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 0.001423/0.001423, allocations: 81.17 kB / 19.87 MB, free: 4.621 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 0.001629/0.001629, allocations: 169 kB / 23.27 MB, free: 1.223 MB / 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 0.9823/0.9823, allocations: 177.2 MB / 203.7 MB, free: 5.52 MB / 186.7 MB
"
[Timeout remaining time 179]
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 0.1034/0.1034, allocations: 17.47 MB / 277.7 MB, free: 11.42 MB / 266.7 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: Performance of FrontEnd - loaded program: time 1.663e-06/1.663e-06, allocations: 0 / 354 MB, free: 9.555 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.283e-05/1.45e-05, allocations: 6.25 kB / 354 MB, free: 9.547 MB / 282.7 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 0.026/0.02601, allocations: 32.87 MB / 386.9 MB, free: 8.789 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01226/0.03827, allocations: 15.43 MB / 402.3 MB, free: 9.305 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007978/0.03907, allocations: 39.69 kB / 402.4 MB, free: 9.266 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0008093/0.03988, allocations: 444.2 kB / 402.8 MB, free: 8.828 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002275/0.04216, allocations: 1.578 MB / 404.4 MB, free: 7.238 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.003355/0.04551, allocations: 2.459 MB / 406.8 MB, free: 4.766 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.1302/0.1757, allocations: 7.628 MB / 414.5 MB, free: 36.32 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004996/0.1807, allocations: 4.553 MB / 419 MB, free: 36.05 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008768/0.1895, allocations: 6.308 MB / 425.3 MB, free: 35.09 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.007618/0.1971, allocations: 4.656 MB / 430 MB, free: 34.04 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.003258/0.2004, allocations: 0.6735 MB / 430.7 MB, free: 34.04 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.007051/0.2074, allocations: 2.084 MB / 432.7 MB, free: 33.79 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.003209/0.2106, allocations: 1.83 MB / 434.6 MB, free: 32.87 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.004883/0.2155, allocations: 2.555 MB / 437.1 MB, free: 31.56 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.01074/0.2263, allocations: 8.489 MB / 445.6 MB, free: 23.64 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 6.773e-06/0.2263, allocations: 0 / 445.6 MB, free: 23.64 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.563e-06/0.2263, allocations: 1.656 kB / 445.6 MB, free: 23.64 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.0003712/0.2266, allocations: 0 / 445.6 MB, free: 23.64 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 0.01055/0.2372, allocations: 6.705 MB / 452.3 MB, free: 17.21 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.39e-05/0.2372, allocations: 8.031 kB / 452.3 MB, free: 17.2 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.003912/0.2411, allocations: 2.043 MB / 454.4 MB, free: 15.15 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.003107/0.2443, allocations: 2.638 MB / 457 MB, free: 12.63 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0002684/0.2445, allocations: 1.005 MB / 458 MB, free: 11.48 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0006305/0.2452, allocations: 0.4948 MB / 458.5 MB, free: 10.99 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.005644/0.2508, allocations: 5.207 MB / 463.7 MB, free: 5.852 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 6.054e-05/0.2509, allocations: 3.469 kB / 463.7 MB, free: 5.852 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004107/0.2513, allocations: 192.4 kB / 463.9 MB, free: 5.664 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.065e-05/0.2513, allocations: 119.9 kB / 464 MB, free: 5.547 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.005367/0.2567, allocations: 4.86 MB / 468.9 MB, free: 0.6758 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 0.0269/0.2836, allocations: 18.64 MB / 487.5 MB, free: 14.67 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.05411/0.3377, allocations: 31.69 MB / 0.507 GB, free: 40 kB / 378.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.009773/0.3475, allocations: 1.86 MB / 0.5089 GB, free: 14.21 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.03759/0.3851, allocations: 10.45 MB / 0.5191 GB, free: 4.086 MB / 394.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.931e-05/0.3851, allocations: 67.94 kB / 0.5191 GB, free: 4.008 MB / 394.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.00588/0.391, allocations: 1.145 MB / 0.5203 GB, free: 2.926 MB / 394.7 MB
Notification: Performance of pre-optimization done (n=324): time 2.051e-05/0.391, allocations: 0 / 0.5203 GB, free: 2.926 MB / 394.7 MB
Notification: Performance of matching and sorting (n=376): time 0.0385/0.4295, allocations: 11.88 MB / 0.5319 GB, free: 7.227 MB / 410.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.221e-05/0.4296, allocations: 93.02 kB / 0.5319 GB, free: 7.125 MB / 410.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00253/0.4321, allocations: 2.662 MB / 0.5345 GB, free: 4.812 MB / 410.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0007803/0.4329, allocations: 85.7 kB / 0.5346 GB, free: 4.723 MB / 410.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001205/0.4341, allocations: 2.43 MB / 0.537 GB, free: 2.398 MB / 410.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001335/0.4354, allocations: 1.425 MB / 0.5384 GB, free: 1.051 MB / 410.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001137/0.4366, allocations: 1.058 MB / 0.5394 GB, free: 80 kB / 410.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001159/0.4367, allocations: 479.1 kB / 0.5399 GB, free: 15.61 MB / 426.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001258/0.4379, allocations: 0.8277 MB / 0.5407 GB, free: 14.78 MB / 426.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002251/0.4402, allocations: 3.085 MB / 0.5437 GB, free: 10.89 MB / 426.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.004038/0.4442, allocations: 4.4 MB / 0.548 GB, free: 5.922 MB / 426.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.169e-05/0.4443, allocations: 12 kB / 0.548 GB, free: 5.91 MB / 426.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02374/0.468, allocations: 7.073 MB / 0.5549 GB, free: 15.25 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 4.8e-05/0.468, allocations: 25.12 kB / 0.5549 GB, free: 15.23 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.824e-05/0.4681, allocations: 48 kB / 0.555 GB, free: 15.18 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01318/0.4813, allocations: 5.716 MB / 0.5606 GB, free: 9.574 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003205/0.4845, allocations: 1.193 MB / 0.5617 GB, free: 8.461 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.1536/0.6381, allocations: 8.404 MB / 0.5699 GB, free: 126.2 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003687/0.6418, allocations: 156 kB / 0.5701 GB, free: 126.2 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009592/0.6428, allocations: 239.7 kB / 0.5703 GB, free: 126.2 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 0.001939/0.6447, allocations: 466 kB / 0.5708 GB, free: 126 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00101/0.6457, allocations: 466.2 kB / 0.5712 GB, free: 126 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01611/0.6618, allocations: 5.1 MB / 0.5762 GB, free: 125.8 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.617e-05/0.6619, allocations: 40.22 kB / 0.5762 GB, free: 125.8 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.402e-05/0.6619, allocations: 3.844 kB / 0.5762 GB, free: 125.8 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001382/0.6621, allocations: 27.77 kB / 0.5763 GB, free: 125.8 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02263/0.6847, allocations: 9.167 MB / 0.5852 GB, free: 124.8 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.975e-05/0.6847, allocations: 3.5 kB / 0.5852 GB, free: 124.8 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00254/0.6873, allocations: 0.7812 MB / 0.586 GB, free: 124.8 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.007666/0.6949, allocations: 2.414 MB / 0.5883 GB, free: 124.8 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0007872/0.6957, allocations: 139.3 kB / 0.5885 GB, free: 124.8 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.008817/0.7046, allocations: 7.331 MB / 0.5956 GB, free: 119.3 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.677e-06/0.7046, allocations: 3.188 kB / 0.5956 GB, free: 119.3 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01665/0.7212, allocations: 6.109 MB / 0.6016 GB, free: 118.5 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001497/0.7227, allocations: 0.6782 MB / 0.6023 GB, free: 118.3 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003406/0.723, allocations: 93.92 kB / 0.6023 GB, free: 118.3 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001047/0.7241, allocations: 80.78 kB / 0.6024 GB, free: 118.3 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0005992/0.7247, allocations: 389.2 kB / 0.6028 GB, free: 118.3 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002114/0.7249, allocations: 124.1 kB / 0.6029 GB, free: 118.3 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001009/0.7259, allocations: 1.236 MB / 0.6041 GB, free: 118.1 MB / 442.7 MB
Notification: Performance of sort global known variables: time 8e-08/0.7259, allocations: 2.594 kB / 0.6041 GB, free: 118.1 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.003958/0.7299, allocations: 1.775 MB / 0.6059 GB, free: 118.1 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 0.001337/0.7312, allocations: 0.8893 MB / 0.6067 GB, free: 117.9 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.005421/0.7366, allocations: 3.782 MB / 0.6104 GB, free: 116.3 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 5.561e-06/0.7366, allocations: 0 / 0.6104 GB, free: 116.3 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002729/0.7394, allocations: 2.21 MB / 0.6126 GB, free: 114.1 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002217/0.7416, allocations: 0.8205 MB / 0.6134 GB, free: 113.4 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 0.01111/0.7527, allocations: 8.566 MB / 0.6217 GB, free: 104.9 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0009297/0.7536, allocations: 1.256 MB / 0.623 GB, free: 103.6 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.002116/0.7557, allocations: 0.6037 MB / 0.6236 GB, free: 103.1 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001741/0.7575, allocations: 1.056 MB / 0.6246 GB, free: 102.1 MB / 442.7 MB
Notification: Performance of SimCode: time 1.422e-06/0.7575, allocations: 2.656 kB / 0.6246 GB, free: 102.1 MB / 442.7 MB
Notification: Performance of Templates: time 0.08869/0.8462, allocations: 92.95 MB / 0.7154 GB, free: 10.48 MB / 442.7 MB
"
[Timeout remaining time 659]
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=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 13.785643958952278]