Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0009029/0.0009029, allocations: 77.09 kB / 20.66 MB, free: 3.844 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.0009749/0.0009749, allocations: 169 kB / 24.06 MB, free: 456 kB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 0.9407/0.9407, allocations: 177.1 MB / 204.5 MB, free: 5.5 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo): time 0.0843/0.0843, allocations: 17.47 MB / 278.5 MB, free: 11.39 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
translateModel(Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.462e-06/1.462e-06, allocations: 0 / 354.8 MB, free: 9.539 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.596e-05/1.742e-05, allocations: 5.688 kB / 354.8 MB, free: 9.535 MB / 282.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Obsolete.mo:14335:7-14335:66: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 master/Obsolete.mo:14335:7-14335:66: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.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC): time 0.02612/0.02614, allocations: 32.85 MB / 387.7 MB, free: 8.793 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0129/0.03904, allocations: 15.43 MB / 403.1 MB, free: 9.301 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0008172/0.03986, allocations: 35.69 kB / 403.1 MB, free: 9.266 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007576/0.04062, allocations: 444.2 kB / 403.6 MB, free: 8.828 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002276/0.04289, allocations: 1.574 MB / 405.1 MB, free: 7.242 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004216/0.04711, allocations: 2.463 MB / 407.6 MB, free: 4.766 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.1303/0.1774, allocations: 7.63 MB / 415.2 MB, free: 36.36 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005169/0.1826, allocations: 4.546 MB / 419.8 MB, free: 36.08 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.01176/0.1944, allocations: 6.305 MB / 426.1 MB, free: 35.08 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007903/0.2023, allocations: 4.661 MB / 430.7 MB, free: 34.04 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.002652/0.2049, allocations: 0.6731 MB / 431.4 MB, free: 34.04 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006499/0.2114, allocations: 2.085 MB / 433.5 MB, free: 33.79 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.003031/0.2145, allocations: 1.832 MB / 435.3 MB, free: 32.84 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.004761/0.2192, allocations: 2.555 MB / 437.9 MB, free: 31.56 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0104/0.2296, allocations: 8.489 MB / 446.4 MB, free: 23.63 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.464e-06/0.2296, allocations: 0 / 446.4 MB, free: 23.63 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.473e-06/0.2296, allocations: 0 / 446.4 MB, free: 23.63 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.0002375/0.2299, allocations: 0 / 446.4 MB, free: 23.63 MB / 330.7 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 0.01102/0.2409, allocations: 6.707 MB / 453.1 MB, free: 17.21 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.677e-05/0.2409, allocations: 8.031 kB / 453.1 MB, free: 17.2 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.004781/0.2457, allocations: 2.046 MB / 455.1 MB, free: 15.15 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.003931/0.2496, allocations: 2.636 MB / 457.8 MB, free: 12.63 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.000328/0.25, allocations: 1.003 MB / 458.8 MB, free: 11.48 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001234/0.2512, allocations: 0.4895 MB / 459.3 MB, free: 10.99 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.006525/0.2577, allocations: 5.209 MB / 464.5 MB, free: 5.852 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 7.069e-05/0.2578, allocations: 3.562 kB / 464.5 MB, free: 5.852 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004263/0.2582, allocations: 195 kB / 464.7 MB, free: 5.664 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.792e-05/0.2583, allocations: 119.9 kB / 464.8 MB, free: 5.547 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.005952/0.2642, allocations: 4.863 MB / 469.6 MB, free: 0.6719 MB / 330.7 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 0.03323/0.2975, allocations: 18.64 MB / 488.3 MB, free: 14.66 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.04034/0.3378, allocations: 31.7 MB / 0.5078 GB, free: 32 kB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.003268/0.3411, allocations: 1.855 MB / 0.5096 GB, free: 14.21 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01666/0.3577, allocations: 10.41 MB / 0.5198 GB, free: 4.066 MB / 394.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.579e-05/0.3578, allocations: 71.69 kB / 0.5198 GB, free: 3.988 MB / 394.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002663/0.3604, allocations: 1.133 MB / 0.5209 GB, free: 2.914 MB / 394.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.077e-05/0.3604, allocations: 2.656 kB / 0.5209 GB, free: 2.914 MB / 394.7 MB
