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 0.001193/0.001193, allocations: 108.7 kB / 16.37 MB, free: 6.48 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001286/0.001286, allocations: 195.8 kB / 17.31 MB, free: 5.82 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.322/1.322, allocations: 222.9 MB / 241 MB, free: 15.18 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08308/0.08308, allocations: 15.31 MB / 306.5 MB, free: 15.44 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001273/0.001273, allocations: 67 kB / 371.7 MB, free: 50.8 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08877/0.09007, allocations: 53.62 MB / 425.4 MB, free: 13.32 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 0.03338/0.1235, allocations: 28.98 MB / 454.3 MB, free: 464 kB / 318.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0273/0.1508, allocations: 26.07 MB / 480.4 MB, free: 6.27 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001364/0.1522, allocations: 23.88 kB / 480.4 MB, free: 6.246 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001375/0.1536, allocations: 0.5931 MB / 481 MB, free: 5.648 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005517/0.1591, allocations: 2.141 MB / 483.2 MB, free: 3.492 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.008601/0.1677, allocations: 3.515 MB / 486.7 MB, free: 15.96 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.008434/0.1762, allocations: 7.398 MB / 494.1 MB, free: 8.527 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006755/0.183, allocations: 5.92 MB / 0.4883 GB, free: 2.539 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.006642/0.1897, allocations: 4.869 MB / 0.493 GB, free: 13.66 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007523/0.1972, allocations: 4.627 MB / 0.4976 GB, free: 9.02 MB / 382.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002378/0.1996, allocations: 0.668 MB / 0.4982 GB, free: 8.352 MB / 382.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01159/0.2112, allocations: 3.324 MB / 0.5015 GB, free: 5.023 MB / 382.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.00317/0.2144, allocations: 1.784 MB / 0.5032 GB, free: 3.234 MB / 382.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.2022/0.4167, allocations: 3.341 MB / 0.5065 GB, free: 31.43 MB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02086/0.4376, allocations: 11.05 MB / 0.5173 GB, free: 31.03 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.765e-06/0.4376, allocations: 1.125 kB / 0.5173 GB, free: 31.03 MB / 382.1 MB
Notification: Performance of FrontEnd: time 2.244e-06/0.4377, allocations: 0 / 0.5173 GB, free: 31.03 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 0.0003401/0.438, allocations: 0.8438 kB / 0.5173 GB, free: 31.03 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 0.02691/0.4649, allocations: 7.431 MB / 0.5245 GB, free: 28.71 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.225e-05/0.465, allocations: 11.19 kB / 0.5245 GB, free: 28.71 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.007917/0.4729, allocations: 1.212 MB / 0.5257 GB, free: 28.41 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.01037/0.4833, allocations: 3.219 MB / 0.5289 GB, free: 27.75 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0005853/0.4839, allocations: 0.6764 MB / 0.5295 GB, free: 27.4 MB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.003071/0.487, allocations: 0.492 MB / 0.53 GB, free: 27.39 MB / 382.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02116/0.5082, allocations: 9.367 MB / 0.5391 GB, free: 26.09 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001748/0.5084, allocations: 3.531 kB / 0.5391 GB, free: 26.09 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.002021/0.5104, allocations: 195.4 kB / 0.5393 GB, free: 25.93 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.354e-05/0.5105, allocations: 117.4 kB / 0.5394 GB, free: 25.93 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0253/0.5358, allocations: 12.59 MB / 0.5517 GB, free: 17.2 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 0.07086/0.6067, allocations: 30.19 MB / 0.5812 GB, free: 2.891 MB / 398.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0668/0.6736, allocations: 41.26 MB / 0.6215 GB, free: 7.141 MB / 446.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01111/0.6847, allocations: 5.071 MB / 0.6265 GB, free: 2.047 MB / 446.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04675/0.7315, allocations: 20.89 MB / 0.6469 GB, free: 12.46 MB / 478.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.344e-05/0.7316, allocations: 69.09 kB / 0.6469 GB, free: 12.38 MB / 478.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004201/0.7358, allocations: 0.9643 MB / 0.6479 GB, free: 11.44 MB / 478.1 MB
Notification: Performance of pre-optimization done (n=324): time 1.561e-05/0.7358, allocations: 4 kB / 0.6479 GB, free: 11.43 MB / 478.1 MB
Notification: Performance of matching and sorting (n=376): time 0.1025/0.8384, allocations: 24.38 MB / 0.6717 GB, free: 3.141 MB / 494.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.73e-05/0.8385, allocations: 90.36 kB / 0.6718 GB, free: 3.039 MB / 494.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004433/0.8429, allocations: 2.958 MB / 0.6747 GB, free: 68 kB / 494.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.001577/0.8445, allocations: 94.08 kB / 0.6748 GB, free: 15.98 MB / 0.4981 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001697/0.8462, allocations: 2.162 MB / 0.6769 GB, free: 13.81 MB / 0.4981 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001904/0.8481, allocations: 1.296 MB / 0.6781 GB, free: 12.53 MB / 0.4981 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001574/0.8497, allocations: 0.9804 MB / 0.6791 GB, free: 11.54 MB / 0.4981 GB
Notification: Performance of setup shared object (initialization): time 9.924e-05/0.8498, allocations: 305.1 kB / 0.6794 GB, free: 11.23 MB / 0.4981 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004795/0.8546, allocations: 2.956 MB / 0.6823 GB, free: 8.273 MB / 0.4981 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.00606/0.8607, allocations: 4.479 MB / 0.6866 GB, free: 3.172 MB / 0.4981 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.2154/1.076, allocations: 7.806 MB / 0.6943 GB, free: 189.8 MB / 0.4981 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.426e-05/1.076, allocations: 15.53 kB / 0.6943 GB, free: 189.8 MB / 0.4981 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.056/1.132, allocations: 13.82 MB / 0.7078 GB, free: 186.6 MB / 0.4981 GB
Notification: Performance of prepare postOptimizeDAE: time 4.998e-05/1.132, allocations: 27.78 kB / 0.7078 GB, free: 186.6 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.991e-05/1.132, allocations: 47.62 kB / 0.7079 GB, free: 186.6 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008446/1.141, allocations: 3.479 MB / 0.7112 GB, free: 185.4 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005672/1.147, allocations: 1.272 MB / 0.7125 GB, free: 185.1 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02968/1.176, allocations: 18.48 MB / 0.7305 GB, free: 168 MB / 0.4981 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.006214/1.183, allocations: 255.8 kB / 0.7308 GB, free: 167.7 MB / 0.4981 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.002295/1.185, allocations: 279.8 kB / 0.731 GB, free: 167.4 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 0.005325/1.19, allocations: 1.446 MB / 0.7325 GB, free: 166 MB / 0.4981 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001401/1.192, allocations: 351.4 kB / 0.7328 GB, free: 165.8 MB / 0.4981 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03328/1.225, allocations: 9.656 MB / 0.7422 GB, free: 156.3 MB / 0.4981 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.76e-05/1.225, allocations: 40 kB / 0.7423 GB, free: 156.2 MB / 0.4981 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.983e-05/1.225, allocations: 4 kB / 0.7423 GB, free: 156.2 MB / 0.4981 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001375/1.225, allocations: 21.33 kB / 0.7423 GB, free: 156.2 MB / 0.4981 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04343/1.269, allocations: 15.45 MB / 0.7574 GB, free: 140.9 MB / 0.4981 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.285e-05/1.269, allocations: 7.938 kB / 0.7574 GB, free: 140.9 MB / 0.4981 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00459/1.273, allocations: 0.8477 MB / 0.7582 GB, free: 140 MB / 0.4981 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005708/1.279, allocations: 2.127 MB / 0.7603 GB, free: 138 MB / 0.4981 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001139/1.28, allocations: 135.9 kB / 0.7604 GB, free: 137.8 MB / 0.4981 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02036/1.301, allocations: 12.68 MB / 0.7728 GB, free: 124.8 MB / 0.4981 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 7.424e-06/1.301, allocations: 4 kB / 0.7728 GB, free: 124.8 MB / 0.4981 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.04167/1.342, allocations: 12.96 MB / 0.7855 GB, free: 111.9 MB / 0.4981 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.00344/1.346, allocations: 0.9347 MB / 0.7864 GB, free: 110.9 MB / 0.4981 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001135/1.347, allocations: 95.97 kB / 0.7865 GB, free: 110.8 MB / 0.4981 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002994/1.35, allocations: 159.8 kB / 0.7866 GB, free: 110.7 MB / 0.4981 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001058/1.351, allocations: 462.4 kB / 0.7871 GB, free: 110.2 MB / 0.4981 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003382/1.351, allocations: 143.9 kB / 0.7872 GB, free: 110.1 MB / 0.4981 GB
Notification: Performance of sorting global known variables: time 0.00242/1.354, allocations: 1.992 MB / 0.7891 GB, free: 108.1 MB / 0.4981 GB
Notification: Performance of sort global known variables: time 3.2e-07/1.354, allocations: 0 / 0.7891 GB, free: 108.1 MB / 0.4981 GB
Notification: Performance of remove unused functions: time 0.008175/1.362, allocations: 2.048 MB / 0.7911 GB, free: 106.2 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 0.003323/1.365, allocations: 1.297 MB / 0.7924 GB, free: 105.2 MB / 0.4981 GB
Notification: Performance of simCode: created initialization part: time 0.0143/1.38, allocations: 7.433 MB / 0.7997 GB, free: 97.72 MB / 0.4981 GB
Notification: Performance of simCode: created event and clocks part: time 8.686e-06/1.38, allocations: 2.656 kB / 0.7997 GB, free: 97.72 MB / 0.4981 GB
Notification: Performance of simCode: created simulation system equations: time 0.008388/1.388, allocations: 4.095 MB / 0.8037 GB, free: 93.6 MB / 0.4981 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.005027/1.393, allocations: 0.7702 MB / 0.8044 GB, free: 92.91 MB / 0.4981 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01862/1.412, allocations: 10.81 MB / 0.815 GB, free: 82.09 MB / 0.4981 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002402/1.414, allocations: 3.301 MB / 0.8182 GB, free: 78.8 MB / 0.4981 GB
Notification: Performance of simCode: alias equations: time 0.004367/1.419, allocations: 1.593 MB / 0.8198 GB, free: 77.35 MB / 0.4981 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00137/1.42, allocations: 463.2 kB / 0.8202 GB, free: 76.89 MB / 0.4981 GB
Notification: Performance of SimCode: time 1.353e-06/1.42, allocations: 0 / 0.8202 GB, free: 76.89 MB / 0.4981 GB
Notification: Performance of Templates: time 0.3251/1.745, allocations: 89.82 MB / 0.9079 GB, free: 171.9 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 gbode -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1)