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 0.001269/0.001269, allocations: 99.64 kB / 18.95 MB, free: 2.668 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 0.00147/0.00147, allocations: 211.8 kB / 22.24 MB, free: 5.258 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 1.409/1.409, allocations: 230.6 MB / 256 MB, free: 7.805 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 0.147/0.147, allocations: 24 MB / 336.4 MB, free: 10.85 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 0.002237/0.002237, allocations: 75.89 kB / 471.8 MB, free: 6.828 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3076/0.3098, allocations: 59.89 MB / 0.5192 GB, free: 9.75 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 0.07448/0.3843, allocations: 29.44 MB / 0.548 GB, free: 10.33 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0337/0.418, allocations: 23.05 MB / 0.5705 GB, free: 5.133 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002126/0.4201, allocations: 31.75 kB / 0.5705 GB, free: 5.102 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.002124/0.4222, allocations: 0.5464 MB / 0.5711 GB, free: 4.551 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.007405/0.4296, allocations: 2.165 MB / 0.5732 GB, free: 2.371 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01105/0.4407, allocations: 3.581 MB / 0.5767 GB, free: 14.77 MB / 430.1 MB
Notification: Performance of NFFlatten.flatten: time 0.01143/0.4521, allocations: 7.398 MB / 0.5839 GB, free: 7.34 MB / 430.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006512/0.4586, allocations: 4.312 MB / 0.5881 GB, free: 2.953 MB / 430.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0076/0.4662, allocations: 4.971 MB / 0.593 GB, free: 13.97 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009126/0.4753, allocations: 4.951 MB / 0.5978 GB, free: 9.008 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002482/0.4778, allocations: 0.6758 MB / 0.5985 GB, free: 8.332 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01157/0.4894, allocations: 3.187 MB / 0.6016 GB, free: 5.141 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.002933/0.4923, allocations: 1.804 MB / 0.6033 GB, free: 3.332 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.005129/0.4975, allocations: 2.903 MB / 0.6062 GB, free: 428 kB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02119/0.5186, allocations: 11.63 MB / 0.6175 GB, free: 4.746 MB / 462.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.202e-06/0.5187, allocations: 4 kB / 0.6175 GB, free: 4.742 MB / 462.1 MB
Notification: Performance of FrontEnd: time 2.044e-06/0.5187, allocations: 0 / 0.6175 GB, free: 4.742 MB / 462.1 MB
Notification: Performance of Transformations before backend: time 0.0002614/0.5189, allocations: 0 / 0.6175 GB, free: 4.742 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 0.01931/0.5382, allocations: 7.237 MB / 0.6246 GB, free: 13.43 MB / 478.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.735e-05/0.5383, allocations: 8.031 kB / 0.6246 GB, free: 13.43 MB / 478.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006145/0.5444, allocations: 1.245 MB / 0.6258 GB, free: 12.18 MB / 478.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.008496/0.5529, allocations: 3.329 MB / 0.6291 GB, free: 8.789 MB / 478.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0009765/0.5539, allocations: 1.007 MB / 0.6301 GB, free: 7.633 MB / 478.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002566/0.5565, allocations: 0.4885 MB / 0.6305 GB, free: 7.145 MB / 478.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02208/0.5785, allocations: 9.466 MB / 0.6398 GB, free: 13.57 MB / 494.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.000119/0.5787, allocations: 7.984 kB / 0.6398 GB, free: 13.56 MB / 494.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001148/0.5798, allocations: 192 kB / 0.64 GB, free: 13.38 MB / 494.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001022/0.5799, allocations: 116 kB / 0.6401 GB, free: 13.26 MB / 494.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02626/0.6062, allocations: 12.67 MB / 0.6524 GB, free: 0.5742 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 0.06496/0.6711, allocations: 26.72 MB / 0.6785 GB, free: 5.613 MB / 0.5138 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.05777/0.7289, allocations: 26.14 MB / 0.7041 GB, free: 12.39 MB / 0.545 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.00951/0.7384, allocations: 4.72 MB / 0.7087 GB, free: 7.641 MB / 0.545 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.03757/0.776, allocations: 16.89 MB / 0.7252 GB, free: 6.676 MB / 0.5606 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.757e-05/0.776, allocations: 73.05 kB / 0.7252 GB, free: 6.594 MB / 0.5606 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004732/0.7808, allocations: 1.25 MB / 0.7265 GB, free: 5.34 MB / 0.5606 GB
Notification: Performance of pre-optimization done (n=324): time 1.432e-05/0.7808, allocations: 0 / 0.7265 GB, free: 5.34 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=376): time 0.3063/1.087, allocations: 24.15 MB / 0.7501 GB, free: 168.9 MB / 0.5606 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.908e-05/1.087, allocations: 90.33 kB / 0.7501 GB, free: 168.8 MB / 0.5606 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003497/1.091, allocations: 2.838 MB / 0.7529 GB, free: 167.8 MB / 0.5606 GB
Notification: Performance of collectPreVariables (initialization): time 0.0008073/1.091, allocations: 89.52 kB / 0.753 GB, free: 167.7 MB / 0.5606 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001081/1.093, allocations: 2.223 MB / 0.7552 GB, free: 166.3 MB / 0.5606 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001202/1.094, allocations: 1.366 MB / 0.7565 GB, free: 165.4 MB / 0.5606 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001333/1.095, allocations: 0.9841 MB / 0.7575 GB, free: 165 MB / 0.5606 GB
