Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr BioChem_BioChem.Examples.GMO.cell.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/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: "" <> buildModelFMU(BioChem.Examples.GMO.cell,fileNamePrefix="BioChem_BioChem_Examples_GMO_cell",fmuType="me",version="2.0",platforms={"static"})
"" <> buildModelFMU(BioChem.Examples.GMO.cell,fileNamePrefix="BioChem_BioChem_Examples_GMO_cell",fmuType="me",version="2.0",platforms={"static"})
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008609/0.0008608, allocations: 87.11 kB / 15.06 MB, free: 1.09 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00104/0.00104, allocations: 168.7 kB / 15.95 MB, free: 204 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.471/1.471, allocations: 223.3 MB / 240 MB, free: 5.438 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo): time 0.2263/0.2263, allocations: 12.21 MB / 303.3 MB, free: 1.895 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0002857/0.0002857, allocations: 12 kB / 367 MB, free: 9.527 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.101/0.1013, allocations: 53.08 MB / 420.1 MB, free: 4.355 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005132/0.1065, allocations: 3.817 MB / 423.9 MB, free: 0.5234 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0004591/0.107, allocations: 307.2 kB / 424.2 MB, free: 224 kB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 8.971e-05/0.1071, allocations: 16 kB / 424.2 MB, free: 208 kB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 6.922e-05/0.1072, allocations: 43.72 kB / 424.2 MB, free: 164 kB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001458/0.1073, allocations: 55.48 kB / 424.3 MB, free: 108 kB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001639/0.1075, allocations: 55.94 kB / 424.3 MB, free: 52 kB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.1777/0.2852, allocations: 269.7 kB / 424.6 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002549/0.2855, allocations: 122.9 kB / 424.7 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001019/0.2856, allocations: 101 kB / 424.8 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001461/0.2858, allocations: 121.4 kB / 424.9 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.486e-05/0.2858, allocations: 15.78 kB / 425 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.656e-05/0.2859, allocations: 18.06 kB / 425 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.233e-05/0.2859, allocations: 50.84 kB / 425 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 5.436e-05/0.286, allocations: 79.3 kB / 425.1 MB, free: 35.04 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002489/0.2862, allocations: 253.8 kB / 425.4 MB, free: 35.04 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 1.318e-05/0.2863, allocations: 0.8125 kB / 425.4 MB, free: 35.04 MB / 350.1 MB
Notification: Performance of FrontEnd: time 3.817e-06/0.2863, allocations: 0 / 425.4 MB, free: 35.04 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 4.101e-05/0.2863, allocations: 0 / 425.4 MB, free: 35.04 MB / 350.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 96
 * Number of variables: 96
Notification: Performance of Generate backend data structure: time 0.000757/0.2871, allocations: 0.546 MB / 425.9 MB, free: 34.61 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.467e-05/0.2871, allocations: 9.969 kB / 425.9 MB, free: 34.61 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 5.964e-05/0.2872, allocations: 78.52 kB / 426 MB, free: 34.57 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.16e-05/0.2873, allocations: 34.02 kB / 426 MB, free: 34.55 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 9.618e-05/0.2874, allocations: 209.5 kB / 426.2 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.414e-05/0.2874, allocations: 28.81 kB / 426.3 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.76e-05/0.2875, allocations: 38.34 kB / 426.3 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004506/0.2879, allocations: 303.6 kB / 426.6 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.644e-05/0.2879, allocations: 4.812 kB / 426.6 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.846e-05/0.288, allocations: 22.02 kB / 426.6 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.548e-06/0.288, allocations: 10.19 kB / 426.6 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004536/0.2885, allocations: 239.2 kB / 426.9 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001431/0.2899, allocations: 1.033 MB / 427.9 MB, free: 33.95 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002676/0.2902, allocations: 178.7 kB / 428.1 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002372/0.2904, allocations: 132.5 kB / 428.2 MB, free: 33.92 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.527e-05/0.2905, allocations: 192 / 428.2 MB, free: 33.92 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.233e-05/0.2905, allocations: 37.69 kB / 428.2 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.092e-06/0.2905, allocations: 0 / 428.2 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001601/0.2921, allocations: 0.8976 MB / 429.1 MB, free: 33.57 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 1.981e-05/0.2921, allocations: 58.23 kB / 429.2 MB, free: 33.51 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001706/0.2923, allocations: 167.6 kB / 429.3 MB, free: 33.4 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.68e-05/0.2923, allocations: 31.83 kB / 429.4 MB, free: 33.37 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 6.669e-05/0.2924, allocations: 210 kB / 429.6 MB, free: 33.21 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.25e-05/0.2925, allocations: 100.9 kB / 429.7 MB, free: 33.15 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.289e-05/0.2925, allocations: 6.688 kB / 429.7 MB, free: 33.15 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 4.279e-05/0.2925, allocations: 332 kB / 430 MB, free: 32.84 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001169/0.2927, allocations: 77.73 kB / 430.1 MB, free: 32.83 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001373/0.2928, allocations: 198.3 kB / 430.3 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001484/0.293, allocations: 119.5 kB / 430.4 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.174e-06/0.293, allocations: 5.656 kB / 430.4 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004006/0.2934, allocations: 344.8 kB / 430.7 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.218e-05/0.2934, allocations: 5.875 kB / 430.7 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.021e-06/0.2934, allocations: 2.812 kB / 430.8 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.392e-05/0.2934, allocations: 7.406 kB / 430.8 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002762/0.2937, allocations: 83.05 kB / 430.8 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.016e-05/0.2937, allocations: 11.17 kB / 430.9 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001468/0.2939, allocations: 20.64 kB / 430.9 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.781e-05/0.2939, allocations: 17.5 kB / 430.9 MB, free: 32.65 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         C.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         M.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         X.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 16
 * 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 (46):
 * Single equations (assignments): 46
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001883/0.2941, allocations: 166 kB / 431.1 MB, free: 32.52 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 6.965e-05/0.2942, allocations: 15.78 kB / 431.1 MB, free: 32.52 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001252/0.2943, allocations: 29.44 kB / 431.1 MB, free: 32.51 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.506e-06/0.2943, allocations: 8.484 kB / 431.1 MB, free: 32.51 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.96e-06/0.2943, allocations: 0 / 431.1 MB, free: 32.51 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.909e-06/0.2943, allocations: 4.516 kB / 431.1 MB, free: 32.51 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003472/0.2947, allocations: 362.3 kB / 431.5 MB, free: 32.32 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.244e-06/0.2947, allocations: 0.5625 kB / 431.5 MB, free: 32.32 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002528/0.295, allocations: 45.05 kB / 431.5 MB, free: 32.32 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.547e-06/0.295, allocations: 4.094 kB / 431.5 MB, free: 32.32 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.764e-05/0.295, allocations: 6.531 kB / 431.5 MB, free: 32.32 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.893e-06/0.295, allocations: 0 / 431.5 MB, free: 32.32 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 7.61e-07/0.295, allocations: 0 / 431.5 MB, free: 32.32 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004114/0.2954, allocations: 446.7 kB / 432 MB, free: 32.16 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.596e-05/0.2955, allocations: 90.78 kB / 432 MB, free: 32.06 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.895e-05/0.2955, allocations: 13.81 kB / 432.1 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001446/0.2957, allocations: 9.062 kB / 432.1 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.881e-05/0.2957, allocations: 16.91 kB / 432.1 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.225e-05/0.2957, allocations: 5.906 kB / 432.1 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.21e-05/0.2958, allocations: 118.1 kB / 432.2 MB, free: 31.98 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.6e-07/0.2958, allocations: 1.281 kB / 432.2 MB, free: 31.98 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.000323/0.2961, allocations: 69.14 kB / 432.3 MB, free: 31.98 MB / 350.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,C.n,M.n,X.n,ambientSubstance.n)
 * 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 (26):
 * Single equations (assignments): 26
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0006507/0.2968, allocations: 0.952 MB / 433.2 MB, free: 31.3 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003563/0.2971, allocations: 245.9 kB / 433.5 MB, free: 31.29 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.764e-06/0.2972, allocations: 1.25 kB / 433.5 MB, free: 31.29 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001365/0.2973, allocations: 112.2 kB / 433.6 MB, free: 31.28 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002991/0.2976, allocations: 22.28 kB / 433.6 MB, free: 31.28 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001922/0.2995, allocations: 1.723 MB / 435.3 MB, free: 30.36 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001481/0.2997, allocations: 0.7728 MB / 436.1 MB, free: 29.66 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0001121/0.2998, allocations: 19.22 kB / 436.1 MB, free: 29.65 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001159/0.2999, allocations: 100.1 kB / 436.2 MB, free: 29.64 MB / 350.1 MB
Notification: Performance of SimCode: time 7.32e-07/0.2999, allocations: 0 / 436.2 MB, free: 29.64 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.01328/0.3132, allocations: 3.879 MB / 440.1 MB, free: 29.41 MB / 350.1 MB
Notification: Performance of buildModelFMU: configured platform static using cached values: time 0.0001113/0.3134, allocations: 158.4 kB / 440.2 MB, free: 29.17 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 1.757/2.07, allocations: 0 / 440.2 MB, free: 29.17 MB / 350.1 MB
(rm -f BioChem_BioChem.Examples.GMO.cell.pipe ; mkfifo BioChem_BioChem.Examples.GMO.cell.pipe ; head -c 1048576 < BioChem_BioChem.Examples.GMO.cell.pipe >> ../files/BioChem_BioChem.Examples.GMO.cell.sim & /home/hudson/saved_omc/OMSimulator/install/linux/bin/OMSimulator  --tempDir=temp_BioChem_BioChem_Examples_GMO_cell_fmu --startTime=0 --stopTime=100 --timeout=50 --tolerance=1e-06 BioChem_BioChem_Examples_GMO_cell.fmu > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1)
Environment - environmentSimulation: