Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001352/0.001352, allocations: 102.3 kB / 16.4 MB, free: 6.508 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001482/0.001482, allocations: 198.7 kB / 19.35 MB, free: 3.73 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.404/1.404, allocations: 222.9 MB / 245 MB, free: 15.02 MB / 206.1 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08845/0.08845, allocations: 15.3 MB / 312.5 MB, free: 13.32 MB / 254.1 MB
"
[Timeout remaining time 180]
Using package Chemical with version 1.4.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC")
translateModel(Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 0.001965/0.001965, allocations: 67.89 kB / 433.9 MB, free: 8.848 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1044/0.1063, allocations: 53.59 MB / 487.5 MB, free: 3.199 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66: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 1.4.1-master/package.mo:4740:7-4740:66: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.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC): time 0.04566/0.152, allocations: 30.06 MB / 0.5054 GB, free: 5.207 MB / 382.1 MB
Notification: Performance of NFInst.instExpressions: time 0.254/0.4061, allocations: 26.07 MB / 0.5309 GB, free: 13.42 MB / 382.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001958/0.4081, allocations: 23.59 kB / 0.5309 GB, free: 13.41 MB / 382.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.001902/0.41, allocations: 0.5957 MB / 0.5315 GB, free: 13.09 MB / 382.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0101/0.4201, allocations: 2.143 MB / 0.5336 GB, free: 11.9 MB / 382.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.01681/0.437, allocations: 3.519 MB / 0.537 GB, free: 9.875 MB / 382.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0103/0.4473, allocations: 7.394 MB / 0.5443 GB, free: 6.27 MB / 382.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.007902/0.4552, allocations: 5.917 MB / 0.55 GB, free: 3.133 MB / 382.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.009158/0.4644, allocations: 4.867 MB / 0.5548 GB, free: 352 kB / 382.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.01107/0.4755, allocations: 4.63 MB / 0.5593 GB, free: 11.7 MB / 398.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.003065/0.4786, allocations: 0.668 MB / 0.56 GB, free: 11.04 MB / 398.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.01814/0.4968, allocations: 3.324 MB / 0.5632 GB, free: 7.707 MB / 398.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.005073/0.5019, allocations: 1.777 MB / 0.5649 GB, free: 5.926 MB / 398.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.008893/0.5108, allocations: 3.348 MB / 0.5682 GB, free: 2.566 MB / 398.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.02826/0.5391, allocations: 11.15 MB / 0.5791 GB, free: 7.379 MB / 414.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.895e-06/0.5392, allocations: 0 / 0.5791 GB, free: 7.379 MB / 414.1 MB
Notification: Performance of FrontEnd: time 1.674e-06/0.5392, allocations: 0 / 0.5791 GB, free: 7.379 MB / 414.1 MB
Notification: Performance of Transformations before backend: time 0.0003489/0.5395, allocations: 0 / 0.5791 GB, free: 7.379 MB / 414.1 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 0.02358/0.5631, allocations: 7.584 MB / 0.5865 GB, free: 15.79 MB / 430.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.657e-05/0.5632, allocations: 8.031 kB / 0.5865 GB, free: 15.78 MB / 430.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006556/0.5697, allocations: 1.236 MB / 0.5877 GB, free: 14.54 MB / 430.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.007754/0.5775, allocations: 3.237 MB / 0.5909 GB, free: 11.24 MB / 430.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0007046/0.5783, allocations: 0.6688 MB / 0.5915 GB, free: 10.5 MB / 430.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002041/0.5803, allocations: 0.4924 MB / 0.592 GB, free: 10.01 MB / 430.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0254/0.6057, allocations: 9.366 MB / 0.6012 GB, free: 0.543 MB / 430.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001059/0.6059, allocations: 3.938 kB / 0.6012 GB, free: 0.5391 MB / 430.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0009606/0.6068, allocations: 200 kB / 0.6014 GB, free: 352 kB / 430.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001096/0.607, allocations: 122.6 kB / 0.6015 GB, free: 232 kB / 430.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.02644/0.6334, allocations: 12.59 MB / 0.6138 GB, free: 3.617 MB / 446.1 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 0.07617/0.7096, allocations: 30.2 MB / 0.6433 GB, free: 4.758 MB / 478.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.07313/0.7828, allocations: 41.28 MB / 0.6836 GB, free: 8.938 MB / 0.5137 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01056/0.7934, allocations: 5.075 MB / 0.6885 GB, free: 3.836 MB / 0.5137 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.04542/0.8389, allocations: 20.91 MB / 0.709 GB, free: 13.98 MB / 0.545 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.93e-05/0.839, allocations: 67.73 kB / 0.709 GB, free: 13.91 MB / 0.545 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003933/0.843, allocations: 0.9757 MB / 0.71 GB, free: 12.93 MB / 0.545 GB
Notification: Performance of pre-optimization done (n=324): time 1.215e-05/0.843, allocations: 0 / 0.71 GB, free: 12.93 MB / 0.545 GB
Notification: Performance of matching and sorting (n=376): time 0.3906/1.234, allocations: 24.47 MB / 0.7339 GB, free: 185.1 MB / 0.545 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.025e-05/1.234, allocations: 90.11 kB / 0.734 GB, free: 185.1 MB / 0.545 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.004432/1.238, allocations: 2.961 MB / 0.7369 GB, free: 184.1 MB / 0.545 GB
Notification: Performance of collectPreVariables (initialization): time 0.001092/1.239, allocations: 86.83 kB / 0.7369 GB, free: 184 MB / 0.545 GB
Notification: Performance of collectInitialEqns (initialization): time 0.00147/1.241, allocations: 2.221 MB / 0.7391 GB, free: 182.5 MB / 0.545 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001821/1.243, allocations: 1.369 MB / 0.7404 GB, free: 181.6 MB / 0.545 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001633/1.244, allocations: 0.9813 MB / 0.7414 GB, free: 181.2 MB / 0.545 GB
Notification: Performance of setup shared object (initialization): time 5.306e-05/1.244, allocations: 305.4 kB / 0.7417 GB, free: 181 MB / 0.545 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.004735/1.249, allocations: 2.956 MB / 0.7446 GB, free: 180 MB / 0.545 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.005746/1.255, allocations: 4.485 MB / 0.749 GB, free: 177.2 MB / 0.545 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01012/1.265, allocations: 7.804 MB / 0.7566 GB, free: 172.4 MB / 0.545 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.363e-05/1.265, allocations: 18.22 kB / 0.7566 GB, free: 172.4 MB / 0.545 GB
Notification: Performance of matching and sorting (n=617) (initialization): time 0.05576/1.321, allocations: 13.84 MB / 0.7701 GB, free: 165 MB / 0.545 GB
Notification: Performance of prepare postOptimizeDAE: time 7.855e-05/1.321, allocations: 28 kB / 0.7701 GB, free: 164.9 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.996e-05/1.321, allocations: 48 kB / 0.7702 GB, free: 164.9 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.008327/1.329, allocations: 3.464 MB / 0.7736 GB, free: 161.6 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005745/1.335, allocations: 1.268 MB / 0.7748 GB, free: 160.3 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02881/1.364, allocations: 18.49 MB / 0.7929 GB, free: 141.5 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.004909/1.369, allocations: 254.4 kB / 0.7931 GB, free: 141.2 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0009904/1.37, allocations: 283.8 kB / 0.7934 GB, free: 140.9 MB / 0.545 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 0.002882/1.373, allocations: 1.451 MB / 0.7948 GB, free: 139.5 MB / 0.545 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00098/1.374, allocations: 357.7 kB / 0.7951 GB, free: 139.2 MB / 0.545 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03392/1.408, allocations: 9.662 MB / 0.8046 GB, free: 129.6 MB / 0.545 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.607e-05/1.408, allocations: 46.67 kB / 0.8046 GB, free: 129.5 MB / 0.545 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.545e-05/1.408, allocations: 4 kB / 0.8046 GB, free: 129.5 MB / 0.545 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0001265/1.408, allocations: 19.92 kB / 0.8046 GB, free: 129.5 MB / 0.545 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.04385/1.452, allocations: 15.44 MB / 0.8197 GB, free: 114.1 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 8.894e-05/1.452, allocations: 4 kB / 0.8197 GB, free: 114.1 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.005266/1.457, allocations: 0.8491 MB / 0.8206 GB, free: 113.3 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005779/1.463, allocations: 2.125 MB / 0.8226 GB, free: 111.1 MB / 0.545 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001243/1.464, allocations: 143.8 kB / 0.8228 GB, free: 111 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.02071/1.485, allocations: 12.67 MB / 0.8351 GB, free: 97.91 MB / 0.545 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.871e-06/1.485, allocations: 7.938 kB / 0.8351 GB, free: 97.9 MB / 0.545 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03913/1.524, allocations: 12.99 MB / 0.8478 GB, free: 84.8 MB / 0.545 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003127/1.527, allocations: 0.9502 MB / 0.8488 GB, free: 83.84 MB / 0.545 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0008154/1.528, allocations: 95.97 kB / 0.8489 GB, free: 83.74 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002425/1.531, allocations: 167.8 kB / 0.849 GB, free: 83.58 MB / 0.545 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001108/1.532, allocations: 454.4 kB / 0.8494 GB, free: 83.13 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003123/1.532, allocations: 151.9 kB / 0.8496 GB, free: 82.98 MB / 0.545 GB
Notification: Performance of sorting global known variables: time 0.002294/1.534, allocations: 1.989 MB / 0.8515 GB, free: 81 MB / 0.545 GB
Notification: Performance of sort global known variables: time 1.3e-07/1.534, allocations: 0 / 0.8515 GB, free: 81 MB / 0.545 GB
Notification: Performance of remove unused functions: time 0.007286/1.542, allocations: 2.07 MB / 0.8536 GB, free: 79.09 MB / 0.545 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 0.002616/1.544, allocations: 1.312 MB / 0.8548 GB, free: 77.91 MB / 0.545 GB
Notification: Performance of simCode: created initialization part: time 0.01271/1.557, allocations: 7.429 MB / 0.8621 GB, free: 70.45 MB / 0.545 GB
Notification: Performance of simCode: created event and clocks part: time 7.694e-06/1.557, allocations: 1 kB / 0.8621 GB, free: 70.45 MB / 0.545 GB
Notification: Performance of simCode: created simulation system equations: time 0.007106/1.564, allocations: 4.096 MB / 0.8661 GB, free: 66.32 MB / 0.545 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003793/1.568, allocations: 0.778 MB / 0.8669 GB, free: 65.6 MB / 0.545 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01829/1.586, allocations: 10.95 MB / 0.8775 GB, free: 54.57 MB / 0.545 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.002227/1.589, allocations: 3.307 MB / 0.8808 GB, free: 51.23 MB / 0.545 GB
Notification: Performance of simCode: alias equations: time 0.004087/1.593, allocations: 1.586 MB / 0.8823 GB, free: 49.67 MB / 0.545 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001604/1.594, allocations: 458 kB / 0.8828 GB, free: 49.23 MB / 0.545 GB
Notification: Performance of SimCode: time 1.543e-06/1.594, allocations: 0 / 0.8828 GB, free: 49.23 MB / 0.545 GB
Notification: Performance of Templates: time 0.3975/1.992, allocations: 91.17 MB / 0.9718 GB, free: 154.6 MB / 0.545 GB
"
[Timeout remaining time 658]
make -j1 -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.makefile [Timeout 660]
(rm -f Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.sim & ./Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.Allosteric_Hemoglobin2_MWC.pipe 2>&1) [Timeout 480]
[Calling os._exit(0), Time elapsed: 9.397164849564433]