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/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 1.4.0-master/package.mo", uses=false)
Using package Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-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.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/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001251/0.00125, allocations: 99.16 kB / 15.05 MB, free: 1.105 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001491/0.001491, allocations: 177.3 kB / 15.95 MB, free: 216 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.341/1.341, allocations: 223.2 MB / 239.9 MB, free: 5.457 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.1985/0.1985, allocations: 15.26 MB / 306.2 MB, free: 15.78 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.0005019/0.000502, allocations: 8 kB / 371.4 MB, free: 4.047 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3505/0.351, allocations: 54.62 MB / 426 MB, free: 40.03 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65: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:3011:6-3011:65: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 0.01628/0.3673, allocations: 20.04 MB / 446 MB, free: 29.11 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.06164/0.429, allocations: 61.35 MB / 0.4955 GB, free: 1.008 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.005586/0.4346, allocations: 95.5 kB / 0.4956 GB, free: 0.9609 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.006153/0.4408, allocations: 1.501 MB / 0.497 GB, free: 156 kB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0203/0.4611, allocations: 5.739 MB / 0.5026 GB, free: 12.38 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.03686/0.498, allocations: 8.804 MB / 0.5112 GB, free: 4.508 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.02406/0.5221, allocations: 15.91 MB / 0.5268 GB, free: 4.566 MB / 398.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.02026/0.5424, allocations: 16.06 MB / 0.5425 GB, free: 4.426 MB / 414.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.02378/0.5662, allocations: 14.54 MB / 0.5567 GB, free: 5.84 MB / 430.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.02612/0.5924, allocations: 13.06 MB / 0.5694 GB, free: 8.738 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.007436/0.5999, allocations: 1.43 MB / 0.5708 GB, free: 7.309 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.5177/1.118, allocations: 9.97 MB / 0.5805 GB, free: 36.54 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.01219/1.13, allocations: 4.851 MB / 0.5853 GB, free: 36.54 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.01163/1.141, allocations: 3.224 MB / 0.5884 GB, free: 36.51 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.05467/1.196, allocations: 30.25 MB / 0.618 GB, free: 31.61 MB / 446.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.414e-06/1.196, allocations: 2.078 kB / 0.618 GB, free: 31.61 MB / 446.1 MB
Notification: Performance of FrontEnd: time 4.218e-06/1.196, allocations: 0 / 0.618 GB, free: 31.61 MB / 446.1 MB
Notification: Performance of Transformations before backend: time 0.002043/1.198, allocations: 0 / 0.618 GB, free: 31.61 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: 3808
 * Number of variables: 3808
Notification: Performance of Generate backend data structure: time 0.08538/1.284, allocations: 20.26 MB / 0.6378 GB, free: 21.6 MB / 446.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.319e-05/1.284, allocations: 6.438 kB / 0.6378 GB, free: 21.6 MB / 446.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02878/1.313, allocations: 3.889 MB / 0.6416 GB, free: 18.38 MB / 446.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.03269/1.345, allocations: 10.89 MB / 0.6522 GB, free: 10.99 MB / 446.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.00217/1.348, allocations: 2.134 MB / 0.6543 GB, free: 9.137 MB / 446.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.01608/1.364, allocations: 1.526 MB / 0.6558 GB, free: 8.113 MB / 446.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.1106/1.474, allocations: 34.56 MB / 0.6895 GB, free: 300 kB / 462.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0008159/1.475, allocations: 10.84 kB / 0.6895 GB, free: 296 kB / 462.