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 0.001646/0.001646, allocations: 96.42 kB / 19.7 MB, free: 2.133 MB / 14.72 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 0.001425/0.001425, allocations: 210.1 kB / 22.99 MB, free: 4.957 MB / 14.72 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 1.423/1.423, allocations: 230.6 MB / 256.8 MB, free: 7.793 MB / 206.1 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 0.138/0.138, allocations: 23.92 MB / 337.1 MB, free: 10.92 MB / 270.1 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: Chemical requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.002035/0.002035, allocations: 59.91 kB / 472.4 MB, free: 6.93 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3101/0.3121, allocations: 59.87 MB / 0.5198 GB, free: 9.793 MB / 382.1 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 0.07083/0.3829, allocations: 29.3 MB / 0.5485 GB, free: 10.52 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03113/0.414, allocations: 23.04 MB / 0.571 GB, free: 5.414 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001803/0.4159, allocations: 35.75 kB / 0.571 GB, free: 5.379 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001619/0.4175, allocations: 0.5464 MB / 0.5715 GB, free: 4.828 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.006474/0.4239, allocations: 2.161 MB / 0.5736 GB, free: 2.652 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01047/0.4344, allocations: 3.585 MB / 0.5771 GB, free: 15.05 MB / 430.1 MB
Notification: Performance of NFFlatten.flatten: time 0.008936/0.4433, allocations: 7.398 MB / 0.5844 GB, free: 7.617 MB / 430.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006153/0.4495, allocations: 4.339 MB / 0.5886 GB, free: 3.203 MB / 430.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007911/0.4574, allocations: 4.971 MB / 0.5935 GB, free: 14.22 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008166/0.4656, allocations: 4.76 MB / 0.5981 GB, free: 9.449 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.00239/0.468, allocations: 0.6797 MB / 0.5988 GB, free: 8.77 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01006/0.478, allocations: 3.249 MB / 0.6019 GB, free: 5.516 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.002667/0.4807, allocations: 1.808 MB / 0.6037 GB, free: 3.703 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.005238/0.4859, allocations: 2.903 MB / 0.6065 GB, free: 0.7891 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02263/0.5086, allocations: 11.63 MB / 0.6179 GB, free: 5.117 MB / 462.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.735e-06/0.5086, allocations: 0 / 0.6179 GB, free: 5.117 MB / 462.1 MB
Notification: Performance of FrontEnd: time 1.953e-06/0.5086, allocations: 0 / 0.6179 GB, free: 5.117 MB / 462.1 MB
Notification: Performance of Transformations before backend: time 0.0003612/0.5089, allocations: 0 / 0.6179 GB, free: 5.117 MB / 462.1 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 0.02679/0.5357, allocations: 7.237 MB / 0.625 GB, free: 13.81 MB / 478.1 MB
Notification: Performance of prepare preOptimizeDAE: time 7.274e-05/0.5358, allocations: 12.03 kB / 0.625 GB, free: 13.8 MB / 478.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.008962/0.5448, allocations: 1.241 MB / 0.6262 GB, free: 12.55 MB / 478.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.01115/0.5559, allocations: 3.317 MB / 0.6294 GB, free: 9.176 MB / 478.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001105/0.557, allocations: 1.003 MB / 0.6304 GB, free: 8.023 MB / 478.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.00283/0.5598, allocations: 0.4963 MB / 0.6309 GB, free: 7.527 MB / 478.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02405/0.5839, allocations: 9.466 MB / 0.6401 GB, free: 13.95 MB / 494.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.000195/0.5841, allocations: 4 kB / 0.6401 GB, free: 13.95 MB / 494.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.00179/0.5859, allocations: 192 kB / 0.6403 GB, free: 13.76 MB / 494.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001087/0.586, allocations: 116 kB / 0.6404 GB, free: 13.64 MB / 494.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0252/0.6112, allocations: 12.66 MB / 0.6528 GB, free: 0.9609 MB / 494.1 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 0.07106/0.6822, allocations: 26.72 MB / 0.6789 GB, free: 6 MB / 0.5137 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.06001/0.7422, allocations: 26.13 MB / 0.7044 GB, free: 12.77 MB / 0.545 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.00856/0.7508, allocations: 4.72 MB / 0.709 GB, free: 8.027 MB / 0.545 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.03838/0.7892, allocations: 16.88 MB / 0.7255 GB, free: 7.074 MB / 0.5606 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.098e-05/0.7892, allocations: 69.11 kB / 0.7256 GB, free: 6.996 MB / 0.5606 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004982/0.7942, allocations: 1.254 MB / 0.7268 GB, free: 5.738 MB / 0.5606 GB
Notification: Performance of pre-optimization done (n=324): time 1.162e-05/0.7942, allocations: 0 / 0.7268 GB, free: 5.738 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=376): time 0.3789/1.173, allocations: 24.17 MB / 0.7504 GB, free: 169.9 MB / 0.5606 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 9.305e-05/1.173, allocations: 89.89 kB / 0.7505 GB, free: 169.8 MB / 0.5606 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004648/1.178, allocations: 2.841 MB / 0.7533 GB, free: 168.9 MB / 0.5606 GB
Notification: Performance of collectPreVariables (initialization): time 0.001205/1.179, allocations: 86.58 kB / 0.7533 GB, free: 168.8 MB / 0.5606 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001645/1.181, allocations: 2.221 MB / 0.7555 GB, free: 167.3 MB / 0.5606 GB
Notification: Performance of collectInitialBindings (initialization): time 0.00237/1.183, allocations: 1.361 MB / 0.7568 GB, free: 166.4 MB / 0.5606 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001739/1.185, allocations: 0.9845 MB / 0.7578 GB, free: 166.1 MB / 0.5606 GB
