Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.conf.json loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/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/ModelicaServices 4.0.0+maint.om/package.mo", uses=false) Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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 Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo) Running command: translateModel(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") translateModel(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.1189/0.1189, allocations: 15.28 MB / 31.08 MB, free: 3.113 MB / 24.77 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001089/0.001089, allocations: 198 kB / 36.14 MB, free: 2.145 MB / 24.77 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.323/1.323, allocations: 222.9 MB / 264 MB, free: 5.062 MB / 202.7 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009929/0.0009928, allocations: 107.1 kB / 318.4 MB, free: 3.461 MB / 250.7 MB Notification: Performance of FrontEnd - loaded program: time 0.001035/0.001035, allocations: 57.83 kB / 382.7 MB, free: 48.99 MB / 298.7 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.09264/0.09369, allocations: 53.62 MB / 436.3 MB, free: 1.059 MB / 298.7 MB [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated. [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66:writable] Notification: The diagnostics message for the missing inner is: Your model is using an outer "system" component but an inner "system" component is not defined. For simulation drag Modelica.Fluid.System into your model to specify system properties. Notification: Performance of NFInst.instantiate(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery): time 0.04315/0.1369, allocations: 41.77 MB / 478.1 MB, free: 7.332 MB / 346.7 MB Notification: Performance of NFInst.instExpressions: time 0.2598/0.3967, allocations: 71.89 MB / 0.5371 GB, free: 15.75 MB / 378.7 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.005748/0.4024, allocations: 108.2 kB / 0.5372 GB, free: 15.75 MB / 378.7 MB Notification: Performance of NFTyping.typeComponents: time 0.005494/0.408, allocations: 1.456 MB / 0.5386 GB, free: 15.72 MB / 378.7 MB Notification: Performance of NFTyping.typeBindings: time 0.01828/0.4263, allocations: 5.003 MB / 0.5435 GB, free: 14.23 MB / 378.7 MB Notification: Performance of NFTyping.typeClassSections: time 0.03129/0.4576, allocations: 9.005 MB / 0.5523 GB, free: 11.23 MB / 378.7 MB Notification: Performance of NFFlatten.flatten: time 0.02778/0.4854, allocations: 25.84 MB / 0.5775 GB, free: 11.65 MB / 394.7 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02201/0.5075, allocations: 17.93 MB / 0.595 GB, free: 10.68 MB / 410.7 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02715/0.5346, allocations: 16.22 MB / 0.6109 GB, free: 10.67 MB / 426.7 MB Notification: Performance of NFSimplifyModel.simplify: time 0.02586/0.5605, allocations: 14.87 MB / 0.6254 GB, free: 12.24 MB / 442.7 MB Notification: Performance of NFPackage.collectConstants: time 0.008895/0.5695, allocations: 1.69 MB / 0.6271 GB, free: 10.55 MB / 442.7 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03671/0.6062, allocations: 9.052 MB / 0.6359 GB, free: 1.57 MB / 442.7 MB Notification: Performance of NFScalarize.scalarize: time 0.01131/0.6176, allocations: 5.396 MB / 0.6412 GB, free: 12.38 MB / 458.7 MB Notification: Performance of NFVerifyModel.verify: time 0.02371/0.6413, allocations: 10.51 MB / 0.6514 GB, free: 2.027 MB / 458.7 MB Notification: Performance of NFConvertDAE.convert: time 0.5632/1.205, allocations: 39.58 MB / 0.6901 GB, free: 63.2 MB / 490.8 MB Notification: Performance of FrontEnd - DAE generated: time 6.723e-06/1.205, allocations: 0 / 0.6901 GB, free: 63.2 MB / 490.8 MB Notification: Performance of FrontEnd: time 1.903e-06/1.205, allocations: 0 / 0.6901 GB, free: 63.2 MB / 490.8 MB Notification: Performance of Transformations before backend: time 0.001227/1.206, allocations: 0 / 0.6901 GB, free: 63.2 MB / 490.8 MB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 3808 * Number of variables: 3808 Notification: Performance of Generate backend data structure: time 0.1015/1.307, allocations: 24.72 MB / 0.7142 GB, free: 57.07 MB / 490.8 MB Notification: Performance of prepare preOptimizeDAE: time 5.013e-05/1.307, allocations: 10.94 kB / 0.7142 GB, free: 57.07 MB / 490.8 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02726/1.335, allocations: 3.884 MB / 0.718 GB, free: 56.14 MB / 490.8 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03937/1.374, allocations: 11.77 MB / 0.7295 GB, free: 54.54 MB / 490.8 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002559/1.377, allocations: 2.134 MB / 0.7316 GB, free: 53.42 MB / 490.8 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01444/1.391, allocations: 1.53 MB / 0.7331 GB, free: 53.38 MB / 490.8 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.09902/1.49, allocations: 34.79 MB / 0.7671 GB, free: 34.94 MB / 490.8 MB Notification: Performance of preOpt findStateOrder (simulation): time 0.0005563/1.491, allocations: 10.19 kB / 0.7671 GB, free: 34.94 MB / 490.8 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01121/1.502, allocations: 0.5888 MB / 0.7677 GB, free: 34.35 MB / 490.8 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002423/1.502, allocations: 364.3 kB / 0.768 GB, free: 34 MB / 490.8 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.08677/1.589, allocations: 46.83 MB / 0.8137 GB, free: 3.176 MB / 0.4949 GB Warning: The model contains alias variables with redundant start and/or conflicting nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts. Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.5146/2.104, allocations: 128.1 MB / 0.9388 GB, free: 182.8 MB / 0.573 GB Notification: Performance of preOpt comSubExp (simulation): time 0.7672/2.871, allocations: 276 MB / 1.208 GB, free: 156.1 MB / 0.573 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03418/2.905, allocations: 19.81 MB / 1.228 GB, free: 152.8 MB / 0.573 GB Notification: Performance of preOpt evalFunc (simulation): time 0.1548/3.06, allocations: 87.58 MB / 1.313 GB, free: 93.46 MB / 0.573 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 8.354e-05/3.06, allocations: 143.4 kB / 1.313 GB, free: 93.32 MB / 0.573 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.0218/3.082, allocations: 4.421 MB / 1.318 GB, free: 89 MB / 0.573 GB Notification: Performance of pre-optimization done (n=995): time 5.964e-05/3.082, allocations: 0 / 1.318 GB, free: 89 MB / 0.573 GB Notification: Performance of matching and sorting (n=1129): time 0.8059/3.888, allocations: 130.7 MB / 1.445 GB, free: 198.8 MB / 0.573 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001035/3.888, allocations: 166.3 kB / 1.446 GB, free: 198.7 MB / 0.573 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01274/3.901, allocations: 10.16 MB / 1.455 GB, free: 193.7 MB / 0.573 GB Notification: Performance of collectPreVariables (initialization): time 0.00414/3.905, allocations: 213 kB / 1.456 GB, free: 193.5 MB / 0.573 GB Notification: Performance of collectInitialEqns (initialization): time 0.004772/3.91, allocations: 6.881 MB / 1.462 GB, free: 189.1 MB / 0.573 GB Notification: Performance of collectInitialBindings (initialization): time 0.006476/3.916, allocations: 3.908 MB / 1.466 GB, free: 185.7 MB / 0.573 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.007858/3.924, allocations: 3.257 MB / 1.469 GB, free: 183.9 MB / 0.573 GB Notification: Performance of setup shared object (initialization): time 4.78e-05/3.924, allocations: 310.3 kB / 1.47 GB, free: 183.6 MB / 0.573 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.01667/3.941, allocations: 11.82 MB / 1.481 GB, free: 177.1 MB / 0.573 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02128/3.962, allocations: 16.56 MB / 1.497 GB, free: 164.4 MB / 0.573 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.04133/4.004, allocations: 