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 0.001494/0.001494, allocations: 112.4 kB / 17.13 MB, free: 6.008 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 0.001682/0.001682, allocations: 211.2 kB / 20.1 MB, free: 3.055 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 1.476/1.476, allocations: 230.6 MB / 253.5 MB, free: 15.12 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 0.135/0.135, allocations: 23.9 MB / 333.4 MB, free: 1.176 MB / 254.1 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 0.002077/0.002077, allocations: 67.62 kB / 467.3 MB, free: 30.56 MB / 350.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09196/0.09404, allocations: 59.83 MB / 0.5147 GB, free: 12.39 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 0.04316/0.1372, allocations: 30.53 MB / 0.5445 GB, free: 13.88 MB / 414.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03263/0.1698, allocations: 26.23 MB / 0.5702 GB, free: 3.559 MB / 430.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001294/0.1711, allocations: 35.69 kB / 0.5702 GB, free: 3.523 MB / 430.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001565/0.1727, allocations: 0.6048 MB / 0.5708 GB, free: 2.914 MB / 430.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.005621/0.1783, allocations: 2.153 MB / 0.5729 GB, free: 0.7461 MB / 430.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.008903/0.1872, allocations: 3.55 MB / 0.5763 GB, free: 13.18 MB / 446.1 MB
Notification: Performance of NFFlatten.flatten: time 0.008197/0.1954, allocations: 7.402 MB / 0.5836 GB, free: 5.742 MB / 446.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006515/0.2019, allocations: 5.12 MB / 0.5886 GB, free: 0.5469 MB / 446.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.225/0.4269, allocations: 4.963 MB / 0.5934 GB, free: 24.09 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.008758/0.4357, allocations: 4.76 MB / 0.5981 GB, free: 23.63 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.00238/0.438, allocations: 0.6746 MB / 0.5987 GB, free: 23.63 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01155/0.4496, allocations: 3.368 MB / 0.602 GB, free: 23.63 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003282/0.4529, allocations: 1.799 MB / 0.6038 GB, free: 23.44 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.005676/0.4585, allocations: 3.358 MB / 0.6071 GB, free: 22.68 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.01615/0.4747, allocations: 11.61 MB / 0.6184 GB, free: 19.88 MB / 446.1 MB
Notification: Performance of FrontEnd - DAE generated: time 1.075e-05/0.4747, allocations: 10.78 kB / 0.6184 GB, free: 19.87 MB / 446.1 MB
Notification: Performance of FrontEnd: time 3.146e-06/0.4747, allocations: 0 / 0.6184 GB, free: 19.87 MB / 446.1 MB
Notification: Performance of Transformations before backend: time 0.0001943/0.4749, allocations: 0 / 0.6184 GB, free: 19.87 MB / 446.1 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 0.01692/0.4918, allocations: 7.321 MB / 0.6256 GB, free: 16.12 MB / 446.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.451e-05/0.4918, allocations: 10.16 kB / 0.6256 GB, free: 16.12 MB / 446.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.005981/0.4978, allocations: 1.241 MB / 0.6268 GB, free: 15.56 MB / 446.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.005836/0.5037, allocations: 3.277 MB / 0.63 GB, free: 13.79 MB / 446.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004003/0.5041, allocations: 0.678 MB / 0.6306 GB, free: 13.26 MB / 446.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001269/0.5053, allocations: 0.4934 MB / 0.6311 GB, free: 12.92 MB / 446.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0137/0.519, allocations: 9.446 MB / 0.6403 GB, free: 3.383 MB / 446.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 7.298e-05/0.5191, allocations: 4 kB / 0.6404 GB, free: 3.379 MB / 446.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0006903/0.5198, allocations: 196 kB / 0.6405 GB, free: 3.188 MB / 446.