Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_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 0.0009117/0.0009117, allocations: 81.17 kB / 19.87 MB, free: 4.621 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 0.001405/0.001405, allocations: 169 kB / 23.27 MB, free: 1.219 MB / 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 0.8981/0.8981, allocations: 177.1 MB / 203.7 MB, free: 5.504 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.08735/0.08735, allocations: 17.38 MB / 277.6 MB, free: 11.48 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/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_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_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.242e-06/1.242e-06, allocations: 0 / 353.9 MB, free: 9.676 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.096e-05/1.22e-05, allocations: 2.312 kB / 353.9 MB, free: 9.672 MB / 282.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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 0.04488/0.04489, allocations: 32.87 MB / 386.8 MB, free: 8.91 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01336/0.05825, allocations: 15.43 MB / 402.2 MB, free: 9.422 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000856/0.0591, allocations: 35.69 kB / 402.2 MB, free: 9.387 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0007441/0.05985, allocations: 448.2 kB / 402.7 MB, free: 8.945 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.00258/0.06243, allocations: 1.578 MB / 404.3 MB, free: 7.355 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.003694/0.06612, allocations: 2.463 MB / 406.7 MB, free: 4.879 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.1334/0.1995, allocations: 7.621 MB / 414.3 MB, free: 36.35 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005862/0.2054, allocations: 4.553 MB / 418.9 MB, free: 36.07 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.00693/0.2123, allocations: 6.311 MB / 425.2 MB, free: 35.11 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0037/0.216, allocations: 4.653 MB / 429.9 MB, free: 34.11 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0008137/0.2168, allocations: 0.676 MB / 430.5 MB, free: 34.11 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.003088/0.2199, allocations: 2.087 MB / 432.6 MB, free: 33.86 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0009159/0.2208, allocations: 1.833 MB / 434.5 MB, free: 32.95 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0017/0.2225, allocations: 2.551 MB / 437 MB, free: 31.72 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.004766/0.2273, allocations: 8.482 MB / 445.5 MB, free: 23.8 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.108e-06/0.2273, allocations: 4 kB / 445.5 MB, free: 23.79 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.272e-06/0.2273, allocations: 0 / 445.5 MB, free: 23.79 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 3.968e-05/0.2273, allocations: 0 / 445.5 MB, free: 23.79 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 0.006145/0.2335, allocations: 6.706 MB / 452.2 MB, free: 17.37 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.451e-05/0.2335, allocations: 12.02 kB / 452.2 MB, free: 17.36 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.003007/0.2365, allocations: 2.05 MB / 454.3 MB, free: 15.3 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.002383/0.2389, allocations: 2.63 MB / 456.9 MB, free: 12.79 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0002845/0.2392, allocations: 1.003 MB / 457.9 MB, free: 11.63 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0005742/0.2398, allocations: 0.4921 MB / 458.4 MB, free: 11.15 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.004364/0.2441, allocations: 5.207 MB / 463.6 MB, free: 6.008 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 5.878e-05/0.2442, allocations: 3.375 kB / 463.6 MB, free: 6.008 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0003941/0.2446, allocations: 192.4 kB / 463.8 MB, free: 5.82 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.434e-05/0.2446, allocations: 122.6 kB / 463.9 MB, free: 5.703 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.004633/0.2493, allocations: 4.859 MB / 468.8 MB, free: 0.8281 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 0.02029/0.2696, allocations: 18.64 MB / 487.4 MB, free: 14.82 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.04127/0.3108, allocations: 31.7 MB / 0.5069 GB, free: 192 kB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.003303/0.3141, allocations: 1.854 MB / 0.5087 GB, free: 14.36 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01739/0.3315, allocations: 10.46 MB / 0.519 GB, free: 4.234 MB / 394.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.495e-05/0.3316, allocations: 71.88 kB / 0.519 GB, free: 4.152 MB / 394.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002943/0.3345, allocations: 1.143 MB / 0.5201 GB, free: 3.07 MB / 394.7 MB
Notification: Performance of pre-optimization done (n=324): time 6.763e-06/0.3345, allocations: 0 / 0.5201 GB, free: 3.07 MB / 394.7 MB
Notification: Performance of matching and sorting (n=376): time 0.03938/0.3739, allocations: 11.88 MB / 0.5317 GB, free: 7.375 MB / 410.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.119e-05/0.374, allocations: 94.36 kB / 0.5318 GB, free: 7.27 MB / 410.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002117/0.3761, allocations: 2.654 MB / 0.5344 GB, free: 4.965 MB / 410.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0002711/0.3763, allocations: 85.7 kB / 0.5345 GB, free: 4.875 MB / 410.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001115/0.3775, allocations: 2.434 MB / 0.5369 GB, free: 2.551 MB / 410.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0008767/0.3783, allocations: 1.424 MB / 0.5383 GB, free: 1.203 MB / 410.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001039/0.3794, allocations: 1.059 MB / 0.5393 GB, free: 236 kB / 410.7 MB
