Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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/Chemical 1.4.1-master/package.mo", uses=false)
Using package Chemical with version 1.4.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-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(Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
translateModel(Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.008283/0.008283, allocations: 99.64 kB / 15.73 MB, free: 6.465 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001961/0.001961, allocations: 190.8 kB / 16.67 MB, free: 6.379 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.39/1.39, allocations: 222.9 MB / 240.4 MB, free: 4.332 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2551/0.2551, allocations: 15.31 MB / 305.8 MB, free: 15.29 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.00114/0.00114, allocations: 67.89 kB / 425.2 MB, free: 13.11 MB / 366.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3094/0.3106, allocations: 53.6 MB / 478.8 MB, free: 25.79 MB / 366.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66: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 1.4.1-master/package.mo:4740:7-4740:66: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.Allosteric_Hemoglobin2_MWC): time 0.04187/0.3525, allocations: 29.19 MB / 0.4961 GB, free: 5.473 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03276/0.3853, allocations: 26.09 MB / 0.5216 GB, free: 11.28 MB / 398.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.003364/0.3887, allocations: 23.88 kB / 0.5216 GB, free: 11.26 MB / 398.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.00198/0.3907, allocations: 0.5931 MB / 0.5222 GB, free: 10.66 MB / 398.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.009289/0.4, allocations: 2.133 MB / 0.5243 GB, free: 8.512 MB / 398.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01219/0.4123, allocations: 3.522 MB / 0.5277 GB, free: 4.969 MB / 398.1 MB
Notification: Performance of NFFlatten.flatten: time 0.01098/0.4233, allocations: 7.39 MB / 0.5349 GB, free: 13.55 MB / 414.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.008862/0.4322, allocations: 5.927 MB / 0.5407 GB, free: 7.547 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.009074/0.4413, allocations: 4.869 MB / 0.5455 GB, free: 2.668 MB / 414.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009634/0.4509, allocations: 4.627 MB / 0.55 GB, free: 14.03 MB / 430.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002871/0.4538, allocations: 0.668 MB / 0.5506 GB, free: 13.36 MB / 430.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01554/0.4694, allocations: 3.324 MB / 0.5539 GB, free: 10.03 MB / 430.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.004071/0.4735, allocations: 1.784 MB / 0.5556 GB, free: 8.242 MB / 430.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.00857/0.4821, allocations: 3.338 MB / 0.5589 GB, free: 4.891 MB / 430.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02572/0.5079, allocations: 11.1 MB / 0.5697 GB, free: 9.754 MB / 446.1 MB
Notification: Performance of FrontEnd - DAE generated: time 1.055e-05/0.5079, allocations: 3.984 kB / 0.5697 GB, free: 9.75 MB / 446.1 MB
Notification: Performance of FrontEnd: time 2.354e-06/0.508, allocations: 4 kB / 0.5697 GB, free: 9.746 MB / 446.1 MB
Notification: Performance of Transformations before backend: time 0.0003211/0.5083, allocations: 0 / 0.5697 GB, free: 9.746 MB / 446.1 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 0.02275/0.531, allocations: 7.427 MB / 0.577 GB, free: 2.238 MB / 446.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.536e-05/0.5311, allocations: 12.03 kB / 0.577 GB, free: 2.227 MB / 446.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006903/0.538, allocations: 1.215 MB / 0.5782 GB, free: 1.004 MB / 446.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.009733/0.5478, allocations: 3.212 MB / 0.5813 GB, free: 13.71 MB / 462.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001014/0.5489, allocations: 0.6766 MB / 0.582 GB, free: 12.96 MB / 462.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.003647/0.5525, allocations: 0.4923 MB / 0.5825 GB, free: 12.47 MB / 462.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02687/0.5794, allocations: 9.368 MB / 0.5916 GB, free: 2.996 MB / 462.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002848/0.5798, allocations: 7.938 kB / 0.5916 GB, free: 2.988 MB / 462.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.002788/0.5826, allocations: 195.9 kB / 0.5918 GB, free: 2.797 MB / 462.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.000135/0.5827, allocations: 116 kB / 0.5919 GB, free: 2.684 MB / 462.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02676/0.6095, allocations: 12.59 MB / 0.6042 GB, free: 6.074 MB / 478.1 MB
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 0.4044/1.014, allocations: 30.17 MB / 0.6337 GB, free: 97.73 MB / 478.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06285/1.077, allocations: 41.27 MB / 0.674 GB, free: 66.68 MB / 478.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.009854/1.087, allocations: 5.071 MB / 0.6789 GB, free: 61.59 MB / 478.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04094/1.128, allocations: 20.9 MB / 0.6993 GB, free: 40.01 MB / 478.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.124e-05/1.128, allocations: 63.8 kB / 0.6994 GB, free: 39.94 MB / 478.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003611/1.131, allocations: 0.9719 MB / 0.7004 GB, free: 38.99 MB / 478.1 MB
Notification: Performance of pre-optimization done (n=324): time 1.767e-05/1.131, allocations: 0 / 0.7004 GB, free: 38.99 MB / 478.1 MB
Notification: Performance of matching and sorting (n=376): time 0.09757/1.229, allocations: 24.41 MB / 0.7242 GB, free: 14.65 MB / 478.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.209e-05/1.229, allocations: 93.02 kB / 0.7243 GB, free: 14.55 MB / 478.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00382/1.233, allocations: 2.958 MB / 0.7272 GB, free: 11.57 MB / 478.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.001348/1.234, allocations: 85.7 kB / 0.7273 GB, free: 11.48 MB / 478.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.00111/1.236, allocations: 2.153 MB / 0.7294 GB, free: 9.316 MB / 478.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001612/1.237, allocations: 1.301 MB / 0.7306 GB, free: 8.027 MB / 478.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001367/1.239, allocations: 0.9804 MB / 0.7316 GB, free: 7.035 MB / 478.1 MB
Notification: Performance of setup shared object (initialization): time 4.756e-05/1.239, allocations: 303.8 kB / 0.7319 GB, free: 6.738 MB / 478.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.003843/1.242, allocations: 2.956 MB / 0.7348 GB, free: 3.773 MB / 478.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004886/1.247, allocations: 4.483 MB / 0.7391 GB, free: 14.64 MB / 494.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01143/1.259, allocations: 7.803 MB / 0.7468 GB, free: 6.25 MB / 494.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.535e-05/1.259, allocations: 16 kB / 0.7468 GB, free: 6.234 MB / 494.1 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05957/1.318, allocations: 13.83 MB / 0.7603 GB, free: 8.543 MB / 0.4981 GB
Notification: Performance of prepare postOptimizeDAE: time 0.0001189/1.319, allocations: 24 kB / 0.7603 GB, free: 8.52 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001391/1.319, allocations: 48 kB / 0.7603 GB, free: 8.473 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01042/1.329, allocations: 3.478 MB / 0.7637 GB, free: 5.086 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.006589/1.336, allocations: 1.258 MB / 0.765 GB, free: 3.828 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03827/1.374, allocations: 18.49 MB / 0.783 GB, free: 0.9805 MB / 0.5137 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.006263/1.38, allocations: 255.7 kB / 0.7833 GB, free: 0.7305 MB / 0.5137 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001856/1.382, allocations: 279.8 kB / 0.7835 GB, free: 468 kB / 0.5137 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 0.005124/1.387, allocations: 1.455 MB / 0.785 GB, free: 14.99 MB / 0.5294 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.002081/1.39, allocations: 343.6 kB / 0.7853 GB, free: 14.65 MB / 0.5294 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.04128/1.431, allocations: 9.659 MB / 0.7947 GB, free: 5.07 MB / 0.5294 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.599e-05/1.431, allocations: 40.69 kB / 0.7948 GB, free: 5.031 MB / 0.5294 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.511e-05/1.431, allocations: 11.88 kB / 0.7948 GB, free: 5.02 MB / 0.5294 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001993/1.431, allocations: 20.48 kB / 0.7948 GB, free: 5 MB / 0.5294 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.06098/1.492, allocations: 15.43 MB / 0.8099 GB, free: 5.555 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.249e-05/1.492, allocations: 4 kB / 0.8099 GB, free: 5.551 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.005219/1.498, allocations: 0.8463 MB / 0.8107 GB, free: 4.707 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006572/1.504, allocations: 2.132 MB / 0.8128 GB, free: 2.594 MB / 0.545 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001198/1.505, allocations: 139.9 kB / 0.8129 GB, free: 2.457 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.3781/1.884, allocations: 12.66 MB / 0.8253 GB, free: 177.5 MB / 0.545 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.155e-05/1.884, allocations: 7.656 kB / 0.8253 GB, free: 177.5 MB / 0.545 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.04323/1.927, allocations: 12.97 MB / 0.8379 GB, free: 173.5 MB / 0.545 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003367/1.93, allocations: 0.9273 MB / 0.8388 GB, free: 173.3 MB / 0.545 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0006887/1.931, allocations: 96.14 kB / 0.8389 GB, free: 173.2 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002489/1.934, allocations: 168.8 kB / 0.8391 GB, free: 173.1 MB / 0.545 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001206/1.935, allocations: 457.5 kB / 0.8395 GB, free: 173.1 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.000337/1.935, allocations: 144.1 kB / 0.8397 GB, free: 173.1 MB / 0.545 GB
Notification: Performance of sorting global known variables: time 0.003033/1.938, allocations: 1.991 MB / 0.8416 GB, free: 172.4 MB / 0.545 GB
Notification: Performance of sort global known variables: time 1.864e-06/1.938, allocations: 0 / 0.8416 GB, free: 172.4 MB / 0.545 GB
Notification: Performance of remove unused functions: time 0.00853/1.947, allocations: 2.054 MB / 0.8436 GB, free: 172.2 MB / 0.545 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 0.002935/1.95, allocations: 1.293 MB / 0.8449 GB, free: 172 MB / 0.545 GB
Notification: Performance of simCode: created initialization part: time 0.01371/1.963, allocations: 7.431 MB / 0.8521 GB, free: 168.2 MB / 0.545 GB
Notification: Performance of simCode: created event and clocks part: time 9.538e-06/1.963, allocations: 0 / 0.8521 GB, free: 168.2 MB / 0.545 GB
Notification: Performance of simCode: created simulation system equations: time 0.007913/1.971, allocations: 4.089 MB / 0.8561 GB, free: 166 MB / 0.545 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004037/1.975, allocations: 0.7766 MB / 0.8569 GB, free: 165.6 MB / 0.545 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01934/1.995, allocations: 10.8 MB / 0.8674 GB, free: 157.1 MB / 0.545 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002799/1.998, allocations: 3.309 MB / 0.8707 GB, free: 153.9 MB / 0.545 GB
Notification: Performance of simCode: alias equations: time 0.004611/2.002, allocations: 1.582 MB / 0.8722 GB, free: 152.4 MB / 0.545 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001349/2.004, allocations: 457.4 kB / 0.8727 GB, free: 152 MB / 0.545 GB
Notification: Performance of SimCode: time 1.844e-06/2.004, allocations: 0 / 0.8727 GB, free: 152 MB / 0.545 GB
Notification: Performance of Templates: time 0.1282/2.132, allocations: 92.55 MB / 0.963 GB, free: 60.41 MB / 0.545 GB
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile
(rm -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1)