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 0.001411/0.001411, allocations: 104.4 kB / 19.7 MB, free: 2.125 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 0.001483/0.001483, allocations: 215.9 kB / 22.99 MB, free: 4.945 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 1.423/1.423, allocations: 230.6 MB / 256.8 MB, free: 7.812 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 0.1365/0.1365, allocations: 24 MB / 337.2 MB, free: 10.86 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 0.002086/0.002086, allocations: 67.89 kB / 472.6 MB, free: 6.832 MB / 334.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3224/0.3245, allocations: 59.89 MB / 0.52 GB, free: 9.77 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 0.07585/0.4003, allocations: 29.45 MB / 0.5487 GB, free: 10.29 MB / 398.1 MB
Notification: Performance of NFInst.instExpressions: time 0.033/0.4333, allocations: 23.05 MB / 0.5712 GB, free: 5.133 MB / 414.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.002481/0.4358, allocations: 31.75 kB / 0.5713 GB, free: 5.102 MB / 414.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001862/0.4377, allocations: 0.5503 MB / 0.5718 GB, free: 4.547 MB / 414.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.007438/0.4451, allocations: 2.161 MB / 0.5739 GB, free: 2.371 MB / 414.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01097/0.4561, allocations: 3.581 MB / 0.5774 GB, free: 14.77 MB / 430.1 MB
Notification: Performance of NFFlatten.flatten: time 0.009163/0.4653, allocations: 7.39 MB / 0.5846 GB, free: 7.348 MB / 430.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.005917/0.4712, allocations: 4.315 MB / 0.5888 GB, free: 2.957 MB / 430.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.007927/0.4791, allocations: 4.967 MB / 0.5937 GB, free: 13.98 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009366/0.4885, allocations: 4.959 MB / 0.5985 GB, free: 9.008 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.002877/0.4913, allocations: 0.6719 MB / 0.5992 GB, free: 8.336 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01276/0.5041, allocations: 3.183 MB / 0.6023 GB, free: 5.148 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.003543/0.5076, allocations: 1.808 MB / 0.6041 GB, free: 3.336 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.005935/0.5136, allocations: 2.9 MB / 0.6069 GB, free: 436 kB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02165/0.5352, allocations: 11.63 MB / 0.6183 GB, free: 4.754 MB / 462.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.915e-06/0.5352, allocations: 4 kB / 0.6183 GB, free: 4.75 MB / 462.1 MB
Notification: Performance of FrontEnd: time 2.014e-06/0.5352, allocations: 4 kB / 0.6183 GB, free: 4.746 MB / 462.1 MB
Notification: Performance of Transformations before backend: time 0.000316/0.5355, allocations: 0 / 0.6183 GB, free: 4.746 MB / 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 0.02121/0.5568, allocations: 7.233 MB / 0.6253 GB, free: 13.44 MB / 478.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.369e-05/0.5568, allocations: 8.031 kB / 0.6253 GB, free: 13.43 MB / 478.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006175/0.563, allocations: 1.241 MB / 0.6266 GB, free: 12.19 MB / 478.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.009548/0.5725, allocations: 3.325 MB / 0.6298 GB, free: 8.805 MB / 478.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.000912/0.5734, allocations: 1.003 MB / 0.6308 GB, free: 7.652 MB / 478.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001994/0.5754, allocations: 0.4924 MB / 0.6313 GB, free: 7.16 MB / 478.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01819/0.5936, allocations: 9.47 MB / 0.6405 GB, free: 13.58 MB / 494.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 8.88e-05/0.5937, allocations: 4 kB / 0.6405 GB, free: 13.58 MB / 494.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0006818/0.5944, allocations: 192 kB / 0.6407 GB, free: 13.39 MB / 494.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001007/0.5945, allocations: 116 kB / 0.6408 GB, free: 13.28 MB / 494.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02334/0.6178, allocations: 12.67 MB / 0.6532 GB, free: 0.5898 MB / 494.1 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 0.05932/0.6772, allocations: 26.73 MB / 0.6793 GB, free: 5.621 MB / 0.5137 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.05596/0.7331, allocations: 26.12 MB / 0.7048 GB, free: 12.41 MB / 0.545 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.008287/0.7414, allocations: 4.724 MB / 0.7094 GB, free: 7.66 MB / 0.545 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.03313/0.7745, allocations: 16.89 MB / 0.7259 GB, free: 6.695 MB / 0.5606 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.452e-05/0.7746, allocations: 73.05 kB / 0.726 GB, free: 6.613 MB / 0.5606 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004528/0.7791, allocations: 1.25 MB / 0.7272 GB, free: 5.359 MB / 0.5606 GB
Notification: Performance of pre-optimization done (n=324): time 8.285e-06/0.7791, allocations: 0 / 0.7272 GB, free: 5.359 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=376): time 0.3293/1.108, allocations: 24.16 MB / 0.7508 GB, free: 169 MB / 0.5606 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.182e-05/1.109, allocations: 89.77 kB / 0.7509 GB, free: 168.9 MB / 0.5606 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004203/1.113, allocations: 2.84 MB / 0.7536 GB, free: 167.9 MB / 0.5606 GB
Notification: Performance of collectPreVariables (initialization): time 0.001158/1.114, allocations: 88.83 kB / 0.7537 GB, free: 167.9 MB / 0.5606 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001515/1.115, allocations: 2.226 MB / 0.7559 GB, free: 166.4 MB / 0.5606 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001978/1.117, allocations: 1.36 MB / 0.7572 GB, free: 165.5 MB / 0.5606 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001554/1.119, allocations: 0.9806 MB / 0.7582 GB, free: 165.1 MB / 0.5606 GB
Notification: Performance of setup shared object (initialization): time 5.052e-05/1.119, allocations: 306.2 kB / 0.7585 GB, free: 164.8 MB / 0.5606 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004344/1.123, allocations: 2.962 MB / 0.7614 GB, free: 163.3 MB / 0.5606 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004975/1.128, allocations: 4.493 MB / 0.7658 GB, free: 159.8 MB / 0.5606 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01152/1.14, allocations: 7.809 MB / 0.7734 GB, free: 154.6 MB / 0.5606 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.835e-05/1.14, allocations: 18.66 kB / 0.7734 GB, free: 154.6 MB / 0.5606 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05812/1.198, allocations: 13.82 MB / 0.7869 GB, free: 144.8 MB / 0.5606 GB
Notification: Performance of prepare postOptimizeDAE: time 5.342e-05/1.198, allocations: 28 kB / 0.7869 GB, free: 144.8 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.266e-05/1.198, allocations: 48 kB / 0.787 GB, free: 144.8 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008096/1.206, allocations: 3.469 MB / 0.7903 GB, free: 141.5 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005408/1.212, allocations: 1.27 MB / 0.7916 GB, free: 140.2 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02851/1.24, allocations: 17.87 MB / 0.809 GB, free: 122 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004956/1.245, allocations: 251.8 kB / 0.8093 GB, free: 121.8 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009125/1.246, allocations: 282.5 kB / 0.8096 GB, free: 121.5 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 0.002759/1.249, allocations: 1.453 MB / 0.811 GB, free: 120.1 MB / 0.5606 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0009045/1.25, allocations: 345.7 kB / 0.8113 GB, free: 119.8 MB / 0.5606 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03468/1.284, allocations: 9.612 MB / 0.8207 GB, free: 110.2 MB / 0.5606 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.39e-05/1.284, allocations: 40 kB / 0.8207 GB, free: 110.2 MB / 0.5606 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.961e-05/1.284, allocations: 4 kB / 0.8207 GB, free: 110.2 MB / 0.5606 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001199/1.285, allocations: 23.92 kB / 0.8208 GB, free: 110.2 MB / 0.5606 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04523/1.33, allocations: 14.37 MB / 0.8348 GB, free: 95.86 MB / 0.5606 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.785e-05/1.33, allocations: 3.281 kB / 0.8348 GB, free: 95.86 MB / 0.5606 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004548/1.334, allocations: 0.8551 MB / 0.8356 GB, free: 95.01 MB / 0.5606 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005852/1.34, allocations: 2.126 MB / 0.8377 GB, free: 92.91 MB / 0.5606 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.000943/1.341, allocations: 135.9 kB / 0.8378 GB, free: 92.78 MB / 0.5606 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02119/1.362, allocations: 12.1 MB / 0.8496 GB, free: 80.4 MB / 0.5606 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.19e-06/1.362, allocations: 13.47 kB / 0.8497 GB, free: 80.39 MB / 0.5606 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03948/1.402, allocations: 12.93 MB / 0.8623 GB, free: 67.39 MB / 0.5606 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003347/1.405, allocations: 0.9 MB / 0.8632 GB, free: 66.49 MB / 0.5606 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001023/1.406, allocations: 95.97 kB / 0.8633 GB, free: 66.4 MB / 0.5606 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002923/1.409, allocations: 162.5 kB / 0.8634 GB, free: 66.24 MB / 0.5606 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0009975/1.41, allocations: 470.2 kB / 0.8639 GB, free: 65.78 MB / 0.5606 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003235/1.41, allocations: 147.9 kB / 0.864 GB, free: 65.64 MB / 0.5606 GB
Notification: Performance of sorting global known variables: time 0.002172/1.413, allocations: 1.847 MB / 0.8658 GB, free: 63.79 MB / 0.5606 GB
Notification: Performance of sort global known variables: time 9e-08/1.413, allocations: 0 / 0.8658 GB, free: 63.79 MB / 0.5606 GB
Notification: Performance of remove unused functions: time 0.007182/1.42, allocations: 2.061 MB / 0.8678 GB, free: 61.79 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 0.002603/1.422, allocations: 1.325 MB / 0.8691 GB, free: 60.65 MB / 0.5606 GB
Notification: Performance of simCode: created initialization part: time 0.01296/1.435, allocations: 7.077 MB / 0.876 GB, free: 53.55 MB / 0.5606 GB
Notification: Performance of simCode: created event and clocks part: time 1.074e-05/1.435, allocations: 2.719 kB / 0.876 GB, free: 53.55 MB / 0.5606 GB
Notification: Performance of simCode: created simulation system equations: time 0.007563/1.443, allocations: 3.766 MB / 0.8797 GB, free: 49.75 MB / 0.5606 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003964/1.447, allocations: 0.7644 MB / 0.8805 GB, free: 49.07 MB / 0.5606 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01706/1.464, allocations: 10.94 MB / 0.8911 GB, free: 38.1 MB / 0.5606 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001956/1.466, allocations: 2.699 MB / 0.8938 GB, free: 35.41 MB / 0.5606 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001881/1.468, allocations: 490 kB / 0.8942 GB, free: 34.93 MB / 0.5606 GB
Notification: Performance of SimCode: time 9.82e-07/1.468, allocations: 0 / 0.8942 GB, free: 34.93 MB / 0.5606 GB
Notification: Performance of Templates: time 0.3986/1.866, allocations: 148.8 MB / 1.04 GB, free: 142.2 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: 14.763719691894948]
Failed to read output from testmodel.py, exit status != 0:
1.8757027722895145 1.884516609 1.346770667
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7fb95b6eafe0>