Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.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 0.001319/0.001319, allocations: 101.5 kB / 19.73 MB, free: 2.23 MB / 14.72 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 0.001471/0.001471, allocations: 217.5 kB / 23.04 MB, free: 5.074 MB / 14.72 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 1.495/1.495, allocations: 230.6 MB / 256.8 MB, free: 7.965 MB / 206.1 MB " [Timeout remaining time 178] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.1367/0.1367, allocations: 23.85 MB / 337.1 MB, free: 11.18 MB / 270.1 MB " [Timeout remaining time 180] Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/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: "" <> buildModelFMU(Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,fileNamePrefix="Chemical_Chemical_Obsolete_Examples_Hemoglobin_Allosteric_Hemoglobin2_MWC",fmuType="cs",version="2.0",platforms={"static"}) "" <> buildModelFMU(Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,fileNamePrefix="Chemical_Chemical_Obsolete_Examples_Hemoglobin_Allosteric_Hemoglobin2_MWC",fmuType="cs",version="2.0",platforms={"static"}) [Timeout 660] "Notification: Chemical requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed. Notification: Performance of FrontEnd - loaded program: time 0.002049/0.002049, allocations: 71.91 kB / 472 MB, free: 7.641 MB / 334.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.3019/0.3039, allocations: 59.85 MB / 0.5194 GB, free: 9.613 MB / 382.1 MB [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC): time 0.04221/0.3461, allocations: 30.32 MB / 0.549 GB, free: 9.719 MB / 398.1 MB Notification: Performance of NFInst.instExpressions: time 0.0355/0.3816, allocations: 26.29 MB / 0.5746 GB, free: 1.473 MB / 414.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.001805/0.3834, allocations: 35.69 kB / 0.5747 GB, free: 1.438 MB / 414.1 MB Notification: Performance of NFTyping.typeComponents: time 0.001789/0.3852, allocations: 0.597 MB / 0.5753 GB, free: 0.8359 MB / 414.1 MB Notification: Performance of NFTyping.typeBindings: time 0.006584/0.3918, allocations: 2.18 MB / 0.5774 GB, free: 14.64 MB / 430.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.01002/0.4018, allocations: 3.581 MB / 0.5809 GB, free: 11.04 MB / 430.1 MB Notification: Performance of NFFlatten.flatten: time 0.009653/0.4115, allocations: 7.402 MB / 0.5881 GB, free: 3.605 MB / 430.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.006481/0.418, allocations: 4.331 MB / 0.5924 GB, free: 15.2 MB / 446.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.008033/0.426, allocations: 4.963 MB / 0.5972 GB, free: 10.23 MB / 446.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.00859/0.4346, allocations: 4.764 MB / 0.6018 GB, free: 5.449 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.002623/0.4372, allocations: 0.6758 MB / 0.6025 GB, free: 4.773 MB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.01152/0.4487, allocations: 3.363 MB / 0.6058 GB, free: 1.406 MB / 446.1 MB Notification: Performance of NFScalarize.scalarize: time 0.003868/0.4526, allocations: 1.812 MB / 0.6076 GB, free: 15.59 MB / 462.1 MB Notification: Performance of NFVerifyModel.verify: time 0.007363/0.46, allocations: 3.358 MB / 0.6108 GB, free: 12.21 MB / 462.1 MB Notification: Performance of NFConvertDAE.convert: time 0.02126/0.4812, allocations: 11.62 MB / 0.6222 GB, free: 0.5547 MB / 462.1 MB Notification: Performance of FrontEnd - DAE generated: time 5.19e-06/0.4812, allocations: 3.938 kB / 0.6222 GB, free: 0.5508 MB / 462.1 MB Notification: Performance of FrontEnd: time 1.212e-06/0.4812, allocations: 0 / 0.6222 GB, free: 0.5508 MB / 462.1 MB Notification: Performance of Transformations before backend: time 0.0002646/0.4815, allocations: 0 / 0.6222 GB, free: 0.5508 MB / 462.1 MB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 1226 * Number of variables: 1226 Notification: Performance of Generate backend data structure: time 0.02091/0.5024, allocations: 7.241 MB / 0.6293 GB, free: 9.234 MB / 478.1 MB Notification: Performance of prepare preOptimizeDAE: time 5.068e-05/0.5024, allocations: 12.03 kB / 0.6293 GB, free: 9.223 MB / 478.1 MB Notification: Performance of preOpt introduceOutputRealDerivatives (simulation): time 0.0001519/0.5026, allocations: 121.8 kB / 0.6294 GB, free: 9.102 MB / 478.1 MB Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.001456/0.5041, allocations: 0.6579 MB / 0.63 GB, free: 8.434 MB / 478.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006252/0.5103, allocations: 1.241 MB / 0.6312 GB, free: 7.188 MB / 478.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.007755/0.5181, allocations: 3.313 MB / 0.6345 GB, free: 3.816 MB / 478.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0009045/0.519, allocations: 1.007 MB / 0.6355 GB, free: 2.66 MB / 478.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.00187/0.5208, allocations: 0.5039 MB / 0.636 GB, free: 2.156 MB / 478.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0212/0.542, allocations: 9.454 MB / 0.6452 GB, free: 8.598 MB / 494.1 MB Notification: Performance of preOpt findStateOrder (simulation): time 0.0001004/0.5421, allocations: 7.938 kB / 0.6452 GB, free: 8.59 MB / 494.1 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0009832/0.5431, allocations: 196 kB / 0.6454 GB, free: 8.398 MB / 494.1 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.000103/0.5432, allocations: 116 kB / 0.6455 GB, free: 8.285 MB / 494.1 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02488/0.5681, allocations: 12.75 MB / 0.6579 GB, free: 11.52 MB / 0.4981 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 0.06884/0.6369, allocations: 30.79 MB / 0.688 GB, free: 11.99 MB / 0.5294 GB Notification: Performance of preOpt comSubExp (simulation): time 0.06226/0.6992, allocations: 26.86 MB / 0.7142 GB, free: 2.039 MB / 0.545 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.01009/0.7093, allocations: 4.721 MB / 0.7189 GB, free: 13.29 MB / 0.5606 GB Notification: Performance of preOpt evalFunc (simulation): time 0.2707/0.98, allocations: 17.74 MB / 0.7362 GB, free: 169.6 MB / 0.5606 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.418e-05/0.98, allocations: 64.14 kB / 0.7362 GB, free: 169.5 MB / 0.5606 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.004793/0.9848, allocations: 1.28 MB / 0.7375 GB, free: 169.5 MB / 0.5606 GB Notification: Performance of pre-optimization done (n=324): time 1.292e-05/0.9848, allocations: 0 / 0.7375 GB, free: 169.5 MB / 0.5606 GB Notification: Performance of matching and sorting (n=376): time 0.09521/1.08, allocations: 24.18 MB / 0.7611 GB, free: 162.4 MB / 0.5606 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.966e-05/1.08, allocations: 93.77 kB / 0.7612 GB, free: 162.3 MB / 0.5606 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003601/1.084, allocations: 2.979 MB / 0.7641 GB, free: 160.8 MB / 0.5606 GB Notification: Performance of collectPreVariables (initialization): time 0.001112/1.085, allocations: 85.52 kB / 0.7642 GB, free: 160.7 MB / 0.5606 GB Notification: Performance of collectInitialEqns (initialization): time 0.001053/1.086, allocations: 2.225 MB / 0.7664 GB, free: 159.1 MB / 0.5606 GB Notification: Performance of collectInitialBindings (initialization): time 0.001731/1.088, allocations: 1.362 MB / 0.7677 GB, free: 158.1 MB / 0.5606 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.001575/1.089, allocations: 0.9801 MB / 0.7686 GB, free: 157.5 MB / 0.5606 GB Notification: Performance of setup shared object (initialization): time 4.591e-05/1.089, allocations: 307.8 kB / 