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 0.001263/0.001264, allocations: 105.2 kB / 16.36 MB, free: 6.285 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001333/0.001333, allocations: 192 kB / 17.29 MB, free: 5.863 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.308/1.308, allocations: 222.9 MB / 241 MB, free: 15.16 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.07828/0.07828, allocations: 15.31 MB / 306.5 MB, free: 15.41 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001174/0.001175, allocations: 60.23 kB / 371.7 MB, free: 50.74 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09594/0.09713, allocations: 53.62 MB / 425.4 MB, free: 13.29 MB / 302.1 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 0.03529/0.1325, allocations: 28.98 MB / 454.3 MB, free: 428 kB / 318.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02748/0.16, allocations: 26.08 MB / 480.4 MB, free: 6.234 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001569/0.1616, allocations: 23.88 kB / 480.4 MB, free: 6.211 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001513/0.1631, allocations: 0.6048 MB / 481 MB, free: 5.602 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.006036/0.1691, allocations: 2.133 MB / 483.2 MB, free: 3.453 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.008268/0.1774, allocations: 3.526 MB / 486.7 MB, free: 15.91 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.006978/0.1844, allocations: 7.39 MB / 494.1 MB, free: 8.484 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.007003/0.1914, allocations: 5.92 MB / 0.4883 GB, free: 2.496 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008691/0.2002, allocations: 4.869 MB / 0.493 GB, free: 13.62 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009077/0.2093, allocations: 4.627 MB / 0.4976 GB, free: 8.977 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.00237/0.2117, allocations: 0.668 MB / 0.4982 GB, free: 8.309 MB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01145/0.2232, allocations: 3.324 MB / 0.5015 GB, free: 4.98 MB / 382.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003577/0.2268, allocations: 1.788 MB / 0.5032 GB, free: 3.188 MB / 382.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.2305/0.4573, allocations: 3.332 MB / 0.5065 GB, free: 31.32 MB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0194/0.4768, allocations: 11.06 MB / 0.5173 GB, free: 30.92 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.594e-06/0.4768, allocations: 3 kB / 0.5173 GB, free: 30.92 MB / 382.1 MB
Notification: Performance of FrontEnd: time 2.033e-06/0.4768, allocations: 0 / 0.5173 GB, free: 30.92 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 0.000344/0.4772, allocations: 1 kB / 0.5173 GB, free: 30.92 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 0.02909/0.5063, allocations: 7.425 MB / 0.5245 GB, free: 28.59 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.701e-05/0.5064, allocations: 9.625 kB / 0.5245 GB, free: 28.59 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.009477/0.5158, allocations: 1.214 MB / 0.5257 GB, free: 28.3 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0122/0.5281, allocations: 3.216 MB / 0.5289 GB, free: 27.64 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0008969/0.529, allocations: 0.6799 MB / 0.5295 GB, free: 27.29 MB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.005024/0.5341, allocations: 0.4946 MB / 0.53 GB, free: 27.27 MB / 382.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02736/0.5615, allocations: 9.367 MB / 0.5391 GB, free: 26 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0002164/0.5617, allocations: 0 / 0.5391 GB, free: 26 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.002973/0.5647, allocations: 193.2 kB / 0.5393 GB, free: 25.85 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.106e-05/0.5648, allocations: 117.4 kB / 0.5394 GB, free: 25.85 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0275/0.5923, allocations: 12.6 MB / 0.5517 GB, free: 17.07 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 0.07206/0.6644, allocations: 30.18 MB / 0.5812 GB, free: 2.762 MB / 398.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06432/0.7288, allocations: 41.26 MB / 0.6215 GB, free: 7.004 MB / 446.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0102/0.739, allocations: 5.068 MB / 0.6265 GB, free: 1.91 MB / 446.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04391/0.783, allocations: 20.9 MB / 0.6469 GB, free: 12.32 MB / 478.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.144e-05/0.7831, allocations: 69.14 kB / 0.6469 GB, free: 12.24 MB / 478.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003787/0.7869, allocations: 0.9594 MB / 0.6479 GB, free: 11.3 MB / 478.1 MB
Notification: Performance of pre-optimization done (n=324): time 1.268e-05/0.7869, allocations: 2.656 kB / 0.6479 GB, free: 11.3 MB / 478.1 MB
Notification: Performance of matching and sorting (n=376): time 0.09151/0.8784, allocations: 24.39 MB / 0.6717 GB, free: 3.004 MB / 494.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.793e-05/0.8785, allocations: 94.34 kB / 0.6718 GB, free: 2.898 MB / 494.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003839/0.8824, allocations: 2.958 MB / 0.6747 GB, free: 15.93 MB / 0.4981 GB
Notification: Performance of collectPreVariables (initialization): time 0.001554/0.8839, allocations: 89.7 kB / 0.6748 GB, free: 15.83 MB / 0.4981 GB
Notification: Performance of collectInitialEqns (initialization): time 0.00156/0.8855, allocations: 2.156 MB / 0.6769 GB, free: 13.66 MB / 0.4981 GB
Notification: Performance of collectInitialBindings (initialization): time 0.002136/0.8877, allocations: 1.296 MB / 0.6781 GB, free: 12.38 MB / 0.4981 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001774/0.8894, allocations: 0.9725 MB / 0.6791 GB, free: 11.39 MB / 0.4981 GB
Notification: Performance of setup shared object (initialization): time 0.0001106/0.8896, allocations: 312.6 kB / 0.6794 GB, free: 11.09 MB / 0.4981 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.00504/0.8946, allocations: 2.959 MB / 0.6823 GB, free: 8.125 MB / 0.4981 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.006591/0.9012, allocations: 4.475 MB / 0.6866 GB, free: 3.027 MB / 0.4981 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.2534/1.155, allocations: 7.807 MB / 0.6943 GB, free: 189.7 MB / 0.4981 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.6e-05/1.155, allocations: 14.25 kB / 0.6943 GB, free: 189.7 MB / 0.4981 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05404/1.209, allocations: 13.82 MB / 0.7078 GB, free: 186.4 MB / 0.4981 GB
Notification: Performance of prepare postOptimizeDAE: time 7.616e-05/1.209, allocations: 27.78 kB / 0.7078 GB, free: 186.4 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001097/1.209, allocations: 50.44 kB / 0.7078 GB, free: 186.4 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008269/1.217, allocations: 3.475 MB / 0.7112 GB, free: 185.2 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00565/1.223, allocations: 1.273 MB / 0.7125 GB, free: 184.9 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02877/1.252, allocations: 18.47 MB / 0.7305 GB, free: 167.8 MB / 0.4981 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005363/1.257, allocations: 251.8 kB / 0.7308 GB, free: 167.5 MB / 0.4981 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00152/1.259, allocations: 283.8 kB / 0.731 GB, free: 167.3 MB / 0.4981 GB
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 0.003917/1.263, allocations: 1.449 MB / 0.7325 GB, free: 165.8 MB / 0.4981 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001221/1.264, allocations: 354.3 kB / 0.7328 GB, free: 165.7 MB / 0.4981 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.033/1.297, allocations: 9.658 MB / 0.7422 GB, free: 156.1 MB / 0.4981 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.112e-05/1.297, allocations: 42.66 kB / 0.7423 GB, free: 156.1 MB / 0.4981 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.847e-05/1.297, allocations: 4 kB / 0.7423 GB, free: 156.1 MB / 0.4981 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001336/1.297, allocations: 19.92 kB / 0.7423 GB, free: 156 MB / 0.4981 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04333/1.341, allocations: 15.44 MB / 0.7574 GB, free: 140.7 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.061e-05/1.341, allocations: 7.938 kB / 0.7574 GB, free: 140.7 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004612/1.345, allocations: 0.8529 MB / 0.7582 GB, free: 139.8 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005552/1.351, allocations: 2.124 MB / 0.7603 GB, free: 137.8 MB / 0.4981 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001074/1.352, allocations: 142.6 kB / 0.7604 GB, free: 137.6 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02012/1.372, allocations: 12.67 MB / 0.7728 GB, free: 124.6 MB / 0.4981 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.048e-06/1.372, allocations: 4.938 kB / 0.7728 GB, free: 124.6 MB / 0.4981 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03698/1.409, allocations: 12.96 MB / 0.7854 GB, free: 111.7 MB / 0.4981 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003205/1.412, allocations: 0.9321 MB / 0.7864 GB, free: 110.8 MB / 0.4981 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0007139/1.413, allocations: 91.97 kB / 0.7864 GB, free: 110.7 MB / 0.4981 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002264/1.415, allocations: 174.5 kB / 0.7866 GB, free: 110.5 MB / 0.4981 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009747/1.416, allocations: 452.9 kB / 0.787 GB, free: 110.1 MB / 0.4981 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003122/1.417, allocations: 147.9 kB / 0.7872 GB, free: 109.9 MB / 0.4981 GB
Notification: Performance of sorting global known variables: time 0.002287/1.419, allocations: 1.991 MB / 0.7891 GB, free: 107.9 MB / 0.4981 GB
Notification: Performance of sort global known variables: time 3.2e-07/1.419, allocations: 0 / 0.7891 GB, free: 107.9 MB / 0.4981 GB
Notification: Performance of remove unused functions: time 0.007795/1.427, allocations: 2.054 MB / 0.7911 GB, free: 106 MB / 0.4981 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 0.003224/1.43, allocations: 1.304 MB / 0.7924 GB, free: 105 MB / 0.4981 GB
Notification: Performance of simCode: created initialization part: time 0.01292/1.443, allocations: 7.423 MB / 0.7997 GB, free: 97.55 MB / 0.4981 GB
Notification: Performance of simCode: created event and clocks part: time 7.083e-06/1.443, allocations: 0 / 0.7997 GB, free: 97.55 MB / 0.4981 GB
Notification: Performance of simCode: created simulation system equations: time 0.007401/1.45, allocations: 4.1 MB / 0.8037 GB, free: 93.42 MB / 0.4981 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004047/1.455, allocations: 0.7767 MB / 0.8044 GB, free: 92.72 MB / 0.4981 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01696/1.471, allocations: 10.81 MB / 0.815 GB, free: 81.91 MB / 0.4981 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00212/1.474, allocations: 3.303 MB / 0.8182 GB, free: 78.62 MB / 0.4981 GB
Notification: Performance of simCode: alias equations: time 0.003843/1.478, allocations: 1.592 MB / 0.8197 GB, free: 77.17 MB / 0.4981 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001223/1.479, allocations: 457.1 kB / 0.8202 GB, free: 76.72 MB / 0.4981 GB
Notification: Performance of SimCode: time 1.493e-06/1.479, allocations: 0 / 0.8202 GB, free: 76.72 MB / 0.4981 GB
Notification: Performance of Templates: time 0.3691/1.848, allocations: 89.82 MB / 0.9079 GB, free: 171.7 MB / 0.4981 GB
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 -s cvode -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1)