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.733e-06/0.09752, allocations: 0 / 0.4957 GB, free: 12.8 MB / 366.1 MB Notification: Performance of matching and sorting (n=46) (initialization): time 0.0005253/0.09804, allocations: 345.1 kB / 0.496 GB, free: 12.46 MB / 366.1 MB Notification: Performance of prepare postOptimizeDAE: time 1.504e-05/0.09806, allocations: 8.469 kB / 0.496 GB, free: 12.45 MB / 366.1 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.705e-06/0.09807, allocations: 8 kB / 0.496 GB, free: 12.45 MB / 366.1 MB Notification: Performance of postOpt tearingSystem (initialization): time 1.742e-05/0.09808, allocations: 4 kB / 0.496 GB, free: 12.44 MB / 366.1 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003161/0.0984, allocations: 79.89 kB / 0.4961 GB, free: 12.36 MB / 366.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.119e-05/0.09841, allocations: 7.938 kB / 0.4961 GB, free: 12.36 MB / 366.1 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001408/0.09855, allocations: 12 kB / 0.4961 GB, free: 12.34 MB / 366.1 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.053e-05/0.09857, allocations: 12 kB / 0.4962 GB, free: 12.33 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 ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real X.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real M.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real C.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: 16 * 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 (46): * Single equations (assignments): 46 * 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 0.000264/0.09884, allocations: 169.4 kB / 0.4963 GB, free: 12.16 MB / 366.1 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 4.655e-05/0.09888, allocations: 19.86 kB / 0.4963 GB, free: 12.14 MB / 366.1 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.437e-05/0.09896, allocations: 29.88 kB / 0.4964 GB, free: 12.11 MB / 366.1 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.911e-06/0.09896, allocations: 4 kB / 0.4964 GB, free: 12.11 MB / 366.1 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 4.167e-06/0.09897, allocations: 3.938 kB / 0.4964 GB, free: 12.1 MB / 366.1 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.32e-06/0.09897, allocations: 3.984 kB / 0.4964 GB, free: 12.1 MB / 366.1 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000503/0.09947, allocations: 373.3 kB / 0.4967 GB, free: 11.68 MB / 366.1 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.603e-06/0.09948, allocations: 0 / 0.4967 GB, free: 11.68 MB / 366.1 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002835/0.09976, allocations: 43.97 kB / 0.4968 GB, free: 11.64 MB / 366.1 MB Notification: Performance of postOpt tearingSystem (simulation): time 2.194e-06/0.09976, allocations: 0 / 0.4968 GB, free: 11.64 MB / 366.1 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.233e-05/0.09978, allocations: 11.98 kB / 0.4968 GB, free: 11.63 MB / 366.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.667e-06/0.09979, allocations: 4 kB / 0.4968 GB, free: 11.62 MB / 366.1 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.31e-07/0.09979, allocations: 0 / 0.4968 GB, free: 11.62 MB / 366.1 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005827/0.1004, allocations: 435.3 kB / 0.4972 GB, free: 11.18 MB / 366.1 MB Notification: Performance of postOpt removeConstants (simulation): time 8.486e-05/0.1005, allocations: 100.9 kB / 0.4973 GB, free: 11.07 MB / 366.1 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.354e-05/0.1005, allocations: 8.062 kB / 0.4973 GB, free: 11.06 MB / 366.1 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001438/0.1006, allocations: 0 / 0.4973 GB, free: 11.06 MB / 366.1 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 4.255e-05/0.1007, allocations: 19.97 kB / 0.4973 GB, free: 11.04 MB / 366.1 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.404e-05/0.1007, allocations: 4 kB / 0.4973 GB, free: 11.04 MB / 366.1 MB Notification: Performance of sorting global known variables: time 8.708e-05/0.1008, allocations: 117.8 kB / 0.4974 GB, free: 10.92 MB / 366.1 MB Notification: Performance of sort global known variables: time 7e-08/0.1008, allocations: 0 / 0.4974 GB, free: 10.92 MB / 366.1 MB Notification: Performance of remove unused functions: time 0.0003352/0.1011, allocations: 64 kB / 0.4975 GB, free: 10.86 MB / 366.1 MB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 5 (V,C.n,M.n,X.n,ambientSubstance.n) * 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 (26): * Single equations (assignments): 26 * 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 0.0001122/0.1012, allocations: 103.2 kB / 0.4976 GB, free: 10.75 MB / 366.1 MB Notification: Performance of simCode: created initialization part: time 0.0004408/0.1017, allocations: 231.8 kB / 0.4978 GB, free: 10.52 MB / 366.1 MB Notification: Performance of simCode: created event and clocks part: time 2.144e-06/0.1017, allocations: 0 / 0.4978 GB, free: 10.52 MB / 366.1 MB Notification: Performance of simCode: created simulation system equations: time 0.0001562/0.1018, allocations: 103.9 kB / 0.4979 GB, free: 10.42 MB / 366.1 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003022/0.1021, allocations: 24.86 kB / 0.4979 GB, free: 10.39 MB / 366.1 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001388/0.1035, allocations: 0.7796 MB / 0.4987 GB, free: 9.586 MB / 366.1 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000381/0.1039, allocations: 0.7714 MB / 0.4995 GB, free: 8.789 MB / 366.1 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 9.331e-05/0.104, allocations: 23.44 kB / 0.4995 GB, free: 8.77 MB / 366.1 MB Notification: Performance of SimCode: time 2.004e-06/0.104, allocations: 0 / 0.4995 GB, free: 8.77 MB / 366.1 MB Notification: Performance of Templates: time 0.005137/0.1091, allocations: 2.86 MB / 0.5023 GB, free: 5.902 MB / 366.1 MB " [Timeout remaining time 660] make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile [Timeout 660] (rm -f BioChem_BioChem.Examples.GMO.cell.pipe ; mkfifo BioChem_BioChem.Examples.GMO.cell.pipe ; head -c 1048576 < BioChem_BioChem.Examples.GMO.cell.pipe >> ../files/BioChem_BioChem.Examples.GMO.cell.sim & ./BioChem_BioChem.Examples.GMO.cell -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1) [Timeout 480] [Calling sys.exit(0), Time elapsed: 7.212884235996171] Failed to read output from testmodel.py, exit status != 0: 0.11633453700051177 0.130554364 0.040314952 Calling exit ...