Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.conf.json
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/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/package.mo", uses=false)
Using package Physiolibrary with version 3.0.0-beta1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/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)
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)
Running command: translateModel(Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
translateModel(Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001168/0.001168, allocations: 183.2 kB / 15.98 MB, free: 5.77 MB / 13.93 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.346/1.346, allocations: 222.9 MB / 239.7 MB, free: 10.98 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001041/0.00104, allocations: 117.7 kB / 289.9 MB, free: 10.92 MB / 234.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/package.mo): time 0.4502/0.4502, allocations: 36.67 MB / 376.7 MB, free: 41.42 MB / 298.7 MB
Notification: Performance of FrontEnd - loaded program: time 0.001209/0.00121, allocations: 63.91 kB / 446.4 MB, free: 11.81 MB / 330.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1209/0.1222, allocations: 58.91 MB / 0.4935 GB, free: 0.8398 MB / 378.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/Chemical.mo:4671:7-4671:66:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Physiolibrary 3.0.0-master/Chemical.mo:4671:7-4671:66: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(Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC): time 0.2694/0.3917, allocations: 27.5 MB / 0.5203 GB, free: 31.08 MB / 378.7 MB
Notification: Performance of NFInst.instExpressions: time 0.02539/0.4171, allocations: 25.83 MB / 0.5456 GB, free: 12.5 MB / 378.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.003/0.4201, allocations: 42.53 kB / 0.5456 GB, free: 12.48 MB / 378.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.002158/0.4223, allocations: 0.5336 MB / 0.5461 GB, free: 12.2 MB / 378.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.008951/0.4313, allocations: 1.811 MB / 0.5479 GB, free: 11.1 MB / 378.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01198/0.4433, allocations: 3.083 MB / 0.5509 GB, free: 9.285 MB / 378.7 MB
Notification: Performance of NFFlatten.flatten: time 0.008681/0.452, allocations: 7.339 MB / 0.5581 GB, free: 5.969 MB / 378.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.00635/0.4584, allocations: 4.999 MB / 0.5629 GB, free: 1.984 MB / 378.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008972/0.4674, allocations: 4.765 MB / 0.5676 GB, free: 13.91 MB / 394.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.01017/0.4777, allocations: 4.384 MB / 0.5719 GB, free: 10.38 MB / 394.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.003679/0.4814, allocations: 480 kB / 0.5723 GB, free: 9.914 MB / 394.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01593/0.4973, allocations: 3.054 MB / 0.5753 GB, free: 6.855 MB / 394.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.004181/0.5016, allocations: 1.538 MB / 0.5768 GB, free: 5.312 MB / 394.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.00786/0.5095, allocations: 3.084 MB / 0.5798 GB, free: 2.215 MB / 394.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.02197/0.5315, allocations: 10.83 MB / 0.5904 GB, free: 7.352 MB / 410.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.575e-06/0.5315, allocations: 4 kB / 0.5904 GB, free: 7.348 MB / 410.7 MB
Notification: Performance of FrontEnd: time 3.657e-06/0.5315, allocations: 0 / 0.5904 GB, free: 7.348 MB / 410.7 MB
Notification: Performance of Transformations before backend: time 0.0003847/0.5319, allocations: 7.938 kB / 0.5904 GB, free: 7.34 MB / 410.7 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 0.02369/0.5556, allocations: 7.455 MB / 0.5977 GB, free: 15.8 MB / 426.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.423e-05/0.5557, allocations: 8.031 kB / 0.5977 GB, free: 15.8 MB / 426.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006762/0.5625, allocations: 1.206 MB / 0.5989 GB, free: 14.59 MB / 426.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.008703/0.5712, allocations: 3.161 MB / 0.602 GB, free: 11.35 MB / 426.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.000885/0.5721, allocations: 0.6922 MB / 0.6027 GB, free: 10.59 MB / 426.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002608/0.5747, allocations: 496.1 kB / 0.6031 GB, free: 10.1 MB / 426.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0239/0.5987, allocations: 9.403 MB / 0.6123 GB, free: 0.5898 MB / 426.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002482/0.599, allocations: 3.938 kB / 0.6123 GB, free: 0.5859 MB / 426.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.002451/0.6014, allocations: 196 kB / 0.6125 GB, free: 404 kB / 426.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.699e-05/0.6015, allocations: 116 kB / 0.6126 GB, free: 288 kB / 426.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02723/0.6288, allocations: 12.61 MB / 0.6249 GB, free: 3.648 MB / 442.7 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 0.0732/0.702, allocations: 30.36 MB / 0.6546 GB, free: 4.57 MB / 474.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.3267/1.029, allocations: 41.28 MB / 0.6949 GB, free: 110.1 MB / 490.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.009464/1.038, allocations: 5.101 MB / 0.6999 GB, free: 110 MB / 490.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04333/1.082, allocations: 20.98 MB / 0.7204 GB, free: 99.56 MB / 490.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.685e-05/1.082, allocations: 67.77 kB / 0.7204 GB, free: 99.5 MB / 490.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.005543/1.087, allocations: 0.9764 MB / 0.7214 GB, free: 99.21 MB / 490.7 MB
Notification: Performance of pre-optimization done (n=324): time 3.419e-05/1.087, allocations: 0 / 0.7214 GB, free: 99.21 MB / 490.7 MB
Notification: Performance of matching and sorting (n=376): time 0.1162/1.204, allocations: 25.31 MB / 0.7461 GB, free: 90.26 MB / 490.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.459e-05/1.204, allocations: 90.33 kB / 0.7462 GB, free: 90.19 MB / 490.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003452/1.207, allocations: 2.951 MB / 0.7491 GB, free: 88.66 MB / 490.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.001144/1.208, allocations: 91.08 kB / 0.7492 GB, free: 88.58 MB / 490.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.00125/1.21, allocations: 2.164 MB / 0.7513 GB, free: 86.68 MB / 490.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001927/1.212, allocations: 1.295 MB / 0.7525 GB, free: 85.57 MB / 490.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001991/1.214, allocations: 0.9823 MB / 0.7535 GB, free: 85.03 MB / 490.7 MB
Notification: Performance of setup shared object (initialization): time 6.281e-05/1.214, allocations: 301.1 kB / 0.7538 GB, free: 84.73 MB / 490.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004889/1.219, allocations: 2.984 MB / 0.7567 GB, free: 83.04 MB / 490.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005678/1.224, allocations: 4.508 MB / 0.7611 GB, free: 77.91 MB / 490.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01135/1.236, allocations: 7.859 MB / 0.7688 GB, free: 69.62 MB / 490.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.989e-05/1.236, allocations: 16 kB / 0.7688 GB, free: 69.6 MB / 490.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.06061/1.296, allocations: 14.49 MB / 0.7829 GB, free: 55.29 MB / 490.7 MB
Notification: Performance of prepare postOptimizeDAE: time 5.732e-05/1.297, allocations: 24 kB / 0.783 GB, free: 55.27 MB / 490.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.427e-05/1.297, allocations: 48.52 kB / 0.783 GB, free: 55.22 MB / 490.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.009248/1.306, allocations: 3.627 MB / 0.7865 GB, free: 51.75 MB / 490.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005618/1.312, allocations: 1.263 MB / 0.7878 GB, free: 50.49 MB / 490.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03012/1.342, allocations: 17 MB / 0.8044 GB, free: 33.16 MB / 490.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00501/1.347, allocations: 381.4 kB / 0.8047 GB, free: 32.8 MB / 490.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001149/1.348, allocations: 275.8 kB / 0.805 GB, free: 32.54 MB / 490.7 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 0.003237/1.351, allocations: 1.457 MB / 0.8064 GB, free: 31.07 MB / 490.