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 0.001229/0.001229, allocations: 111.3 kB / 15.23 MB, free: 0.6602 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001381/0.001381, allocations: 196.2 kB / 16.14 MB, free: 6.676 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.439/1.439, allocations: 222.9 MB / 239.8 MB, free: 4.605 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2472/0.2472, allocations: 15.31 MB / 305.3 MB, free: 15.27 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.002111/0.002111, allocations: 75.86 kB / 369.7 MB, free: 4.426 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1251/0.1272, allocations: 53.61 MB / 423.3 MB, free: 14.77 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 0.3881/0.5153, allocations: 30.9 MB / 454.2 MB, free: 38.52 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02596/0.5413, allocations: 26.03 MB / 480.2 MB, free: 25.45 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002515/0.5439, allocations: 43.5 kB / 480.2 MB, free: 25.43 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001961/0.5459, allocations: 0.5323 MB / 480.8 MB, free: 25.16 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.008618/0.5545, allocations: 1.868 MB / 482.6 MB, free: 24.02 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01403/0.5686, allocations: 3.077 MB / 485.7 MB, free: 22.21 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.009364/0.578, allocations: 7.267 MB / 493 MB, free: 18.9 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.007335/0.5853, allocations: 4.991 MB / 498 MB, free: 16.93 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.01108/0.5964, allocations: 4.728 MB / 0.4909 GB, free: 14.98 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009707/0.6062, allocations: 4.387 MB / 0.4952 GB, free: 11.52 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.00385/0.6101, allocations: 484 kB / 0.4957 GB, free: 11.04 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01745/0.6276, allocations: 3.135 MB / 0.4987 GB, free: 8.203 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.004311/0.6319, allocations: 1.545 MB / 0.5002 GB, free: 7.016 MB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0086/0.6405, allocations: 3.083 MB / 0.5032 GB, free: 4.254 MB / 366.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02544/0.666, allocations: 10.49 MB / 0.5135 GB, free: 9.848 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.053e-06/0.666, allocations: 0 / 0.5135 GB, free: 9.848 MB / 382.1 MB
Notification: Performance of FrontEnd: time 2.204e-06/0.6661, allocations: 0 / 0.5135 GB, free: 9.848 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 0.0003375/0.6664, allocations: 0 / 0.5135 GB, free: 9.848 MB / 382.1 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 0.02864/0.695, allocations: 7.439 MB / 0.5207 GB, free: 2.324 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 6.708e-05/0.6951, allocations: 8.031 kB / 0.5208 GB, free: 2.316 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.009013/0.7042, allocations: 1.219 MB / 0.5219 GB, free: 1.094 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.01101/0.7152, allocations: 3.13 MB / 0.525 GB, free: 13.88 MB / 398.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0009216/0.7162, allocations: 0.6727 MB / 0.5257 GB, free: 13.14 MB / 398.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.003377/0.7196, allocations: 0.4921 MB / 0.5261 GB, free: 12.65 MB / 398.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.03005/0.7496, allocations: 9.368 MB / 0.5353 GB, free: 3.176 MB / 398.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002696/0.75, allocations: 7.938 kB / 0.5353 GB, free: 3.168 MB / 398.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.002778/0.7528, allocations: 195.9 kB / 0.5355 GB, free: 2.977 MB / 398.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001398/0.7529, allocations: 116 kB / 0.5356 GB, free: 2.863 MB / 398.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.03311/0.786, allocations: 12.59 MB / 0.5479 GB, free: 6.25 MB / 414.1 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 0.08499/0.8711, allocations: 30.23 MB / 0.5774 GB, free: 7.316 MB / 446.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.3234/1.195, allocations: 41.27 MB / 0.6177 GB, free: 107 MB / 462.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.008703/1.203, allocations: 5.073 MB / 0.6227 GB, free: 106.9 MB / 462.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04292/1.246, allocations: 20.92 MB / 0.6431 GB, free: 96.95 MB / 462.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.789e-05/1.246, allocations: 70.02 kB / 0.6432 GB, free: 96.88 MB / 462.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004832/1.251, allocations: 0.9466 MB / 0.6441 GB, free: 96.6 MB / 462.1 MB
Notification: Performance of pre-optimization done (n=324): time 2.35e-05/1.251, allocations: 0 / 0.6441 GB, free: 96.6 MB / 462.1 MB
Notification: Performance of matching and sorting (n=376): time 0.1066/1.358, allocations: 24.39 MB / 0.6679 GB, free: 88.72 MB / 462.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001022/1.358, allocations: 89.8 kB / 0.668 GB, free: 88.66 MB / 462.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00551/1.364, allocations: 2.961 MB / 0.6709 GB, free: 87.11 MB / 462.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.001522/1.365, allocations: 88.11 kB / 0.671 GB, free: 87.04 MB / 462.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001604/1.367, allocations: 2.159 MB / 0.6731 GB, free: 85.14 MB / 462.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.00246/1.369, allocations: 1.3 MB / 0.6744 GB, free: 84.02 MB / 462.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.003738/1.373, allocations: 0.9812 MB / 0.6753 GB, free: 83.48 MB / 462.1 MB