Notification: Performance of setup shared object (initialization): time 0.000105/0.3795, allocations: 480.8 kB / 0.5398 GB, free: 15.76 MB / 426.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001028/0.3805, allocations: 0.8277 MB / 0.5406 GB, free: 14.93 MB / 426.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002116/0.3826, allocations: 3.08 MB / 0.5436 GB, free: 11.04 MB / 426.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003546/0.3862, allocations: 4.402 MB / 0.5479 GB, free: 6.07 MB / 426.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.669e-05/0.3862, allocations: 12 kB / 0.5479 GB, free: 6.059 MB / 426.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02241/0.4086, allocations: 7.071 MB / 0.5548 GB, free: 15.41 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 3.715e-05/0.4086, allocations: 27.98 kB / 0.5548 GB, free: 15.38 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.881e-05/0.4087, allocations: 48 kB / 0.5549 GB, free: 15.34 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01275/0.4214, allocations: 5.715 MB / 0.5605 GB, free: 9.723 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003013/0.4245, allocations: 1.198 MB / 0.5616 GB, free: 8.605 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.1601/0.5846, allocations: 8.394 MB / 0.5698 GB, free: 127 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003171/0.5878, allocations: 152.2 kB / 0.57 GB, free: 127 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0004335/0.5882, allocations: 247.5 kB / 0.5702 GB, free: 127 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 0.001407/0.5896, allocations: 465.3 kB / 0.5706 GB, free: 126.9 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0007571/0.5904, allocations: 466.2 kB / 0.5711 GB, free: 126.9 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01454/0.6049, allocations: 5.106 MB / 0.5761 GB, free: 126.7 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.832e-05/0.6049, allocations: 42.56 kB / 0.5761 GB, free: 126.7 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.175e-05/0.605, allocations: 4.125 kB / 0.5761 GB, free: 126.7 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 2.423e-05/0.605, allocations: 19.69 kB / 0.5761 GB, free: 126.7 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01906/0.624, allocations: 9.161 MB / 0.5851 GB, free: 125.7 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.608e-06/0.6241, allocations: 5.969 kB / 0.5851 GB, free: 125.7 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001907/0.626, allocations: 0.7781 MB / 0.5858 GB, free: 125.7 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.007442/0.6334, allocations: 2.419 MB / 0.5882 GB, free: 125.6 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0003299/0.6337, allocations: 141.9 kB / 0.5883 GB, free: 125.6 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.008093/0.6418, allocations: 7.333 MB / 0.5955 GB, free: 120.1 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.725e-06/0.6418, allocations: 2.719 kB / 0.5955 GB, free: 120.1 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01507/0.6569, allocations: 6.112 MB / 0.6015 GB, free: 119.4 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001175/0.6581, allocations: 0.6712 MB / 0.6021 GB, free: 119.2 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003121/0.6584, allocations: 92.02 kB / 0.6022 GB, free: 119.2 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001005/0.6594, allocations: 82.28 kB / 0.6023 GB, free: 119.2 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0005145/0.6599, allocations: 389.3 kB / 0.6027 GB, free: 119.2 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.000188/0.6601, allocations: 122.2 kB / 0.6028 GB, free: 119.2 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.0009704/0.6611, allocations: 1.239 MB / 0.604 GB, free: 118.9 MB / 442.7 MB
Notification: Performance of sort global known variables: time 2.71e-07/0.6611, allocations: 0 / 0.604 GB, free: 118.9 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.003764/0.6648, allocations: 1.778 MB / 0.6057 GB, free: 118.8 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 0.001051/0.6659, allocations: 0.8777 MB / 0.6066 GB, free: 118.6 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.004567/0.6704, allocations: 3.793 MB / 0.6103 GB, free: 117.1 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.336e-06/0.6704, allocations: 0 / 0.6103 GB, free: 117.1 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002331/0.6728, allocations: 2.209 MB / 0.6125 GB, free: 114.9 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001758/0.6745, allocations: 0.8156 MB / 0.6132 GB, free: 114.2 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 0.01037/0.6849, allocations: 8.572 MB / 0.6216 GB, free: 105.7 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0007736/0.6857, allocations: 1.264 MB / 0.6229 GB, free: 104.4 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.001494/0.6872, allocations: 0.5963 MB / 0.6234 GB, free: 103.9 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001588/0.6888, allocations: 1.063 MB / 0.6245 GB, free: 102.9 MB / 442.7 MB
Notification: Performance of SimCode: time 1.293e-06/0.6888, allocations: 0 / 0.6245 GB, free: 102.9 MB / 442.7 MB
Notification: Performance of Templates: time 0.07956/0.7683, allocations: 92.94 MB / 0.7152 GB, free: 11.29 MB / 442.7 MB
"
[Timeout remaining time 659]
make -j1 -f Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 12.931633607950062]