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 0.0007915/0.0007916, allocations: 98.48 kB / 16.02 MB, free: 76 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0008714/0.0008715, allocations: 187.2 kB / 16.92 MB, free: 6.75 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.321/1.321, allocations: 223.3 MB / 241 MB, free: 5.34 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.1957/0.1957, allocations: 15.27 MB / 307.4 MB, free: 15.8 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.0003306/0.0003307, allocations: 8 kB / 372.7 MB, free: 3.617 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3018/0.3021, allocations: 54.63 MB / 427.4 MB, free: 40.09 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:3019:6-3019:65: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 1.4.1-master/package.mo:3019:6-3019:65: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 0.03102/0.3332, allocations: 29.46 MB / 456.8 MB, free: 29 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.02604/0.3592, allocations: 25.76 MB / 482.6 MB, free: 10.38 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002022/0.3613, allocations: 39.69 kB / 482.6 MB, free: 10.34 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001854/0.3632, allocations: 0.5321 MB / 483.2 MB, free: 9.941 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.00648/0.3697, allocations: 1.868 MB / 485 MB, free: 8.383 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.009087/0.3788, allocations: 3.067 MB / 488.1 MB, free: 5.852 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.006595/0.3854, allocations: 7.259 MB / 495.4 MB, free: 15.46 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.00657/0.392, allocations: 4.786 MB / 0.4884 GB, free: 11.6 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007862/0.3999, allocations: 4.546 MB / 0.4929 GB, free: 7.695 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008915/0.4088, allocations: 4.141 MB / 0.4969 GB, free: 4.422 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002647/0.4115, allocations: 396 kB / 0.4973 GB, free: 4.035 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01257/0.4241, allocations: 3.059 MB / 0.5003 GB, free: 1.02 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003292/0.4274, allocations: 1.413 MB / 0.5016 GB, free: 15.6 MB / 382.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.006186/0.4336, allocations: 2.965 MB / 0.5045 GB, free: 12.62 MB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01203/0.4457, allocations: 8.231 MB / 0.5126 GB, free: 4.359 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.069e-06/0.4457, allocations: 7.938 kB / 0.5126 GB, free: 4.352 MB / 382.1 MB
Notification: Performance of FrontEnd: time 1.623e-06/0.4458, allocations: 0 / 0.5126 GB, free: 4.352 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 0.0003016/0.4461, allocations: 0 / 0.5126 GB, free: 4.352 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 0.01673/0.4628, allocations: 6.043 MB / 0.5185 GB, free: 14.23 MB / 398.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.434e-05/0.4629, allocations: 12.02 kB / 0.5185 GB, free: 14.22 MB / 398.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006533/0.4694, allocations: 1.208 MB / 0.5197 GB, free: 13 MB / 398.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00659/0.476, allocations: 3.051 MB / 0.5227 GB, free: 9.875 MB / 398.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0007384/0.4768, allocations: 0.6766 MB / 0.5233 GB, free: 9.129 MB / 398.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002146/0.479, allocations: 0.4884 MB / 0.5238 GB, free: 8.641 MB / 398.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01979/0.4988, allocations: 9.368 MB / 0.5329 GB, free: 15.16 MB / 414.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001681/0.499, allocations: 3.938 kB / 0.533 GB, free: 15.16 MB / 414.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001438/0.5004, allocations: 200 kB / 0.5331 GB, free: 14.96 MB / 414.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.468e-05/0.5005, allocations: 116 kB / 0.5333 GB, free: 14.85 MB / 414.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02262/0.5232, allocations: 12.59 MB / 0.5456 GB, free: 2.238 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 0.06254/0.5857, allocations: 30.07 MB / 0.5749 GB, free: 3.457 MB / 446.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.2713/0.8571, allocations: 41.26 MB / 0.6152 GB, free: 93.71 MB / 446.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.008446/0.8656, allocations: 5.073 MB / 0.6202 GB, free: 91.82 MB / 446.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.03639/0.902, allocations: 20.76 MB / 0.6404 GB, free: 81.02 MB / 446.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.411e-05/0.9021, allocations: 63.77 kB / 0.6405 GB, free: 80.95 MB / 446.1 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003656/0.9057, allocations: 0.9637 MB / 0.6415 GB, free: 80.22 MB / 446.1 MB
Notification: Performance of pre-optimization done (n=324): time 1.314e-05/0.9058, allocations: 0 / 0.6415 GB, free: 80.22 MB / 446.1 MB
Notification: Performance of matching and sorting (n=376): time 0.09966/1.005, allocations: 24.48 MB / 0.6654 GB, free: 57.91 MB / 446.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.003e-05/1.006, allocations: 90.36 kB / 0.6654 GB, free: 57.81 MB / 446.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004008/1.01, allocations: 2.954 MB / 0.6683 GB, free: 54.84 MB / 446.1 MB
Notification: Performance of collectPreVariables (initialization): time 0.00103/1.011, allocations: 89.7 kB / 0.6684 GB, free: 54.75 MB / 446.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001168/1.012, allocations: 2.165 MB / 0.6705 GB, free: 52.57 MB / 446.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001626/1.013, allocations: 1.292 MB / 0.6718 GB, free: 51.29 MB / 446.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001181/1.015, allocations: 390.9 kB / 0.6722 GB, free: 50.91 MB / 446.1 MB
Notification: Performance of setup shared object (initialization): time 5.071e-05/1.015, allocations: 301.1 kB / 0.6724 GB, free: 50.61 MB / 446.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004704/1.019, allocations: 2.956 MB / 0.6753 GB, free: 47.64 MB / 446.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005176/1.025, allocations: 4.489 MB / 0.6797 GB, free: 42.51 MB / 446.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01011/1.035, allocations: 7.808 MB / 0.6873 GB, free: 34.11 MB / 446.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.512e-05/1.035, allocations: 12 kB / 0.6874 GB, free: 34.1 MB / 446.1 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.0587/1.093, allocations: 13.85 MB / 0.7009 GB, free: 20.39 MB / 446.1 MB
Notification: Performance of prepare postOptimizeDAE: time 7.8e-05/1.094, allocations: 24 kB / 0.7009 GB, free: 20.36 MB / 446.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.303e-05/1.094, allocations: 48 kB / 0.701 GB, free: 20.32 MB / 446.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.009118/1.103, allocations: 3.486 MB / 0.7044 GB, free: 16.97 MB / 446.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005681/1.109, allocations: 1.27 MB / 0.7056 GB, free: 15.7 MB / 446.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03074/1.139, allocations: 16.64 MB / 0.7218 GB, free: 14.71 MB / 462.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005505/1.145, allocations: 358 kB / 0.7222 GB, free: 14.38 MB / 462.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001311/1.146, allocations: 279.8 kB / 0.7225 GB, free: 14.1 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 0.004122/1.15, allocations: 1.45 MB / 0.7239 GB, free: 12.64 MB / 462.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001338/1.152, allocations: 343.6 kB / 0.7242 GB, free: 12.3 MB / 462.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.04241/1.194, allocations: 9.685 MB / 0.7337 GB, free: 2.699 MB / 462.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.236e-05/1.194, allocations: 39.98 kB / 0.7337 GB, free: 2.66 MB / 462.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.762e-05/1.194, allocations: 8 kB / 0.7337 GB, free: 2.652 MB / 462.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001553/1.194, allocations: 18.28 kB / 0.7337 GB, free: 2.637 MB / 462.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.05392/1.248, allocations: 15.46 MB / 0.7488 GB, free: 3.195 MB / 478.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.585e-05/1.249, allocations: 4 kB / 0.7488 GB, free: 3.191 MB / 478.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.005351/1.254, allocations: 0.8424 MB / 0.7496 GB, free: 2.352 MB / 478.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006915/1.261, allocations: 2.141 MB / 0.7517 GB, free: 236 kB / 478.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0009995/1.262, allocations: 135.9 kB / 0.7519 GB, free: 100 kB / 478.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.2479/1.51, allocations: 11.45 MB / 0.763 GB, free: 132.4 MB / 478.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.141e-06/1.51, allocations: 12.97 kB / 0.7631 GB, free: 132.4 MB / 478.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.04187/1.552, allocations: 12.98 MB / 0.7757 GB, free: 129.4 MB / 478.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.002975/1.555, allocations: 0.9384 MB / 0.7766 GB, free: 129.1 MB / 478.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0006918/1.555, allocations: 95.88 kB / 0.7767 GB, free: 129 MB / 478.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002879/1.558, allocations: 255 kB / 0.777 GB, free: 129 MB / 478.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001241/1.56, allocations: 450.9 kB / 0.7774 GB, free: 128.9 MB / 478.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0004132/1.56, allocations: 146.3 kB / 0.7776 GB, free: 128.9 MB / 478.1 MB
Notification: Performance of sorting global known variables: time 0.003271/1.563, allocations: 1.993 MB / 0.7795 GB, free: 128.2 MB / 478.1 MB
Notification: Performance of sort global known variables: time 3.21e-07/1.563, allocations: 0 / 0.7795 GB, free: 128.2 MB / 478.1 MB
Notification: Performance of remove unused functions: time 0.007976/1.571, allocations: 2.042 MB / 0.7815 GB, free: 128.1 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 0.002723/1.574, allocations: 1.292 MB / 0.7828 GB, free: 127.9 MB / 478.1 MB
Notification: Performance of simCode: created initialization part: time 0.01562/1.59, allocations: 7.407 MB / 0.79 GB, free: 125.3 MB / 478.1 MB
Notification: Performance of simCode: created event and clocks part: time 9.959e-06/1.59, allocations: 1.094 kB / 0.79 GB, free: 125.3 MB / 478.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.008379/1.598, allocations: 4.087 MB / 0.794 GB, free: 123.7 MB / 478.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.005761/1.604, allocations: 0.7291 MB / 0.7947 GB, free: 123.4 MB / 478.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01858/1.622, allocations: 13 MB / 0.8074 GB, free: 117.2 MB / 478.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002236/1.625, allocations: 3.21 MB / 0.8105 GB, free: 116.2 MB / 478.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002048/1.627, allocations: 0.4891 MB / 0.811 GB, free: 116.2 MB / 478.1 MB
Notification: Performance of SimCode: time 7.11e-07/1.627, allocations: 6.625 kB / 0.811 GB, free: 116.2 MB / 478.1 MB
Notification: Performance of Templates: time 0.3922/2.019, allocations: 145.5 MB / 0.9531 GB, free: 129.5 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)