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 0.0009062/0.0009061, allocations: 99.62 kB / 15.05 MB, free: 1.105 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0009801/0.0009801, allocations: 177.3 kB / 15.95 MB, free: 216 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.282/1.282, allocations: 223.2 MB / 239.9 MB, free: 5.465 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo): time 0.2466/0.2466, allocations: 12.19 MB / 303.2 MB, free: 1.836 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0002783/0.0002783, allocations: 8 kB / 366.8 MB, free: 9.582 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08669/0.08698, allocations: 53.09 MB / 419.9 MB, free: 4.406 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.00428/0.0913, allocations: 3.665 MB / 423.6 MB, free: 0.7266 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003188/0.09164, allocations: 327.2 kB / 423.9 MB, free: 412 kB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 8.123e-05/0.09173, allocations: 16 kB / 423.9 MB, free: 396 kB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 6.373e-05/0.0918, allocations: 35.8 kB / 424 MB, free: 360 kB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001421/0.09195, allocations: 71.78 kB / 424 MB, free: 288 kB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001444/0.0921, allocations: 51.94 kB / 424.1 MB, free: 236 kB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002106/0.09232, allocations: 200 kB / 424.3 MB, free: 36 kB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.1439/0.2362, allocations: 133.4 kB / 424.4 MB, free: 35.11 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001765/0.2364, allocations: 90.75 kB / 424.5 MB, free: 35.11 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001493/0.2366, allocations: 121.8 kB / 424.6 MB, free: 35.11 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 2.88e-05/0.2366, allocations: 16.09 kB / 424.6 MB, free: 35.11 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.286e-05/0.2367, allocations: 16.12 kB / 424.7 MB, free: 35.11 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 3.605e-05/0.2367, allocations: 47.47 kB / 424.7 MB, free: 35.11 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 5.23e-05/0.2368, allocations: 80.61 kB / 424.8 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002255/0.237, allocations: 254.3 kB / 425 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.056e-06/0.237, allocations: 1.75 kB / 425 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.273e-06/0.237, allocations: 1.75 kB / 425 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 5.19e-06/0.237, allocations: 0 / 425 MB, free: 35.07 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 0.000688/0.2377, allocations: 0.5488 MB / 425.6 MB, free: 34.65 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.226e-05/0.2377, allocations: 10.72 kB / 425.6 MB, free: 34.65 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 6.799e-05/0.2378, allocations: 78.42 kB / 425.7 MB, free: 34.61 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.062e-05/0.2379, allocations: 31.66 kB / 425.7 MB, free: 34.59 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 8.85e-05/0.238, allocations: 202.9 kB / 425.9 MB, free: 34.38 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.399e-05/0.238, allocations: 30.78 kB / 425.9 MB, free: 34.38 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.238e-05/0.2381, allocations: 36.41 kB / 426 MB, free: 34.38 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000405/0.2385, allocations: 304.4 kB / 426.3 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.371e-05/0.2385, allocations: 0 / 426.3 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.009e-05/0.2385, allocations: 22.48 kB / 426.3 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.097e-05/0.2385, allocations: 10.8 kB / 426.3 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003231/0.2389, allocations: 239.4 kB / 426.5 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001401/0.2403, allocations: 1.04 MB / 427.6 MB, free: 33.99 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002621/0.2406, allocations: 183 kB / 427.7 MB, free: 33.96 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.5e-05/0.2406, allocations: 3.75 kB / 427.7 MB, free: 33.96 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.092e-05/0.2406, allocations: 34.12 kB / 427.8 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.263e-06/0.2406, allocations: 1.531 kB / 427.8 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001558/0.2422, allocations: 0.893 MB / 428.7 MB, free: 33.62 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 1.97e-05/0.2422, allocations: 58.36 kB / 428.7 MB, free: 33.55 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.007e-05/0.2423, allocations: 169.5 kB / 428.9 MB, free: 33.45 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.507e-05/0.2423, allocations: 30.58 kB / 428.9 MB, free: 33.41 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 5.782e-05/0.2424, allocations: 212.4 kB / 429.1 MB, free: 33.25 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 3.999e-05/0.2424, allocations: 91.95 kB / 429.2 MB, free: 33.2 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.226e-05/0.2424, allocations: 11.06 kB / 429.2 MB, free: 33.2 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 