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 0.0009035/0.0009035, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 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 0.001073/0.001073, allocations: 173.3 kB / 23.03 MB, free: 1.547 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 0.9849/0.9849, allocations: 177.1 MB / 203.4 MB, free: 5.641 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 0.08533/0.08533, allocations: 17.38 MB / 277.3 MB, free: 11.65 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 1.202e-06/1.202e-06, allocations: 0 / 353.5 MB, free: 9.965 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.084e-05/2.204e-05, allocations: 2.312 kB / 353.5 MB, free: 9.961 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 0.02795/0.02797, allocations: 33 MB / 386.5 MB, free: 9.074 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.01405/0.04203, allocations: 15.78 MB / 402.2 MB, free: 9.234 MB / 330.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0009044/0.04293, allocations: 31.75 kB / 402.3 MB, free: 9.203 MB / 330.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0008254/0.04376, allocations: 444.2 kB / 402.7 MB, free: 8.766 MB / 330.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.002717/0.04647, allocations: 1.578 MB / 404.3 MB, free: 7.176 MB / 330.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.004476/0.05095, allocations: 2.459 MB / 406.7 MB, free: 4.703 MB / 330.7 MB
Notification: Performance of NFFlatten.flatten: time 0.1355/0.1865, allocations: 7.626 MB / 414.4 MB, free: 36.11 MB / 330.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004686/0.1912, allocations: 4.553 MB / 418.9 MB, free: 35.83 MB / 330.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007093/0.1983, allocations: 6.304 MB / 425.2 MB, free: 34.84 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.005099/0.2034, allocations: 4.664 MB / 429.9 MB, free: 33.74 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.002368/0.2057, allocations: 0.676 MB / 430.6 MB, free: 33.74 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.004446/0.2102, allocations: 2.078 MB / 432.6 MB, free: 33.49 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.001248/0.2114, allocations: 1.833 MB / 434.5 MB, free: 32.57 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.003039/0.2145, allocations: 2.551 MB / 437 MB, free: 31.34 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0112/0.2257, allocations: 8.488 MB / 445.5 MB, free: 23.82 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.845e-06/0.2257, allocations: 0 / 445.5 MB, free: 23.82 MB / 330.7 MB
Notification: Performance of FrontEnd: time 2.284e-06/0.2257, allocations: 0 / 445.5 MB, free: 23.82 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 0.000286/0.226, allocations: 0 / 445.5 MB, free: 23.82 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 0.01275/0.2387, allocations: 7.3 MB / 452.8 MB, free: 16.53 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 5.825e-05/0.2388, allocations: 8.031 kB / 452.8 MB, free: 16.52 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.004943/0.2437, allocations: 2.047 MB / 454.9 MB, free: 14.47 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.004501/0.2482, allocations: 2.904 MB / 457.8 MB, free: 11.68 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0003831/0.2486, allocations: 0.999 MB / 458.8 MB, free: 10.53 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001085/0.2497, allocations: 0.4945 MB / 459.3 MB, free: 10.04 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.008337/0.258, allocations: 5.729 MB / 465 MB, free: 4.191 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 6.732e-05/0.2581, allocations: 4.188 kB / 465 MB, free: 4.188 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.000472/0.2586, allocations: 196.4 kB / 465.2 MB, free: 3.996 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.753e-05/0.2586, allocations: 119.9 kB / 465.3 MB, free: 3.879 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.008166/0.2668, allocations: 5.955 MB / 471.3 MB, free: 13.93 MB / 346.7 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 0.02707/0.2939, allocations: 20.15 MB / 491.4 MB, free: 10.05 MB / 362.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03658/0.3304, allocations: 32.16 MB / 0.5113 GB, free: 10.87 MB / 394.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.003794/0.3342, allocations: 2.182 MB / 0.5134 GB, free: 8.66 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.01553/0.3498, allocations: 10.97 MB / 0.5241 GB, free: 13.84 MB / 410.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.363e-05/0.3498, allocations: 67.94 kB / 0.5242 GB, free: 13.76 MB / 410.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.002461/0.3523, allocations: 1.189 MB / 0.5254 GB, free: 12.63 MB / 410.7 MB
Notification: Performance of pre-optimization done (n=324): time 1.335e-05/0.3523, allocations: 0 / 0.5254 GB, free: 12.63 MB / 410.7 MB
