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 0.001344/0.001344, allocations: 92.22 kB / 19.65 MB, free: 276 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 0.00155/0.00155, allocations: 169 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 1.041/1.041, allocations: 177.1 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 0.08113/0.08113, allocations: 9.55 MB / 269.5 MB, free: 3.941 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 1.664e-06/1.664e-06, allocations: 0 / 342 MB, free: 8.676 MB / 314.7 MB Notification: Performance of FrontEnd - Absyn->SCode: time 3.076e-05/3.242e-05, allocations: 2.312 kB / 342 MB, free: 8.672 MB / 314.7 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.centralMetabolism.extra_cellular): time 0.005787/0.00582, allocations: 5.296 MB / 347.3 MB, free: 3.355 MB / 314.7 MB Notification: Performance of NFInst.instExpressions: time 0.003052/0.008872, allocations: 1.266 MB / 348.6 MB, free: 2.086 MB / 314.7 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.0007165/0.009588, allocations: 56 kB / 348.6 MB, free: 2.031 MB / 314.7 MB Notification: Performance of NFTyping.typeComponents: time 0.0004967/0.01009, allocations: 194.3 kB / 348.8 MB, free: 1.84 MB / 314.7 MB Notification: Performance of NFTyping.typeBindings: time 0.0006947/0.01078, allocations: 309 kB / 349.1 MB, free: 1.535 MB / 314.7 MB Notification: Performance of NFTyping.typeClassSections: time 0.0006232/0.0114, allocations: 355.5 kB / 349.5 MB, free: 1.188 MB / 314.7 MB Notification: Performance of NFFlatten.flatten: time 0.001335/0.01274, allocations: 1.414 MB / 350.9 MB, free: 15.77 MB / 330.7 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0006206/0.01336, allocations: 428.8 kB / 351.3 MB, free: 15.33 MB / 330.7 MB Notification: Performance of NFEvalConstants.evaluate: time 0.001111/0.01447, allocations: 0.8813 MB / 352.2 MB, free: 14.45 MB / 330.7 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0006087/0.01508, allocations: 0.4947 MB / 352.7 MB, free: 13.95 MB / 330.7 MB Notification: Performance of NFPackage.collectConstants: time 0.0002387/0.01532, allocations: 188 kB / 352.9 MB, free: 13.77 MB / 330.7 MB Notification: Performance of NFFlatten.collectFunctions: time 0.0001883/0.01551, allocations: 192 kB / 353.1 MB, free: 13.58 MB / 330.7 MB Notification: Performance of NFScalarize.scalarize: time 0.0002207/0.01573, allocations: 362.8 kB / 353.4 MB, free: 13.23 MB / 330.7 MB Notification: Performance of NFVerifyModel.verify: time 0.0004359/0.01616, allocations: 490.9 kB / 353.9 MB, free: 12.75 MB / 330.7 MB Notification: Performance of NFConvertDAE.convert: time 0.001005/0.01717, allocations: 1.067 MB / 355 MB, free: 11.68 MB / 330.7 MB Notification: Performance of FrontEnd - DAE generated: time 3.917e-06/0.01717, allocations: 0 / 355 MB, free: 11.68 MB / 330.7 MB Notification: Performance of FrontEnd: time 1.322e-06/0.01717, allocations: 0 / 355 MB, free: 11.68 MB / 330.7 MB Notification: Performance of Transformations before backend: time 2.813e-05/0.0172, allocations: 0 / 355 MB, free: 11.68 MB / 330.7 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 0.00232/0.01952, allocations: 1.582 MB / 356.5 MB, free: 10.05 MB / 330.7 MB Notification: Performance of prepare preOptimizeDAE: time 4.721e-05/0.01957, allocations: 12.03 kB / 356.6 MB, free: 10.04 MB / 330.7 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002739/0.01984, allocations: 256 kB / 356.8 MB, free: 9.789 MB / 330.7 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0005604/0.0204, allocations: 0.4915 MB / 357.3 MB, free: 9.266 MB / 330.7 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.615e-05/0.02046, allocations: 99.16 kB / 357.4 MB, free: 9.168 MB / 330.7 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001464/0.02061, allocations: 144.3 kB / 357.5 MB, free: 9.027 MB / 330.7 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.001256/0.02186, allocations: 0.9928 MB / 358.5 MB, free: 8 MB / 330.7 MB Notification: Performance of preOpt findStateOrder (simulation): time 4.033e-05/0.0219, allocations: 4.188 kB / 358.5 MB, free: 7.996 MB / 330.7 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.632e-05/0.02198, allocations: 60.36 kB / 358.6 MB, free: 7.938 MB / 330.7 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.548e-05/0.022, allocations: 32.38 kB / 358.6 MB, free: 7.906 MB / 330.7 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009103/0.02291, allocations: 0.5662 MB / 359.2 MB, free: 7.332 MB / 330.7 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004829/0.02774, allocations: 3.715 MB / 362.9 MB, free: 3.5 MB / 330.7 MB Notification: Performance of preOpt comSubExp (simulation): time 0.000905/0.02865, allocations: 0.7754 MB / 363.7 MB, free: 2.719 MB / 330.7 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0003559/0.029, allocations: 300.7 kB / 364 MB, free: 2.43 MB / 330.7 MB Notification: Performance of preOpt evalFunc (simulation): time 4.541e-05/0.02905, allocations: 13 kB / 364 MB, free: 2.418 MB / 330.7 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.185e-05/0.02908, allocations: 50.39 kB / 364 MB, free: 2.359 MB / 330.7 MB Notification: Performance of pre-optimization done (n=96): time 4.87e-06/0.02909, allocations: 4 kB / 364 MB, free: 2.355 MB / 330.7 MB Notification: Performance of matching and sorting (n=114): time 0.004408/0.03349, allocations: 2.849 MB / 366.9 MB, free: 15.51 MB / 346.7 MB Notification: Performance of inlineWhenForInitialization (initialization): time 3.629e-05/0.03353, allocations: 64.41 kB / 367 MB, free: 15.43 MB / 346.7 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002951/0.03382, allocations: 422.5 kB / 367.4 MB, free: 15 MB / 346.7 MB Notification: Performance of collectPreVariables (initialization): time 4.846e-05/0.03387, allocations: 49.64 kB / 367.4 MB, free: 14.95 MB / 346.7 MB Notification: Performance of collectInitialEqns (initialization): time 0.0002526/0.03413, allocations: 0.585 MB / 368 MB, free: 14.36 MB / 346.7 MB Notification: Performance of collectInitialBindings (initialization): time 0.0002547/0.03438, allocations: 428.3 kB / 368.4 MB, free: 13.93 MB / 346.7 MB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002188/0.0346, allocations: 208.5 kB / 368.6 MB, free: 13.72 MB / 346.7 MB Notification: Performance of setup shared object (initialization): time 0.000166/0.03477, allocations: 0.5508 MB / 369.2 MB, free: 13.16 MB / 346.7 MB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003599/0.03513, allocations: 242.4 kB / 369.4 MB, free: 12.92 MB / 346.7 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0008355/0.03596, allocations: 0.5965 MB / 370 MB, free: 12.18 MB / 346.7 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.001345/0.03731, allocations: 1.246 MB / 371.2 MB, free: 10.79 MB / 346.7 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.25e-06/0.03731, allocations: 4 kB / 371.3 MB, free: 10.79 MB / 346.7 MB Notification: Performance of matching and sorting (n=165) (initialization): time 0.001399/0.03871, allocations: 1.113 MB / 372.4 MB, free: 9.656 MB / 346.7 MB Notification: Performance of prepare postOptimizeDAE: time 2.32e-05/0.03873, allocations: 9.562 kB / 372.4 MB, free: 9.648 MB / 346.7 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.176e-05/0.03874, allocations: 8 kB / 372.4 MB, free: 9.641 MB / 346.7 MB Notification: Performance of postOpt tearingSystem (initialization): time 0.0004536/0.0392, allocations: 127.4 kB / 372.5 MB, free: 9.508 MB / 346.7 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007679/0.03997, allocations: 295.6 kB / 372.8 MB, free: 9.219 MB / 346.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.002543/0.04251, allocations: 4.2 MB / 377 MB, free: 4.777 MB / 346.7 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003865/0.0429, allocations: 39.94 kB / 377 MB, free: 4.738 MB / 346.7 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.097e-05/0.04295, allocations: 44 kB / 377.1 MB, free: 4.695 MB / 346.7 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 0.0004352/0.04338, allocations: 291.8 kB / 377.4 MB, free: 4.406 MB / 346.7 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001306/0.04351, allocations: 107.6 kB / 377.5 MB, free: 4.301 MB / 346.7 