0.7689 GB, free: 157.2 MB / 0.5606 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.004153/1.093, allocations: 2.961 MB / 0.7718 GB, free: 155.7 MB / 0.5606 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.004737/1.098, allocations: 4.488 MB / 0.7762 GB, free: 152.2 MB / 0.5606 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.009361/1.107, allocations: 7.807 MB / 0.7838 GB, free: 147 MB / 0.5606 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.873e-05/1.107, allocations: 14.5 kB / 0.7838 GB, free: 147 MB / 0.5606 GB Notification: Performance of matching and sorting (n=617) (initialization): time 0.05467/1.162, allocations: 13.83 MB / 0.7974 GB, free: 134.1 MB / 0.5606 GB Notification: Performance of prepare postOptimizeDAE: time 5.599e-05/1.162, allocations: 30.66 kB / 0.7974 GB, free: 134 MB / 0.5606 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.26e-05/1.162, allocations: 48 kB / 0.7974 GB, free: 134 MB / 0.5606 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.008069/1.17, allocations: 3.48 MB / 0.8008 GB, free: 130.7 MB / 0.5606 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005384/1.176, allocations: 1.265 MB / 0.8021 GB, free: 129.4 MB / 0.5606 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02872/1.204, allocations: 18.15 MB / 0.8198 GB, free: 110.9 MB / 0.5606 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00432/1.209, allocations: 247.8 kB / 0.82 GB, free: 110.7 MB / 0.5606 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.000711/1.21, allocations: 283.8 kB / 0.8203 GB, free: 110.4 MB / 0.5606 GB Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 218 * 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 (599): * Single equations (assignments): 596 * 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 {(9,4,100.0%), (1,3,100.0%)} * Non-linear torn systems (#iteration vars, #inner vars): 1 system {(1,3)} Notification: Performance of prepare postOptimizeDAE: time 0.002351/1.212, allocations: 1.45 MB / 0.8217 GB, free: 109 MB / 0.5606 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0008632/1.213, allocations: 361.6 kB / 0.8221 GB, free: 108.6 MB / 0.5606 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03424/1.247, allocations: 9.631 MB / 0.8315 GB, free: 99.11 MB / 0.5606 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.797e-05/1.247, allocations: 42.69 kB / 0.8315 GB, free: 99.07 MB / 0.5606 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 1.913e-05/1.247, allocations: 4 kB / 0.8315 GB, free: 99.06 MB / 0.5606 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001351/1.247, allocations: 23.86 kB / 0.8315 GB, free: 99.04 MB / 0.5606 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04466/1.292, allocations: 15.5 MB / 0.8467 GB, free: 83.58 MB / 0.5606 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.536e-05/1.292, allocations: 6.625 kB / 0.8467 GB, free: 83.57 MB / 0.5606 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004397/1.296, allocations: 0.8477 MB / 0.8475 GB, free: 82.73 MB / 0.5606 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.005547/1.302, allocations: 2.126 MB / 0.8496 GB, free: 80.64 MB / 0.5606 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0007919/1.303, allocations: 139.9 kB / 0.8497 GB, free: 80.5 MB / 0.5606 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02056/1.323, allocations: 12.32 MB / 0.8617 GB, free: 67.88 MB / 0.5606 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.13e-06/1.323, allocations: 11.88 kB / 0.8617 GB, free: 67.86 MB / 0.5606 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03822/1.361, allocations: 12.96 MB / 0.8744 GB, free: 54.85 MB / 0.5606 GB Notification: Performance of postOpt removeConstants (simulation): time 0.002816/1.364, allocations: 0.9159 MB / 0.8753 GB, free: 53.93 MB / 0.5606 