Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.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.HemoglobinCarboxylation,tolerance=1e-05,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation")
translateModel(Chemical.Examples.Hemoglobin.HemoglobinCarboxylation,tolerance=1e-05,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001319/0.001319, allocations: 103.5 kB / 16.41 MB, free: 6.5 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00125/0.00125, allocations: 183 kB / 17.34 MB, free: 5.766 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.311/1.311, allocations: 222.9 MB / 241 MB, free: 15.15 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08422/0.08422, allocations: 15.31 MB / 306.5 MB, free: 15.4 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001235/0.001235, allocations: 60.12 kB / 425.9 MB, free: 11.41 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1118/0.1131, allocations: 53.61 MB / 479.5 MB, free: 5.75 MB / 350.1 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.HemoglobinCarboxylation): time 0.5169/0.63, allocations: 41.59 MB / 0.5089 GB, free: 2.922 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.07849/0.7085, allocations: 72.71 MB / 0.5799 GB, free: 5.375 MB / 430.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.005469/0.714, allocations: 63.38 kB / 0.5799 GB, free: 5.352 MB / 430.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.005903/0.72, allocations: 1.612 MB / 0.5815 GB, free: 4.066 MB / 430.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.02179/0.7418, allocations: 5.923 MB / 0.5873 GB, free: 15.39 MB / 446.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.03232/0.7741, allocations: 10.22 MB / 0.5973 GB, free: 7.355 MB / 446.1 MB
Notification: Performance of NFFlatten.flatten: time 0.03199/0.8062, allocations: 26.69 MB / 0.6233 GB, free: 15.73 MB / 478.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.02813/0.8343, allocations: 21.97 MB / 0.6448 GB, free: 9.645 MB / 494.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.02961/0.864, allocations: 17.48 MB / 0.6619 GB, free: 8.137 MB / 0.4982 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.03081/0.8948, allocations: 16.19 MB / 0.6777 GB, free: 7.898 MB / 0.5138 GB
Notification: Performance of NFPackage.collectConstants: time 0.01292/0.9078, allocations: 3.094 MB / 0.6807 GB, free: 4.805 MB / 0.5138 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.04404/0.9519, allocations: 10.7 MB / 0.6911 GB, free: 10.1 MB / 0.5294 GB
Notification: Performance of NFScalarize.scalarize: time 0.01421/0.9661, allocations: 6.981 MB / 0.698 GB, free: 3.102 MB / 0.5294 GB
Notification: Performance of NFVerifyModel.verify: time 0.02727/0.9934, allocations: 12.15 MB / 0.7098 GB, free: 6.906 MB / 0.545 GB
Notification: Performance of NFConvertDAE.convert: time 0.3819/1.375, allocations: 42.21 MB / 0.751 GB, free: 60.4 MB / 0.545 GB
Notification: Performance of FrontEnd - DAE generated: time 9.508e-06/1.375, allocations: 0 / 0.751 GB, free: 60.4 MB / 0.545 GB
Notification: Performance of FrontEnd: time 2.004e-06/1.375, allocations: 1.312 kB / 0.751 GB, free: 60.4 MB / 0.545 GB
Notification: Performance of Transformations before backend: time 0.001321/1.377, allocations: 2.656 kB / 0.751 GB, free: 60.4 MB / 0.545 GB
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 0.1012/1.478, allocations: 24.72 MB / 0.7752 GB, free: 53.52 MB / 0.545 GB
Notification: Performance of prepare preOptimizeDAE: time 4.999e-05/1.478, allocations: 18.55 kB / 0.7752 GB, free: 53.52 MB / 0.545 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.03018/1.508, allocations: 3.892 MB / 0.779 GB, free: 52.04 MB / 0.545 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0324/1.541, allocations: 12.01 MB / 0.7907 GB, free: 48.61 MB / 0.545 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002379/1.543, allocations: 2.139 MB / 0.7928 GB, free: 47.44 MB / 0.545 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.01336/1.556, allocations: 1.526 MB / 0.7943 GB, free: 47.39 MB / 0.545 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.09387/1.65, allocations: 34.79 MB / 0.8283 GB, free: 15.76 MB / 0.545 GB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0008069/1.651, allocations: 11.03 kB / 0.8283 GB, free: 15.76 MB / 0.545 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01169/1.663, allocations: 0.5886 MB / 0.8289 GB, free: 15.17 MB / 0.545 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002775/1.663, allocations: 360 kB / 0.8292 GB, free: 14.82 MB / 0.545 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1001/1.763, allocations: 46.83 MB / 0.8749 GB, free: 15.99 MB / 0.5919 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 0.624/2.387, allocations: 127.8 MB / 0.9997 GB, free: 173.8 MB / 0.6544 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.8836/3.271, allocations: 276 MB / 1.269 GB, free: 183.7 MB / 0.6544 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.03713/3.308, allocations: 19.81 MB / 1.289 GB, free: 179.7 MB / 0.6544 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.1624/3.471, allocations: 87.46 MB / 1.374 GB, free: 108.5 MB / 0.6544 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 9.892e-05/3.471, allocations: 144.1 kB / 1.374 GB, free: 108.3 MB / 0.6544 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.02214/3.493, allocations: 4.518 MB / 1.379 GB, free: 103.9 MB / 0.6544 GB
Notification: Performance of pre-optimization done (n=995): time 6.032e-05/3.493, allocations: 3.938 kB / 1.379 GB, free: 103.9 MB / 0.6544 GB
Notification: Performance of matching and sorting (n=1129): time 1.043/4.536, allocations: 135.9 MB / 1.511 GB, free: 238.9 MB / 0.6544 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001019/4.536, allocations: 165.5 kB / 1.512 GB, free: 238.8 MB / 0.6544 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0168/4.553, allocations: 10.15 MB / 1.521 GB, free: 234.8 MB / 0.6544 GB
Notification: Performance of collectPreVariables (initialization): time 0.004817/4.557, allocations: 213.3 kB / 1.522 GB, free: 234.6 MB / 0.6544 GB
Notification: Performance of collectInitialEqns (initialization): time 0.005615/4.563, allocations: 6.891 MB / 1.528 GB, free: 230.1 MB / 0.6544 GB
Notification: Performance of collectInitialBindings (initialization): time 0.00783/4.571, allocations: 3.909 MB / 1.532 GB, free: 226.8 MB / 0.6544 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.01665/4.588, allocations: 3.264 MB / 1.535 GB, free: 225 MB / 0.6544 GB
Notification: Performance of setup shared object (initialization): time 4.721e-05/4.588, allocations: 301.1 kB / 1.536 GB, free: 224.7 MB / 0.6544 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.02159/4.609, allocations: 11.82 MB / 1.547 GB, free: 218.2 MB / 0.6544 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.02507/4.634, allocations: 16.55 MB / 1.563 GB, free: 205.6 MB / 0.6544 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.05011/4.685, allocations: 29.74 MB / 1.592 GB, free: 178.4 MB / 0.6544 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002077/4.685, allocations: 44 kB / 1.592 GB, free: 178.4 MB / 0.6544 GB
Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4474/5.132, allocations: 81.46 MB / 1.672 GB, free: 96.77 MB / 0.6544 GB
Notification: Performance of prepare postOptimizeDAE: time 0.0001024/5.132, allocations: 68 kB / 1.672 GB, free: 96.7 MB / 0.6544 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.00019/5.133, allocations: 152.1 kB / 1.672 GB, free: 96.55 MB / 0.6544 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.05727/5.19, allocations: 22.38 MB / 1.694 GB, free: 74.31 MB / 0.6544 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01839/5.208, allocations: 3.727 MB / 1.698 GB, free: 70.58 MB / 0.6544 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.5489/5.757, allocations: 93.94 MB / 1.789 GB, free: 193.4 MB / 0.6544 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02107/5.778, allocations: 0.8338 MB / 1.79 GB, free: 192.5 MB / 0.6544 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00678/5.785, allocations: 0.9368 MB / 1.791 GB, free: 191.6 MB / 0.6544 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 0.01983/5.805, allocations: 5.371 MB / 1.796 GB, free: 186.5 MB / 0.6544 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.007898/5.813, allocations: 1.056 MB / 1.797 GB, free: 186 MB / 0.6544 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2772/6.09, allocations: 48.59 MB / 1.845 GB, free: 138.2 MB / 0.6544 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001567/6.09, allocations: 120 kB / 1.845 GB, free: 138.1 MB / 0.6544 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001778/6.09, allocations: 18.69 kB / 1.845 GB, free: 138 MB / 0.6544 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0005009/6.091, allocations: 63.77 kB / 1.845 GB, free: 138 MB / 0.6544 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3294/6.42, allocations: 73.04 MB / 1.916 GB, free: 65.29 MB / 0.6544 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001324/6.421, allocations: 4 kB / 1.916 GB, free: 65.29 MB / 0.6544 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01497/6.436, allocations: 2.415 MB / 1.919 GB, free: 62.87 MB / 0.6544 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.355/6.791, allocations: 11.88 MB / 1.93 GB, free: 220.9 MB / 0.6544 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.005031/6.796, allocations: 475.2 kB / 1.931 GB, free: 220.9 MB / 0.6544 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1086/6.904, allocations: 46.94 MB / 1.977 GB, free: 208.1 MB / 0.6544 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.5e-06/6.904, allocations: 9.5 kB / 1.977 GB, free: 208.1 MB / 0.6544 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2931/7.197, allocations: 62.73 MB / 2.038 GB, free: 168 MB / 0.6544 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.01192/7.209, allocations: 3.291 MB / 2.041 GB, free: 165.3 MB / 0.6544 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.007649/7.217, allocations: 291.9 kB / 2.041 GB, free: 165 MB / 0.6544 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01577/7.233, allocations: 0.5267 MB / 2.042 GB, free: 164.5 MB / 0.6544 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.008462/7.241, allocations: 1.503 MB / 2.043 GB, free: 163 MB / 0.6544 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.004259/7.246, allocations: 471.6 kB / 2.044 GB, free: 162.5 MB / 0.6544 GB
Notification: Performance of sorting global known variables: time 0.01408/7.26, allocations: 6.966 MB / 2.051 GB, free: 155.6 MB / 0.6544 GB
Notification: Performance of sort global known variables: time 6.51e-07/7.26, allocations: 0 / 2.051 GB, free: 155.6 MB / 0.6544 GB
Notification: Performance of remove unused functions: time 0.03658/7.296, allocations: 6.679 MB / 2.057 GB, free: 149.4 MB / 0.6544 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 0.01394/7.31, allocations: 3.539 MB / 2.061 GB, free: 146.6 MB / 0.6544 GB
Notification: Performance of simCode: created initialization part: time 0.07496/7.385, allocations: 27.79 MB / 2.088 GB, free: 118.8 MB / 0.6544 GB
Notification: Performance of simCode: created event and clocks part: time 1.25e-05/7.385, allocations: 0 / 2.088 GB, free: 118.8 MB / 0.6544 GB
Notification: Performance of simCode: created simulation system equations: time 0.0434/7.429, allocations: 14.87 MB / 2.102 GB, free: 103.9 MB / 0.6544 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02572/7.455, allocations: 2.499 MB / 2.105 GB, free: 101.5 MB / 0.6544 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.1031/7.558, allocations: 37.51 MB / 2.141 GB, free: 63.93 MB / 0.6544 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.329/7.887, allocations: 9.631 MB / 2.151 GB, free: 217.9 MB / 0.6544 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01019/7.897, allocations: 1.563 MB / 2.152 GB, free: 217.9 MB / 0.6544 GB
Notification: Performance of SimCode: time 9.32e-07/7.897, allocations: 0 / 2.152 GB, free: 217.9 MB / 0.6544 GB
Notification: Performance of Templates: time 1.283/9.18, allocations: 0.5111 GB / 2.663 GB, free: 198.2 MB / 0.6544 GB
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.makefile
(rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe 2>&1)