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001092/0.04362, allocations: 123 kB / 377.6 MB, free: 4.176 MB / 346.7 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.171e-06/0.04363, allocations: 12 kB / 377.6 MB, free: 4.164 MB / 346.7 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 1.405e-05/0.04364, allocations: 8 kB / 377.6 MB, free: 4.156 MB / 346.7 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.953e-06/0.04365, allocations: 3.984 kB / 377.6 MB, free: 4.152 MB / 346.7 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.00247/0.04612, allocations: 1.91 MB / 379.5 MB, free: 2.188 MB / 346.7 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.007e-06/0.04612, allocations: 4.031 kB / 379.5 MB, free: 2.184 MB / 346.7 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0006293/0.04675, allocations: 215.7 kB / 379.7 MB, free: 1.973 MB / 346.7 MB Notification: Performance of postOpt tearingSystem (simulation): time 0.0003046/0.04706, allocations: 131.2 kB / 379.9 MB, free: 1.836 MB / 346.7 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.566e-05/0.04712, allocations: 31.98 kB / 379.9 MB, free: 1.805 MB / 346.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.002399/0.04952, allocations: 4.193 MB / 384.1 MB, free: 13.38 MB / 362.7 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.867e-06/0.04953, allocations: 11.94 kB / 384.1 MB, free: 13.37 MB / 362.7 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001517/0.05104, allocations: 1.334 MB / 385.4 MB, free: 12 MB / 362.7 MB Notification: Performance of postOpt removeConstants (simulation): time 5.879e-05/0.0511, allocations: 55.53 kB / 385.5 MB, free: 11.95 MB / 362.7 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.801e-05/0.05117, allocations: 32.03 kB / 385.5 MB, free: 11.91 MB / 362.7 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002465/0.05142, allocations: 23.98 kB / 385.5 MB, free: 11.89 MB / 362.7 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 9.67e-05/0.05151, allocations: 72.8 kB / 385.6 MB, free: 11.82 MB / 362.7 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.973e-05/0.05155, allocations: 31.98 kB / 385.6 MB, free: 11.79 MB / 362.7 MB Notification: Performance of sorting global known variables: time 0.0001587/0.05171, allocations: 259.1 kB / 385.9 MB, free: 11.54 MB / 362.7 MB Notification: Performance of sort global known variables: time 8e-08/0.05171, allocations: 0 / 385.9 MB, free: 11.54 MB / 362.7 MB Notification: Performance of remove unused functions: time 0.0006644/0.05238, allocations: 276 kB / 386.2 MB, free: 11.27 MB / 362.7 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 0.000144/0.05252, allocations: 135.9 kB / 386.3 MB, free: 11.12 MB / 362.7 MB Notification: Performance of simCode: created initialization part: time 0.001287/0.05381, allocations: 1.158 MB / 387.5 MB, free: 9.93 MB / 362.7 MB Notification: Performance of simCode: created event and clocks part: time 2.585e-06/0.05381, allocations: 0 / 387.5 MB, free: 9.93 MB / 362.7 MB Notification: Performance of simCode: created simulation system equations: time 0.0007204/0.05453, allocations: 0.7683 MB / 388.2 MB, free: 9.121 MB / 362.7 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004255/0.05496, allocations: 123.4 kB / 388.3 MB, free: 9.004 MB / 362.7 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002905/0.05786, allocations: 2.376 MB / 390.7 MB, free: 6.574 MB / 362.7 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004666/0.05833, allocations: 212.5 kB / 390.9 MB, free: 6.344 MB / 362.7 MB Notification: Performance of simCode: alias equations: time 0.0003022/0.05863, allocations: 89.7 kB / 391 MB, free: 6.254 MB / 362.7 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002026/0.05883, allocations: 64.48 kB / 391.1 MB, free: 6.191 MB / 362.7 MB Notification: Performance of SimCode: time 1.714e-06/0.05883, allocations: 0 / 391.1 MB, free: 6.191 MB / 362.7 MB Notification: Performance of Templates: time 0.01539/0.07423, allocations: 10.74 MB / 401.8 MB, free: 11.6 MB / 378.7 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: 3.3739133048802614]