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01236/1.488, allocations: 0.5842 MB / 0.6901 GB, free: 172 kB / 462.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003971/1.488, allocations: 364 kB / 0.6905 GB, free: 15.81 MB / 478.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.11/1.598, allocations: 46.74 MB / 0.7361 GB, free: 9.273 MB / 0.4982 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 0.6305/2.228, allocations: 127.1 MB / 0.8602 GB, free: 83.57 MB / 0.5294 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.9225/3.151, allocations: 276 MB / 1.13 GB, free: 125.7 MB / 0.5763 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.1739/3.325, allocations: 86.93 MB / 1.215 GB, free: 40.84 MB / 0.5763 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 8.885e-05/3.325, allocations: 141.2 kB / 1.215 GB, free: 40.7 MB / 0.5763 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.02322/3.348, allocations: 4.431 MB / 1.219 GB, free: 36.36 MB / 0.5763 GB
Notification: Performance of pre-optimization done (n=995): time 4.367e-05/3.348, allocations: 0 / 1.219 GB, free: 36.36 MB / 0.5763 GB
Notification: Performance of matching and sorting (n=1129): time 1.005/4.354, allocations: 130.9 MB / 1.347 GB, free: 176.3 MB / 0.5763 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001599/4.354, allocations: 168.2 kB / 1.347 GB, free: 176.2 MB / 0.5763 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.02207/4.376, allocations: 10.08 MB / 1.357 GB, free: 166.1 MB / 0.5763 GB
Notification: Performance of collectPreVariables (initialization): time 0.005149/4.381, allocations: 217.6 kB / 1.357 GB, free: 165.9 MB / 0.5763 GB
Notification: Performance of collectInitialEqns (initialization): time 0.005534/4.387, allocations: 6.876 MB / 1.364 GB, free: 159 MB / 0.5763 GB
Notification: Performance of collectInitialBindings (initialization): time 0.008091/4.395, allocations: 3.914 MB / 1.368 GB, free: 155.2 MB / 0.5763 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.005197/4.4, allocations: 297.6 kB / 1.368 GB, free: 154.9 MB / 0.5763 GB
Notification: Performance of setup shared object (initialization): time 0.00138/4.402, allocations: 0.9022 MB / 1.369 GB, free: 154 MB / 0.5763 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.02352/4.425, allocations: 11.77 MB / 1.38 GB, free: 142.2 MB / 0.5763 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.02798/4.453, allocations: 16.44 MB / 1.396 GB, free: 123.7 MB / 0.5763 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.02944/4.483, allocations: 14.09 MB / 1.41 GB, free: 109.5 MB / 0.5763 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001714/4.483, allocations: 40 kB / 1.41 GB, free: 109.5 MB / 0.5763 GB
Notification: Performance of matching and sorting (n=1889) (initialization): time 0.7255/5.208, allocations: 81.41 MB / 1.49 GB, free: 191.8 MB / 0.5763 GB
Notification: Performance of prepare postOptimizeDAE: time 0.0001591/5.209, allocations: 69.27 kB / 1.49 GB, free: 191.8 MB / 0.5763 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002315/5.209, allocations: 149.1 kB / 1.49 GB, free: 191.8 MB / 0.5763 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.06168/5.27, allocations: 22.55 MB / 1.512 GB, free: 182.5 MB / 0.5763 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01971/5.29, allocations: 3.723 MB / 1.516 GB, free: 181.8 MB / 0.5763 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.1872/5.477, allocations: 93.73 MB / 1.607 GB, free: 92.61 MB / 0.5763 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0235/5.501, allocations: 1.143 MB / 1.608 GB, free: 91.5 MB / 0.5763 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.006333/5.507, allocations: 0.9328 MB / 1.609 GB, free: 90.57 MB / 0.5763 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 (linear and non-linear blocks): 0
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 2 {(1,100.0%) 3,(33,82.4%) 10}
