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 0.001651/0.001651, allocations: 99.75 kB / 18.95 MB, free: 2.832 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 0.002092/0.002092, allocations: 216.8 kB / 22.25 MB, free: 5.105 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 1.454/1.454, allocations: 230.6 MB / 256 MB, free: 7.82 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 0.1428/0.1428, allocations: 23.92 MB / 336.3 MB, free: 10.93 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 0.002121/0.002121, allocations: 75.89 kB / 471.7 MB, free: 6.934 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2995/0.3016, allocations: 59.87 MB / 0.5191 GB, free: 9.734 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 0.0752/0.3768, allocations: 29.32 MB / 0.5478 GB, free: 10.54 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03418/0.411, allocations: 23.05 MB / 0.5703 GB, free: 5.43 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002605/0.4136, allocations: 39.62 kB / 0.5703 GB, free: 5.391 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.002314/0.4159, allocations: 0.5465 MB / 0.5708 GB, free: 4.84 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.00825/0.4241, allocations: 2.161 MB / 0.5729 GB, free: 2.664 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01048/0.4346, allocations: 3.577 MB / 0.5764 GB, free: 15.07 MB / 430.1 MB
Notification: Performance of NFFlatten.flatten: time 0.009321/0.4439, allocations: 7.406 MB / 0.5837 GB, free: 7.629 MB / 430.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006409/0.4503, allocations: 4.331 MB / 0.5879 GB, free: 3.223 MB / 430.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0114/0.4617, allocations: 4.967 MB / 0.5927 GB, free: 14.25 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.01373/0.4755, allocations: 4.768 MB / 0.5974 GB, free: 9.465 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.003721/0.4792, allocations: 0.6758 MB / 0.5981 GB, free: 8.789 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01578/0.495, allocations: 3.257 MB / 0.6012 GB, free: 5.527 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.005423/0.5004, allocations: 1.8 MB / 0.603 GB, free: 3.723 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.008719/0.5091, allocations: 2.907 MB / 0.6058 GB, free: 0.8047 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02726/0.5364, allocations: 11.64 MB / 0.6172 GB, free: 5.125 MB / 462.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.514e-06/0.5364, allocations: 0 / 0.6172 GB, free: 5.125 MB / 462.1 MB
Notification: Performance of FrontEnd: time 2.014e-06/0.5364, allocations: 0 / 0.6172 GB, free: 5.125 MB / 462.1 MB
Notification: Performance of Transformations before backend: time 0.0003064/0.5367, allocations: 0 / 0.6172 GB, free: 5.125 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 0.02417/0.5609, allocations: 7.233 MB / 0.6243 GB, free: 13.82 MB / 478.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.821e-05/0.5609, allocations: 12.03 kB / 0.6243 GB, free: 13.81 MB / 478.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.007563/0.5685, allocations: 1.241 MB / 0.6255 GB, free: 12.56 MB / 478.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.009882/0.5784, allocations: 3.321 MB / 0.6287 GB, free: 9.184 MB / 478.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0009255/0.5793, allocations: 1.011 MB / 0.6297 GB, free: 8.023 MB / 478.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002262/0.5815, allocations: 0.4924 MB / 0.6302 GB, free: 7.531 MB / 478.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02521/0.6068, allocations: 9.462 MB / 0.6394 GB, free: 13.96 MB / 494.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001968/0.6069, allocations: 4 kB / 0.6394 GB, free: 13.96 MB / 494.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.00194/0.6089, allocations: 192 kB / 0.6396 GB, free: 13.77 MB / 494.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001198/0.609, allocations: 124 kB / 0.6397 GB, free: 13.65 MB / 494.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02696/0.636, allocations: 12.66 MB / 0.6521 GB, free: 0.9688 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 0.07053/0.7065, allocations: 26.73 MB / 0.6782 GB, free: 6 MB / 0.5137 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.06243/0.7689, allocations: 26.11 MB / 0.7037 GB, free: 12.79 MB / 0.545 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01026/0.7792, allocations: 4.724 MB / 0.7083 GB, free: 8.039 MB / 0.545 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.04347/0.8227, allocations: 16.9 MB / 0.7248 GB, free: 7.07 MB / 0.5606 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 7.029e-05/0.8227, allocations: 65.11 kB / 0.7249 GB, free: 6.996 MB / 0.5606 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.005648/0.8284, allocations: 1.254 MB / 0.7261 GB, free: 5.738 MB / 0.5606 GB
Notification: Performance of pre-optimization done (n=324): time 1.374e-05/0.8284, allocations: 0 / 0.7261 GB, free: 5.738 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=376): time 0.3502/1.179, allocations: 24.16 MB / 0.7497 GB, free: 170.9 MB / 0.5606 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.323e-05/1.179, allocations: 90.64 kB / 0.7498 GB, free: 170.8 MB / 0.5606 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003909/1.183, allocations: 2.842 MB / 0.7526 GB, free: 169.8 MB / 0.5606 GB
Notification: Performance of collectPreVariables (initialization): time 0.000899/1.183, allocations: 86.27 kB / 0.7527 GB, free: 169.8 MB / 0.5606 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001106/1.185, allocations: 2.224 MB / 0.7548 GB, free: 168.1 MB / 0.5606 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001442/1.186, allocations: 1.361 MB / 0.7562 GB, free: 167.1 MB / 0.5606 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001601/1.188, allocations: 0.9806 MB / 0.7571 GB, free: 166.7 MB / 0.5606 GB
Notification: Performance of setup shared object (initialization): time 3.997e-05/1.188, allocations: 306.8 kB / 0.7574 GB, free: 166.4 MB / 0.5606 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004645/1.192, allocations: 2.961 MB / 0.7603 GB, free: 165 MB / 0.5606 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005543/1.198, allocations: 4.489 MB / 0.7647 GB, free: 161.5 MB / 0.5606 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01028/1.208, allocations: 7.815 MB / 0.7723 GB, free: 156.3 MB / 0.5606 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.854e-05/1.208, allocations: 15.25 kB / 0.7723 GB, free: 156.3 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.06025/1.268, allocations: 13.81 MB / 0.7858 GB, free: 146.5 MB / 0.5606 GB
Notification: Performance of prepare postOptimizeDAE: time 0.0001224/1.269, allocations: 24 kB / 0.7858 GB, free: 146.4 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001152/1.269, allocations: 48 kB / 0.7859 GB, free: 146.4 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.009267/1.278, allocations: 3.469 MB / 0.7893 GB, free: 143.1 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005808/1.284, allocations: 1.272 MB / 0.7905 GB, free: 141.8 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03225/1.316, allocations: 17.88 MB / 0.808 GB, free: 123.6 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005213/1.321, allocations: 247.8 kB / 0.8082 GB, free: 123.4 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001187/1.322, allocations: 282.5 kB / 0.8085 GB, free: 123.1 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 0.003626/1.326, allocations: 1.448 MB / 0.8099 GB, free: 121.7 MB / 0.5606 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001403/1.327, allocations: 349.7 kB / 0.8102 GB, free: 121.3 MB / 0.5606 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03841/1.366, allocations: 9.617 MB / 0.8196 GB, free: 111.8 MB / 0.5606 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.799e-05/1.366, allocations: 42.66 kB / 0.8197 GB, free: 111.7 MB / 0.5606 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.822e-05/1.366, allocations: 4 kB / 0.8197 GB, free: 111.7 MB / 0.5606 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001235/1.366, allocations: 19.92 kB / 0.8197 GB, free: 111.7 MB / 0.5606 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0533/1.419, allocations: 14.36 MB / 0.8337 GB, free: 97.43 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.488e-05/1.419, allocations: 6.688 kB / 0.8337 GB, free: 97.42 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004918/1.424, allocations: 0.8489 MB / 0.8345 GB, free: 96.57 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006539/1.431, allocations: 2.132 MB / 0.8366 GB, free: 94.47 MB / 0.5606 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001051/1.432, allocations: 138.1 kB / 0.8367 GB, free: 94.34 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02277/1.455, allocations: 12.1 MB / 0.8486 GB, free: 81.96 MB / 0.5606 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.51e-06/1.455, allocations: 4 kB / 0.8486 GB, free: 81.95 MB / 0.5606 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0443/1.499, allocations: 12.94 MB / 0.8612 GB, free: 68.95 MB / 0.5606 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003948/1.503, allocations: 0.8996 MB / 0.8621 GB, free: 68.04 MB / 0.5606 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001587/1.504, allocations: 95.97 kB / 0.8622 GB, free: 67.95 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.003636/1.508, allocations: 163.8 kB / 0.8623 GB, free: 67.79 MB / 0.5606 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.00145/1.51, allocations: 468.9 kB / 0.8628 GB, free: 67.33 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0006715/1.51, allocations: 147.9 kB / 0.8629 GB, free: 67.19 MB / 0.5606 GB
Notification: Performance of sorting global known variables: time 0.00285/1.513, allocations: 1.843 MB / 0.8647 GB, free: 65.34 MB / 0.5606 GB
Notification: Performance of sort global known variables: time 1e-07/1.513, allocations: 0 / 0.8647 GB, free: 65.34 MB / 0.5606 GB
Notification: Performance of remove unused functions: time 0.007893/1.521, allocations: 2.066 MB / 0.8667 GB, free: 63.27 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 0.003166/1.524, allocations: 1.326 MB / 0.868 GB, free: 62.14 MB / 0.5606 GB
Notification: Performance of simCode: created initialization part: time 0.01372/1.538, allocations: 7.078 MB / 0.875 GB, free: 55.04 MB / 0.5606 GB
Notification: Performance of simCode: created event and clocks part: time 8.155e-06/1.538, allocations: 0 / 0.875 GB, free: 55.04 MB / 0.5606 GB
Notification: Performance of simCode: created simulation system equations: time 0.007713/1.546, allocations: 3.773 MB / 0.8786 GB, free: 51.23 MB / 0.5606 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004872/1.55, allocations: 0.7709 MB / 0.8794 GB, free: 50.55 MB / 0.5606 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.02034/1.571, allocations: 10.99 MB / 0.8901 GB, free: 39.53 MB / 0.5606 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.003306/1.574, allocations: 2.783 MB / 0.8928 GB, free: 36.75 MB / 0.5606 GB
Notification: Performance of simCode: alias equations: time 0.004769/1.579, allocations: 1.558 MB / 0.8944 GB, free: 35.3 MB / 0.5606 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001811/1.581, allocations: 453.8 kB / 0.8948 GB, free: 34.86 MB / 0.5606 GB
Notification: Performance of SimCode: time 1.021e-06/1.581, allocations: 0 / 0.8948 GB, free: 34.86 MB / 0.5606 GB
Notification: Performance of Templates: time 0.3632/1.944, allocations: 100.1 MB / 0.9925 GB, free: 182.4 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: 9.690968678332865]
Failed to read output from testmodel.py, exit status != 0:
1.9534350377507508 1.9627828 1.423738145
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fe92e7def50>