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 0.0009917/0.0009917, 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 0.001669/0.001669, allocations: 165.3 kB / 23.02 MB, free: 1.547 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 1.01/1.01, 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 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 0.08616/0.08616, allocations: 17.38 MB / 277.3 MB, free: 11.65 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 1.724e-06/1.724e-06, allocations: 0 / 353.5 MB, free: 9.961 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.418e-05/3.591e-05, allocations: 2.312 kB / 353.5 MB, free: 9.957 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 0.04473/0.04477, allocations: 32.99 MB / 386.5 MB, free: 9.074 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0206/0.06537, allocations: 15.77 MB / 402.2 MB, free: 9.242 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.00131/0.06668, allocations: 35.69 kB / 402.3 MB, free: 9.207 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001192/0.06787, allocations: 444.1 kB / 402.7 MB, free: 8.77 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003779/0.07165, allocations: 1.582 MB / 404.3 MB, free: 7.176 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004335/0.07598, allocations: 2.455 MB / 406.7 MB, free: 4.707 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.1304/0.2064, allocations: 7.627 MB / 414.4 MB, free: 36.16 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004884/0.2113, allocations: 4.553 MB / 418.9 MB, free: 35.88 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007101/0.2184, allocations: 6.3 MB / 425.2 MB, free: 34.89 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.005423/0.2238, allocations: 4.648 MB / 429.9 MB, free: 33.79 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.001171/0.225, allocations: 0.6756 MB / 430.5 MB, free: 33.79 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.003321/0.2283, allocations: 2.083 MB / 432.6 MB, free: 33.54 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.0009813/0.2293, allocations: 1.828 MB / 434.4 MB, free: 32.61 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.001851/0.2311, allocations: 2.553 MB / 437 MB, free: 31.39 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.005437/0.2366, allocations: 8.485 MB / 445.5 MB, free: 23.86 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.308e-06/0.2366, allocations: 0 / 445.5 MB, free: 23.86 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.372e-06/0.2366, allocations: 0 / 445.5 MB, free: 23.86 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 5.187e-05/0.2366, allocations: 0 / 445.5 MB, free: 23.86 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 0.007316/0.2439, allocations: 7.3 MB / 452.8 MB, free: 16.57 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.566e-05/0.244, allocations: 8.031 kB / 452.8 MB, free: 16.56 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.003479/0.2475, allocations: 2.05 MB / 454.8 MB, free: 14.51 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.003276/0.2507, allocations: 2.916 MB / 457.8 MB, free: 11.71 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0002917/0.251, allocations: 0.999 MB / 458.8 MB, free: 10.56 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0006204/0.2516, allocations: 0.4885 MB / 459.2 MB, free: 10.07 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.006313/0.258, allocations: 5.729 MB / 465 MB, free: 4.227 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 5.847e-05/0.258, allocations: 192 / 465 MB, free: 4.227 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004188/0.2584, allocations: 192.4 kB / 465.2 MB, free: 4.039 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.621e-05/0.2585, allocations: 122.6 kB / 465.3 MB, free: 3.922 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.007459/0.2659, allocations: 5.952 MB / 471.2 MB, free: 13.97 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 0.02444/0.2904, allocations: 20.14 MB / 491.4 MB, free: 10.09 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.04333/0.3337, allocations: 32.16 MB / 0.5113 GB, free: 10.91 MB / 394.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.004384/0.3381, allocations: 2.186 MB / 0.5134 GB, free: 8.699 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01877/0.3569, allocations: 10.97 MB / 0.5241 GB, free: 13.88 MB / 410.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.148e-05/0.3569, allocations: 63.94 kB / 0.5242 GB, free: 13.8 MB / 410.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002713/0.3596, allocations: 1.194 MB / 0.5253 GB, free: 12.67 MB / 410.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.743e-05/0.3596, allocations: 0 / 0.5253 GB, free: 12.67 MB / 410.7 MB
Notification: Performance of matching and sorting (n=376): time 0.04563/0.4053, allocations: 13.97 MB / 0.539 GB, free: 14.82 MB / 426.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.575e-05/0.4053, allocations: 90.36 kB / 0.5391 GB, free: 14.72 MB / 426.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002748/0.4081, allocations: 2.709 MB / 0.5417 GB, free: 11.97 MB / 426.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0007351/0.4088, allocations: 89.7 kB / 0.5418 GB, free: 11.88 MB / 426.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001197/0.41, allocations: 2.415 MB / 0.5442 GB, free: 9.457 MB / 426.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001377/0.4114, allocations: 1.415 MB / 0.5455 GB, free: 8.059 MB / 426.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001539/0.4129, allocations: 1.04 MB / 0.5466 GB, free: 7.008 MB / 426.7 MB
Notification: Performance of setup shared object (initialization): time 0.000125/0.4131, allocations: 480.8 kB / 0.547 GB, free: 6.535 MB / 426.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002081/0.4151, allocations: 1.052 MB / 0.548 GB, free: 5.477 MB / 426.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002952/0.4181, allocations: 3.299 MB / 0.5513 GB, free: 1.262 MB / 426.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.004979/0.4231, allocations: 4.809 MB / 0.556 GB, free: 11.77 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.14e-05/0.4231, allocations: 14.66 kB / 0.556 GB, free: 11.76 MB / 442.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02624/0.4493, allocations: 7.809 MB / 0.5636 GB, free: 4.363 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 5.355e-05/0.4494, allocations: 29.31 kB / 0.5636 GB, free: 4.34 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.017e-05/0.4495, allocations: 48 kB / 0.5637 GB, free: 4.293 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.162/0.6114, allocations: 5.813 MB / 0.5694 GB, free: 128 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.004412/0.6158, allocations: 1.279 MB / 0.5706 GB, free: 128 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01808/0.6339, allocations: 8.766 MB / 0.5792 GB, free: 122.4 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003817/0.6377, allocations: 248.9 kB / 0.5794 GB, free: 122.4 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0005762/0.6383, allocations: 280.7 kB / 0.5797 GB, free: 122.4 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 0.001401/0.6397, allocations: 469.8 kB / 0.5801 GB, free: 122.2 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0008982/0.6406, allocations: 462.5 kB / 0.5806 GB, free: 122.2 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01844/0.6591, allocations: 5.952 MB / 0.5864 GB, free: 122 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.837e-05/0.6591, allocations: 39.67 kB / 0.5864 GB, free: 122 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.571e-05/0.6591, allocations: 3.531 kB / 0.5864 GB, free: 122 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.853e-05/0.6592, allocations: 23.7 kB / 0.5864 GB, free: 122 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02342/0.6826, allocations: 9.924 MB / 0.5961 GB, free: 121 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.62e-05/0.6827, allocations: 8.812 kB / 0.5961 GB, free: 121 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00272/0.6854, allocations: 0.8542 MB / 0.597 GB, free: 121 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.008106/0.6935, allocations: 2.521 MB / 0.5994 GB, free: 121 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0005931/0.6941, allocations: 134.4 kB / 0.5996 GB, free: 120.9 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.009667/0.7038, allocations: 7.694 MB / 0.6071 GB, free: 114.1 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.757e-06/0.7038, allocations: 6.625 kB / 0.6071 GB, free: 114.1 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01882/0.7226, allocations: 6.969 MB / 0.6139 GB, free: 111.1 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001758/0.7243, allocations: 0.7687 MB / 0.6146 GB, free: 110.8 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000431/0.7248, allocations: 94.62 kB / 0.6147 GB, free: 110.7 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001323/0.7261, allocations: 155.8 kB / 0.6149 GB, free: 110.6 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000774/0.7269, allocations: 0.4977 MB / 0.6154 GB, free: 110.1 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002465/0.7271, allocations: 147.9 kB / 0.6155 GB, free: 109.9 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001386/0.7285, allocations: 1.32 MB / 0.6168 GB, free: 108.6 MB / 442.7 MB
Notification: Performance of sort global known variables: time 2.31e-07/0.7285, allocations: 0 / 0.6168 GB, free: 108.6 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.004352/0.7329, allocations: 1.78 MB / 0.6185 GB, free: 106.9 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 0.001375/0.7342, allocations: 0.8375 MB / 0.6193 GB, free: 106.3 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.006383/0.7406, allocations: 4.313 MB / 0.6236 GB, free: 102.1 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 4.819e-06/0.7406, allocations: 4 kB / 0.6236 GB, free: 102.1 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.003113/0.7437, allocations: 2.495 MB / 0.626 GB, free: 99.67 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002219/0.7459, allocations: 0.8246 MB / 0.6268 GB, free: 98.93 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 0.01143/0.7574, allocations: 8.771 MB / 0.6354 GB, free: 90.12 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0009618/0.7583, allocations: 1.264 MB / 0.6366 GB, free: 88.82 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.003279/0.7616, allocations: 1.29 MB / 0.6379 GB, free: 87.69 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001146/0.7628, allocations: 460.2 kB / 0.6383 GB, free: 87.24 MB / 442.7 MB
Notification: Performance of SimCode: time 1.843e-06/0.7628, allocations: 0 / 0.6383 GB, free: 87.24 MB / 442.7 MB
Notification: Performance of Templates: time 0.09342/0.8562, allocations: 85.97 MB / 0.7223 GB, free: 2.535 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 os._exit(0), Time elapsed: 5.64356949320063]