 * Non-linear torn systems: 1 {1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.02024/5.528, allocations: 5.378 MB / 1.614 GB, free: 85.41 MB / 0.5763 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.007186/5.535, allocations: 1.051 MB / 1.615 GB, free: 84.91 MB / 0.5763 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.5691/6.104, allocations: 48.53 MB / 1.663 GB, free: 193.2 MB / 0.5763 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0003136/6.104, allocations: 119.4 kB / 1.663 GB, free: 193.2 MB / 0.5763 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001929/6.104, allocations: 18.88 kB / 1.663 GB, free: 193.2 MB / 0.5763 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0005024/6.105, allocations: 61.16 kB / 1.663 GB, free: 193.2 MB / 0.5763 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3145/6.42, allocations: 72.83 MB / 1.734 GB, free: 159.8 MB / 0.5763 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0002155/6.42, allocations: 4 kB / 1.734 GB, free: 159.8 MB / 0.5763 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01707/6.437, allocations: 2.417 MB / 1.736 GB, free: 157.4 MB / 0.5763 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.03244/6.469, allocations: 11.75 MB / 1.748 GB, free: 145.7 MB / 0.5763 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.005923/6.475, allocations: 479.5 kB / 1.748 GB, free: 145.2 MB / 0.5763 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1126/6.588, allocations: 44.76 MB / 1.792 GB, free: 100.1 MB / 0.5763 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.777e-06/6.588, allocations: 7.938 kB / 1.792 GB, free: 100.1 MB / 0.5763 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.5792/7.167, allocations: 63.31 MB / 1.854 GB, free: 179.4 MB / 0.5763 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.01526/7.183, allocations: 3.279 MB / 1.857 GB, free: 178.9 MB / 0.5763 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.007575/7.19, allocations: 295.3 kB / 1.857 GB, free: 178.7 MB / 0.5763 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01843/7.209, allocations: 0.7909 MB / 1.858 GB, free: 178.6 MB / 0.5763 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.008478/7.217, allocations: 1.495 MB / 1.86 GB, free: 178.4 MB / 0.5763 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.004593/7.222, allocations: 475.5 kB / 1.86 GB, free: 178.3 MB / 0.5763 GB
Notification: Performance of sorting global known variables: time 0.0179/7.24, allocations: 6.89 MB / 1.867 GB, free: 175.9 MB / 0.5763 GB
Notification: Performance of sort global known variables: time 8.12e-07/7.24, allocations: 0 / 1.867 GB, free: 175.9 MB / 0.5763 GB
Notification: Performance of remove unused functions: time 0.04263/7.282, allocations: 6.588 MB / 1.873 GB, free: 175.3 MB / 0.5763 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 (linear and non-linear blocks): 0
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 2 {(1,100.0%) 3,(33,82.4%) 10}
 * Non-linear torn systems: 1 {1 3}
Notification: Performance of Backend phase and start with SimCode phase: time 0.01106/7.294, allocations: 3.45 MB / 1.877 GB, free: 174.5 MB / 0.5763 GB
Notification: Performance of simCode: created initialization part: time 0.0734/7.367, allocations: 27.63 MB / 1.904 GB, free: 164.3 MB / 0.5763 GB
Notification: Performance of simCode: created event and clocks part: time 9.037e-06/7.367, allocations: 0.7812 kB / 1.904 GB, free: 164.3 MB / 0.5763 GB
Notification: Performance of simCode: created simulation system equations: time 0.0465/7.413, allocations: 14.83 MB / 1.918 GB, free: 157.1 MB / 0.5763 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.01928/7.433, allocations: 2.177 MB / 1.92 GB, free: 155.4 MB / 0.5763 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.09348/7.526, allocations: 43.19 MB / 1.962 GB, free: 117.8 MB / 0.5763 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0118/7.538, allocations: 10.22 MB / 1.972 GB, free: 110.2 MB / 0.5763 GB
Notification: Performance of simCode: alias equations: time 0.01813/7.556, allocations: 5.305 MB / 1.978 GB, free: 104.9 MB / 0.5763 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.006001/7.562, allocations: 1.424 MB / 1.979 GB, free: 103.5 MB / 0.5763 GB
Notification: Performance of SimCode: time 1.443e-06/7.562, allocations: 0 / 1.979 GB, free: 103.5 MB / 0.5763 GB
Notification: Performance of Templates: time 1.031/8.594, allocations: 300.6 MB / 2.273 GB, free: 173.9 MB / 0.5763 GB
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.makefile
Environment - environmentSimulation:
(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)
Environment - environmentSimulation: