Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_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 0.001479/0.001479, allocations: 73.97 kB / 20.66 MB, free: 3.844 MB / 18.57 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 0.001487/0.001487, allocations: 169 kB / 24.06 MB, free: 456 kB / 18.57 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 0.9556/0.9556, allocations: 177.1 MB / 204.5 MB, free: 5.488 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.09492/0.09492, allocations: 17.37 MB / 278.4 MB, free: 11.47 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/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_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_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.284e-06/2.284e-06, allocations: 0 / 354.7 MB, free: 9.648 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.469e-05/2.697e-05, allocations: 2.312 kB / 354.7 MB, free: 9.645 MB / 282.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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 0.03001/0.03004, allocations: 32.84 MB / 387.5 MB, free: 8.926 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01453/0.04457, allocations: 15.43 MB / 403 MB, free: 9.434 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001377/0.04595, allocations: 31.75 kB / 403 MB, free: 9.402 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0009933/0.04694, allocations: 444.2 kB / 403.4 MB, free: 8.965 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.003712/0.05066, allocations: 1.582 MB / 405 MB, free: 7.371 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004955/0.05561, allocations: 2.463 MB / 407.5 MB, free: 4.895 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.1395/0.1952, allocations: 7.628 MB / 415.1 MB, free: 36.35 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005886/0.201, allocations: 4.55 MB / 419.7 MB, free: 36.07 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.01225/0.2133, allocations: 6.304 MB / 426 MB, free: 35.16 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007944/0.2212, allocations: 4.661 MB / 430.6 MB, free: 34.16 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.002774/0.224, allocations: 0.6779 MB / 431.3 MB, free: 34.16 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.008825/0.2328, allocations: 2.082 MB / 433.4 MB, free: 33.91 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.003152/0.236, allocations: 1.827 MB / 435.2 MB, free: 32.98 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.005514/0.2415, allocations: 2.557 MB / 437.8 MB, free: 31.75 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01188/0.2534, allocations: 8.482 MB / 446.3 MB, free: 23.84 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.344e-06/0.2534, allocations: 1.125 kB / 446.3 MB, free: 23.84 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.092e-06/0.2534, allocations: 0 / 446.3 MB, free: 23.84 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.0003256/0.2537, allocations: 0 / 446.3 MB, free: 23.84 MB / 330.7 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 0.01208/0.2658, allocations: 6.701 MB / 453 MB, free: 17.42 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.252e-05/0.2659, allocations: 14.69 kB / 453 MB, free: 17.41 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.004578/0.2704, allocations: 2.043 MB / 455 MB, free: 15.36 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.003931/0.2744, allocations: 2.637 MB / 457.6 MB, free: 12.84 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0003299/0.2747, allocations: 0.9985 MB / 458.6 MB, free: 11.69 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0008433/0.2755, allocations: 0.49 MB / 459.1 MB, free: 11.21 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.006569/0.2821, allocations: 5.212 MB / 464.3 MB, free: 6.062 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 7.389e-05/0.2822, allocations: 2.844 kB / 464.4 MB, free: 6.062 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004723/0.2826, allocations: 196.4 kB / 464.5 MB, free: 5.871 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.599e-05/0.2827, allocations: 119.9 kB / 464.7 MB, free: 5.754 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.005655/0.2883, allocations: 4.862 MB / 469.5 MB, free: 0.8828 MB / 330.7 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 0.02927/0.3176, allocations: 18.64 MB / 488.2 MB, free: 14.88 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0371/0.3547, allocations: 31.7 MB / 0.5077 GB, free: 248 kB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.003058/0.3578, allocations: 1.861 MB / 0.5095 GB, free: 14.41 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01562/0.3734, allocations: 10.4 MB / 0.5197 GB, free: 4.277 MB / 394.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.774e-05/0.3735, allocations: 70.56 kB / 0.5197 GB, free: 4.199 MB / 394.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.00259/0.376, allocations: 1.136 MB / 0.5208 GB, free: 3.121 MB / 394.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.112e-05/0.3761, allocations: 0 / 0.5208 GB, free: 3.121 MB / 394.7 MB
Notification: Performance of matching and sorting (n=376): time 0.03976/0.4158, allocations: 11.88 MB / 0.5324 GB, free: 7.422 MB / 410.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.055e-05/0.4159, allocations: 93.83 kB / 0.5325 GB, free: 7.32 MB / 410.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.002725/0.4186, allocations: 2.656 MB / 0.5351 GB, free: 5.016 MB / 410.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.001058/0.4197, allocations: 85.7 kB / 0.5352 GB, free: 4.926 MB / 410.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001966/0.4216, allocations: 2.435 MB / 0.5376 GB, free: 2.598 MB / 410.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001545/0.4232, allocations: 1.427 MB / 0.539 GB, free: 1.25 MB / 410.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001083/0.4242, allocations: 1.059 MB / 0.54 GB, free: 280 kB / 410.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001231/0.4244, allocations: 480.8 kB / 0.5405 GB, free: 15.8 MB / 426.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001123/0.4255, allocations: 0.8239 MB / 0.5413 GB, free: 14.97 MB / 426.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002437/0.4279, allocations: 3.085 MB / 0.5443 GB, free: 11.09 MB / 426.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003735/0.4317, allocations: 4.399 MB / 0.5486 GB, free: 6.117 MB / 426.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.444e-05/0.4317, allocations: 12 kB / 0.5486 GB, free: 6.105 MB / 426.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02481/0.4565, allocations: 7.07 MB / 0.5555 GB, free: 15.45 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 4.736e-05/0.4565, allocations: 24 kB / 0.5555 GB, free: 15.43 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.927e-05/0.4566, allocations: 48 kB / 0.5556 GB, free: 15.38 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01386/0.4705, allocations: 5.718 MB / 0.5611 GB, free: 9.77 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003437/0.4739, allocations: 1.193 MB / 0.5623 GB, free: 8.656 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01337/0.4873, allocations: 8.414 MB / 0.5705 GB, free: 40 kB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.147/0.6343, allocations: 146.7 kB / 0.5707 GB, free: 127.3 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009082/0.6352, allocations: 241.1 kB / 0.5709 GB, free: 127.3 MB / 442.7 MB
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 0.001578/0.6368, allocations: 464.7 kB / 0.5713 GB, free: 127.1 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001001/0.6378, allocations: 465.4 kB / 0.5718 GB, free: 127.1 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01627/0.6541, allocations: 5.098 MB / 0.5768 GB, free: 126.9 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.947e-05/0.6541, allocations: 45.62 kB / 0.5768 GB, free: 126.9 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.596e-05/0.6541, allocations: 3.562 kB / 0.5768 GB, free: 126.9 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.427e-05/0.6542, allocations: 25.45 kB / 0.5768 GB, free: 126.9 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02338/0.6776, allocations: 9.159 MB / 0.5858 GB, free: 125.9 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.394e-05/0.6776, allocations: 3.375 kB / 0.5858 GB, free: 125.9 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00243/0.6801, allocations: 0.7787 MB / 0.5865 GB, free: 125.9 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.007638/0.6877, allocations: 2.419 MB / 0.5889 GB, free: 125.8 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0006048/0.6883, allocations: 132.8 kB / 0.589 GB, free: 125.8 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.008712/0.697, allocations: 7.329 MB / 0.5962 GB, free: 120.3 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.359e-06/0.697, allocations: 11.75 kB / 0.5962 GB, free: 120.3 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01651/0.7135, allocations: 6.101 MB / 0.6022 GB, free: 119.6 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001482/0.715, allocations: 0.6749 MB / 0.6028 GB, free: 119.4 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003838/0.7154, allocations: 94.08 kB / 0.6029 GB, free: 119.4 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001086/0.7165, allocations: 81.09 kB / 0.603 GB, free: 119.4 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0006152/0.7171, allocations: 397.7 kB / 0.6034 GB, free: 119.4 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002047/0.7173, allocations: 118.2 kB / 0.6035 GB, free: 119.4 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001065/0.7184, allocations: 1.238 MB / 0.6047 GB, free: 119.2 MB / 442.7 MB
Notification: Performance of sort global known variables: time 2.3e-07/0.7184, allocations: 0 / 0.6047 GB, free: 119.2 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.004281/0.7226, allocations: 1.781 MB / 0.6064 GB, free: 119.2 MB / 442.7 MB
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 0.001432/0.7241, allocations: 0.8811 MB / 0.6073 GB, free: 119 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.005476/0.7295, allocations: 3.781 MB / 0.611 GB, free: 117.3 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 5.05e-06/0.7296, allocations: 0 / 0.611 GB, free: 117.3 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.00286/0.7324, allocations: 2.212 MB / 0.6131 GB, free: 115.2 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.00239/0.7348, allocations: 0.8172 MB / 0.6139 GB, free: 114.4 MB / 442.7 MB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01102/0.7458, allocations: 8.577 MB / 0.6223 GB, free: 105.9 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0008328/0.7467, allocations: 1.264 MB / 0.6235 GB, free: 104.6 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.001973/0.7486, allocations: 0.6009 MB / 0.6241 GB, free: 104.1 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00166/0.7503, allocations: 1.049 MB / 0.6251 GB, free: 103.1 MB / 442.7 MB
Notification: Performance of SimCode: time 1.683e-06/0.7503, allocations: 0 / 0.6251 GB, free: 103.1 MB / 442.7 MB
Notification: Performance of Templates: time 0.08579/0.8361, allocations: 94.66 MB / 0.7176 GB, free: 9.773 MB / 442.7 MB
"
[Timeout remaining time 659]
make -j1 -f Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 240]
[Calling os._exit(0), Time elapsed: 5.708573704585433]