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 0.001616/0.001616, 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 0.002049/0.002049, 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 0.9786/0.9786, allocations: 177.1 MB / 203.4 MB, free: 5.637 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 0.08414/0.08414, allocations: 17.46 MB / 277.4 MB, free: 11.55 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 1.733e-06/1.733e-06, allocations: 3.938 kB / 353.6 MB, free: 9.828 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.935e-05/3.108e-05, allocations: 9.547 kB / 353.6 MB, free: 9.82 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 0.03067/0.0307, allocations: 33 MB / 386.6 MB, free: 8.926 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01504/0.04574, allocations: 15.77 MB / 402.4 MB, free: 9.094 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.00125/0.04699, allocations: 35.69 kB / 402.4 MB, free: 9.059 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009166/0.04791, allocations: 432.2 kB / 402.8 MB, free: 8.633 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003768/0.05168, allocations: 1.59 MB / 404.4 MB, free: 7.031 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.00508/0.05676, allocations: 2.455 MB / 406.9 MB, free: 4.562 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.1427/0.1995, allocations: 7.626 MB / 414.5 MB, free: 36.22 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005009/0.2045, allocations: 4.545 MB / 419 MB, free: 35.94 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.01172/0.2162, allocations: 6.307 MB / 425.3 MB, free: 34.88 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007372/0.2236, allocations: 4.658 MB / 430 MB, free: 33.76 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.002463/0.226, allocations: 0.6747 MB / 430.7 MB, free: 33.76 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.006207/0.2322, allocations: 2.081 MB / 432.8 MB, free: 33.51 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.002729/0.235, allocations: 1.834 MB / 434.6 MB, free: 32.53 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.004854/0.2398, allocations: 2.555 MB / 437.1 MB, free: 31.3 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01189/0.2517, allocations: 8.49 MB / 445.6 MB, free: 23.68 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 6.502e-06/0.2517, allocations: 0 / 445.6 MB, free: 23.68 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.613e-06/0.2517, allocations: 3.562 kB / 445.6 MB, free: 23.68 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.0002479/0.252, allocations: 0 / 445.6 MB, free: 23.68 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 0.01048/0.2624, allocations: 7.299 MB / 452.9 MB, free: 16.39 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.708e-05/0.2625, allocations: 11.5 kB / 452.9 MB, free: 16.38 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.004082/0.2666, allocations: 2.05 MB / 455 MB, free: 14.33 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.004473/0.271, allocations: 2.906 MB / 457.9 MB, free: 11.54 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004525/0.2715, allocations: 1.003 MB / 458.9 MB, free: 10.38 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001371/0.2729, allocations: 0.4885 MB / 459.4 MB, free: 9.895 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.008491/0.2814, allocations: 5.726 MB / 465.1 MB, free: 4.047 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 7.29e-05/0.2814, allocations: 6.031 kB / 465.1 MB, free: 4.047 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004816/0.2819, allocations: 192.4 kB / 465.3 MB, free: 3.859 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.309e-05/0.282, allocations: 119.9 kB / 465.4 MB, free: 3.742 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.009388/0.2914, allocations: 5.95 MB / 471.4 MB, free: 13.79 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 0.03543/0.3268, allocations: 20.15 MB / 491.5 MB, free: 9.91 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03648/0.3633, allocations: 32.16 MB / 0.5114 GB, free: 10.73 MB / 394.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.004131/0.3674, allocations: 2.179 MB / 0.5135 GB, free: 8.52 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01846/0.3859, allocations: 10.97 MB / 0.5242 GB, free: 13.7 MB / 410.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.87e-05/0.3859, allocations: 67.94 kB / 0.5243 GB, free: 13.62 MB / 410.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.00355/0.3895, allocations: 1.193 MB / 0.5255 GB, free: 12.49 MB / 410.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.999e-05/0.3895, allocations: 5.297 kB / 0.5255 GB, free: 12.49 MB / 410.7 MB
Notification: Performance of matching and sorting (n=376): time 0.05812/0.4476, allocations: 13.96 MB / 0.5391 GB, free: 14.65 MB / 426.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.3e-05/0.4477, allocations: 93.83 kB / 0.5392 GB, free: 14.55 MB / 426.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002988/0.4507, allocations: 2.705 MB / 0.5419 GB, free: 11.8 MB / 426.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0008782/0.4515, allocations: 93.7 kB / 0.5419 GB, free: 11.7 MB / 426.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001265/0.4528, allocations: 2.416 MB / 0.5443 GB, free: 9.281 MB / 426.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001497/0.4543, allocations: 1.417 MB / 0.5457 GB, free: 7.883 MB / 426.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001212/0.4555, allocations: 1.04 MB / 0.5467 GB, free: 6.832 MB / 426.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001047/0.4556, allocations: 476.8 kB / 0.5472 GB, free: 6.363 MB / 426.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001835/0.4575, allocations: 1.056 MB / 0.5482 GB, free: 5.301 MB / 426.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.003301/0.4608, allocations: 3.304 MB / 0.5514 GB, free: 1.082 MB / 426.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005452/0.4662, allocations: 4.803 MB / 0.5561 GB, free: 11.6 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.465e-05/0.4663, allocations: 18.62 kB / 0.5561 GB, free: 11.58 MB / 442.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.0261/0.4924, allocations: 7.808 MB / 0.5637 GB, free: 4.191 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 5.232e-05/0.4924, allocations: 30.81 kB / 0.5638 GB, free: 4.164 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.323e-05/0.4925, allocations: 48 kB / 0.5638 GB, free: 4.117 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.1586/0.6511, allocations: 5.814 MB / 0.5695 GB, free: 128 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003306/0.6544, allocations: 1.273 MB / 0.5707 GB, free: 128 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01418/0.6686, allocations: 8.758 MB / 0.5793 GB, free: 122.3 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003257/0.6718, allocations: 246.8 kB / 0.5795 GB, free: 122.3 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001103/0.6729, allocations: 284.9 kB / 0.5798 GB, free: 122.3 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 0.001738/0.6747, allocations: 473 kB / 0.5803 GB, free: 122.2 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001064/0.6757, allocations: 464.9 kB / 0.5807 GB, free: 122.2 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.02138/0.6971, allocations: 5.95 MB / 0.5865 GB, free: 122 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.14e-05/0.6971, allocations: 37.28 kB / 0.5865 GB, free: 122 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.576e-05/0.6972, allocations: 6.75 kB / 0.5865 GB, free: 122 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.871e-05/0.6973, allocations: 18.7 kB / 0.5866 GB, free: 122 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0271/0.7244, allocations: 9.934 MB / 0.5963 GB, free: 120.9 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.98e-05/0.7244, allocations: 8.125 kB / 0.5963 GB, free: 120.9 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.003605/0.728, allocations: 0.85 MB / 0.5971 GB, free: 120.9 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.009876/0.7379, allocations: 2.525 MB / 0.5996 GB, free: 120.9 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0007504/0.7386, allocations: 131.2 kB / 0.5997 GB, free: 120.8 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.009137/0.7478, allocations: 7.696 MB / 0.6072 GB, free: 113.9 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.376e-06/0.7478, allocations: 3.719 kB / 0.6072 GB, free: 113.9 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01774/0.7655, allocations: 6.968 MB / 0.614 GB, free: 110.9 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001852/0.7674, allocations: 0.7636 MB / 0.6148 GB, free: 110.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0005137/0.7679, allocations: 91.97 kB / 0.6149 GB, free: 110.4 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001324/0.7692, allocations: 162.5 kB / 0.615 GB, free: 110.2 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0007755/0.77, allocations: 0.5006 MB / 0.6155 GB, free: 109.7 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002441/0.7702, allocations: 150.7 kB / 0.6156 GB, free: 109.6 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001466/0.7717, allocations: 1.32 MB / 0.6169 GB, free: 108.2 MB / 442.7 MB
Notification: Performance of sort global known variables: time 4e-08/0.7717, allocations: 0 / 0.6169 GB, free: 108.2 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.005144/0.7768, allocations: 1.773 MB / 0.6187 GB, free: 106.6 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 0.001541/0.7784, allocations: 0.8444 MB / 0.6195 GB, free: 106 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.007064/0.7854, allocations: 4.308 MB / 0.6237 GB, free: 101.8 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 8.666e-06/0.7854, allocations: 4 kB / 0.6237 GB, free: 101.8 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.003608/0.7891, allocations: 2.492 MB / 0.6261 GB, free: 99.33 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002505/0.7916, allocations: 0.8238 MB / 0.6269 GB, free: 98.59 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 0.01346/0.805, allocations: 8.779 MB / 0.6355 GB, free: 89.78 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001076/0.8061, allocations: 1.264 MB / 0.6367 GB, free: 88.48 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.002959/0.809, allocations: 1.281 MB / 0.638 GB, free: 87.35 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001106/0.8102, allocations: 466.9 kB / 0.6384 GB, free: 86.9 MB / 442.7 MB
Notification: Performance of SimCode: time 3.276e-06/0.8102, allocations: 0 / 0.6384 GB, free: 86.9 MB / 442.7 MB
Notification: Performance of Templates: time 0.08465/0.8948, allocations: 90.99 MB / 0.7273 GB, free: 13.21 MB / 458.7 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: 6.026295270305127]