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 0.001095/0.001095, allocations: 92.2 kB / 20.19 MB, free: 4.359 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 0.001303/0.001303, allocations: 173 kB / 23.49 MB, free: 1.055 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 0.9314/0.9314, allocations: 177.1 MB / 203.8 MB, free: 5.613 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 0.08538/0.08538, allocations: 17.38 MB / 277.6 MB, free: 11.7 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 1.513e-06/1.513e-06, allocations: 0 / 353.5 MB, free: 10.29 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.646e-05/2.797e-05, allocations: 9.547 kB / 353.5 MB, free: 10.28 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 0.02866/0.02869, allocations: 33.28 MB / 386.8 MB, free: 9.125 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.1824/0.2111, allocations: 26.34 MB / 413.1 MB, free: 33.62 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.004491/0.2156, allocations: 38.09 kB / 413.1 MB, free: 33.62 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001477/0.2171, allocations: 0.5499 MB / 413.7 MB, free: 33.62 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0115/0.2286, allocations: 2.246 MB / 415.9 MB, free: 33.28 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01288/0.2415, allocations: 3.681 MB / 419.6 MB, free: 32.57 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.007237/0.2487, allocations: 7.635 MB / 427.2 MB, free: 30.76 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004728/0.2534, allocations: 4.558 MB / 431.8 MB, free: 28.44 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008042/0.2615, allocations: 6.344 MB / 438.1 MB, free: 25.68 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.005985/0.2675, allocations: 4.637 MB / 442.8 MB, free: 23.55 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.001452/0.2689, allocations: 0.6752 MB / 443.5 MB, free: 23.18 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007336/0.2762, allocations: 3.211 MB / 446.7 MB, free: 20.14 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.00175/0.278, allocations: 1.836 MB / 448.5 MB, free: 18.45 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.003823/0.2818, allocations: 2.548 MB / 451 MB, free: 16.04 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01592/0.2977, allocations: 9.925 MB / 461 MB, free: 6.824 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.023e-06/0.2977, allocations: 2.562 kB / 461 MB, free: 6.824 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.723e-06/0.2977, allocations: 0 / 461 MB, free: 6.824 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.0001556/0.2979, allocations: 0 / 461 MB, free: 6.824 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 0.009012/0.3069, allocations: 7.54 MB / 468.5 MB, free: 15.31 MB / 346.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.194e-05/0.307, allocations: 8.031 kB / 468.5 MB, free: 15.3 MB / 346.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.004603/0.3116, allocations: 2.048 MB / 470.6 MB, free: 13.25 MB / 346.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.004432/0.316, allocations: 2.919 MB / 473.5 MB, free: 10.44 MB / 346.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004769/0.3165, allocations: 1.006 MB / 474.5 MB, free: 9.289 MB / 346.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0008919/0.3174, allocations: 496.2 kB / 475 MB, free: 8.805 MB / 346.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.007762/0.3251, allocations: 5.734 MB / 480.7 MB, free: 2.957 MB / 346.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 6.225e-05/0.3252, allocations: 192 / 480.7 MB, free: 2.957 MB / 346.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004696/0.3257, allocations: 192.4 kB / 480.9 MB, free: 2.77 MB / 346.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.373e-05/0.3257, allocations: 119.9 kB / 481 MB, free: 2.652 MB / 346.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.008727/0.3344, allocations: 5.96 MB / 487 MB, free: 12.7 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 0.02838/0.3628, allocations: 20.18 MB / 0.4953 GB, free: 8.77 MB / 378.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03687/0.3997, allocations: 32.16 MB / 0.5267 GB, free: 9.59 MB / 410.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.004548/0.4042, allocations: 2.182 MB / 0.5288 GB, free: 7.383 MB / 410.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.02106/0.4253, allocations: 11.53 MB / 0.5401 GB, free: 12.01 MB / 426.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.061e-05/0.4254, allocations: 71.94 kB / 0.5401 GB, free: 11.93 MB / 426.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003427/0.4288, allocations: 1.197 MB / 0.5413 GB, free: 10.79 MB / 426.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.66e-05/0.4288, allocations: 0 / 0.5413 GB, free: 10.79 MB / 426.7 MB