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0008999/1.365, allocations: 99.91 kB / 0.8754 GB, free: 53.84 MB / 0.5606 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002678/1.368, allocations: 172.8 kB / 0.8756 GB, free: 53.67 MB / 0.5606 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009961/1.369, allocations: 470.2 kB / 0.876 GB, free: 53.21 MB / 0.5606 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003533/1.369, allocations: 143.9 kB / 0.8761 GB, free: 53.07 MB / 0.5606 GB Notification: Performance of sorting global known variables: time 0.002222/1.371, allocations: 1.996 MB / 0.8781 GB, free: 51.07 MB / 0.5606 GB Notification: Performance of sort global known variables: time 9e-08/1.371, allocations: 3.812 kB / 0.8781 GB, free: 51.07 MB / 0.5606 GB Notification: Performance of remove unused functions: time 0.00697/1.378, allocations: 2.065 MB / 0.8801 GB, free: 49.03 MB / 0.5606 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 15 * Number of states: 19 (solution.temperature,OxyRHm[1].logn,OxyRHm[2].logn,OxyRHm[3].logn,OxyRHm[4].logn,DeoxyRHm[1].logn,DeoxyRHm[2].logn,DeoxyRHm[3].logn,DeoxyRHm[4].logn,OxyTHm[1].logn,OxyTHm[2].logn,OxyTHm[3].logn,OxyTHm[4].logn,DeoxyTHm[1].logn,DeoxyTHm[2].logn,DeoxyTHm[3].logn,DeoxyTHm[4].logn,oxygen_unbound.logn,H2O.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 (408): * Single equations (assignments): 405 * 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%), (9,4,100.0%)} * Non-linear torn systems (#iteration vars, #inner vars): 1 system {(1,3)} Notification: Performance of Backend phase and start with SimCode phase: time 0.04032/1.419, allocations: 14.74 MB / 0.8945 GB, free: 34.4 MB / 0.5606 GB Notification: Performance of simCode: created initialization part: time 0.014/1.433, allocations: 7.078 MB / 0.9014 GB, free: 27.29 MB / 0.5606 GB Notification: Performance of simCode: created event and clocks part: time 1.016e-05/1.433, allocations: 0 / 0.9014 GB, free: 27.29 MB / 0.5606 GB Notification: Performance of simCode: created simulation system equations: time 0.007698/1.44, allocations: 3.775 MB / 0.9051 GB, free: 23.48 MB / 0.5606 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004348/1.445, allocations: 0.7718 MB / 0.9059 GB, free: 22.76 MB / 0.5606 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3898/1.834, allocations: 54.82 MB / 0.9594 GB, free: 191.1 MB / 0.5919 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.003518/1.838, allocations: 3.304 MB / 0.9626 GB, free: 190.3 MB / 0.5919 GB Notification: Performance of simCode: alias equations: time 0.004351/1.842, allocations: 1.579 MB / 0.9642 GB, free: 190.3 MB / 0.5919 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002993/1.845, allocations: 2.047 MB / 0.9662 GB, free: 190.3 MB / 0.5919 GB Notification: Performance of SimCode: time 7.01e-07/1.845, allocations: 0.5 kB / 0.9662 GB, free: 190.3 MB / 0.5919 GB Notification: Performance of buildModelFMU: Generate the FMI files: time 0.2027/2.048, allocations: 133.2 MB / 1.096 GB, free: 85.52 MB / 0.5919 GB Notification: Performance of buildModelFMU: Generate platform static: time 36.71/38.76, allocations: 11.33 kB / 1.096 GB, free: 85.52 MB / 0.5919 GB " [Timeout remaining time 621] (rm -f Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & /home/hudson/saved_omc/OMSimulator/install/bin/OMSimulator --tempDir=temp_Chemical_Chemical_Obsolete_Examples_Hemoglobin_Allosteric_Hemoglobin2_MWC_fmu --startTime=0 --stopTime=15000 --stepSize=6 --timeout=50 --tolerance=1e-06 Chemical_Chemical_Obsolete_Examples_Hemoglobin_Allosteric_Hemoglobin2_MWC.fmu > Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 52.5] [Calling sys.exit(0), Time elapsed: 42.08471683005337] Failed to read output from testmodel.py, exit status != 0: 39.00092431996018 39.016748866 38.531902762 Calling exit ...