Notification: Performance of matching and sorting (n=376): time 0.05699/0.4093, allocations: 13.96 MB / 0.539 GB, free: 14.8 MB / 426.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.793e-05/0.4093, allocations: 94.34 kB / 0.5391 GB, free: 14.69 MB / 426.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00273/0.4121, allocations: 2.712 MB / 0.5417 GB, free: 11.94 MB / 426.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0007574/0.4128, allocations: 85.7 kB / 0.5418 GB, free: 11.85 MB / 426.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.001197/0.414, allocations: 2.425 MB / 0.5442 GB, free: 9.422 MB / 426.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001244/0.4153, allocations: 1.415 MB / 0.5456 GB, free: 8.023 MB / 426.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001197/0.4165, allocations: 1.033 MB / 0.5466 GB, free: 6.977 MB / 426.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001041/0.4166, allocations: 480.8 kB / 0.547 GB, free: 6.504 MB / 426.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001768/0.4183, allocations: 1.065 MB / 0.5481 GB, free: 5.438 MB / 426.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002698/0.421, allocations: 3.29 MB / 0.5513 GB, free: 1.227 MB / 426.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005192/0.4262, allocations: 4.803 MB / 0.556 GB, free: 11.74 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.562e-05/0.4263, allocations: 16 kB / 0.556 GB, free: 11.73 MB / 442.7 MB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.02567/0.4519, allocations: 7.814 MB / 0.5636 GB, free: 4.332 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 4.975e-05/0.452, allocations: 28 kB / 0.5637 GB, free: 4.305 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.647e-05/0.452, allocations: 48 kB / 0.5637 GB, free: 4.258 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.2166/0.6686, allocations: 5.814 MB / 0.5694 GB, free: 128.1 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.003524/0.6721, allocations: 1.277 MB / 0.5706 GB, free: 128.1 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.01757/0.6897, allocations: 8.76 MB / 0.5792 GB, free: 122.5 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003614/0.6933, allocations: 244 kB / 0.5794 GB, free: 122.5 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0007452/0.694, allocations: 283.3 kB / 0.5797 GB, free: 122.5 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 0.001571/0.6956, allocations: 473.1 kB / 0.5801 GB, free: 122.3 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000998/0.6966, allocations: 463.6 kB / 0.5806 GB, free: 122.3 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.02171/0.7183, allocations: 5.952 MB / 0.5864 GB, free: 122.1 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.979e-05/0.7184, allocations: 40.47 kB / 0.5864 GB, free: 122.1 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.884e-05/0.7184, allocations: 5.031 kB / 0.5864 GB, free: 122.1 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001099/0.7185, allocations: 16.45 kB / 0.5864 GB, free: 122.1 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02626/0.7448, allocations: 9.935 MB / 0.5961 GB, free: 121.1 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.366e-05/0.7448, allocations: 7.219 kB / 0.5962 GB, free: 121.1 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.002674/0.7475, allocations: 0.8534 MB / 0.597 GB, free: 121.1 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.007802/0.7553, allocations: 2.521 MB / 0.5994 GB, free: 121.1 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001027/0.7563, allocations: 139.4 kB / 0.5996 GB, free: 121 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.0092/0.7655, allocations: 7.693 MB / 0.6071 GB, free: 114.2 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.527e-06/0.7655, allocations: 6.625 kB / 0.6071 GB, free: 114.2 MB / 442.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01748/0.783, allocations: 6.971 MB / 0.6139 GB, free: 111.2 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001718/0.7847, allocations: 0.7629 MB / 0.6147 GB, free: 110.8 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0004339/0.7852, allocations: 91.97 kB / 0.6147 GB, free: 110.7 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001175/0.7863, allocations: 158.5 kB / 0.6149 GB, free: 110.5 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0007912/0.7871, allocations: 0.5016 MB / 0.6154 GB, free: 110 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002224/0.7873, allocations: 147.9 kB / 0.6155 GB, free: 109.9 MB / 442.7 MB
Notification: Performance of sorting global known variables: time 0.001209/0.7885, allocations: 1.316 MB / 0.6168 GB, free: 108.6 MB / 442.7 MB
Notification: Performance of sort global known variables: time 7e-08/0.7885, allocations: 0 / 0.6168 GB, free: 108.6 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.004365/0.7929, allocations: 1.778 MB / 0.6185 GB, free: 106.9 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 0.001289/0.7942, allocations: 0.8526 MB / 0.6194 GB, free: 106.3 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.00637/0.8006, allocations: 4.305 MB / 0.6236 GB, free: 102.1 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 5.801e-06/0.8006, allocations: 0 / 0.6236 GB, free: 102.1 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.003161/0.8037, allocations: 2.488 MB / 0.626 GB, free: 99.66 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.002498/0.8062, allocations: 0.8321 MB / 0.6268 GB, free: 98.92 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 0.01211/0.8184, allocations: 8.777 MB / 0.6354 GB, free: 90.1 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001089/0.8194, allocations: 1.264 MB / 0.6366 GB, free: 88.81 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.003447/0.8229, allocations: 1.286 MB / 0.6379 GB, free: 87.68 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001191/0.8241, allocations: 456.2 kB / 0.6383 GB, free: 87.23 MB / 442.7 MB
Notification: Performance of SimCode: time 1.744e-06/0.8241, allocations: 0 / 0.6383 GB, free: 87.23 MB / 442.7 MB
Notification: Performance of Templates: time 0.09681/0.9209, allocations: 90.99 MB / 0.7272 GB, free: 13.54 MB / 458.7 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: 5.9032412567175925]