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00115/1.352, allocations: 351.4 kB / 0.8068 GB, free: 30.72 MB / 490.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03911/1.392, allocations: 10.32 MB / 0.8168 GB, free: 20.44 MB / 490.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.639e-05/1.392, allocations: 40 kB / 0.8169 GB, free: 20.4 MB / 490.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.27e-05/1.392, allocations: 4 kB / 0.8169 GB, free: 20.39 MB / 490.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001297/1.392, allocations: 26.17 kB / 0.8169 GB, free: 20.37 MB / 490.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04855/1.44, allocations: 16.1 MB / 0.8326 GB, free: 4.223 MB / 490.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.027e-05/1.44, allocations: 4 kB / 0.8326 GB, free: 4.219 MB / 490.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004598/1.445, allocations: 0.8507 MB / 0.8335 GB, free: 3.367 MB / 490.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006723/1.452, allocations: 2.279 MB / 0.8357 GB, free: 1.086 MB / 490.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.00109/1.453, allocations: 131.9 kB / 0.8358 GB, free: 0.957 MB / 490.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02564/1.479, allocations: 11.82 MB / 0.8474 GB, free: 4.742 MB / 0.4948 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.482e-06/1.479, allocations: 4 kB / 0.8474 GB, free: 4.738 MB / 0.4948 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.336/1.815, allocations: 39.65 MB / 0.8861 GB, free: 143.5 MB / 0.5105 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003304/1.818, allocations: 0.9384 MB / 0.887 GB, free: 143.2 MB / 0.5105 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001417/1.819, allocations: 92.59 kB / 0.8871 GB, free: 143.1 MB / 0.5105 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.004005/1.823, allocations: 272.9 kB / 0.8874 GB, free: 143.1 MB / 0.5105 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001417/1.825, allocations: 454.2 kB / 0.8878 GB, free: 143 MB / 0.5105 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003777/1.825, allocations: 145.1 kB / 0.8879 GB, free: 143 MB / 0.5105 GB
Notification: Performance of sorting global known variables: time 0.002625/1.828, allocations: 1.992 MB / 0.8899 GB, free: 142.3 MB / 0.5105 GB
Notification: Performance of sort global known variables: time 2.2e-07/1.828, allocations: 0.6875 kB / 0.8899 GB, free: 142.3 MB / 0.5105 GB
Notification: Performance of remove unused functions: time 0.0109/1.839, allocations: 2.505 MB / 0.8923 GB, free: 142.1 MB / 0.5105 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 0.00352/1.842, allocations: 1.281 MB / 0.8936 GB, free: 141.9 MB / 0.5105 GB
Notification: Performance of simCode: created initialization part: time 0.01775/1.86, allocations: 7.526 MB / 0.9009 GB, free: 139.5 MB / 0.5105 GB
Notification: Performance of simCode: created event and clocks part: time 1.041e-05/1.86, allocations: 0 / 0.9009 GB, free: 139.5 MB / 0.5105 GB
Notification: Performance of simCode: created simulation system equations: time 0.0115/1.872, allocations: 4.18 MB / 0.905 GB, free: 138 MB / 0.5105 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.005168/1.877, allocations: 0.7269 MB / 0.9057 GB, free: 137.7 MB / 0.5105 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.02693/1.904, allocations: 15.54 MB / 0.9209 GB, free: 130 MB / 0.5105 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.005025/1.909, allocations: 3.406 MB / 0.9242 GB, free: 128.9 MB / 0.5105 GB
Notification: Performance of simCode: alias equations: time 0.006206/1.915, allocations: 1.672 MB / 0.9258 GB, free: 128.9 MB / 0.5105 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002136/1.917, allocations: 489 kB / 0.9263 GB, free: 128.8 MB / 0.5105 GB
Notification: Performance of SimCode: time 8.51e-07/1.917, allocations: 0 / 0.9263 GB, free: 128.8 MB / 0.5105 GB
Notification: Performance of Templates: time 0.1365/2.054, allocations: 101.1 MB / 1.025 GB, free: 36.84 MB / 0.5105 GB
make -j1 -f Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile
(rm -f Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Physiolibrary_Physiolibrary.Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1)