29.74 MB / 1.526 GB, free: 134.1 MB / 0.573 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.000186/4.004, allocations: 44 kB / 1.526 GB, free: 134.1 MB / 0.573 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.6588/4.663, allocations: 81.46 MB / 1.606 GB, free: 187.1 MB / 0.573 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001318/4.663, allocations: 73.41 kB / 1.606 GB, free: 187.1 MB / 0.573 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002488/4.663, allocations: 150.6 kB / 1.606 GB, free: 187.1 MB / 0.573 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.0577/4.721, allocations: 22.39 MB / 1.628 GB, free: 185 MB / 0.573 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01583/4.737, allocations: 3.734 MB / 1.632 GB, free: 184.9 MB / 0.573 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.1571/4.894, allocations: 88.27 MB / 1.718 GB, free: 123.8 MB / 0.573 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01709/4.911, allocations: 1.145 MB / 1.719 GB, free: 122.7 MB / 0.573 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.003835/4.915, allocations: 0.9354 MB / 1.72 GB, free: 121.8 MB / 0.573 GB Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 677 * 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 (1841): * Single equations (assignments): 1838 * Array equations: 0 * Algorithm blocks: 0 * Record equations: 0 * When equations: 0 * If-equations: 0 * Equation systems (not torn): 0 * Torn equation systems: 3 * Mixed (continuous/discrete) equation systems: 0 Notification: Torn system details for strict tearing set: * Linear torn systems (#iteration vars, #inner vars, density): 2 systems {(1,3,100.0%), (33,10,82.4%)} * Non-linear torn systems (#iteration vars, #inner vars): 1 system {(1,3)} Notification: Performance of prepare postOptimizeDAE: time 0.01295/4.928, allocations: 5.378 MB / 1.725 GB, free: 116.7 MB / 0.573 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.005778/4.934, allocations: 1.057 MB / 1.726 GB, free: 116.2 MB / 0.573 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2382/5.172, allocations: 48.62 MB / 1.774 GB, free: 67.66 MB / 0.573 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001365/5.172, allocations: 120 kB / 1.774 GB, free: 67.54 MB / 0.573 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 8.206e-05/5.172, allocations: 20 kB / 1.774 GB, free: 67.52 MB / 0.573 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0003669/5.173, allocations: 59.77 kB / 1.774 GB, free: 67.46 MB / 0.573 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.5463/5.719, allocations: 73.04 MB / 1.845 GB, free: 174.4 MB / 0.573 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001178/5.719, allocations: 2.656 kB / 1.845 GB, free: 174.4 MB / 0.573 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01414/5.733, allocations: 2.422 MB / 1.848 GB, free: 174.3 MB / 0.573 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.0314/5.765, allocations: 11.88 MB / 1.859 GB, free: 172.6 MB / 0.573 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.004121/5.769, allocations: 476.6 kB / 1.86 GB, free: 172.3 MB / 0.573 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.08857/5.857, allocations: 42.19 MB / 1.901 GB, free: 136 MB / 0.573 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.318e-06/5.857, allocations: 7.938 kB / 1.901 GB, free: 136 MB / 0.573 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.6571/6.515, allocations: 145.1 MB / 2.043 GB, free: 156.3 MB / 0.573 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01133/6.526, allocations: 3.292 MB / 2.046 GB, free: 154.9 MB / 0.573 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.003559/6.53, allocations: 292.3 kB / 2.046 GB, free: 154.7 MB / 0.573 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01244/6.542, allocations: 0.7923 MB / 2.047 GB, free: 154.5 MB / 0.573 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.005935/6.548, allocations: 1.496 MB / 2.048 GB, free: 154.3 MB / 0.573 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.002002/6.55, allocations: 471.5 kB / 2.049 GB, free: 154.3 MB / 0.573 GB Notification: Performance of sorting global known variables: time 0.01269/6.563, allocations: 6.97 MB / 2.056 GB, free: 151.9 MB / 0.573 GB Notification: Performance of sort global known variables: time 5.11e-07/6.563, allocations: 0 / 2.056 GB, free: 151.9 MB / 0.573 GB Notification: Performance of remove unused functions: time 0.05509/6.618, allocations: 8.265 MB / 2.064 GB, free: 151.1 MB / 0.573 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 15 * Number of states: 60 (solution.temperature,O2_free.logn,H2O.logn,relaxed.OxyHm[1].logn,relaxed.OxyHm[2].logn,relaxed.OxyHm[3].logn,relaxed.OxyHm[4].logn,relaxed.DeoxyHm[1].logn,relaxed.DeoxyHm[2].logn,relaxed.DeoxyHm[3].logn,relaxed.DeoxyHm[4].logn,relaxed.HmAH[1].logn,relaxed.HmAH[2].logn,relaxed.HmAH[3].logn,relaxed.HmAH[4].logn,relaxed.HmA[1].logn,relaxed.HmA[2].logn,relaxed.HmA[3].logn,relaxed.HmA[4].logn,relaxed.HmNH3[1].logn,relaxed.HmNH3[2].logn,relaxed.HmNH3[3].logn,relaxed.HmNH3[4].logn,relaxed.HmNH2[1].logn,relaxed.HmNH2[2].logn,relaxed.HmNH2[3].logn,relaxed.HmNH2[4].logn,relaxed.HmNHCOO[1].logn,relaxed.HmNHCOO[2].logn,relaxed.HmNHCOO[3].logn,relaxed.HmNHCOO[4].logn,tensed.OxyHm[1].logn,tensed.OxyHm[2].logn,tensed.OxyHm[3].logn,tensed.OxyHm[4].logn,tensed.DeoxyHm[1].logn,tensed.DeoxyHm[2].logn,tensed.DeoxyHm[3].logn,tensed.DeoxyHm[4].logn,tensed.HmAH[1].logn,tensed.HmAH[2].logn,tensed.HmAH[3].logn,tensed.HmAH[4].logn,tensed.HmA[1].logn,tensed.HmA[2].logn,tensed.HmA[3].logn,tensed.HmA[4].logn,tensed.HmNH3[1].logn,tensed.HmNH3[2].logn,tensed.HmNH3[3].logn,tensed.HmNH3[4].logn,tensed.HmNH2[1].logn,tensed.HmNH2[2].logn,tensed.HmNH2[3].logn,tensed.HmNH2[4].logn,tensed.HmNHCOO[1].logn,tensed.HmNHCOO[2].logn,tensed.HmNHCOO[3].logn,tensed.HmNHCOO[4].logn,CO2_free.logn) * 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 (1234): * Single equations (assignments): 1231 * Array equations: 0 * Algorithm blocks: 0 * Record equations: 0 * When equations: 0 * If-equations: 0 * Equation systems (not torn): 0 * Torn equation systems: 3 * Mixed (continuous/discrete) equation systems: 0 Notification: Torn system details for strict tearing set: * Linear torn systems (#iteration vars, #inner vars, density): 2 systems {(1,3,100.0%), (33,10,82.4%)} * Non-linear torn systems (#iteration vars, #inner vars): 1 system {(1,3)} Notification: Performance of Backend phase and start with SimCode phase: time 0.01101/6.629, allocations: 3.449 MB / 2.067 GB, free: 148.9 MB / 0.573 GB Notification: Performance of simCode: created initialization part: time 0.06417/6.693, allocations: 27.72 MB / 2.094 GB, free: 125.6 MB / 0.573 GB Notification: Performance of simCode: created event and clocks part: time 1.058e-05/6.693, allocations: 0 / 2.094 GB, free: 125.6 MB / 0.573 GB Notification: Performance of simCode: created simulation system equations: time 0.03821/6.731, allocations: 14.87 MB / 2.109 GB, free: 113.1 MB / 0.573 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.01805/6.749, allocations: 2.335 MB / 2.111 GB, free: 111.4 MB / 0.573 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.08843/6.838, allocations: 52.57 MB / 2.162 GB, free: 62.9 MB / 0.573 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01112/6.849, allocations: 10.24 MB / 2.172 GB, free: 52.78 MB / 0.573 GB Notification: Performance of simCode: alias equations: time 0.2249/7.074, allocations: 5.534 MB / 2.178 GB, free: 156.9 MB / 0.573 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.008231/7.082, allocations: 1.527 MB / 2.179 GB, free: 156.8 MB / 0.573 GB Notification: Performance of SimCode: time 7.11e-07/7.082, allocations: 5.406 kB / 2.179 GB, free: 156.8 MB / 0.573 GB Notification: Performance of Templates: time 0.6699/7.752, allocations: 355.9 MB / 2.527 GB, free: 62.07 MB / 0.573 GB make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.makefile (rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe 2>&1)