Notification: Performance of matching and sorting (n=376): time 0.04093/0.4014, allocations: 11.88 MB / 0.5325 GB, free: 7.211 MB / 410.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.44e-05/0.4014, allocations: 90.36 kB / 0.5326 GB, free: 7.109 MB / 410.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002375/0.4038, allocations: 2.655 MB / 0.5352 GB, free: 4.805 MB / 410.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0007075/0.4045, allocations: 85.7 kB / 0.5353 GB, free: 4.715 MB / 410.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001504/0.406, allocations: 2.439 MB / 0.5377 GB, free: 2.387 MB / 410.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001417/0.4074, allocations: 1.424 MB / 0.5391 GB, free: 1.039 MB / 410.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0011/0.4085, allocations: 1.057 MB / 0.5401 GB, free: 68 kB / 410.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001087/0.4086, allocations: 476.8 kB / 0.5406 GB, free: 15.6 MB / 426.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001119/0.4098, allocations: 0.8278 MB / 0.5414 GB, free: 14.77 MB / 426.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002368/0.4121, allocations: 3.086 MB / 0.5444 GB, free: 10.88 MB / 426.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003737/0.4159, allocations: 4.404 MB / 0.5487 GB, free: 5.906 MB / 426.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.32e-05/0.4159, allocations: 12 kB / 0.5487 GB, free: 5.895 MB / 426.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02521/0.4411, allocations: 7.071 MB / 0.5556 GB, free: 15.24 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 4.693e-05/0.4411, allocations: 28 kB / 0.5556 GB, free: 15.21 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.053e-05/0.4412, allocations: 48 kB / 0.5557 GB, free: 15.17 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.0144/0.4556, allocations: 5.715 MB / 0.5613 GB, free: 9.559 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003529/0.4591, allocations: 1.19 MB / 0.5624 GB, free: 8.445 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.234/0.6932, allocations: 8.39 MB / 0.5706 GB, free: 126.3 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003148/0.6963, allocations: 153.4 kB / 0.5708 GB, free: 126.3 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0005962/0.6969, allocations: 242.8 kB / 0.571 GB, free: 126.3 MB / 442.7 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 0.001592/0.6985, allocations: 468.6 kB / 0.5714 GB, free: 126.2 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009779/0.6995, allocations: 462.9 kB / 0.5719 GB, free: 126.2 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01558/0.7151, allocations: 5.106 MB / 0.5769 GB, free: 126 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.662e-05/0.7151, allocations: 39.75 kB / 0.5769 GB, free: 126 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.388e-05/0.7151, allocations: 3.844 kB / 0.5769 GB, free: 126 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.449e-05/0.7152, allocations: 25.16 kB / 0.5769 GB, free: 126 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02138/0.7366, allocations: 9.165 MB / 0.5859 GB, free: 125 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.271e-05/0.7366, allocations: 3.188 kB / 0.5859 GB, free: 125 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.002479/0.7391, allocations: 0.7769 MB / 0.5866 GB, free: 125 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.008143/0.7472, allocations: 2.414 MB / 0.589 GB, free: 124.9 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0005572/0.7478, allocations: 141.8 kB / 0.5891 GB, free: 124.9 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.009009/0.7568, allocations: 7.324 MB / 0.5963 GB, free: 119.4 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.327e-06/0.7568, allocations: 6.469 kB / 0.5963 GB, free: 119.4 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01779/0.7746, allocations: 6.106 MB / 0.6023 GB, free: 118.7 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001505/0.7761, allocations: 0.6841 MB / 0.6029 GB, free: 118.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0004275/0.7765, allocations: 90.73 kB / 0.603 GB, free: 118.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.00116/0.7777, allocations: 85.64 kB / 0.6031 GB, free: 118.5 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0006646/0.7783, allocations: 393.5 kB / 0.6035 GB, free: 118.5 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002422/0.7786, allocations: 120.1 kB / 0.6036 GB, free: 118.5 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001263/0.7798, allocations: 1.237 MB / 0.6048 GB, free: 118.3 MB / 442.7 MB
Notification: Performance of sort global known variables: time 4.11e-07/0.7798, allocations: 3.531 kB / 0.6048 GB, free: 118.3 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.004354/0.7842, allocations: 1.777 MB / 0.6065 GB, free: 118.2 MB / 442.7 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 0.001227/0.7854, allocations: 0.8803 MB / 0.6074 GB, free: 117.9 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.005467/0.7909, allocations: 3.78 MB / 0.6111 GB, free: 116.3 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 6.362e-06/0.7909, allocations: 0 / 0.6111 GB, free: 116.3 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.003156/0.794, allocations: 2.209 MB / 0.6132 GB, free: 114.2 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002618/0.7967, allocations: 0.8215 MB / 0.614 GB, free: 113.4 MB / 442.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01203/0.8087, allocations: 8.565 MB / 0.6224 GB, free: 104.9 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001003/0.8097, allocations: 1.26 MB / 0.6236 GB, free: 103.6 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.002178/0.8119, allocations: 0.6082 MB / 0.6242 GB, free: 103.2 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001861/0.8137, allocations: 1.051 MB / 0.6253 GB, free: 102.1 MB / 442.7 MB
Notification: Performance of SimCode: time 2.455e-06/0.8137, allocations: 0 / 0.6253 GB, free: 102.1 MB / 442.7 MB
Notification: Performance of Templates: time 0.08563/0.8994, allocations: 94.66 MB / 0.7177 GB, free: 8.785 MB / 442.7 MB
"
[Timeout remaining time 659]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 240]
[Calling os._exit(0), Time elapsed: 5.834183715283871]