4.137e-05/0.2425, allocations: 327.2 kB / 429.6 MB, free: 32.88 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001119/0.2426, allocations: 85.66 kB / 429.6 MB, free: 32.88 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001401/0.2428, allocations: 193.4 kB / 429.8 MB, free: 32.75 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001473/0.2429, allocations: 121.2 kB / 429.9 MB, free: 32.75 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.603e-06/0.2429, allocations: 2.719 kB / 429.9 MB, free: 32.75 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.000374/0.2433, allocations: 348.5 kB / 430.3 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.183e-05/0.2433, allocations: 7.344 kB / 430.3 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.691e-06/0.2433, allocations: 2.875 kB / 430.3 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.249e-05/0.2433, allocations: 5.781 kB / 430.3 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002787/0.2436, allocations: 84.62 kB / 430.4 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.676e-06/0.2436, allocations: 6.719 kB / 430.4 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001494/0.2438, allocations: 16.64 kB / 430.4 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.718e-05/0.2438, allocations: 16.25 kB / 430.4 MB, free: 32.7 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 0.0001772/0.244, allocations: 169.6 kB / 430.6 MB, free: 32.58 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.61e-05/0.244, allocations: 21.62 kB / 430.6 MB, free: 32.57 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.5e-05/0.2441, allocations: 31.38 kB / 430.6 MB, free: 32.57 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.206e-06/0.2441, allocations: 3.812 kB / 430.6 MB, free: 32.57 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.448e-06/0.2441, allocations: 1.906 kB / 430.6 MB, free: 32.57 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.717e-06/0.2441, allocations: 3.938 kB / 430.7 MB, free: 32.57 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003552/0.2445, allocations: 358.9 kB / 431 MB, free: 32.38 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.413e-06/0.2445, allocations: 3.281 kB / 431 MB, free: 32.38 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002341/0.2447, allocations: 42.92 kB / 431 MB, free: 32.38 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.106e-06/0.2448, allocations: 1.281 kB / 431 MB, free: 32.38 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.591e-05/0.2448, allocations: 10.67 kB / 431.1 MB, free: 32.38 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.573e-06/0.2448, allocations: 1.312 kB / 431.1 MB, free: 32.38 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.895e-06/0.2448, allocations: 0.5625 kB / 431.1 MB, free: 32.38 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003819/0.2452, allocations: 440.2 kB / 431.5 MB, free: 32.22 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.595e-05/0.2452, allocations: 87.86 kB / 431.6 MB, free: 32.12 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.756e-05/0.2452, allocations: 7.469 kB / 431.6 MB, free: 32.12 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001424/0.2454, allocations: 12.98 kB / 431.6 MB, free: 32.12 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.666e-05/0.2454, allocations: 17.58 kB / 431.6 MB, free: 32.12 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.149e-05/0.2454, allocations: 8.625 kB / 431.6 MB, free: 32.12 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 4.687e-05/0.2455, allocations: 119.9 kB / 431.7 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.31e-07/0.2455, allocations: 0 / 431.7 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002932/0.2458, allocations: 62.19 kB / 431.8 MB, free: 32.05 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 0.000489/0.2463, allocations: 0.9648 MB / 432.8 MB, free: 31.37 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002777/0.2466, allocations: 247.2 kB / 433 MB, free: 31.36 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.844e-06/0.2466, allocations: 0 / 433 MB, free: 31.36 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001106/0.2467, allocations: 108.2 kB / 433.1 MB, free: 31.36 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0001913/0.2469, allocations: 20.12 kB / 433.1 MB, free: 31.36 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002021/0.2489, allocations: 3.991 MB / 437.1 MB, free: 28.21 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001377/0.2491, allocations: 0.7742 MB / 437.9 MB, free: 27.51 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 9.839e-05/0.2492, allocations: 26 kB / 437.9 MB, free: 27.5 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001011/0.2493, allocations: 92.31 kB / 438 MB, free: 27.5 MB / 350.1 MB
Notification: Performance of SimCode: time 2.2e-07/0.2493, allocations: 0 / 438 MB, free: 27.5 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.01231/0.2616, allocations: 3.856 MB / 441.9 MB, free: 27.3 MB / 350.1 MB
Notification: Performance of buildModelFMU: configured platform static using cached values: time 0.0001271/0.2618, allocations: 151.9 kB / 442 MB, free: 27.05 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 1.659/1.92, allocations: 4 kB / 442 MB, free: 27.05 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: