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 0.00549/0.00549, allocations: 100.3 kB / 15.73 MB, free: 6.059 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001153/0.001153, allocations: 192 kB / 16.67 MB, free: 5.969 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.406/1.406, allocations: 222.9 MB / 240.4 MB, free: 15.14 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08259/0.08259, allocations: 15.3 MB / 305.8 MB, free: 15.4 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.001163/0.001163, allocations: 67.84 kB / 425.2 MB, free: 11.42 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1041/0.1053, allocations: 53.61 MB / 478.8 MB, free: 5.762 MB / 350.1 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 0.04/0.1453, allocations: 29.3 MB / 0.4962 GB, free: 8.531 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.2853/0.4306, allocations: 26.06 MB / 0.5217 GB, free: 15 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001519/0.4322, allocations: 24 kB / 0.5217 GB, free: 14.99 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.00175/0.4339, allocations: 0.5962 MB / 0.5223 GB, free: 14.66 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.008183/0.4421, allocations: 2.148 MB / 0.5244 GB, free: 13.49 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01199/0.4542, allocations: 3.513 MB / 0.5278 GB, free: 11.57 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0091/0.4633, allocations: 7.393 MB / 0.535 GB, free: 8.094 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.008286/0.4716, allocations: 5.92 MB / 0.5408 GB, free: 4.992 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007994/0.4796, allocations: 4.877 MB / 0.5455 GB, free: 2.406 MB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009275/0.4889, allocations: 4.622 MB / 0.5501 GB, free: 13.77 MB / 398.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.003104/0.4921, allocations: 0.668 MB / 0.5507 GB, free: 13.11 MB / 398.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01621/0.5083, allocations: 3.327 MB / 0.554 GB, free: 9.777 MB / 398.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.00383/0.5122, allocations: 1.784 MB / 0.5557 GB, free: 7.988 MB / 398.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.006918/0.5191, allocations: 3.338 MB / 0.559 GB, free: 4.637 MB / 398.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02334/0.5425, allocations: 11.15 MB / 0.5698 GB, free: 9.453 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.276e-06/0.5425, allocations: 0 / 0.5698 GB, free: 9.453 MB / 414.1 MB
Notification: Performance of FrontEnd: time 1.944e-06/0.5425, allocations: 4 kB / 0.5699 GB, free: 9.449 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 0.0003095/0.5429, allocations: 0 / 0.5699 GB, free: 9.449 MB / 414.1 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 0.02001/0.5629, allocations: 7.585 MB / 0.5773 GB, free: 1.855 MB / 414.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.628e-05/0.5629, allocations: 12.03 kB / 0.5773 GB, free: 1.844 MB / 414.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006084/0.569, allocations: 1.235 MB / 0.5785 GB, free: 0.6094 MB / 414.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00661/0.5757, allocations: 3.23 MB / 0.5816 GB, free: 13.32 MB / 430.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0005593/0.5762, allocations: 0.6727 MB / 0.5823 GB, free: 12.57 MB / 430.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001222/0.5775, allocations: 0.4963 MB / 0.5828 GB, free: 12.08 MB / 430.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01689/0.5944, allocations: 9.37 MB / 0.5919 GB, free: 2.605 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 8.388e-05/0.5945, allocations: 4 kB / 0.5919 GB, free: 2.602 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0007185/0.5952, allocations: 194.7 kB / 0.5921 GB, free: 2.414 MB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.471e-05/0.5953, allocations: 119.9 kB / 0.5922 GB, free: 2.297 MB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02217/0.6175, allocations: 12.59 MB / 0.6045 GB, free: 5.691 MB / 446.1 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 0.05878/0.6763, allocations: 30.22 MB / 0.634 GB, free: 6.82 MB / 478.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06292/0.7393, allocations: 41.26 MB / 0.6743 GB, free: 11.01 MB / 0.5137 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01024/0.7496, allocations: 5.075 MB / 0.6793 GB, free: 5.91 MB / 0.5137 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.04028/0.7899, allocations: 20.92 MB / 0.6997 GB, free: 52 kB / 0.5294 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.735e-05/0.79, allocations: 63.84 kB / 0.6998 GB, free: 15.98 MB / 0.545 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003392/0.7934, allocations: 0.9795 MB / 0.7007 GB, free: 15 MB / 0.545 GB
Notification: Performance of pre-optimization done (n=324): time 9.157e-06/0.7934, allocations: 0 / 0.7007 GB, free: 15 MB / 0.545 GB
Notification: Performance of matching and sorting (n=376): time 0.3222/1.116, allocations: 24.47 MB / 0.7246 GB, free: 185.8 MB / 0.545 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.506e-05/1.116, allocations: 90.3 kB / 0.7247 GB, free: 185.8 MB / 0.545 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003931/1.12, allocations: 2.959 MB / 0.7276 GB, free: 184.8 MB / 0.545 GB
Notification: Performance of collectPreVariables (initialization): time 0.0009295/1.121, allocations: 90.02 kB / 0.7277 GB, free: 184.7 MB / 0.545 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001155/1.122, allocations: 2.229 MB / 0.7299 GB, free: 183.2 MB / 0.545 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001247/1.123, allocations: 1.36 MB / 0.7312 GB, free: 182.3 MB / 0.545 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001427/1.124, allocations: 0.9786 MB / 0.7321 GB, free: 181.9 MB / 0.545 GB
Notification: Performance of setup shared object (initialization): time 5.396e-05/1.125, allocations: 302.4 kB / 0.7324 GB, free: 181.6 MB / 0.545 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004147/1.129, allocations: 2.959 MB / 0.7353 GB, free: 180.7 MB / 0.545 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004826/1.134, allocations: 4.484 MB / 0.7397 GB, free: 177.9 MB / 0.545 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.009504/1.143, allocations: 7.812 MB / 0.7473 GB, free: 173.3 MB / 0.545 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.457e-05/1.143, allocations: 17.25 kB / 0.7473 GB, free: 173.3 MB / 0.545 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.0535/1.197, allocations: 13.84 MB / 0.7609 GB, free: 166 MB / 0.545 GB
Notification: Performance of prepare postOptimizeDAE: time 5.399e-05/1.197, allocations: 22.78 kB / 0.7609 GB, free: 166 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.328e-05/1.197, allocations: 52.47 kB / 0.7609 GB, free: 166 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.007721/1.205, allocations: 3.47 MB / 0.7643 GB, free: 163.4 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005153/1.21, allocations: 1.27 MB / 0.7656 GB, free: 162.1 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02791/1.238, allocations: 18.48 MB / 0.7836 GB, free: 143.3 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005757/1.243, allocations: 260.7 kB / 0.7839 GB, free: 143 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001316/1.245, allocations: 282.3 kB / 0.7841 GB, free: 142.8 MB / 0.545 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 0.003112/1.248, allocations: 1.452 MB / 0.7855 GB, free: 141.3 MB / 0.545 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009908/1.249, allocations: 365.6 kB / 0.7859 GB, free: 141 MB / 0.545 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03336/1.282, allocations: 9.664 MB / 0.7953 GB, free: 131.4 MB / 0.545 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.093e-05/1.282, allocations: 40 kB / 0.7954 GB, free: 131.4 MB / 0.545 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.074e-05/1.282, allocations: 6.656 kB / 0.7954 GB, free: 131.4 MB / 0.545 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001329/1.283, allocations: 19.92 kB / 0.7954 GB, free: 131.3 MB / 0.545 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04233/1.325, allocations: 15.44 MB / 0.8105 GB, free: 115.9 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.414e-05/1.325, allocations: 8.062 kB / 0.8105 GB, free: 115.9 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004498/1.329, allocations: 0.8464 MB / 0.8113 GB, free: 115.1 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005474/1.335, allocations: 2.125 MB / 0.8134 GB, free: 112.9 MB / 0.545 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0008543/1.336, allocations: 139.8 kB / 0.8135 GB, free: 112.8 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02035/1.356, allocations: 12.68 MB / 0.8259 GB, free: 99.7 MB / 0.545 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.017e-06/1.356, allocations: 4 kB / 0.8259 GB, free: 99.7 MB / 0.545 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03732/1.394, allocations: 12.99 MB / 0.8386 GB, free: 86.6 MB / 0.545 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002395/1.396, allocations: 0.9503 MB / 0.8395 GB, free: 85.63 MB / 0.545 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0006754/1.397, allocations: 91.97 kB / 0.8396 GB, free: 85.54 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002282/1.399, allocations: 170.5 kB / 0.8398 GB, free: 85.38 MB / 0.545 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009771/1.4, allocations: 463.1 kB / 0.8402 GB, free: 84.93 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.000302/1.4, allocations: 143.9 kB / 0.8403 GB, free: 84.79 MB / 0.545 GB
Notification: Performance of sorting global known variables: time 0.002181/1.402, allocations: 1.992 MB / 0.8423 GB, free: 82.79 MB / 0.545 GB
Notification: Performance of sort global known variables: time 1.2e-07/1.402, allocations: 0 / 0.8423 GB, free: 82.79 MB / 0.545 GB
Notification: Performance of remove unused functions: time 0.006027/1.408, allocations: 2.06 MB / 0.8443 GB, free: 80.89 MB / 0.545 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 0.002338/1.411, allocations: 1.31 MB / 0.8456 GB, free: 79.72 MB / 0.545 GB
Notification: Performance of simCode: created initialization part: time 0.01226/1.423, allocations: 7.438 MB / 0.8528 GB, free: 72.25 MB / 0.545 GB
Notification: Performance of simCode: created event and clocks part: time 8.065e-06/1.423, allocations: 4.062 kB / 0.8528 GB, free: 72.25 MB / 0.545 GB
Notification: Performance of simCode: created simulation system equations: time 0.006812/1.43, allocations: 4.093 MB / 0.8568 GB, free: 68.12 MB / 0.545 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003589/1.434, allocations: 0.7812 MB / 0.8576 GB, free: 67.39 MB / 0.545 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01794/1.452, allocations: 10.95 MB / 0.8683 GB, free: 56.37 MB / 0.545 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00208/1.454, allocations: 3.304 MB / 0.8715 GB, free: 53.03 MB / 0.545 GB
Notification: Performance of simCode: alias equations: time 0.004138/1.458, allocations: 1.576 MB / 0.8731 GB, free: 51.48 MB / 0.545 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001339/1.459, allocations: 466 kB / 0.8735 GB, free: 51.02 MB / 0.545 GB
Notification: Performance of SimCode: time 9.21e-07/1.459, allocations: 0 / 0.8735 GB, free: 51.02 MB / 0.545 GB
Notification: Performance of Templates: time 0.3993/1.859, allocations: 91.17 MB / 0.9625 GB, free: 156.6 MB / 0.545 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 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1)