Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.centralMetabolism.extra_cellular.conf.json loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.001488/0.001488, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.001586/0.001586, allocations: 173.3 kB / 23.02 MB, free: 1.551 MB / 18.57 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 1.012/1.012, allocations: 177.2 MB / 203.4 MB, free: 5.633 MB / 186.7 MB " [Timeout remaining time 179] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo): time 0.04752/0.04752, allocations: 9.556 MB / 269.5 MB, free: 3.938 MB / 250.7 MB " [Timeout remaining time 180] Using package BioChem with version 1.1.3 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo) Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo) Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo) Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo) Running command: translateModel(BioChem.Examples.centralMetabolism.extra_cellular,tolerance=1e-05,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.centralMetabolism.extra_cellular") translateModel(BioChem.Examples.centralMetabolism.extra_cellular,tolerance=1e-05,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.centralMetabolism.extra_cellular") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 2.184e-06/2.184e-06, allocations: 0 / 342 MB, free: 7.609 MB / 266.7 MB Notification: Performance of FrontEnd - Absyn->SCode: time 2.739e-05/2.958e-05, allocations: 6.312 kB / 342 MB, free: 7.602 MB / 266.7 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.centralMetabolism.extra_cellular): time 0.01062/0.01065, allocations: 5.298 MB / 347.3 MB, free: 2.293 MB / 266.7 MB Notification: Performance of NFInst.instExpressions: time 0.001987/0.01264, allocations: 1.27 MB / 348.6 MB, free: 1.02 MB / 266.7 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.00351/0.01615, allocations: 56 kB / 348.7 MB, free: 0.9648 MB / 266.7 MB Notification: Performance of NFTyping.typeComponents: time 0.0003868/0.01654, allocations: 190.4 kB / 348.8 MB, free: 0.7773 MB / 266.7 MB Notification: Performance of NFTyping.typeBindings: time 0.0005187/0.01706, allocations: 317 kB / 349.2 MB, free: 476 kB / 266.7 MB Notification: Performance of NFTyping.typeClassSections: time 0.0004693/0.01753, allocations: 355.5 kB / 349.5 MB, free: 120 kB / 266.7 MB Notification: Performance of NFFlatten.flatten: time 0.00106/0.01858, allocations: 1.406 MB / 350.9 MB, free: 14.71 MB / 282.7 MB Notification: Performance of NFFlatten.resolveConnections: time 0.00362/0.0222, allocations: 432.8 kB / 351.3 MB, free: 14.26 MB / 282.7 MB Notification: Performance of NFEvalConstants.evaluate: time 0.0008177/0.02302, allocations: 0.8813 MB / 352.2 MB, free: 13.38 MB / 282.7 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0005848/0.02361, allocations: 0.4986 MB / 352.7 MB, free: 12.88 MB / 282.7 MB Notification: Performance of NFPackage.collectConstants: time 0.0001978/0.02381, allocations: 188 kB / 352.9 MB, free: 12.69 MB / 282.7 MB Notification: Performance of NFFlatten.collectFunctions: time 0.0001982/0.024, allocations: 188 kB / 353.1 MB, free: 12.51 MB / 282.7 MB Notification: Performance of NFScalarize.scalarize: time 0.0004731/0.02448, allocations: 358.9 kB / 353.4 MB, free: 12.16 MB / 282.7 MB Notification: Performance of NFVerifyModel.verify: time 0.002419/0.0269, allocations: 498.9 kB / 353.9 MB, free: 11.67 MB / 282.7 MB Notification: Performance of NFConvertDAE.convert: time 0.001006/0.0279, allocations: 1.063 MB / 355 MB, free: 10.6 MB / 282.7 MB Notification: Performance of FrontEnd - DAE generated: time 5.451e-06/0.02791, allocations: 0 / 355 MB, free: 10.6 MB / 282.7 MB Notification: Performance of FrontEnd: time 1.623e-06/0.02791, allocations: 0 / 355 MB, free: 10.6 MB / 282.7 MB Notification: Performance of Transformations before backend: time 1.149e-05/0.02792, allocations: 4 kB / 355 MB, free: 10.6 MB / 282.7 MB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 353 * Number of variables: 353 Notification: Performance of Generate backend data structure: time 0.002207/0.03013, allocations: 1.578 MB / 356.6 MB, free: 8.977 MB / 282.7 MB Notification: Performance of prepare preOptimizeDAE: time 5.117e-05/0.03018, allocations: 8.031 kB / 356.6 MB, free: 8.969 MB / 282.7 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002409/0.03042, allocations: 252 kB / 356.8 MB, free: 8.723 MB / 282.7 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004829/0.0309, allocations: 0.4954 MB / 357.3 MB, free: 8.195 MB / 282.7 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.675e-05/0.03096, allocations: 107.1 kB / 357.4 MB, free: 8.09 MB / 282.7 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001238/0.03108, allocations: 144.3 kB / 357.6 MB, free: 7.949 MB / 282.7 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.001138/0.03222, allocations: 0.989 MB / 358.5 MB, free: 6.926 MB / 282.7 MB Notification: Performance of preOpt findStateOrder (simulation): time 3.03e-05/0.03225, allocations: 4.188 kB / 358.5 MB, free: 6.922 MB / 282.7 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.211e-05/0.03232, allocations: 60.38 kB / 358.6 MB, free: 6.863 MB / 282.7 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.527e-05/0.03235, allocations: 36.38 kB / 358.6 MB, free: 6.828 MB / 282.7 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008487/0.0332, allocations: 0.5662 MB / 359.2 MB, free: 6.254 MB / 282.7 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004216/0.03741, allocations: 3.719 MB / 362.9 MB, free: 2.414 MB / 282.7 MB Notification: Performance of preOpt comSubExp (simulation): time 0.0008805/0.03829, allocations: 0.777 MB / 363.7 MB, free: 1.633 MB / 282.7 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0003675/0.03866, allocations: 293.5 kB / 364 MB, free: 1.348 MB / 282.7 MB Notification: Performance of preOpt evalFunc (simulation): time 4.281e-05/0.0387, allocations: 17 kB / 364 MB, free: 1.332 MB / 282.7 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.841e-05/0.03873, allocations: 50.39 kB / 364.1 MB, free: 1.273 MB / 282.7 MB Notification: Performance of pre-optimization done (n=96): time 2.635e-06/0.03873, allocations: 4 kB / 364.1 MB, free: 1.27 MB / 282.7 MB Notification: Performance of matching and sorting (n=114): time 0.004116/0.04285, allocations: 2.849 MB / 366.9 MB, free: 14.43 MB / 298.7 MB Notification: Performance of inlineWhenForInitialization (initialization): time 3.42e-05/0.04288, allocations: 60.41 kB / 367 MB, free: 14.36 MB / 298.7 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000261/0.04315, allocations: 430.4 kB / 367.4 MB, free: 13.92 MB / 298.7 MB Notification: Performance of collectPreVariables (initialization): time 0.0002595/0.04341, allocations: 45.7 kB / 367.4 MB, free: 13.87 MB / 298.7 MB Notification: Performance of collectInitialEqns (initialization): time 0.0002282/0.04363, allocations: 0.5928 MB / 368 MB, free: 13.27 MB / 298.7 MB Notification: Performance of collectInitialBindings (initialization): time 0.0002176/0.04385, allocations: 420.4 kB / 368.4 MB, free: 12.86 MB / 298.7 MB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002195/0.04407, allocations: 208.5 kB / 368.6 MB, free: 12.64 MB / 298.7 MB Notification: Performance of setup shared object (initialization): time 0.0001623/0.04423, allocations: 0.5469 MB / 369.2 MB, free: 12.08 MB / 298.7 MB Notification: Performance of preBalanceInitialSystem (initialization): time 0.000347/0.04458, allocations: 234.5 kB / 369.4 MB, free: 11.86 MB / 298.7 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004891/0.04507, allocations: 0.6044 MB / 370 MB, free: 11.1 MB / 298.7 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.001264/0.04633, allocations: 1.234 MB / 371.3 MB, free: 9.723 MB / 298.7 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.018e-06/0.04634, allocations: 4 kB / 371.3 MB, free: 9.719 MB / 298.7 MB Notification: Performance of matching and sorting (n=165) (initialization): time 0.001317/0.04765, allocations: 1.101 MB / 372.4 MB, free: 8.602 MB / 298.7 MB Notification: Performance of prepare postOptimizeDAE: time 2.559e-05/0.04768, allocations: 15.92 kB / 372.4 MB, free: 8.586 MB / 298.7 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.203e-05/0.04769, allocations: 8 kB / 372.4 MB, free: 8.578 MB / 298.7 MB Notification: Performance of postOpt tearingSystem (initialization): time 0.0003635/0.04806, allocations: 135.6 kB / 372.5 MB, free: 8.438 MB / 298.7 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006988/0.04875, allocations: 295.5 kB / 372.8 MB, free: 8.148 MB / 298.