Notification: Performance of setup shared object (initialization): time 5.143e-05/1.185, allocations: 307.8 kB / 0.7581 GB, free: 165.8 MB / 0.5606 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004671/1.19, allocations: 2.959 MB / 0.761 GB, free: 164.4 MB / 0.5606 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005191/1.195, allocations: 4.49 MB / 0.7654 GB, free: 160.9 MB / 0.5606 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.009882/1.205, allocations: 7.81 MB / 0.773 GB, free: 155.7 MB / 0.5606 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.091e-05/1.205, allocations: 14.81 kB / 0.773 GB, free: 155.7 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05613/1.261, allocations: 13.81 MB / 0.7865 GB, free: 145.4 MB / 0.5606 GB
Notification: Performance of prepare postOptimizeDAE: time 5.827e-05/1.261, allocations: 28 kB / 0.7865 GB, free: 145.4 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.809e-05/1.261, allocations: 48 kB / 0.7866 GB, free: 145.3 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008373/1.269, allocations: 3.471 MB / 0.79 GB, free: 142 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005763/1.275, allocations: 1.266 MB / 0.7912 GB, free: 140.8 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02939/1.305, allocations: 17.89 MB / 0.8087 GB, free: 122.6 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004912/1.309, allocations: 247.8 kB / 0.8089 GB, free: 122.4 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0012/1.311, allocations: 279.8 kB / 0.8092 GB, free: 122.1 MB / 0.5606 GB
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 0.003869/1.314, allocations: 1.446 MB / 0.8106 GB, free: 120.7 MB / 0.5606 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001519/1.316, allocations: 349.7 kB / 0.8109 GB, free: 120.3 MB / 0.5606 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03539/1.351, allocations: 9.62 MB / 0.8203 GB, free: 110.8 MB / 0.5606 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.465e-05/1.351, allocations: 43.98 kB / 0.8204 GB, free: 110.8 MB / 0.5606 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.007e-05/1.351, allocations: 4 kB / 0.8204 GB, free: 110.7 MB / 0.5606 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001392/1.352, allocations: 19.92 kB / 0.8204 GB, free: 110.7 MB / 0.5606 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04538/1.397, allocations: 14.36 MB / 0.8344 GB, free: 96.43 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.67e-05/1.397, allocations: 4 kB / 0.8344 GB, free: 96.43 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004523/1.402, allocations: 0.8515 MB / 0.8352 GB, free: 95.58 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006075/1.408, allocations: 2.122 MB / 0.8373 GB, free: 93.48 MB / 0.5606 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001017/1.409, allocations: 139.9 kB / 0.8374 GB, free: 93.35 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02094/1.43, allocations: 12.11 MB / 0.8493 GB, free: 80.96 MB / 0.5606 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.188e-06/1.43, allocations: 7.938 kB / 0.8493 GB, free: 80.95 MB / 0.5606 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03847/1.468, allocations: 12.93 MB / 0.8619 GB, free: 67.95 MB / 0.5606 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.00306/1.471, allocations: 0.9062 MB / 0.8628 GB, free: 67.05 MB / 0.5606 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000898/1.472, allocations: 93.33 kB / 0.8629 GB, free: 66.96 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002541/1.475, allocations: 163.8 kB / 0.863 GB, free: 66.8 MB / 0.5606 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001038/1.476, allocations: 474.2 kB / 0.8635 GB, free: 66.34 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.000324/1.476, allocations: 142.7 kB / 0.8636 GB, free: 66.2 MB / 0.5606 GB
Notification: Performance of sorting global known variables: time 0.002172/1.478, allocations: 1.847 MB / 0.8654 GB, free: 64.35 MB / 0.5606 GB
Notification: Performance of sort global known variables: time 5.11e-07/1.478, allocations: 0 / 0.8654 GB, free: 64.35 MB / 0.5606 GB
Notification: Performance of remove unused functions: time 0.006458/1.485, allocations: 2.066 MB / 0.8674 GB, free: 62.34 MB / 0.5606 GB
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 0.002382/1.487, allocations: 1.32 MB / 0.8687 GB, free: 61.21 MB / 0.5606 GB
Notification: Performance of simCode: created initialization part: time 0.01247/1.499, allocations: 7.072 MB / 0.8756 GB, free: 54.11 MB / 0.5606 GB
Notification: Performance of simCode: created event and clocks part: time 9.999e-06/1.499, allocations: 4 kB / 0.8756 GB, free: 54.11 MB / 0.5606 GB
Notification: Performance of simCode: created simulation system equations: time 0.007637/1.507, allocations: 3.766 MB / 0.8793 GB, free: 50.31 MB / 0.5606 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003808/1.511, allocations: 0.7762 MB / 0.8801 GB, free: 49.61 MB / 0.5606 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01683/1.528, allocations: 10.99 MB / 0.8908 GB, free: 38.59 MB / 0.5606 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00204/1.53, allocations: 2.786 MB / 0.8935 GB, free: 35.82 MB / 0.5606 GB
Notification: Performance of simCode: alias equations: time 0.003774/1.534, allocations: 1.562 MB / 0.8951 GB, free: 34.37 MB / 0.5606 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001165/1.535, allocations: 459.2 kB / 0.8955 GB, free: 33.93 MB / 0.5606 GB
Notification: Performance of SimCode: time 1.243e-06/1.535, allocations: 0 / 0.8955 GB, free: 33.93 MB / 0.5606 GB
Notification: Performance of Templates: time 0.3879/1.923, allocations: 100.1 MB / 0.9932 GB, free: 181.2 MB / 0.5919 GB
"
[Timeout remaining time 658]
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=480 -s cvode -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 9.486984526010929]
Failed to read output from testmodel.py, exit status != 0:
1.932527911994839 1.942133395 1.431164706
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fea74486f50>