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-master/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-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: "" <> 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 0.001128/0.001128, allocations: 108 kB / 15.61 MB, free: 148 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001185/0.001185, allocations: 193.6 kB / 16.53 MB, free: 6.691 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.293/1.293, allocations: 222.9 MB / 240.2 MB, free: 4.402 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2192/0.2192, allocations: 12.26 MB / 302.7 MB, free: 1.254 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001151/0.001151, allocations: 55.91 kB / 365.9 MB, free: 9.715 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09382/0.09499, allocations: 52.09 MB / 418 MB, free: 5.535 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.007023/0.102, allocations: 4.307 MB / 422.3 MB, free: 1.203 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0005823/0.1027, allocations: 299.2 kB / 422.6 MB, free: 0.9062 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000182/0.1029, allocations: 19.94 kB / 422.6 MB, free: 0.8867 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001465/0.103, allocations: 51.61 kB / 422.6 MB, free: 0.8359 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002333/0.1033, allocations: 71.23 kB / 422.7 MB, free: 0.7656 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001998/0.1035, allocations: 71.89 kB / 422.8 MB, free: 0.6953 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002919/0.1038, allocations: 295.2 kB / 423 MB, free: 416 kB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.000265/0.1041, allocations: 164.4 kB / 423.2 MB, free: 252 kB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001229/0.1042, allocations: 123.6 kB / 423.3 MB, free: 128 kB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.1457/0.2499, allocations: 158.9 kB / 423.5 MB, free: 36.72 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001168/0.25, allocations: 32.34 kB / 423.5 MB, free: 36.72 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 7.166e-05/0.2501, allocations: 34.78 kB / 423.6 MB, free: 36.72 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 5.372e-05/0.2502, allocations: 72.88 kB / 423.6 MB, free: 36.72 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001388/0.2503, allocations: 163.6 kB / 423.8 MB, free: 36.72 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0003532/0.2507, allocations: 347.7 kB / 424.1 MB, free: 36.7 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.53e-06/0.2507, allocations: 0 / 424.1 MB, free: 36.7 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.533e-06/0.2507, allocations: 2 kB / 424.1 MB, free: 36.7 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.355e-05/0.2507, allocations: 1.219 kB / 424.1 MB, free: 36.7 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 0.0008604/0.2516, allocations: 0.6093 MB / 424.7 MB, free: 36.27 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.215e-05/0.2516, allocations: 8.5 kB / 424.7 MB, free: 36.27 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 6.796e-05/0.2517, allocations: 74.44 kB / 424.8 MB, free: 36.23 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.613e-05/0.2518, allocations: 41.66 kB / 424.9 MB, free: 36.21 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 9.502e-05/0.2519, allocations: 199.2 kB / 425.1 MB, free: 36 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.767e-05/0.2519, allocations: 32 kB / 425.1 MB, free: 36 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.819e-05/0.252, allocations: 43.83 kB / 425.1 MB, free: 36 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004899/0.2525, allocations: 308.4 kB / 425.4 MB, free: 35.95 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.723e-05/0.2525, allocations: 4.969 kB / 425.4 MB, free: 35.95 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.748e-05/0.2525, allocations: 15.22 kB / 425.4 MB, free: 35.95 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.058e-05/0.2526, allocations: 8.938 kB / 425.5 MB, free: 35.95 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003601/0.2529, allocations: 244 kB / 425.7 MB, free: 35.95 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001442/0.2544, allocations: 1.037 MB / 426.7 MB, free: 35.61 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002742/0.2547, allocations: 181.8 kB / 426.9 MB, free: 35.58 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001347/0.2548, allocations: 128.5 kB / 427 MB, free: 35.57 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.623e-05/0.2548, allocations: 0.625 kB / 427 MB, free: 35.57 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.234e-05/0.2548, allocations: 40.66 kB / 427.1 MB, free: 35.53 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.203e-06/0.2548, allocations: 0 / 427.1 MB, free: 35.53 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001556/0.2564, allocations: 0.888 MB / 428 MB, free: 35.23 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.04e-05/0.2564, allocations: 54.06 kB / 428 MB, free: 35.16 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.077e-05/0.2565, allocations: 170.9 kB / 428.2 MB, free: 35.05 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.503e-05/0.2566, allocations: 31.98 kB / 428.2 MB, free: 35.02 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 6.536e-05/0.2566, allocations: 208 kB / 428.4 MB, free: 34.86 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.21e-05/0.2567, allocations: 98.98 kB / 428.5 MB, free: 34.8 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.854e-05/0.2568, allocations: 72.62 kB / 428.6 MB, free: 34.78 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 5.414e-05/0.2568, allocations: 333 kB / 428.9 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001145/0.2569, allocations: 85.88 kB / 429 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001564/0.2571, allocations: 192.6 kB / 429.2 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002679/0.2598, allocations: 0.822 MB / 430 MB, free: 34.2 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.244e-06/0.2598, allocations: 5.094 kB / 430 MB, free: 34.2 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0003823/0.2602, allocations: 345.7 kB / 430.3 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.473e-05/0.2602, allocations: 6.938 kB / 430.4 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.692e-06/0.2602, allocations: 4.25 kB / 430.4 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.774e-05/0.2602, allocations: 7.25 kB / 430.4 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002619/0.2605, allocations: 80.08 kB / 430.4 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.427e-06/0.2605, allocations: 9.844 kB / 430.5 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001279/0.2607, allocations: 14 kB / 430.5 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.719e-05/0.2607, allocations: 17.19 kB / 430.5 MB, free: 34.16 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         ambientSubstance.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
         M.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" 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
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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002223/0.2609, allocations: 174.2 kB / 430.7 MB, free: 34.04 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.783e-05/0.261, allocations: 18.84 kB / 430.7 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.332e-05/0.261, allocations: 29.78 kB / 430.7 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.476e-06/0.261, allocations: 4.531 kB / 430.7 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.929e-06/0.261, allocations: 0.9375 kB / 430.7 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.877e-06/0.261, allocations: 3.938 kB / 430.7 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003238/0.2614, allocations: 365 kB / 431.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.423e-06/0.2614, allocations: 0 / 431.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002264/0.2616, allocations: 46.22 kB / 431.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.385e-06/0.2616, allocations: 0 / 431.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.734e-05/0.2616, allocations: 10.72 kB / 431.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.915e-06/0.2617, allocations: 0.5625 kB / 431.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.643e-06/0.2617, allocations: 4.688 kB / 431.1 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004083/0.2621, allocations: 431.1 kB / 431.5 MB, free: 33.69 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.868e-05/0.2621, allocations: 93.44 kB / 431.6 MB, free: 33.59 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.864e-05/0.2621, allocations: 6.844 kB / 431.6 MB, free: 33.59 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001286/0.2623, allocations: 3.562 kB / 431.6 MB, free: 33.59 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.778e-05/0.2623, allocations: 18.22 kB / 431.7 MB, free: 33.58 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.242e-05/0.2623, allocations: 10.38 kB / 431.7 MB, free: 33.58 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 4.929e-05/0.2624, allocations: 123.1 kB / 431.8 MB, free: 33.5 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.21e-07/0.2624, allocations: 2.375 kB / 431.8 MB, free: 33.5 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002968/0.2627, allocations: 67.16 kB / 431.9 MB, free: 33.5 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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.000512/0.2632, allocations: 0.964 MB / 432.8 MB, free: 32.83 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003268/0.2635, allocations: 254.9 kB / 433.1 MB, free: 32.82 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.054e-06/0.2636, allocations: 0 / 433.1 MB, free: 32.82 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001091/0.2637, allocations: 115.9 kB / 433.2 MB, free: 32.82 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002897/0.264, allocations: 27.16 kB / 433.2 MB, free: 32.82 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002189/0.2662, allocations: 2.731 MB / 435.9 MB, free: 30.8 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001376/0.2663, allocations: 0.7787 MB / 436.7 MB, free: 30.09 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0001005/0.2664, allocations: 26.64 kB / 436.8 MB, free: 30.08 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001035/0.2665, allocations: 90.38 kB / 436.8 MB, free: 30.02 MB / 350.1 MB
Notification: Performance of SimCode: time 2.41e-07/0.2665, allocations: 0 / 436.8 MB, free: 30.02 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.02088/0.2874, allocations: 4.252 MB / 441.1 MB, free: 29.58 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 7.123/7.41, allocations: 7.172 kB / 441.1 MB, free: 29.58 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 & python3 -m fmpy simulate  --output-file BioChem_BioChem.Examples.GMO.cell_res.csv --start-time 0 --stop-time 100 --timeout 50 --relative-tolerance 1e-06 --interface-type ModelExchange --solver CVode --output-interval 100 BioChem_BioChem_Examples_GMO_cell.fmu > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1)