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 0.001062/0.001062, allocations: 92.2 kB / 20.19 MB, free: 4.363 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 0.001313/0.001313, allocations: 173.3 kB / 23.49 MB, free: 1.062 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 0.9743/0.9743, allocations: 177.1 MB / 203.8 MB, free: 5.652 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 0.08649/0.08649, allocations: 17.46 MB / 277.7 MB, free: 11.64 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 1.713e-06/1.713e-06, allocations: 0 / 353.6 MB, free: 10.16 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.72e-05/2.891e-05, allocations: 2.312 kB / 353.6 MB, free: 10.16 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 0.0414/0.04142, allocations: 33.28 MB / 386.9 MB, free: 8.992 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.1435/0.1849, allocations: 26.34 MB / 413.2 MB, free: 33.64 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001242/0.1861, allocations: 35.81 kB / 413.2 MB, free: 33.64 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.00116/0.1873, allocations: 0.548 MB / 413.8 MB, free: 33.64 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.004365/0.1917, allocations: 2.247 MB / 416 MB, free: 33.29 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.00714/0.1988, allocations: 3.682 MB / 419.7 MB, free: 32.59 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.006579/0.2054, allocations: 7.639 MB / 427.4 MB, free: 30.77 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004901/0.2103, allocations: 4.552 MB / 431.9 MB, free: 28.43 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007742/0.218, allocations: 6.344 MB / 438.3 MB, free: 25.64 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.00575/0.2238, allocations: 4.644 MB / 442.9 MB, free: 23.52 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.001673/0.2255, allocations: 0.6754 MB / 443.6 MB, free: 23.09 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007437/0.2329, allocations: 3.205 MB / 446.8 MB, free: 20.05 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.002058/0.2349, allocations: 1.834 MB / 448.6 MB, free: 18.36 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.004357/0.2393, allocations: 2.549 MB / 451.2 MB, free: 15.96 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01494/0.2543, allocations: 9.928 MB / 461.1 MB, free: 6.738 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 6.072e-06/0.2543, allocations: 0 / 461.1 MB, free: 6.738 MB / 330.7 MB
Notification: Performance of FrontEnd: time 2.855e-06/0.2543, allocations: 0 / 461.1 MB, free: 6.738 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.000237/0.2545, allocations: 4 kB / 461.1 MB, free: 6.734 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 0.01123/0.2657, allocations: 7.547 MB / 468.6 MB, free: 15.3 MB / 346.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.434e-05/0.2658, allocations: 14.69 kB / 468.7 MB, free: 15.29 MB / 346.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.004633/0.2704, allocations: 2.044 MB / 470.7 MB, free: 13.24 MB / 346.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.004916/0.2753, allocations: 2.926 MB / 473.6 MB, free: 10.43 MB / 346.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004879/0.2758, allocations: 0.999 MB / 474.6 MB, free: 9.281 MB / 346.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001047/0.2769, allocations: 0.4885 MB / 475.1 MB, free: 8.793 MB / 346.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.009953/0.2868, allocations: 5.727 MB / 480.8 MB, free: 2.949 MB / 346.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 7.409e-05/0.2869, allocations: 3.375 kB / 480.8 MB, free: 2.949 MB / 346.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0005489/0.2874, allocations: 195.8 kB / 481 MB, free: 2.762 MB / 346.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.594e-05/0.2875, allocations: 123.9 kB / 481.2 MB, free: 2.641 MB / 346.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01039/0.2979, allocations: 5.954 MB / 487.1 MB, free: 12.68 MB / 362.7 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 0.03015/0.328, allocations: 20.18 MB / 0.4954 GB, free: 8.758 MB / 378.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03714/0.3652, allocations: 32.16 MB / 0.5268 GB, free: 9.578 MB / 410.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.003881/0.3691, allocations: 2.186 MB / 0.5289 GB, free: 7.367 MB / 410.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01666/0.3857, allocations: 11.52 MB / 0.5402 GB, free: 12 MB / 426.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.074e-05/0.3858, allocations: 71.92 kB / 0.5403 GB, free: 11.91 MB / 426.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002877/0.3886, allocations: 1.194 MB / 0.5414 GB, free: 10.78 MB / 426.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.413e-05/0.3887, allocations: 0 / 0.5414 GB, free: 10.78 MB / 426.7 MB
Notification: Performance of matching and sorting (n=376): time 0.0538/0.4425, allocations: 13.96 MB / 0.5551 GB, free: 12.94 MB / 442.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.992e-05/0.4425, allocations: 92.5 kB / 0.5552 GB, free: 12.84 MB / 442.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002809/0.4453, allocations: 2.717 MB / 0.5578 GB, free: 10.08 MB / 442.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0007302/0.4461, allocations: 85.7 kB / 0.5579 GB, free: 9.988 MB / 442.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001179/0.4472, allocations: 2.417 MB / 0.5602 GB, free: 7.566 MB / 442.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001377/0.4486, allocations: 1.419 MB / 0.5616 GB, free: 6.168 MB / 442.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001125/0.4497, allocations: 1.037 MB / 0.5626 GB, free: 5.117 MB / 442.7 MB
Notification: Performance of setup shared object (initialization): time 0.0003574/0.4501, allocations: 476.8 kB / 0.5631 GB, free: 4.648 MB / 442.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001882/0.452, allocations: 1.059 MB / 0.5641 GB, free: 3.586 MB / 442.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.1574/0.6094, allocations: 3.292 MB / 0.5674 GB, free: 123.2 MB / 442.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.006643/0.616, allocations: 4.808 MB / 0.572 GB, free: 120.6 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.883e-05/0.6161, allocations: 12.59 kB / 0.5721 GB, free: 120.6 MB / 442.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02792/0.644, allocations: 7.811 MB / 0.5797 GB, free: 120.4 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 4.786e-05/0.6441, allocations: 26.72 kB / 0.5797 GB, free: 120.4 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.861e-05/0.6441, allocations: 48.69 kB / 0.5798 GB, free: 120.4 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01418/0.6583, allocations: 5.823 MB / 0.5854 GB, free: 120.4 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003286/0.6616, allocations: 1.273 MB / 0.5867 GB, free: 120.4 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01374/0.6753, allocations: 8.761 MB / 0.5952 GB, free: 114.8 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003432/0.6788, allocations: 249.1 kB / 0.5955 GB, free: 114.8 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0004952/0.6793, allocations: 282.6 kB / 0.5958 GB, free: 114.8 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 0.001613/0.6809, allocations: 466 kB / 0.5962 GB, free: 114.6 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0007729/0.6817, allocations: 465.3 kB / 0.5966 GB, free: 114.6 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01597/0.6976, allocations: 5.957 MB / 0.6025 GB, free: 112.6 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.942e-05/0.6977, allocations: 39.69 kB / 0.6025 GB, free: 112.6 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.319e-05/0.6977, allocations: 7.438 kB / 0.6025 GB, free: 112.6 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.197e-05/0.6977, allocations: 19.92 kB / 0.6025 GB, free: 112.6 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02129/0.719, allocations: 9.934 MB / 0.6122 GB, free: 106.9 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.52e-05/0.7191, allocations: 4 kB / 0.6122 GB, free: 106.9 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.002534/0.7216, allocations: 0.8562 MB / 0.6131 GB, free: 106.1 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.008052/0.7297, allocations: 2.518 MB / 0.6155 GB, free: 103.6 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0007384/0.7304, allocations: 138.7 kB / 0.6157 GB, free: 103.5 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.009703/0.7401, allocations: 7.693 MB / 0.6232 GB, free: 95.56 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.727e-06/0.7401, allocations: 4 kB / 0.6232 GB, free: 95.56 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01839/0.7585, allocations: 6.967 MB / 0.63 GB, free: 88.72 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.002066/0.7606, allocations: 0.7708 MB / 0.6307 GB, free: 87.95 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0005131/0.7611, allocations: 91.98 kB / 0.6308 GB, free: 87.86 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001316/0.7624, allocations: 162.5 kB / 0.631 GB, free: 87.7 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0008348/0.7632, allocations: 0.4937 MB / 0.6315 GB, free: 87.21 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002512/0.7635, allocations: 147.9 kB / 0.6316 GB, free: 87.07 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001408/0.7649, allocations: 1.32 MB / 0.6329 GB, free: 85.74 MB / 442.7 MB
Notification: Performance of sort global known variables: time 2e-07/0.7649, allocations: 0 / 0.6329 GB, free: 85.74 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.005092/0.77, allocations: 2.059 MB / 0.6349 GB, free: 83.87 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 0.002415/0.7724, allocations: 1.38 MB / 0.6362 GB, free: 82.92 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.008563/0.7809, allocations: 4.303 MB / 0.6404 GB, free: 78.74 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 6.111e-06/0.781, allocations: 0 / 0.6404 GB, free: 78.74 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.004205/0.7852, allocations: 2.497 MB / 0.6429 GB, free: 76.27 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003035/0.7882, allocations: 0.824 MB / 0.6437 GB, free: 75.53 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 0.01414/0.8023, allocations: 8.778 MB / 0.6523 GB, free: 66.71 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0009423/0.8033, allocations: 1.264 MB / 0.6535 GB, free: 65.42 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.003198/0.8065, allocations: 1.294 MB / 0.6548 GB, free: 64.26 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001189/0.8077, allocations: 457.7 kB / 0.6552 GB, free: 63.82 MB / 442.7 MB
Notification: Performance of SimCode: time 2.194e-06/0.8077, allocations: 0 / 0.6552 GB, free: 63.82 MB / 442.7 MB
Notification: Performance of Templates: time 0.2383/1.046, allocations: 93.4 MB / 0.7464 GB, free: 137.4 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: 5.844280060147867]