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 0.002017/0.002017, allocations: 85.48 kB / 19.44 MB, free: 344 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 0.001963/0.001963, allocations: 173.6 kB / 22.76 MB, free: 1.664 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 1.574/1.574, allocations: 177.1 MB / 203.1 MB, free: 5.617 MB / 186.7 MB
"
[Timeout remaining time 178]
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 0.161/0.161, allocations: 17.46 MB / 277 MB, free: 11.61 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 1.643e-06/1.643e-06, allocations: 0 / 352.9 MB, free: 10.18 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.058e-05/3.222e-05, allocations: 2.312 kB / 352.9 MB, free: 10.18 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 0.04519/0.04522, allocations: 31.01 MB / 383.9 MB, free: 11.3 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.04099/0.08621, allocations: 26.34 MB / 410.2 MB, free: 0.8594 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001547/0.08776, allocations: 35.69 kB / 410.2 MB, free: 0.8242 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.001756/0.08951, allocations: 0.5502 MB / 410.8 MB, free: 276 kB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.1576/0.2472, allocations: 2.238 MB / 413 MB, free: 32.13 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.009049/0.2562, allocations: 3.687 MB / 416.7 MB, free: 31.46 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.007428/0.2636, allocations: 7.632 MB / 424.3 MB, free: 29.65 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005415/0.269, allocations: 4.55 MB / 428.9 MB, free: 27.74 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.009663/0.2787, allocations: 6.343 MB / 435.2 MB, free: 25.48 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008569/0.2873, allocations: 4.647 MB / 439.9 MB, free: 23.35 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.002667/0.2899, allocations: 0.675 MB / 440.6 MB, free: 23.35 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01136/0.3013, allocations: 3.208 MB / 443.8 MB, free: 20.74 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.003027/0.3043, allocations: 1.834 MB / 445.6 MB, free: 19.05 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.00594/0.3103, allocations: 2.56 MB / 448.2 MB, free: 16.63 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01914/0.3294, allocations: 12.35 MB / 460.5 MB, free: 4.98 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.421e-06/0.3294, allocations: 0 / 460.5 MB, free: 4.98 MB / 330.7 MB
Notification: Performance of FrontEnd: time 2.475e-06/0.3294, allocations: 4 kB / 460.5 MB, free: 4.977 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.0002647/0.3297, allocations: 2.656 kB / 460.5 MB, free: 4.977 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 0.02056/0.3503, allocations: 7.646 MB / 468.2 MB, free: 13.34 MB / 346.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.682e-05/0.3503, allocations: 14.69 kB / 468.2 MB, free: 13.32 MB / 346.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.008281/0.3586, allocations: 2.048 MB / 470.2 MB, free: 11.27 MB / 346.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.009772/0.3684, allocations: 2.954 MB / 473.2 MB, free: 8.43 MB / 346.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001066/0.3694, allocations: 0.9951 MB / 474.2 MB, free: 7.285 MB / 346.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002748/0.3722, allocations: 0.4924 MB / 474.7 MB, free: 6.793 MB / 346.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02213/0.3943, allocations: 8.976 MB / 483.7 MB, free: 13.7 MB / 362.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001067/0.3944, allocations: 7.469 kB / 483.7 MB, free: 13.7 MB / 362.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0009936/0.3954, allocations: 196.4 kB / 483.9 MB, free: 13.51 MB / 362.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001181/0.3955, allocations: 123.9 kB / 484 MB, free: 13.39 MB / 362.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02584/0.4214, allocations: 11.37 MB / 495.3 MB, free: 2.012 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 0.07044/0.4918, allocations: 28.78 MB / 0.5118 GB, free: 5.301 MB / 394.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06349/0.5553, allocations: 25.37 MB / 0.5366 GB, free: 12.9 MB / 426.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.009244/0.5645, allocations: 4.185 MB / 0.5407 GB, free: 8.688 MB / 426.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.04256/0.6071, allocations: 16.44 MB / 0.5568 GB, free: 8.371 MB / 442.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 7.657e-05/0.6072, allocations: 69.91 kB / 0.5568 GB, free: 8.293 MB / 442.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004938/0.6121, allocations: 1.198 MB / 0.558 GB, free: 7.156 MB / 442.7 MB
Notification: Performance of pre-optimization done (n=324): time 8.717e-06/0.6121, allocations: 3.938 kB / 0.558 GB, free: 7.152 MB / 442.7 MB
Notification: Performance of matching and sorting (n=376): time 0.2159/0.8281, allocations: 21.9 MB / 0.5794 GB, free: 150.2 MB / 442.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.43e-05/0.8281, allocations: 91.39 kB / 0.5795 GB, free: 150.1 MB / 442.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00369/0.8318, allocations: 3.293 MB / 0.5827 GB, free: 148.8 MB / 442.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0009768/0.8328, allocations: 89.33 kB / 0.5828 GB, free: 148.7 MB / 442.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001289/0.8341, allocations: 2.446 MB / 0.5852 GB, free: 147.1 MB / 442.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.00182/0.8359, allocations: 1.453 MB / 0.5866 GB, free: 146.2 MB / 442.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001522/0.8374, allocations: 1.099 MB / 0.5877 GB, free: 145.6 MB / 442.7 MB
