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 0.000965/0.000965, allocations: 80.81 kB / 19.94 MB, free: 4.543 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 0.001013/0.001013, allocations: 177 kB / 23.36 MB, free: 1.129 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 1.008/1.008, allocations: 177.2 MB / 203.8 MB, free: 5.469 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 0.09139/0.09139, allocations: 17.39 MB / 277.7 MB, free: 11.51 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 1.763e-06/1.763e-06, allocations: 0 / 300.7 MB, free: 1.605 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.525e-05/2.701e-05, allocations: 6.312 kB / 300.7 MB, free: 1.598 MB / 266.7 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 0.04734/0.04737, allocations: 38.71 MB / 339.4 MB, free: 13.66 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01499/0.06236, allocations: 15.7 MB / 355.1 MB, free: 13.89 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001431/0.06379, allocations: 35.69 kB / 355.1 MB, free: 13.86 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009675/0.06476, allocations: 452.1 kB / 355.6 MB, free: 13.41 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003309/0.06807, allocations: 1.562 MB / 357.1 MB, free: 11.84 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004997/0.07307, allocations: 2.451 MB / 359.6 MB, free: 9.375 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.006338/0.0794, allocations: 7.614 MB / 367.2 MB, free: 1.73 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004782/0.08419, allocations: 4.583 MB / 371.8 MB, free: 13.05 MB / 346.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007054/0.09124, allocations: 6.273 MB / 378.1 MB, free: 6.766 MB / 346.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.006718/0.09796, allocations: 4.605 MB / 382.7 MB, free: 2.152 MB / 346.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.001866/0.09982, allocations: 0.6758 MB / 383.3 MB, free: 1.477 MB / 346.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004978/0.1048, allocations: 2.138 MB / 385.5 MB, free: 15.34 MB / 362.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.001432/0.1062, allocations: 1.831 MB / 387.3 MB, free: 13.5 MB / 362.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.003226/0.1095, allocations: 2.554 MB / 389.9 MB, free: 10.94 MB / 362.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01106/0.1205, allocations: 8.493 MB / 398.4 MB, free: 2.422 MB / 362.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.38e-06/0.1205, allocations: 0 / 398.4 MB, free: 2.422 MB / 362.7 MB
Notification: Performance of FrontEnd: time 1.873e-06/0.1205, allocations: 0 / 398.4 MB, free: 2.422 MB / 362.7 MB
Notification: Performance of Transformations before backend: time 0.0002355/0.1208, allocations: 0 / 398.4 MB, free: 2.422 MB / 362.7 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 0.0093/0.1301, allocations: 6.142 MB / 404.5 MB, free: 12.22 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.191e-05/0.1301, allocations: 16.03 kB / 404.5 MB, free: 12.2 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.00393/0.134, allocations: 1.942 MB / 406.5 MB, free: 10.25 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.003033/0.1371, allocations: 1.985 MB / 408.4 MB, free: 8.207 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004578/0.1375, allocations: 0.999 MB / 409.4 MB, free: 7.059 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0007525/0.1383, allocations: 0.4962 MB / 409.9 MB, free: 6.559 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.006036/0.1443, allocations: 5.216 MB / 415.2 MB, free: 1.23 MB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 6.672e-05/0.1444, allocations: 4.172 kB / 415.2 MB, free: 1.227 MB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.000426/0.1448, allocations: 194.8 kB / 415.3 MB, free: 1.039 MB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.101e-05/0.1449, allocations: 116 kB / 415.5 MB, free: 0.9258 MB / 378.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.005468/0.1503, allocations: 4.459 MB / 419.9 MB, free: 12.43 MB / 394.7 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 0.02181/0.1721, allocations: 13.66 MB / 433.6 MB, free: 14.57 MB / 410.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.1794/0.3516, allocations: 29.96 MB / 463.5 MB, free: 101.5 MB / 410.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.002561/0.3541, allocations: 1.536 MB / 465.1 MB, free: 101.5 MB / 410.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01221/0.3663, allocations: 7.791 MB / 472.9 MB, free: 100.8 MB / 410.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.132e-05/0.3664, allocations: 67.61 kB / 472.9 MB, free: 100.8 MB / 410.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002239/0.3686, allocations: 1.147 MB / 474.1 MB, free: 100.2 MB / 410.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.642e-05/0.3686, allocations: 0 / 474.1 MB, free: 100.2 MB / 410.7 MB
Notification: Performance of matching and sorting (n=376): time 0.03721/0.4058, allocations: 11.36 MB / 485.4 MB, free: 91.12 MB / 410.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.956e-05/0.4059, allocations: 90.36 kB / 485.5 MB, free: 91.02 MB / 410.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001764/0.4076, allocations: 2.37 MB / 487.9 MB, free: 89.29 MB / 410.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0006355/0.4083, allocations: 88.52 kB / 488 MB, free: 89.25 MB / 410.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0005291/0.4088, allocations: 1.872 MB / 489.9 MB, free: 87.89 MB / 410.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0009196/0.4097, allocations: 1.361 MB / 491.2 MB, free: 86.91 MB / 410.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0009271/0.4106, allocations: 0.8748 MB / 492.1 MB, free: 86.37 MB / 410.7 MB
Notification: Performance of setup shared object (initialization): time 2.595e-05/0.4107, allocations: 301.1 kB / 492.4 MB, free: 86.07 MB / 410.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001022/0.4117, allocations: 0.8142 MB / 493.2 MB, free: 85.27 MB / 410.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001204/0.4129, allocations: 2.221 MB / 495.4 MB, free: 82.5 MB / 410.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002575/0.4155, allocations: 3.623 MB / 499 MB, free: 78.55 MB / 410.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.126e-05/0.4155, allocations: 18.69 kB / 499.1 MB, free: 78.54 MB / 410.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02068/0.4362, allocations: 6.065 MB / 0.4933 GB, free: 72.9 MB / 410.7 MB
Notification: Performance of prepare postOptimizeDAE: time 4.636e-05/0.4362, allocations: 26.19 kB / 0.4933 GB, free: 72.88 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.443e-05/0.4363, allocations: 51.75 kB / 0.4934 GB, free: 72.83 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01203/0.4483, allocations: 5.623 MB / 0.4989 GB, free: 67.37 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00334/0.4516, allocations: 1.301 MB / 0.5001 GB, free: 66.15 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01026/0.4619, allocations: 6.037 MB / 0.506 GB, free: 59.98 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.002524/0.4644, allocations: 152 kB / 0.5062 GB, free: 59.83 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0004536/0.4649, allocations: 219.8 kB / 0.5064 GB, free: 59.62 MB / 410.7 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 0.001326/0.4662, allocations: 419.6 kB / 0.5068 GB, free: 59.3 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0006701/0.4669, allocations: 319.6 kB / 0.5071 GB, free: 58.99 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01264/0.4795, allocations: 4.439 MB / 0.5114 GB, free: 54.67 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.019e-05/0.4795, allocations: 40 kB / 0.5115 GB, free: 54.63 MB / 410.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.092e-05/0.4796, allocations: 4 kB / 0.5115 GB, free: 54.62 MB / 410.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.164e-05/0.4796, allocations: 22.58 kB / 0.5115 GB, free: 54.61 MB / 410.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01754/0.4972, allocations: 6.86 MB / 0.5182 GB, free: 48.33 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.452e-05/0.4972, allocations: 8.828 kB / 0.5182 GB, free: 48.32 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.002618/0.4998, allocations: 0.8487 MB / 0.519 GB, free: 47.52 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.007121/0.507, allocations: 2.374 MB / 0.5213 GB, free: 45.21 MB / 410.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0007126/0.5077, allocations: 130.5 kB / 0.5215 GB, free: 45.09 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.00747/0.5151, allocations: 5.256 MB / 0.5266 GB, free: 39.67 MB / 410.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.256e-06/0.5151, allocations: 4 kB / 0.5266 GB, free: 39.66 MB / 410.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01428/0.5294, allocations: 5.258 MB / 0.5317 GB, free: 34.45 MB / 410.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001314/0.5307, allocations: 447.7 kB / 0.5322 GB, free: 34.02 MB / 410.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0004107/0.5311, allocations: 95.97 kB / 0.5322 GB, free: 33.93 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001087/0.5322, allocations: 89.27 kB / 0.5323 GB, free: 33.84 MB / 410.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0006512/0.5329, allocations: 374.2 kB / 0.5327 GB, free: 33.48 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002072/0.5331, allocations: 107.9 kB / 0.5328 GB, free: 33.38 MB / 410.7 MB
Notification: Performance of sorting global known variables: time 0.000916/0.534, allocations: 1.138 MB / 0.5339 GB, free: 32.34 MB / 410.7 MB
Notification: Performance of sort global known variables: time 1.9e-07/0.534, allocations: 4 kB / 0.5339 GB, free: 32.33 MB / 410.7 MB
Notification: Performance of remove unused functions: time 0.004028/0.538, allocations: 1.781 MB / 0.5356 GB, free: 30.62 MB / 410.7 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 0.00125/0.5393, allocations: 0.8621 MB / 0.5365 GB, free: 29.91 MB / 410.7 MB
Notification: Performance of simCode: created initialization part: time 0.004921/0.5442, allocations: 3.16 MB / 0.5396 GB, free: 26.95 MB / 410.7 MB
Notification: Performance of simCode: created event and clocks part: time 7.725e-05/0.5443, allocations: 46.53 kB / 0.5396 GB, free: 26.9 MB / 410.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002586/0.5469, allocations: 1.802 MB / 0.5414 GB, free: 25.19 MB / 410.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0025/0.5494, allocations: 0.8179 MB / 0.5422 GB, free: 24.47 MB / 410.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01132/0.5607, allocations: 8.367 MB / 0.5503 GB, free: 16.13 MB / 410.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000866/0.5616, allocations: 1.096 MB / 0.5514 GB, free: 15.01 MB / 410.7 MB
Notification: Performance of simCode: alias equations: time 0.002106/0.5637, allocations: 0.6037 MB / 0.552 GB, free: 14.54 MB / 410.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00183/0.5655, allocations: 0.9466 MB / 0.5529 GB, free: 13.58 MB / 410.7 MB
Notification: Performance of SimCode: time 2.054e-06/0.5655, allocations: 4 kB / 0.5529 GB, free: 13.58 MB / 410.7 MB
Notification: Performance of Templates: time 0.2254/0.7909, allocations: 92.58 MB / 0.6433 GB, free: 106.8 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.586313236039132]