Notification: Performance of matching and sorting (n=376): time 0.05418/0.483, allocations: 13.96 MB / 0.5549 GB, free: 12.95 MB / 442.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.148e-05/0.483, allocations: 90.36 kB / 0.555 GB, free: 12.85 MB / 442.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002922/0.486, allocations: 2.713 MB / 0.5577 GB, free: 10.1 MB / 442.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0008018/0.4868, allocations: 85.7 kB / 0.5578 GB, free: 10.01 MB / 442.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001277/0.488, allocations: 2.417 MB / 0.5601 GB, free: 7.586 MB / 442.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.00152/0.4896, allocations: 1.42 MB / 0.5615 GB, free: 6.188 MB / 442.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001496/0.4911, allocations: 1.037 MB / 0.5625 GB, free: 5.137 MB / 442.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001013/0.4912, allocations: 478.6 kB / 0.563 GB, free: 4.668 MB / 442.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001986/0.4931, allocations: 1.067 MB / 0.564 GB, free: 3.594 MB / 442.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.1527/0.6459, allocations: 3.292 MB / 0.5672 GB, free: 148.7 MB / 442.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.008244/0.6541, allocations: 4.803 MB / 0.5719 GB, free: 146 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.413e-05/0.6542, allocations: 13.97 kB / 0.5719 GB, free: 146 MB / 442.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.0357/0.6899, allocations: 7.815 MB / 0.5796 GB, free: 145.5 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 6.587e-05/0.6899, allocations: 24.94 kB / 0.5796 GB, free: 145.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.809e-05/0.69, allocations: 50.81 kB / 0.5796 GB, free: 145.5 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01433/0.7044, allocations: 5.812 MB / 0.5853 GB, free: 145 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00337/0.7077, allocations: 1.276 MB / 0.5866 GB, free: 144.8 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01342/0.7211, allocations: 8.771 MB / 0.5951 GB, free: 138.2 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.002903/0.724, allocations: 241.5 kB / 0.5953 GB, free: 138 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0004018/0.7244, allocations: 284.5 kB / 0.5956 GB, free: 138 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 0.001244/0.7257, allocations: 471.8 kB / 0.5961 GB, free: 137.6 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0006948/0.7264, allocations: 457 kB / 0.5965 GB, free: 137.5 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01647/0.7429, allocations: 5.956 MB / 0.6023 GB, free: 133.9 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.784e-05/0.7429, allocations: 45.31 kB / 0.6024 GB, free: 133.8 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.633e-05/0.7429, allocations: 4 kB / 0.6024 GB, free: 133.8 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001022/0.743, allocations: 19.92 kB / 0.6024 GB, free: 133.8 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02142/0.7644, allocations: 9.935 MB / 0.6121 GB, free: 124 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.154e-05/0.7645, allocations: 4 kB / 0.6121 GB, free: 124 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.002602/0.7671, allocations: 0.8529 MB / 0.6129 GB, free: 123.1 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.007941/0.775, allocations: 2.514 MB / 0.6154 GB, free: 120.6 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0006887/0.7757, allocations: 141.2 kB / 0.6155 GB, free: 120.5 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.009116/0.7848, allocations: 7.68 MB / 0.623 GB, free: 112.5 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.418e-06/0.7848, allocations: 11.88 kB / 0.623 GB, free: 112.5 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0186/0.8034, allocations: 6.964 MB / 0.6298 GB, free: 105.7 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001767/0.8052, allocations: 0.7752 MB / 0.6306 GB, free: 104.9 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0005411/0.8057, allocations: 87.98 kB / 0.6307 GB, free: 104.8 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001342/0.8071, allocations: 159.8 kB / 0.6308 GB, free: 104.7 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0007662/0.8078, allocations: 0.4982 MB / 0.6313 GB, free: 104.2 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002263/0.8081, allocations: 147.9 kB / 0.6315 GB, free: 104 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001285/0.8093, allocations: 1.316 MB / 0.6327 GB, free: 102.7 MB / 442.7 MB
Notification: Performance of sort global known variables: time 1.7e-07/0.8093, allocations: 2.656 kB / 0.6327 GB, free: 102.7 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.004791/0.8141, allocations: 2.062 MB / 0.6348 GB, free: 100.8 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 0.002093/0.8162, allocations: 1.38 MB / 0.6361 GB, free: 99.82 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.006642/0.8229, allocations: 4.3 MB / 0.6403 GB, free: 95.47 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 5.089e-06/0.8229, allocations: 4 kB / 0.6403 GB, free: 95.47 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.003394/0.8263, allocations: 2.502 MB / 0.6427 GB, free: 92.91 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002842/0.8291, allocations: 0.8253 MB / 0.6436 GB, free: 92.17 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 0.01223/0.8413, allocations: 8.769 MB / 0.6521 GB, free: 83.34 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001056/0.8424, allocations: 1.264 MB / 0.6533 GB, free: 82.05 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.003342/0.8457, allocations: 1.291 MB / 0.6546 GB, free: 80.89 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001136/0.8469, allocations: 461.7 kB / 0.6551 GB, free: 80.45 MB / 442.7 MB
Notification: Performance of SimCode: time 2.514e-06/0.8469, allocations: 0 / 0.6551 GB, free: 80.45 MB / 442.7 MB
Notification: Performance of Templates: time 0.2493/1.096, allocations: 93.39 MB / 0.7463 GB, free: 145.2 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: 5.891865211073309]