Notification: Performance of setup shared object (initialization): time 6.911e-05/0.8375, allocations: 483.4 kB / 0.5881 GB, free: 145.2 MB / 442.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.003663/0.8411, allocations: 2.519 MB / 0.5906 GB, free: 144 MB / 442.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004711/0.8459, allocations: 4.815 MB / 0.5953 GB, free: 139.9 MB / 442.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.009581/0.8554, allocations: 8.242 MB / 0.6033 GB, free: 133 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.899e-05/0.8555, allocations: 16 kB / 0.6033 GB, free: 132.9 MB / 442.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05331/0.9088, allocations: 12.44 MB / 0.6155 GB, free: 120.6 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 6.464e-05/0.9089, allocations: 28 kB / 0.6155 GB, free: 120.6 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.692e-05/0.909, allocations: 48 kB / 0.6156 GB, free: 120.5 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.02559/0.9346, allocations: 7.037 MB / 0.6224 GB, free: 113.6 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005551/0.9401, allocations: 1.269 MB / 0.6237 GB, free: 112.4 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02883/0.9689, allocations: 18.51 MB / 0.6417 GB, free: 93.53 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004507/0.9734, allocations: 243.8 kB / 0.642 GB, free: 93.29 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0008804/0.9743, allocations: 283.8 kB / 0.6422 GB, free: 93.01 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 0.002397/0.9767, allocations: 1.362 MB / 0.6436 GB, free: 91.67 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001094/0.9778, allocations: 472.9 kB / 0.644 GB, free: 91.21 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03375/1.012, allocations: 8.724 MB / 0.6525 GB, free: 82.55 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.84e-05/1.012, allocations: 40 kB / 0.6526 GB, free: 82.52 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.818e-05/1.012, allocations: 4 kB / 0.6526 GB, free: 82.51 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001076/1.012, allocations: 19.92 kB / 0.6526 GB, free: 82.49 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04508/1.057, allocations: 14.03 MB / 0.6663 GB, free: 68.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.959e-05/1.057, allocations: 4 kB / 0.6663 GB, free: 68.5 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004551/1.061, allocations: 0.8554 MB / 0.6671 GB, free: 67.65 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.01639/1.078, allocations: 3.144 MB / 0.6702 GB, free: 64.55 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0009172/1.079, allocations: 135.9 kB / 0.6703 GB, free: 64.42 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02053/1.099, allocations: 13.27 MB / 0.6833 GB, free: 50.8 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.589e-06/1.099, allocations: 7.938 kB / 0.6833 GB, free: 50.79 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03749/1.137, allocations: 11.85 MB / 0.6949 GB, free: 38.84 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.003059/1.14, allocations: 0.7646 MB / 0.6956 GB, free: 38.08 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0008155/1.141, allocations: 91.91 kB / 0.6957 GB, free: 37.99 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002625/1.143, allocations: 155.8 kB / 0.6959 GB, free: 37.84 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001068/1.144, allocations: 0.4983 MB / 0.6964 GB, free: 37.34 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003117/1.145, allocations: 147.8 kB / 0.6965 GB, free: 37.2 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.00208/1.147, allocations: 1.818 MB / 0.6983 GB, free: 35.38 MB / 442.7 MB
Notification: Performance of sort global known variables: time 1.1e-07/1.147, allocations: 0 / 0.6983 GB, free: 35.38 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.00623/1.153, allocations: 2.069 MB / 0.7003 GB, free: 33.49 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 0.002497/1.155, allocations: 1.367 MB / 0.7016 GB, free: 32.41 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.01207/1.167, allocations: 6.892 MB / 0.7084 GB, free: 25.48 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 8.536e-06/1.167, allocations: 2.656 kB / 0.7084 GB, free: 25.48 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.006868/1.174, allocations: 3.611 MB / 0.7119 GB, free: 21.81 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003681/1.178, allocations: 0.8364 MB / 0.7127 GB, free: 21.05 MB / 442.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01607/1.194, allocations: 10.34 MB / 0.7228 GB, free: 10.63 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001867/1.196, allocations: 2.517 MB / 0.7253 GB, free: 8.117 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.003485/1.199, allocations: 1.287 MB / 0.7265 GB, free: 6.961 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001233/1.201, allocations: 456.2 kB / 0.727 GB, free: 6.516 MB / 442.7 MB
Notification: Performance of SimCode: time 1.623e-06/1.201, allocations: 3.938 kB / 0.727 GB, free: 6.512 MB / 442.7 MB
Notification: Performance of Templates: time 0.2412/1.442, allocations: 93.38 MB / 0.8182 GB, free: 75.05 MB / 442.7 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: 9.34714240708854]