Notification: Performance of setup shared object (initialization): time 3.841e-05/1.095, allocations: 301.1 kB / 0.7577 GB, free: 164.7 MB / 0.5606 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004051/1.099, allocations: 2.966 MB / 0.7606 GB, free: 163.1 MB / 0.5606 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004452/1.104, allocations: 4.486 MB / 0.765 GB, free: 159.6 MB / 0.5606 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.008427/1.112, allocations: 7.814 MB / 0.7727 GB, free: 154.4 MB / 0.5606 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.171e-05/1.112, allocations: 15.16 kB / 0.7727 GB, free: 154.4 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05067/1.163, allocations: 13.81 MB / 0.7862 GB, free: 144.8 MB / 0.5606 GB
Notification: Performance of prepare postOptimizeDAE: time 4.607e-05/1.163, allocations: 28 kB / 0.7862 GB, free: 144.8 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.648e-05/1.163, allocations: 48 kB / 0.7862 GB, free: 144.7 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.007624/1.17, allocations: 3.466 MB / 0.7896 GB, free: 141.4 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005013/1.176, allocations: 1.271 MB / 0.7909 GB, free: 140.1 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02783/1.203, allocations: 17.87 MB / 0.8083 GB, free: 122 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004847/1.208, allocations: 251.8 kB / 0.8086 GB, free: 121.8 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0008691/1.209, allocations: 279.8 kB / 0.8088 GB, free: 121.5 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 0.002549/1.212, allocations: 1.453 MB / 0.8102 GB, free: 120 MB / 0.5606 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009099/1.213, allocations: 349.7 kB / 0.8106 GB, free: 119.7 MB / 0.5606 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03254/1.245, allocations: 9.606 MB / 0.82 GB, free: 110.2 MB / 0.5606 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.91e-05/1.245, allocations: 39.98 kB / 0.82 GB, free: 110.1 MB / 0.5606 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.787e-05/1.245, allocations: 14.62 kB / 0.82 GB, free: 110.1 MB / 0.5606 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001082/1.245, allocations: 15.94 kB / 0.82 GB, free: 110.1 MB / 0.5606 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04092/1.286, allocations: 14.36 MB / 0.834 GB, free: 95.82 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.899e-05/1.286, allocations: 0 / 0.834 GB, free: 95.82 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00434/1.291, allocations: 0.8528 MB / 0.8349 GB, free: 94.96 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005466/1.296, allocations: 2.126 MB / 0.837 GB, free: 92.87 MB / 0.5606 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.000845/1.297, allocations: 135.9 kB / 0.8371 GB, free: 92.74 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.0198/1.317, allocations: 12.11 MB / 0.8489 GB, free: 80.35 MB / 0.5606 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.368e-06/1.317, allocations: 7.969 kB / 0.8489 GB, free: 80.34 MB / 0.5606 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03668/1.353, allocations: 12.93 MB / 0.8616 GB, free: 67.34 MB / 0.5606 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002946/1.356, allocations: 0.9058 MB / 0.8624 GB, free: 66.44 MB / 0.5606 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000786/1.357, allocations: 91.98 kB / 0.8625 GB, free: 66.35 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002367/1.359, allocations: 162.5 kB / 0.8627 GB, free: 66.2 MB / 0.5606 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009007/1.36, allocations: 470.2 kB / 0.8631 GB, free: 65.73 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002817/1.361, allocations: 147.9 kB / 0.8633 GB, free: 65.59 MB / 0.5606 GB
Notification: Performance of sorting global known variables: time 0.002001/1.363, allocations: 1.847 MB / 0.8651 GB, free: 63.74 MB / 0.5606 GB
Notification: Performance of sort global known variables: time 1.1e-07/1.363, allocations: 0 / 0.8651 GB, free: 63.74 MB / 0.5606 GB
Notification: Performance of remove unused functions: time 0.006103/1.369, allocations: 2.065 MB / 0.8671 GB, free: 61.73 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 0.002324/1.371, allocations: 1.318 MB / 0.8684 GB, free: 60.61 MB / 0.5606 GB
Notification: Performance of simCode: created initialization part: time 0.01207/1.383, allocations: 7.079 MB / 0.8753 GB, free: 53.51 MB / 0.5606 GB
Notification: Performance of simCode: created event and clocks part: time 8.466e-06/1.383, allocations: 4 kB / 0.8753 GB, free: 53.5 MB / 0.5606 GB
Notification: Performance of simCode: created simulation system equations: time 0.006748/1.39, allocations: 3.77 MB / 0.879 GB, free: 49.7 MB / 0.5606 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003379/1.393, allocations: 0.7634 MB / 0.8797 GB, free: 49.02 MB / 0.5606 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01658/1.41, allocations: 10.99 MB / 0.8905 GB, free: 38 MB / 0.5606 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002102/1.412, allocations: 2.784 MB / 0.8932 GB, free: 35.22 MB / 0.5606 GB
Notification: Performance of simCode: alias equations: time 0.004106/1.416, allocations: 1.559 MB / 0.8947 GB, free: 33.77 MB / 0.5606 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001519/1.418, allocations: 458.4 kB / 0.8951 GB, free: 33.32 MB / 0.5606 GB
Notification: Performance of SimCode: time 2.365e-06/1.418, allocations: 0 / 0.8951 GB, free: 33.32 MB / 0.5606 GB
Notification: Performance of Templates: time 0.3689/1.786, allocations: 98.22 MB / 0.991 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 -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling os._exit(0), Time elapsed: 9.17241551913321]
Failed to read output from testmodel.py, exit status != 0:
1.7959064468741417 1.804621927 1.283627657
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fada01eefe0>