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: translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009283/0.0009284, allocations: 99.86 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 0.0009239/0.000924, 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 1.411/1.411, allocations: 223.2 MB / 239.9 MB, free: 5.438 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1989/0.1989, allocations: 12.24 MB / 303.2 MB, free: 2.07 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003089/0.0003091, allocations: 8 kB / 366.8 MB, free: 9.844 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1089/0.1092, allocations: 53.08 MB / 419.9 MB, free: 4.648 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005404/0.1147, allocations: 3.665 MB / 423.6 MB, free: 0.9688 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003607/0.1151, allocations: 319.2 kB / 423.9 MB, free: 0.6523 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.469e-05/0.1152, allocations: 16 kB / 423.9 MB, free: 0.6367 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 7.407e-05/0.1152, allocations: 43.78 kB / 423.9 MB, free: 0.5938 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002686/0.1155, allocations: 75.77 kB / 424 MB, free: 0.5195 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.000176/0.1157, allocations: 47.94 kB / 424.1 MB, free: 484 kB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002336/0.1159, allocations: 204 kB / 424.3 MB, free: 280 kB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002329/0.1162, allocations: 135.1 kB / 424.4 MB, free: 144 kB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000113/0.1163, allocations: 91.66 kB / 424.5 MB, free: 52 kB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.1953/0.3116, allocations: 124.4 kB / 424.6 MB, free: 35.03 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 8.836e-05/0.3117, allocations: 14.88 kB / 424.6 MB, free: 35.03 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 7.977e-05/0.3118, allocations: 16.38 kB / 424.6 MB, free: 35.03 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 5.348e-05/0.3118, allocations: 48.7 kB / 424.7 MB, free: 35.03 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 8.087e-05/0.3119, allocations: 75.33 kB / 424.8 MB, free: 35 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002976/0.3122, allocations: 255.8 kB / 425 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 2.645e-06/0.3122, allocations: 3.375 kB / 425 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.683e-06/0.3123, allocations: 0 / 425 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 9.147e-06/0.3123, allocations: 0.9062 kB / 425 MB, free: 34.99 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 0.0007923/0.3131, allocations: 0.5429 MB / 425.6 MB, free: 34.56 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.629e-05/0.3131, allocations: 10.77 kB / 425.6 MB, free: 34.56 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.936e-05/0.3132, allocations: 33.47 kB / 425.6 MB, free: 34.55 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001198/0.3133, allocations: 195.3 kB / 425.8 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.546e-05/0.3134, allocations: 31.67 kB / 425.8 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.612e-05/0.3135, allocations: 43.25 kB / 425.9 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004846/0.3139, allocations: 301.4 kB / 426.2 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.885e-05/0.314, allocations: 0.7969 kB / 426.2 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.303e-05/0.314, allocations: 18.02 kB / 426.2 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.356e-05/0.314, allocations: 10.25 kB / 426.2 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003514/0.3144, allocations: 235 kB / 426.4 MB, free: 34.29 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001529/0.3159, allocations: 1.043 MB / 427.5 MB, free: 33.95 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002699/0.3162, allocations: 183 kB / 427.6 MB, free: 33.92 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.401e-05/0.3162, allocations: 3.281 kB / 427.6 MB, free: 33.92 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.394e-05/0.3163, allocations: 34.06 kB / 427.7 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.192e-06/0.3163, allocations: 5.594 kB / 427.7 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001686/0.318, allocations: 0.8963 MB / 428.6 MB, free: 33.58 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.766e-05/0.318, allocations: 51.41 kB / 428.6 MB, free: 33.52 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001038/0.3181, allocations: 176.2 kB / 428.8 MB, free: 33.4 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.773e-05/0.3181, allocations: 29.2 kB / 428.8 MB, free: 33.37 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 7.822e-05/0.3182, allocations: 211.2 kB / 429 MB, free: 33.21 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 5.605e-05/0.3183, allocations: 94.45 kB / 429.1 MB, free: 33.15 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.616e-05/0.3183, allocations: 8.531 kB / 429.1 MB, free: 33.15 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 6.6e-05/0.3184, allocations: 333.2 kB / 429.5 