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002234/0.05099, allocations: 4.201 MB / 377 MB, free: 3.703 MB / 298.7 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002996/0.05129, allocations: 43.98 kB / 377 MB, free: 3.66 MB / 298.7 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.886e-05/0.05134, allocations: 47.94 kB / 377.1 MB, free: 3.613 MB / 298.7 MB Warning: Assuming fixed start value for the following 15 variables: V:VARIABLE(start = 2.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real cytosol.V:VARIABLE(start = 2.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real cytosol.GLY.c:VARIABLE(min = 0.0 start = 1.0 unit = \"mol/l\" fixed = true stateSelect=StateSelect.prefer ) \"Current concentration of substance (mM)\" type: Real cytosol.mitochondria.V:VARIABLE(start = 2.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real LACext.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.mitochondria.NADm.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.mitochondria.NADHm.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.CP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.LAC.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.AMP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.IMP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.ADP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.PYR.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.FDP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytosol.NADH.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: 35 * 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 (157): * Single equations (assignments): 155 * Array equations: 0 * Algorithm blocks: 0 * Record equations: 0 * When equations: 0 * If-equations: 0 * Equation systems (not torn): 0 * Torn equation systems: 2 * Mixed (continuous/discrete) equation systems: 0 Notification: Torn system details for strict tearing set: * Linear torn systems (#iteration vars, #inner vars, density): 2 systems {(1,4,100.0%), (1,4,100.0%)} * Non-linear torn systems (#iteration vars, #inner vars): 0 systems Notification: Performance of prepare postOptimizeDAE: time 0.0003483/0.05168, allocations: 286.4 kB / 377.4 MB, free: 3.324 MB / 298.7 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001142/0.0518, allocations: 107.5 kB / 377.5 MB, free: 3.219 MB / 298.7 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001024/0.0519, allocations: 127.1 kB / 377.6 MB, free: 3.094 MB / 298.7 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.801e-06/0.05191, allocations: 12 kB / 377.6 MB, free: 3.082 MB / 298.7 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 9.267e-06/0.05192, allocations: 0 / 377.6 MB, free: 3.082 MB / 298.7 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.007e-06/0.05193, allocations: 7.969 kB / 377.6 MB, free: 3.074 MB / 298.7 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.002249/0.05417, allocations: 1.903 MB / 379.5 MB, free: 1.113 MB / 298.7 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.979e-06/0.05418, allocations: 11.86 kB / 379.5 MB, free: 1.102 MB / 298.7 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0006084/0.05479, allocations: 211.8 kB / 379.7 MB, free: 0.8945 MB / 298.7 MB Notification: Performance of postOpt tearingSystem (simulation): time 0.0002968/0.05508, allocations: 127.2 kB / 379.9 MB, free: 0.7617 MB / 298.7 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.211e-05/0.05516, allocations: 31.98 kB / 379.9 MB, free: 0.7305 MB / 298.