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.197e-05/0.5198, allocations: 118.7 kB / 0.6407 GB, free: 3.074 MB / 446.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02169/0.5415, allocations: 12.73 MB / 0.6531 GB, free: 6.34 MB / 462.1 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 0.05941/0.601, allocations: 30.62 MB / 0.683 GB, free: 7.566 MB / 494.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.06579/0.6667, allocations: 40.96 MB / 0.723 GB, free: 12.11 MB / 0.5294 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.008757/0.6755, allocations: 4.724 MB / 0.7276 GB, free: 7.355 MB / 0.5294 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.03592/0.7114, allocations: 21.22 MB / 0.7483 GB, free: 1.426 MB / 0.545 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.466e-05/0.7115, allocations: 69.09 kB / 0.7484 GB, free: 1.348 MB / 0.545 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004999/0.7165, allocations: 1.268 MB / 0.7496 GB, free: 136 kB / 0.545 GB
Notification: Performance of pre-optimization done (n=324): time 2.198e-05/0.7165, allocations: 0 / 0.7496 GB, free: 136 kB / 0.545 GB
Notification: Performance of matching and sorting (n=376): time 0.09915/0.8156, allocations: 24.42 MB / 0.7735 GB, free: 7.824 MB / 0.5762 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.689e-05/0.8157, allocations: 90.36 kB / 0.7736 GB, free: 7.723 MB / 0.5762 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004678/0.8204, allocations: 2.958 MB / 0.7764 GB, free: 4.75 MB / 0.5762 GB
Notification: Performance of collectPreVariables (initialization): time 0.000852/0.8213, allocations: 92.33 kB / 0.7765 GB, free: 4.656 MB / 0.5762 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001781/0.823, allocations: 2.224 MB / 0.7787 GB, free: 2.426 MB / 0.5762 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001631/0.8247, allocations: 1.361 MB / 0.78 GB, free: 1.082 MB / 0.5762 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001737/0.8264, allocations: 0.9808 MB / 0.781 GB, free: 92 kB / 0.5762 GB
Notification: Performance of setup shared object (initialization): time 0.0001383/0.8265, allocations: 306.8 kB / 0.7813 GB, free: 15.79 MB / 0.5919 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.005082/0.8316, allocations: 2.959 MB / 0.7842 GB, free: 12.82 MB / 0.5919 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.006324/0.8379, allocations: 4.482 MB / 0.7886 GB, free: 7.719 MB / 0.5919 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01198/0.8499, allocations: 7.803 MB / 0.7962 GB, free: 15.53 MB / 0.6075 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.496e-05/0.85, allocations: 14.66 kB / 0.7962 GB, free: 15.52 MB / 0.6075 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.06167/0.9116, allocations: 13.81 MB / 0.8097 GB, free: 2.141 MB / 0.6075 GB
Notification: Performance of prepare postOptimizeDAE: time 5.896e-05/0.9117, allocations: 28 kB / 0.8097 GB, free: 2.113 MB / 0.6075 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.216e-05/0.9118, allocations: 50.69 kB / 0.8098 GB, free: 2.066 MB / 0.6075 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.2283/1.14, allocations: 3.467 MB / 0.8131 GB, free: 217.6 MB / 0.6075 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.006038/1.146, allocations: 1.271 MB / 0.8144 GB, free: 217.6 MB / 0.6075 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.03387/1.18, allocations: 18.44 MB / 0.8324 GB, free: 211.4 MB / 0.6075 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004517/1.185, allocations: 250.9 kB / 0.8326 GB, free: 211.4 MB / 0.6075 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0005885/1.185, allocations: 287.2 kB / 0.8329 GB, free: 211.3 MB / 0.6075 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 0.002309/1.187, allocations: 1.452 MB / 0.8343 GB, free: 210.8 MB / 0.6075 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0007982/1.188, allocations: 366.1 kB / 0.8347 GB, free: 210.8 MB / 0.6075 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03654/1.225, allocations: 