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 1.4.0-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.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 0.0009643/0.0009643, allocations: 99.86 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 0.0009133/0.0009134, allocations: 177.3 kB / 15.94 MB, free: 228 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.318/1.318, allocations: 223.2 MB / 239.9 MB, free: 5.332 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.1977/0.1977, allocations: 15.26 MB / 306.3 MB, free: 15.76 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.0003001/0.0003002, allocations: 8 kB / 371.4 MB, free: 4.012 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2962/0.2965, allocations: 54.63 MB / 426 MB, free: 39.97 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.Allosteric_Hemoglobin2_MWC): time 0.007282/0.3038, allocations: 8.638 MB / 434.6 MB, free: 37.04 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02042/0.3243, allocations: 22.06 MB / 456.7 MB, free: 21.21 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002186/0.3265, allocations: 38.59 kB / 456.7 MB, free: 21.2 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001655/0.3282, allocations: 0.5487 MB / 457.3 MB, free: 20.9 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.00719/0.3354, allocations: 2.105 MB / 459.4 MB, free: 19.51 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.011/0.3464, allocations: 3.128 MB / 462.5 MB, free: 17.61 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.006125/0.3526, allocations: 4.72 MB / 467.2 MB, free: 15.11 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006882/0.3595, allocations: 4.372 MB / 471.6 MB, free: 13.54 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008649/0.3681, allocations: 4.204 MB / 475.8 MB, free: 11.48 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009285/0.3774, allocations: 3.849 MB / 479.6 MB, free: 10.16 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.00275/0.3802, allocations: 397.8 kB / 480 MB, free: 10.16 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01412/0.3944, allocations: 3.388 MB / 483.4 MB, free: 9.586 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.004316/0.3987, allocations: 1.37 MB / 484.8 MB, free: 8.91 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.004115/0.4029, allocations: 0.9523 MB / 485.7 MB, free: 8.445 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01477/0.4177, allocations: 7.459 MB / 493.2 MB, free: 2.855 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.208e-06/0.4177, allocations: 4 kB / 493.2 MB, free: 2.852 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.685e-06/0.4177, allocations: 0 / 493.2 MB, free: 2.852 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 0.0002355/0.418, allocations: 0 / 493.2 MB, free: 2.852 MB / 350.1 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 0.01666/0.4346, allocations: 6.074 MB / 499.3 MB, free: 12.7 MB / 366.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.337e-05/0.4347, allocations: 12.03 kB / 499.3 MB, free: 12.69 MB / 366.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006821/0.4415, allocations: 1.211 MB / 0.4888 GB, free: 11.47 MB / 366.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.007625/0.4492, allocations: 2.868 MB / 0.4916 GB, free: 8.523 MB / 366.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0005754/0.4498, allocations: 0.6682 MB / 0.4922 GB, free: 7.785 MB / 366.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001686/0.4515, allocations: 0.4958 MB / 0.4927 GB, free: 7.289 MB / 366.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0205/0.472, allocations: 9.294 MB / 0.5018 GB, free: 13.88 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001887/0.4722, allocations: 3.938 kB / 0.5018 GB, free: 13.88 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001473/0.4737, allocations: 200 kB / 0.502 GB, free: 13.68 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001072/0.4738, allocations: 116 kB / 0.5021 GB, free: 13.57 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02447/0.4983, allocations: 12.56 MB / 0.5144 GB, free: 0.9844 MB / 382.1 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 0.0713/0.5697, allocations: 29.85 MB / 0.5435 GB, free: 2.426 MB / 414.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06274/0.6324, allocations: 41.24 MB / 0.5838 GB, free: 6.645 MB / 462.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.2393/0.8718, allocations: 20.68 MB / 0.604 GB, free: 132.3 MB / 462.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.616e-05/0.8718, allocations: 65.61 kB / 0.604 GB, free: 132.2 MB / 462.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003432/0.8753, allocations: 0.9535 MB / 0.605 GB, free: 132 MB / 462.1 MB
Notification: Performance of pre-optimization done (n=324): time 8.947e-06/0.8753, allocations: 0 / 0.605 GB, free: 132 MB / 462.1 MB
Notification: Performance of matching and sorting (n=376): time 0.09071/0.966, allocations: 24.44 MB / 0.6288 GB, free: 124.7 MB / 462.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.728e-05/0.9661, allocations: 89.42 kB / 0.6289 GB, free: 124.6 MB / 462.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004961/0.9711, allocations: 2.935 MB / 0.6318 GB, free: 123.2 MB / 462.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.001279/0.9724, allocations: 94.48 kB / 0.6319 GB, free: 123.1 MB / 462.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001602/0.974, allocations: 2.162 MB / 0.634 GB, free: 121.3 MB / 462.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001992/0.976, allocations: 1.297 MB / 0.6353 GB, free: 120.1 MB / 462.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0003269/0.9763, allocations: 94.44 kB / 0.6353 GB, free: 120.1 MB / 462.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002266/0.9766, allocations: 0.4984 MB / 0.6358 GB, free: 119.6 MB / 462.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.003938/0.9805, allocations: 2.936 MB / 0.6387 GB, free: 118.1 MB / 462.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004601/0.9851, allocations: 4.45 MB / 0.643 GB, free: 114.5 MB / 462.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.004778/0.9899, allocations: 3.567 MB / 0.6465 GB, free: 111.1 MB / 462.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.471e-05/0.99, allocations: 12 kB / 0.6465 GB, free: 111.1 MB / 462.1 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05399/1.044, allocations: 13.8 MB / 0.66 GB, free: 97.21 MB / 462.1 MB