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002206/0.05736, allocations: 4.193 MB / 384.1 MB, free: 12.3 MB / 314.7 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.294e-06/0.05737, allocations: 0 / 384.1 MB, free: 12.3 MB / 314.7 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001551/0.05892, allocations: 1.346 MB / 385.4 MB, free: 10.93 MB / 314.7 MB Notification: Performance of postOpt removeConstants (simulation): time 4.996e-05/0.05897, allocations: 59.53 kB / 385.5 MB, free: 10.87 MB / 314.7 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.684e-05/0.05903, allocations: 28 kB / 385.5 MB, free: 10.84 MB / 314.7 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002421/0.05928, allocations: 19.98 kB / 385.5 MB, free: 10.82 MB / 314.7 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001024/0.05938, allocations: 72.8 kB / 385.6 MB, free: 10.75 MB / 314.7 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.945e-05/0.05942, allocations: 31.98 kB / 385.6 MB, free: 10.72 MB / 314.7 MB Notification: Performance of sorting global known variables: time 0.0001473/0.05956, allocations: 267 kB / 385.9 MB, free: 10.46 MB / 314.7 MB Notification: Performance of sort global known variables: time 6e-08/0.05956, allocations: 0 / 385.9 MB, free: 10.46 MB / 314.7 MB Notification: Performance of remove unused functions: time 0.000621/0.06019, allocations: 276 kB / 386.2 MB, free: 10.19 MB / 314.7 MB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 2 * Number of states: 17 (V,cytosol.V,cytosol.NADH.n,cytosol.FDP.n,cytosol.PYR.n,cytosol.ADP.n,cytosol.IMP.n,cytosol.AMP.n,cytosol.LAC.n,cytosol.CP.n,cytosol.GLY.c,cytosol.G6P.c,cytosol.mitochondria.V,cytosol.mitochondria.NADHm.n,cytosol.mitochondria.NADm.n,cytosol.DHAP.c,LACext.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 (106): * Single equations (assignments): 104 * Array equations: 0 * Algorithm blocks: 0 * Record equations: 0 * When equations: 0 * If-equations: 0 * Equation systems (not torn): 0 * Torn equation systems: 2 * Mixed (continuous/discrete) equation systems: 0 Notification: Torn system details for strict tearing set: * Linear torn systems (#iteration vars, #inner vars, density): 2 systems {(1,4,100.0%), (1,4,100.0%)} * Non-linear torn systems (#iteration vars, #inner vars): 0 systems Notification: Performance of Backend phase and start with SimCode phase: time 0.0001448/0.06033, allocations: 128 kB / 386.3 MB, free: 10.05 MB / 314.7 MB Notification: Performance of simCode: created initialization part: time 0.001265/0.06159, allocations: 1.146 MB / 387.4 MB, free: 8.867 MB / 314.7 MB Notification: Performance of simCode: created event and clocks part: time 2.956e-06/0.0616, allocations: 8 kB / 387.5 MB, free: 8.859 MB / 314.7 MB Notification: Performance of simCode: created simulation system equations: time 0.0006986/0.0623, allocations: 0.7685 MB / 388.2 MB, free: 8.051 MB / 314.7 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004324/0.06273, allocations: 125.5 kB / 388.3 MB, free: 7.93 MB / 314.7 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002915/0.06564, allocations: 2.379 MB / 390.7 MB, free: 5.508 MB / 314.7 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001311/0.06577, allocations: 204.5 kB / 390.9 MB, free: 5.289 MB / 314.7 MB Notification: Performance of simCode: alias equations: time 0.0002864/0.06606, allocations: 93.7 kB / 391 MB, free: 5.195 MB / 314.7 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001909/0.06625, allocations: 68.47 kB / 391.1 MB, free: 5.129 MB / 314.7 MB Notification: Performance of SimCode: time 1.393e-06/0.06625, allocations: 0 / 391.1 MB, free: 5.129 MB / 314.7 MB Notification: Performance of Templates: time 0.01346/0.07972, allocations: 11.13 MB / 402.2 MB, free: 10.15 MB / 330.7 MB " [Timeout remaining time 660] make -j1 -f BioChem_BioChem.Examples.centralMetabolism.extra_cellular.makefile [Timeout 660] (rm -f BioChem_BioChem.Examples.centralMetabolism.extra_cellular.pipe ; mkfifo BioChem_BioChem.Examples.centralMetabolism.extra_cellular.pipe ; head -c 1048576 < BioChem_BioChem.Examples.centralMetabolism.extra_cellular.pipe >> ../files/BioChem_BioChem.Examples.centralMetabolism.extra_cellular.sim & ./BioChem_BioChem.Examples.centralMetabolism.extra_cellular -abortSlowSimulation -alarm=240 -lv LOG_STATS > BioChem_BioChem.Examples.centralMetabolism.extra_cellular.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 3.3828905331902206]