9.632 MB / 0.8441 GB, free: 207.7 MB / 0.6075 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.353e-05/1.225, allocations: 43.25 kB / 0.8441 GB, free: 207.7 MB / 0.6075 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.558e-05/1.225, allocations: 3.938 kB / 0.8441 GB, free: 207.7 MB / 0.6075 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.903e-05/1.225, allocations: 21.61 kB / 0.8441 GB, free: 207.6 MB / 0.6075 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04304/1.268, allocations: 15.42 MB / 0.8592 GB, free: 198.6 MB / 0.6075 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.343e-05/1.268, allocations: 4 kB / 0.8592 GB, free: 198.6 MB / 0.6075 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004613/1.273, allocations: 0.8451 MB / 0.86 GB, free: 197.7 MB / 0.6075 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005854/1.278, allocations: 2.136 MB / 0.8621 GB, free: 195.7 MB / 0.6075 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0007486/1.279, allocations: 135.9 kB / 0.8622 GB, free: 195.6 MB / 0.6075 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02151/1.301, allocations: 12.63 MB / 0.8746 GB, free: 182.6 MB / 0.6075 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.677e-06/1.301, allocations: 7.984 kB / 0.8746 GB, free: 182.6 MB / 0.6075 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03907/1.34, allocations: 12.96 MB / 0.8872 GB, free: 169.8 MB / 0.6075 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.00219/1.342, allocations: 0.9535 MB / 0.8882 GB, free: 168.9 MB / 0.6075 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0006688/1.343, allocations: 92.73 kB / 0.8883 GB, free: 168.8 MB / 0.6075 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002456/1.345, allocations: 162.5 kB / 0.8884 GB, free: 168.7 MB / 0.6075 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009968/1.346, allocations: 458.4 kB / 0.8889 GB, free: 168.2 MB / 0.6075 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003056/1.346, allocations: 143.9 kB / 0.889 GB, free: 168.1 MB / 0.6075 GB
Notification: Performance of sorting global known variables: time 0.002243/1.349, allocations: 1.991 MB / 0.8909 GB, free: 166.1 MB / 0.6075 GB
Notification: Performance of sort global known variables: time 8e-08/1.349, allocations: 0 / 0.8909 GB, free: 166.1 MB / 0.6075 GB
Notification: Performance of remove unused functions: time 0.006086/1.355, allocations: 2.07 MB / 0.893 GB, free: 164.2 MB / 0.6075 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 0.002287/1.357, allocations: 1.342 MB / 0.8943 GB, free: 163.1 MB / 0.6075 GB
Notification: Performance of simCode: created initialization part: time 0.01197/1.369, allocations: 7.054 MB / 0.9012 GB, free: 156 MB / 0.6075 GB
Notification: Performance of simCode: created event and clocks part: time 5.661e-06/1.369, allocations: 0 / 0.9012 GB, free: 156 MB / 0.6075 GB
Notification: Performance of simCode: created simulation system equations: time 0.006543/1.376, allocations: 3.774 MB / 0.9048 GB, free: 152.2 MB / 0.6075 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003349/1.379, allocations: 0.7848 MB / 0.9056 GB, free: 151.5 MB / 0.6075 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01534/1.394, allocations: 10.9 MB / 0.9162 GB, free: 140.6 MB / 0.6075 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001949/1.396, allocations: 3.217 MB / 0.9194 GB, free: 137.4 MB / 0.6075 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00185/1.398, allocations: 0.4901 MB / 0.9199 GB, free: 136.9 MB / 0.6075 GB
Notification: Performance of SimCode: time 1.041e-06/1.398, allocations: 0 / 0.9199 GB, free: 136.9 MB / 0.6075 GB
Notification: Performance of Templates: time 0.3469/1.745, allocations: 147.4 MB / 1.064 GB, free: 201.5 MB / 0.6075 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 sys.exit(0), Time elapsed: 14.288119270000607]
Failed to read output from testmodel.py, exit status != 0:
1.7535314690030646 1.762795173 1.285674618
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f89ecd4ef50>