MB, free: 32.84 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001237/0.3185, allocations: 81.69 kB / 429.5 MB, free: 32.83 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001518/0.3187, allocations: 191.7 kB / 429.7 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001606/0.3188, allocations: 120.5 kB / 429.8 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.693e-06/0.3188, allocations: 0.625 kB / 429.8 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004084/0.3193, allocations: 350.8 kB / 430.2 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.614e-05/0.3193, allocations: 5.594 kB / 430.2 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.266e-06/0.3193, allocations: 5.125 kB / 430.2 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.807e-05/0.3193, allocations: 7.188 kB / 430.2 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002901/0.3196, allocations: 83.27 kB / 430.3 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.045e-05/0.3196, allocations: 5.531 kB / 430.3 MB, free: 32.66 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000162/0.3198, allocations: 20.92 kB / 430.3 MB, free: 32.65 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.92e-05/0.3198, allocations: 17.81 kB / 430.3 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 0.0002303/0.3201, allocations: 167.6 kB / 430.5 MB, free: 32.53 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.715e-05/0.3201, allocations: 14.38 kB / 430.5 MB, free: 32.52 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.547e-05/0.3202, allocations: 31.88 kB / 430.5 MB, free: 32.52 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.308e-06/0.3202, allocations: 3.281 kB / 430.5 MB, free: 32.52 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.262e-06/0.3202, allocations: 2.297 kB / 430.5 MB, free: 32.52 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.508e-06/0.3202, allocations: 3.234 kB / 430.5 MB, free: 32.52 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003854/0.3206, allocations: 361.3 kB / 430.9 MB, free: 32.33 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.895e-06/0.3206, allocations: 2.906 kB / 430.9 MB, free: 32.33 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002538/0.3209, allocations: 48.69 kB / 430.9 MB, free: 32.33 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.045e-06/0.3209, allocations: 4.344 kB / 430.9 MB, free: 32.33 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.909e-05/0.3209, allocations: 6.719 kB / 431 MB, free: 32.33 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.805e-06/0.3209, allocations: 2.625 kB / 431 MB, free: 32.33 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.82e-07/0.3209, allocations: 0.5 kB / 431 MB, free: 32.33 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004502/0.3214, allocations: 437.2 kB / 431.4 MB, free: 32.18 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.719e-05/0.3214, allocations: 91.25 kB / 431.5 MB, free: 32.08 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.101e-05/0.3215, allocations: 3 kB / 431.5 MB, free: 32.08 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001465/0.3216, allocations: 17.66 kB / 431.5 MB, free: 32.08 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.631e-05/0.3217, allocations: 17.36 kB / 431.5 MB, free: 32.08 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.222e-05/0.3217, allocations: 10 kB / 431.5 MB, free: 32.08 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.906e-05/0.3217, allocations: 121.3 kB / 431.6 MB, free: 32 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.3217, allocations: 2.688 kB / 431.6 MB, free: 32 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0003572/0.3221, allocations: 60.59 kB / 431.7 MB, free: 32 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 8.668e-05/0.3222, allocations: 101.4 kB / 431.8 MB, free: 31.92 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003433/0.3225, allocations: 249.2 kB / 432 MB, free: 31.91 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.723e-06/0.3226, allocations: 0 / 432 MB, free: 31.91 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001155/0.3227, allocations: 112.1 kB / 432.2 MB, free: 31.91 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002075/0.3229, allocations: 22.02 kB / 432.2 MB, free: 31.91 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001202/0.3241, allocations: 0.9063 MB / 433.1 MB, free: 31.38 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001587/0.3243, allocations: 0.7754 MB / 433.9 MB, free: 30.68 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0001041/0.3244, allocations: 30.83 kB / 433.9 MB, free: 30.68 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.211e-05/0.3245, allocations: 23.91 kB / 433.9 MB, free: 30.67 MB / 350.1 MB
Notification: Performance of SimCode: time 2.11e-07/0.3245, allocations: 0 / 433.9 MB, free: 30.67 MB / 350.1 MB
Notification: Performance of Templates: time 0.0041/0.3286, allocations: 1.843 MB / 435.8 MB, free: 30.59 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile
Environment - environmentSimulation:
(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 & ./BioChem_BioChem.Examples.GMO.cell  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1)
Environment - environmentSimulation: