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 0.0008938/0.0008938, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 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 0.001252/0.001252, allocations: 169 kB / 23.02 MB, free: 1.551 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 0.9687/0.9687, allocations: 177.1 MB / 203.4 MB, free: 5.613 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 0.08894/0.08894, allocations: 17.46 MB / 277.4 MB, free: 11.54 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 1.302e-06/1.302e-06, allocations: 0 / 353.6 MB, free: 9.828 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.248e-05/1.379e-05, allocations: 2.312 kB / 353.6 MB, free: 9.824 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 0.02698/0.027, allocations: 33 MB / 386.6 MB, free: 8.93 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0143/0.0413, allocations: 15.77 MB / 402.3 MB, free: 9.105 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001107/0.0424, allocations: 35.69 kB / 402.4 MB, free: 9.07 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009415/0.04335, allocations: 444.2 kB / 402.8 MB, free: 8.633 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.00306/0.04641, allocations: 1.582 MB / 404.4 MB, free: 7.039 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004437/0.05084, allocations: 2.455 MB / 406.9 MB, free: 4.57 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.1319/0.1828, allocations: 7.638 MB / 414.5 MB, free: 36.22 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004747/0.1875, allocations: 4.543 MB / 419 MB, free: 35.95 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008657/0.1962, allocations: 6.303 MB / 425.3 MB, free: 34.88 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.005944/0.2021, allocations: 4.645 MB / 430 MB, free: 33.75 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.001728/0.2038, allocations: 0.6749 MB / 430.7 MB, free: 33.75 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.003847/0.2077, allocations: 2.079 MB / 432.7 MB, free: 33.5 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0009696/0.2087, allocations: 1.836 MB / 434.6 MB, free: 32.56 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.002094/0.2107, allocations: 2.557 MB / 437.1 MB, free: 31.33 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.007943/0.2187, allocations: 8.483 MB / 445.6 MB, free: 23.72 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.394e-06/0.2187, allocations: 2.688 kB / 445.6 MB, free: 23.72 MB / 330.7 MB
Notification: Performance of FrontEnd: time 2.315e-06/0.2187, allocations: 3.938 kB / 445.6 MB, free: 23.71 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.0002207/0.2189, allocations: 0 / 445.6 MB, free: 23.71 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 0.01031/0.2292, allocations: 7.301 MB / 452.9 MB, free: 16.43 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.452e-05/0.2293, allocations: 8.031 kB / 452.9 MB, free: 16.42 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.00535/0.2346, allocations: 2.043 MB / 455 MB, free: 14.37 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.01061/0.2452, allocations: 2.908 MB / 457.9 MB, free: 11.57 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0003604/0.2456, allocations: 1.005 MB / 458.9 MB, free: 10.42 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0008787/0.2465, allocations: 0.4885 MB / 459.4 MB, free: 9.934 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01782/0.2643, allocations: 5.723 MB / 465.1 MB, free: 4.09 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 7.572e-05/0.2644, allocations: 3.656 kB / 465.1 MB, free: 4.09 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0005642/0.2649, allocations: 192.4 kB / 465.3 MB, free: 3.902 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.129e-05/0.265, allocations: 119.9 kB / 465.4 MB, free: 3.785 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02541/0.2904, allocations: 5.952 MB / 471.4 MB, free: 13.83 MB / 346.7 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 0.03578/0.3262, allocations: 20.15 MB / 491.5 MB, free: 9.945 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03704/0.3632, allocations: 32.16 MB / 0.5114 GB, free: 10.77 MB / 394.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.004513/0.3677, allocations: 2.182 MB / 0.5135 GB, free: 8.559 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01729/0.385, allocations: 10.96 MB / 0.5242 GB, free: 13.74 MB / 410.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.99e-05/0.3851, allocations: 67.94 kB / 0.5243 GB, free: 13.66 MB / 410.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002627/0.3877, allocations: 1.193 MB / 0.5255 GB, free: 12.54 MB / 410.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.649e-05/0.3877, allocations: 0 / 0.5255 GB, free: 12.54 MB / 410.7 MB
Notification: Performance of matching and sorting (n=376): time 0.04358/0.4313, allocations: 13.96 MB / 0.5391 GB, free: 14.69 MB / 426.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.743e-05/0.4314, allocations: 96.39 kB / 0.5392 GB, free: 14.59 MB / 426.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002686/0.4341, allocations: 2.709 MB / 0.5418 GB, free: 11.84 MB / 426.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0005134/0.4346, allocations: 89.7 kB / 0.5419 GB, free: 11.75 MB / 426.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001197/0.4358, allocations: 2.411 MB / 0.5443 GB, free: 9.328 MB / 426.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0015/0.4373, allocations: 1.416 MB / 0.5457 GB, free: 7.93 MB / 426.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001298/0.4386, allocations: 1.037 MB / 0.5467 GB, free: 6.879 MB / 426.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001322/0.4387, allocations: 476.8 kB / 0.5471 GB, free: 6.41 MB / 426.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002182/0.4409, allocations: 1.062 MB / 0.5482 GB, free: 5.344 MB / 426.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002793/0.4437, allocations: 3.299 MB / 0.5514 GB, free: 1.129 MB / 426.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005134/0.4488, allocations: 4.803 MB / 0.5561 GB, free: 11.64 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.421e-05/0.4488, allocations: 16 kB / 0.5561 GB, free: 11.63 MB / 442.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02598/0.4748, allocations: 7.814 MB / 0.5637 GB, free: 4.234 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 5.211e-05/0.4749, allocations: 28 kB / 0.5637 GB, free: 4.207 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.365e-05/0.4749, allocations: 48 kB / 0.5638 GB, free: 4.16 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.1649/0.6399, allocations: 5.822 MB / 0.5695 GB, free: 128.1 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.004328/0.6442, allocations: 1.272 MB / 0.5707 GB, free: 128.1 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01873/0.6629, allocations: 8.76 MB / 0.5793 GB, free: 122.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00367/0.6666, allocations: 250 kB / 0.5795 GB, free: 122.5 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0007454/0.6673, allocations: 280.9 kB / 0.5798 GB, free: 122.5 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 0.001649/0.669, allocations: 466.7 kB / 0.5802 GB, free: 122.3 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009627/0.6699, allocations: 461.3 kB / 0.5807 GB, free: 122.3 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.02079/0.6907, allocations: 5.953 MB / 0.5865 GB, free: 122.1 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.364e-05/0.6908, allocations: 39.69 kB / 0.5865 GB, free: 122.1 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.633e-05/0.6908, allocations: 7.594 kB / 0.5865 GB, free: 122.1 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.439e-05/0.6909, allocations: 19.03 kB / 0.5865 GB, free: 122.1 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02228/0.7132, allocations: 9.932 MB / 0.5962 GB, free: 121.1 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.587e-05/0.7132, allocations: 6.75 kB / 0.5962 GB, free: 121.1 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00272/0.7159, allocations: 0.8547 MB / 0.5971 GB, free: 121.1 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.008517/0.7244, allocations: 2.519 MB / 0.5995 GB, free: 121 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0008257/0.7252, allocations: 141 kB / 0.5997 GB, free: 120.9 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.009706/0.735, allocations: 7.691 MB / 0.6072 GB, free: 114 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.976e-06/0.735, allocations: 3.656 kB / 0.6072 GB, free: 114 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01868/0.7536, allocations: 6.972 MB / 0.614 GB, free: 111 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001861/0.7555, allocations: 0.7657 MB / 0.6147 GB, free: 110.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003966/0.7559, allocations: 91.97 kB / 0.6148 GB, free: 110.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001177/0.7571, allocations: 155.8 kB / 0.615 GB, free: 110.3 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0007229/0.7578, allocations: 0.502 MB / 0.6155 GB, free: 109.8 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002148/0.758, allocations: 147.9 kB / 0.6156 GB, free: 109.7 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001316/0.7593, allocations: 1.316 MB / 0.6169 GB, free: 108.3 MB / 442.7 MB
Notification: Performance of sort global known variables: time 2.1e-07/0.7593, allocations: 2.688 kB / 0.6169 GB, free: 108.3 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.004675/0.764, allocations: 1.782 MB / 0.6186 GB, free: 106.7 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 0.001401/0.7654, allocations: 0.8336 MB / 0.6195 GB, free: 106.1 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.006603/0.772, allocations: 4.312 MB / 0.6237 GB, free: 101.9 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 5.55e-06/0.772, allocations: 2.656 kB / 0.6237 GB, free: 101.9 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.003347/0.7754, allocations: 2.495 MB / 0.6261 GB, free: 99.41 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002524/0.7779, allocations: 0.83 MB / 0.6269 GB, free: 98.68 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 0.01167/0.7895, allocations: 8.773 MB / 0.6355 GB, free: 89.87 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0007761/0.7903, allocations: 1.267 MB / 0.6367 GB, free: 88.57 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.002693/0.793, allocations: 1.279 MB / 0.638 GB, free: 87.43 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0009647/0.794, allocations: 456.2 kB / 0.6384 GB, free: 86.99 MB / 442.7 MB
Notification: Performance of SimCode: time 1.613e-06/0.794, allocations: 0 / 0.6384 GB, free: 86.99 MB / 442.7 MB
Notification: Performance of Templates: time 0.07657/0.8706, allocations: 85.97 MB / 0.7224 GB, free: 2.285 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: 5.64007778884843]