Notification: Performance of setup shared object (initialization): time 6.083e-05/1.373, allocations: 301.1 kB / 0.6756 GB, free: 83.19 MB / 462.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.005274/1.378, allocations: 2.956 MB / 0.6785 GB, free: 81.66 MB / 462.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005951/1.384, allocations: 4.481 MB / 0.6829 GB, free: 77.91 MB / 462.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01103/1.395, allocations: 7.805 MB / 0.6905 GB, free: 69.71 MB / 462.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.309e-05/1.396, allocations: 12 kB / 0.6905 GB, free: 69.7 MB / 462.1 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05833/1.454, allocations: 13.82 MB / 0.704 GB, free: 56.25 MB / 462.1 MB
Notification: Performance of prepare postOptimizeDAE: time 9.988e-05/1.454, allocations: 30.69 kB / 0.704 GB, free: 56.23 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001054/1.454, allocations: 48 kB / 0.7041 GB, free: 56.18 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008776/1.463, allocations: 3.474 MB / 0.7075 GB, free: 52.86 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005702/1.469, allocations: 1.27 MB / 0.7087 GB, free: 51.59 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03006/1.499, allocations: 16.61 MB / 0.7249 GB, free: 34.62 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.006039/1.505, allocations: 358.6 kB / 0.7253 GB, free: 34.29 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001522/1.506, allocations: 283.8 kB / 0.7255 GB, free: 34.01 MB / 462.1 MB
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 0.004746/1.511, allocations: 1.447 MB / 0.727 GB, free: 32.55 MB / 462.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001861/1.513, allocations: 343.7 kB / 0.7273 GB, free: 32.21 MB / 462.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03949/1.553, allocations: 9.666 MB / 0.7367 GB, free: 22.63 MB / 462.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.921e-05/1.553, allocations: 40 kB / 0.7368 GB, free: 22.59 MB / 462.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.18e-05/1.553, allocations: 4 kB / 0.7368 GB, free: 22.59 MB / 462.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001566/1.553, allocations: 23.86 kB / 0.7368 GB, free: 22.57 MB / 462.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.05271/1.606, allocations: 15.45 MB / 0.7519 GB, free: 7.133 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.535e-05/1.606, allocations: 6.531 kB / 0.7519 GB, free: 7.129 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004885/1.611, allocations: 0.8444 MB / 0.7527 GB, free: 6.285 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006227/1.617, allocations: 2.13 MB / 0.7548 GB, free: 4.203 MB / 462.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001693/1.619, allocations: 143.9 kB / 0.7549 GB, free: 4.062 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02352/1.642, allocations: 11.42 MB / 0.7661 GB, free: 8.27 MB / 478.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.606e-06/1.642, allocations: 7.938 kB / 0.7661 GB, free: 8.262 MB / 478.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.3113/1.954, allocations: 12.96 MB / 0.7787 GB, free: 132.1 MB / 478.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.003192/1.957, allocations: 0.9377 MB / 0.7797 GB, free: 132 MB / 478.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001095/1.958, allocations: 91.83 kB / 0.7797 GB, free: 132 MB / 478.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.003219/1.961, allocations: 252.6 kB / 0.78 GB, free: 132 MB / 478.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001163/1.962, allocations: 454.4 kB / 0.7804 GB, free: 132 MB / 478.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003476/1.963, allocations: 150.6 kB / 0.7806 GB, free: 132 MB / 478.1 MB
Notification: Performance of sorting global known variables: time 0.002757/1.965, allocations: 1.99 MB / 0.7825 GB, free: 131.8 MB / 478.1 MB
Notification: Performance of sort global known variables: time 2.3e-07/1.965, allocations: 0 / 0.7825 GB, free: 131.8 MB / 478.1 MB
Notification: Performance of remove unused functions: time 0.008911/1.974, allocations: 2.042 MB / 0.7845 GB, free: 131.8 MB / 478.1 MB
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 0.003231/1.978, allocations: 1.291 MB / 0.7858 GB, free: 131.7 MB / 478.1 MB
Notification: Performance of simCode: created initialization part: time 0.01577/1.993, allocations: 7.418 MB / 0.793 GB, free: 129.5 MB / 478.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.19e-05/1.994, allocations: 1.125 kB / 0.793 GB, free: 129.5 MB / 478.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.01034/2.004, allocations: 4.083 MB / 0.797 GB, free: 128 MB / 478.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.005618/2.01, allocations: 0.7229 MB / 0.7977 GB, free: 127.8 MB / 478.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.02555/2.035, allocations: 12.93 MB / 0.8103 GB, free: 121.6 MB / 478.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.004275/2.039, allocations: 3.311 MB / 0.8135 GB, free: 120.6 MB / 478.1 MB
Notification: Performance of simCode: alias equations: time 0.006638/2.046, allocations: 1.6 MB / 0.8151 GB, free: 120.5 MB / 478.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001867/2.048, allocations: 453.7 kB / 0.8155 GB, free: 120.5 MB / 478.1 MB
Notification: Performance of SimCode: time 1.453e-06/2.048, allocations: 2.625 kB / 0.8155 GB, free: 120.5 MB / 478.1 MB
Notification: Performance of Templates: time 0.1221/2.17, allocations: 88.16 MB / 0.9016 GB, free: 48.41 MB / 478.1 MB
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)