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 0.001396/0.001396, allocations: 110.2 kB / 19.69 MB, free: 2.254 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 0.001531/0.001531, allocations: 218.4 kB / 23.01 MB, free: 4.566 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 1.432/1.432, allocations: 230.6 MB / 256.8 MB, free: 8.02 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 0.1385/0.1385, allocations: 23.89 MB / 337.1 MB, free: 11.18 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 0.002072/0.002072, allocations: 67.89 kB / 472.5 MB, free: 7.125 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3777/0.3798, allocations: 59.87 MB / 0.5199 GB, free: 9.82 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 0.045/0.4248, allocations: 30.58 MB / 0.5498 GB, free: 9.48 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.03634/0.4612, allocations: 26.29 MB / 0.5754 GB, free: 1.148 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002424/0.4636, allocations: 35.69 kB / 0.5755 GB, free: 1.113 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.002179/0.4658, allocations: 0.6009 MB / 0.5761 GB, free: 0.5078 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.00782/0.4736, allocations: 2.169 MB / 0.5782 GB, free: 14.32 MB / 430.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01166/0.4852, allocations: 3.589 MB / 0.5817 GB, free: 10.71 MB / 430.1 MB
Notification: Performance of NFFlatten.flatten: time 0.009758/0.495, allocations: 7.402 MB / 0.5889 GB, free: 3.281 MB / 430.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.006535/0.5015, allocations: 4.331 MB / 0.5931 GB, free: 14.88 MB / 446.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008911/0.5104, allocations: 4.963 MB / 0.598 GB, free: 9.902 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.01009/0.5205, allocations: 4.768 MB / 0.6026 GB, free: 5.121 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.003012/0.5235, allocations: 0.6758 MB / 0.6033 GB, free: 4.445 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01383/0.5374, allocations: 3.363 MB / 0.6066 GB, free: 1.078 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.00402/0.5414, allocations: 1.812 MB / 0.6084 GB, free: 15.26 MB / 462.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.007407/0.5488, allocations: 3.358 MB / 0.6116 GB, free: 11.89 MB / 462.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02393/0.5727, allocations: 11.61 MB / 0.623 GB, free: 244 kB / 462.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.687e-06/0.5727, allocations: 7.938 kB / 0.623 GB, free: 236 kB / 462.1 MB
Notification: Performance of FrontEnd: time 2.505e-06/0.5727, allocations: 0 / 0.623 GB, free: 236 kB / 462.1 MB
Notification: Performance of Transformations before backend: time 0.0003418/0.5731, allocations: 0 / 0.623 GB, free: 236 kB / 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 0.0241/0.5972, allocations: 7.249 MB / 0.6301 GB, free: 8.91 MB / 478.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.477e-05/0.5972, allocations: 8.031 kB / 0.6301 GB, free: 8.902 MB / 478.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.007408/0.6046, allocations: 1.241 MB / 0.6313 GB, free: 7.656 MB / 478.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.00907/0.6137, allocations: 3.317 MB / 0.6345 GB, free: 4.281 MB / 478.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001022/0.6147, allocations: 1.003 MB / 0.6355 GB, free: 3.129 MB / 478.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002497/0.6172, allocations: 0.4924 MB / 0.636 GB, free: 2.637 MB / 478.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.02314/0.6404, allocations: 9.47 MB / 0.6452 GB, free: 9.059 MB / 494.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001071/0.6405, allocations: 0 / 0.6452 GB, free: 9.059 MB / 494.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.001294/0.6418, allocations: 196 kB / 0.6454 GB, free: 8.867 MB / 494.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001133/0.6419, allocations: 116 kB / 0.6455 GB, free: 8.754 MB / 494.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02678/0.6687, allocations: 12.75 MB / 0.658 GB, free: 11.98 MB / 0.4981 GB
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 0.07325/0.7419, allocations: 30.78 MB / 0.688 GB, free: 12.46 MB / 0.5294 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.06064/0.8025, allocations: 26.87 MB / 0.7143 GB, free: 2.5 MB / 0.545 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.009438/0.812, allocations: 4.721 MB / 0.7189 GB, free: 13.75 MB / 0.5606 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.2985/1.11, allocations: 17.73 MB / 0.7362 GB, free: 168.9 MB / 0.5606 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.608e-05/1.111, allocations: 71.22 kB / 0.7363 GB, free: 168.9 MB / 0.5606 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004967/1.116, allocations: 1.278 MB / 0.7375 GB, free: 168.9 MB / 0.5606 GB
Notification: Performance of pre-optimization done (n=324): time 1.882e-05/1.116, allocations: 0 / 0.7375 GB, free: 168.9 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=376): time 0.09573/1.211, allocations: 24.18 MB / 0.7611 GB, free: 162.2 MB / 0.5606 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.486e-05/1.211, allocations: 95.83 kB / 0.7612 GB, free: 162.1 MB / 0.5606 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003743/1.215, allocations: 2.973 MB / 0.7641 GB, free: 160.6 MB / 0.5606 GB
Notification: Performance of collectPreVariables (initialization): time 0.001152/1.216, allocations: 85.61 kB / 0.7642 GB, free: 160.5 MB / 0.5606 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001239/1.217, allocations: 2.231 MB / 0.7664 GB, free: 158.8 MB / 0.5606 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001634/1.219, allocations: 1.361 MB / 0.7677 GB, free: 157.8 MB / 0.5606 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001265/1.22, allocations: 0.9826 MB / 0.7687 GB, free: 157.3 MB / 0.5606 GB
Notification: Performance of setup shared object (initialization): time 4.77e-05/1.22, allocations: 303.3 kB / 0.769 GB, free: 157 MB / 0.5606 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.003839/1.224, allocations: 2.963 MB / 0.7719 GB, free: 155.4 MB / 0.5606 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004329/1.229, allocations: 4.489 MB / 0.7762 GB, free: 151.9 MB / 0.5606 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.00901/1.238, allocations: 7.808 MB / 0.7839 GB, free: 146.7 MB / 0.5606 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.529e-05/1.238, allocations: 11.78 kB / 0.7839 GB, free: 146.7 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05303/1.291, allocations: 13.83 MB / 0.7974 GB, free: 134.3 MB / 0.5606 GB
Notification: Performance of prepare postOptimizeDAE: time 5.573e-05/1.291, allocations: 28 kB / 0.7974 GB, free: 134.3 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.405e-05/1.291, allocations: 53.22 kB / 0.7975 GB, free: 134.2 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.007851/1.299, allocations: 3.473 MB / 0.8008 GB, free: 130.9 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00518/1.304, allocations: 1.27 MB / 0.8021 GB, free: 129.6 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02853/1.332, allocations: 18.14 MB / 0.8198 GB, free: 111.2 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00475/1.337, allocations: 255.8 kB / 0.82 GB, free: 111 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001066/1.338, allocations: 279.8 kB / 0.8203 GB, free: 110.7 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 0.003269/1.341, allocations: 1.454 MB / 0.8217 GB, free: 109.2 MB / 0.5606 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001164/1.343, allocations: 361.6 kB / 0.8221 GB, free: 108.9 MB / 0.5606 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03295/1.376, allocations: 9.631 MB / 0.8315 GB, free: 99.36 MB / 0.5606 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.988e-05/1.376, allocations: 40 kB / 0.8315 GB, free: 99.32 MB / 0.5606 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.799e-05/1.376, allocations: 11.92 kB / 0.8315 GB, free: 99.3 MB / 0.5606 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001136/1.376, allocations: 15.94 kB / 0.8315 GB, free: 99.29 MB / 0.5606 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04292/1.419, allocations: 15.49 MB / 0.8467 GB, free: 83.83 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.287e-05/1.419, allocations: 6.688 kB / 0.8467 GB, free: 83.82 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004325/1.423, allocations: 0.8481 MB / 0.8475 GB, free: 82.98 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005622/1.429, allocations: 2.127 MB / 0.8496 GB, free: 80.89 MB / 0.5606 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0008792/1.43, allocations: 143.8 kB / 0.8497 GB, free: 80.75 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02012/1.45, allocations: 12.32 MB / 0.8617 GB, free: 68.12 MB / 0.5606 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.819e-06/1.45, allocations: 14.91 kB / 0.8618 GB, free: 68.11 MB / 0.5606 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03746/1.487, allocations: 12.95 MB / 0.8744 GB, free: 55.1 MB / 0.5606 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003038/1.49, allocations: 0.9288 MB / 0.8753 GB, free: 54.18 MB / 0.5606 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0009124/1.491, allocations: 91.55 kB / 0.8754 GB, free: 54.09 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.00261/1.494, allocations: 164.4 kB / 0.8756 GB, free: 53.93 MB / 0.5606 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000923/1.495, allocations: 474.7 kB / 0.876 GB, free: 53.47 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002978/1.495, allocations: 147.9 kB / 0.8762 GB, free: 53.32 MB / 0.5606 GB
Notification: Performance of sorting global known variables: time 0.002186/1.497, allocations: 1.992 MB / 0.8781 GB, free: 51.33 MB / 0.5606 GB
Notification: Performance of sort global known variables: time 8e-08/1.497, allocations: 0 / 0.8781 GB, free: 51.33 MB / 0.5606 GB
Notification: Performance of remove unused functions: time 0.006412/1.503, allocations: 2.07 MB / 0.8801 GB, free: 49.28 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 0.002382/1.506, allocations: 1.323 MB / 0.8814 GB, free: 48.14 MB / 0.5606 GB
Notification: Performance of simCode: created initialization part: time 0.01221/1.518, allocations: 7.079 MB / 0.8883 GB, free: 41.04 MB / 0.5606 GB
Notification: Performance of simCode: created event and clocks part: time 9.939e-06/1.518, allocations: 0 / 0.8883 GB, free: 41.04 MB / 0.5606 GB
Notification: Performance of simCode: created simulation system equations: time 0.006958/1.525, allocations: 3.769 MB / 0.892 GB, free: 37.24 MB / 0.5606 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003667/1.529, allocations: 0.7801 MB / 0.8928 GB, free: 36.54 MB / 0.5606 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01718/1.546, allocations: 10.96 MB / 0.9035 GB, free: 25.52 MB / 0.5606 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002018/1.548, allocations: 3.207 MB / 0.9066 GB, free: 22.27 MB / 0.5606 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.002037/1.55, allocations: 0.4944 MB / 0.9071 GB, free: 21.78 MB / 0.5606 GB
Notification: Performance of SimCode: time 1.172e-06/1.55, allocations: 0 / 0.9071 GB, free: 21.78 MB / 0.5606 GB
Notification: Performance of Templates: time 0.3917/1.942, allocations: 147.4 MB / 1.051 GB, free: 130.5 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 sys.exit(0), Time elapsed: 14.873994566005422]
Failed to read output from testmodel.py, exit status != 0:
1.9518673109996598 1.960772167 1.385538946
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f85f83def50>