Notification: Performance of prepare postOptimizeDAE: time 5.893e-05/1.044, allocations: 34.53 kB / 0.66 GB, free: 97.18 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.635e-05/1.044, allocations: 48 kB / 0.6601 GB, free: 97.13 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008274/1.052, allocations: 3.502 MB / 0.6635 GB, free: 93.65 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005593/1.058, allocations: 1.263 MB / 0.6647 GB, free: 92.39 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02882/1.087, allocations: 17.55 MB / 0.6819 GB, free: 74.45 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005979/1.093, allocations: 359.4 kB / 0.6822 GB, free: 74.09 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00111/1.094, allocations: 279.8 kB / 0.6825 GB, free: 73.82 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 (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 {(9,100.0%) 4,(1,100.0%) 3}
 * Non-linear torn systems: 1 {1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.003563/1.098, allocations: 1.445 MB / 0.6839 GB, free: 72.36 MB / 462.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009103/1.099, allocations: 347.6 kB / 0.6842 GB, free: 72.02 MB / 462.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03323/1.132, allocations: 9.678 MB / 0.6937 GB, free: 62.31 MB / 462.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.918e-05/1.132, allocations: 40 kB / 0.6937 GB, free: 62.27 MB / 462.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.079e-05/1.132, allocations: 4 kB / 0.6937 GB, free: 62.27 MB / 462.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001542/1.132, allocations: 23.92 kB / 0.6938 GB, free: 62.25 MB / 462.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04596/1.178, allocations: 15.4 MB / 0.7088 GB, free: 46.8 MB / 462.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.619e-05/1.178, allocations: 7.953 kB / 0.7088 GB, free: 46.8 MB / 462.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004674/1.183, allocations: 0.8466 MB / 0.7096 GB, free: 45.95 MB / 462.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005658/1.189, allocations: 2.135 MB / 0.7117 GB, free: 43.81 MB / 462.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0009878/1.19, allocations: 143.9 kB / 0.7119 GB, free: 43.67 MB / 462.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02044/1.21, allocations: 11.96 MB / 0.7235 GB, free: 31.32 MB / 462.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.132e-06/1.21, allocations: 11.92 kB / 0.7235 GB, free: 31.31 MB / 462.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0391/1.249, allocations: 13.24 MB / 0.7365 GB, free: 17.84 MB / 462.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.003561/1.253, allocations: 0.9257 MB / 0.7374 GB, free: 16.89 MB / 462.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001133/1.254, allocations: 91.97 kB / 0.7375 GB, free: 16.8 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.003196/1.257, allocations: 259.6 kB / 0.7377 GB, free: 16.55 MB / 462.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009161/1.258, allocations: 454.9 kB / 0.7381 GB, free: 16.1 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.000296/1.258, allocations: 147.9 kB / 0.7383 GB, free: 15.96 MB / 462.1 MB
Notification: Performance of sorting global known variables: time 0.002547/1.261, allocations: 1.969 MB / 0.7402 GB, free: 13.99 MB / 462.1 MB
Notification: Performance of sort global known variables: time 1.6e-07/1.261, allocations: 0 / 0.7402 GB, free: 13.99 MB / 462.1 MB
Notification: Performance of remove unused functions: time 0.00841/1.269, allocations: 2.026 MB / 0.7422 GB, free: 12.08 MB / 462.1 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 (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,(9,100.0%) 4}
 * Non-linear torn systems: 1 {1 3}
Notification: Performance of Backend phase and start with SimCode phase: time 0.003347/1.273, allocations: 1.25 MB / 0.7434 GB, free: 11.08 MB / 462.1 MB
Notification: Performance of simCode: created initialization part: time 0.01392/1.287, allocations: 7.376 MB / 0.7506 GB, free: 3.664 MB / 462.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.027e-05/1.287, allocations: 4.812 kB / 0.7506 GB, free: 3.66 MB / 462.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.008366/1.295, allocations: 4.075 MB / 0.7546 GB, free: 15.55 MB / 478.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003937/1.299, allocations: 0.6852 MB / 0.7553 GB, free: 14.86 MB / 478.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.2366/1.536, allocations: 12.57 MB / 0.7675 GB, free: 137.9 MB / 478.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002571/1.538, allocations: 3.398 MB / 0.7709 GB, free: 137.1 MB / 478.1 MB
Notification: Performance of simCode: alias equations: time 0.004832/1.543, allocations: 1.596 MB / 0.7724 GB, free: 137 MB / 478.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001283/1.544, allocations: 457.9 kB / 0.7728 GB, free: 137 MB / 478.1 MB
Notification: Performance of SimCode: time 1.433e-06/1.544, allocations: 0.9375 kB / 0.7728 GB, free: 137 MB / 478.1 MB
Notification: Performance of Templates: time 0.1201/1.665, allocations: 84.03 MB / 0.8549 GB, free: 79.88 MB / 478.1 MB
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile
Environment - environmentSimulation:
(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)
Environment - environmentSimulation: