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 0.00152/0.00152, allocations: 108 kB / 15.61 MB, free: 152 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.002312/0.002312, allocations: 194.6 kB / 16.53 MB, free: 6.699 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.382/1.382, allocations: 222.9 MB / 240.2 MB, free: 4.391 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2501/0.2501, allocations: 12.27 MB / 302.6 MB, free: 1.234 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001232/0.001233, allocations: 67.89 kB / 365.8 MB, free: 9.777 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09985/0.1011, allocations: 52.08 MB / 417.8 MB, free: 5.605 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.00626/0.1074, allocations: 4.307 MB / 422.1 MB, free: 1.273 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003874/0.1078, allocations: 291.3 kB / 422.4 MB, free: 0.9844 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001082/0.1079, allocations: 16 kB / 422.4 MB, free: 0.9688 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001158/0.1081, allocations: 59.53 kB / 422.5 MB, free: 0.9102 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001767/0.1083, allocations: 71.28 kB / 422.6 MB, free: 0.8398 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001786/0.1085, allocations: 67.91 kB / 422.6 MB, free: 0.7734 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002643/0.1087, allocations: 303.1 kB / 422.9 MB, free: 488 kB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002842/0.109, allocations: 168.4 kB / 423.1 MB, free: 320 kB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001084/0.1091, allocations: 127.6 kB / 423.2 MB, free: 192 kB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001757/0.1093, allocations: 155.3 kB / 423.4 MB, free: 36 kB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.661e-05/0.1094, allocations: 32 kB / 423.4 MB, free: 4 kB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.1891/0.2985, allocations: 31.45 kB / 423.4 MB, free: 36.79 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.000122/0.2987, allocations: 76.31 kB / 423.5 MB, free: 36.79 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002761/0.299, allocations: 162.7 kB / 423.7 MB, free: 36.79 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0004602/0.2995, allocations: 351.7 kB / 424 MB, free: 36.77 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.362e-06/0.2995, allocations: 1.219 kB / 424 MB, free: 36.77 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.054e-06/0.2995, allocations: 0.9688 kB / 424 MB, free: 36.77 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 9.638e-06/0.2995, allocations: 0 / 424 MB, free: 36.77 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 0.001092/0.3006, allocations: 0.605 MB / 424.6 MB, free: 36.34 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.613e-05/0.3007, allocations: 8.094 kB / 424.6 MB, free: 36.34 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 9.528e-05/0.3008, allocations: 34.34 kB / 424.7 MB, free: 36.32 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000124/0.3009, allocations: 205.6 kB / 424.9 MB, free: 36.1 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.351e-05/0.3009, allocations: 27.91 kB / 424.9 MB, free: 36.1 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 7.119e-05/0.301, allocations: 42.62 kB / 424.9 MB, free: 36.1 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0006626/0.3017, allocations: 307.9 kB / 425.2 MB, free: 36.06 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.534e-05/0.3017, allocations: 4.281 kB / 425.2 MB, free: 36.06 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.361e-05/0.3018, allocations: 17.09 kB / 425.3 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.807e-05/0.3018, allocations: 9.234 kB / 425.3 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005809/0.3024, allocations: 240.4 kB / 425.5 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002138/0.3046, allocations: 1.048 MB / 426.5 MB, free: 35.7 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000394/0.305, allocations: 183.4 kB / 426.7 MB, free: 35.68 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002056/0.3052, allocations: 121.3 kB / 426.8 MB, free: 35.67 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.44e-05/0.3052, allocations: 4.938 kB / 426.9 MB, free: 35.67 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.668e-05/0.3052, allocations: 36.53 kB / 426.9 MB, free: 35.63 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 2.084e-06/0.3053, allocations: 4.375 kB / 426.9 MB, free: 35.63 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.002223/0.3075, allocations: 0.8905 MB / 427.8 MB, free: 35.32 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.159e-05/0.3075, allocations: 56.62 kB / 427.8 MB, free: 35.26 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001288/0.3077, allocations: 166.8 kB / 428 MB, free: 35.15 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.991e-05/0.3077, allocations: 29.2 kB / 428 MB, free: 35.12 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 8.995e-05/0.3078, allocations: 212.2 kB / 428.2 MB, free: 34.96 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 5.941e-05/0.3079, allocations: 99.45 kB / 428.3 MB, free: 34.9 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.682e-05/0.308, allocations: 67.97 kB / 428.4 MB, free: 34.88 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 6.242e-05/0.308, allocations: 332.5 kB / 428.7 MB, free: 34.57 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001557/0.3082, allocations: 83.36 kB / 428.8 MB, free: 34.57 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001991/0.3084, allocations: 188.8 kB / 429 MB, free: 34.44 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003614/0.312, allocations: 0.8291 MB / 429.8 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.466e-06/0.3121, allocations: 3.562 kB / 429.8 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0005903/0.3127, allocations: 345.7 kB / 430.2 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.949e-05/0.3127, allocations: 11.53 kB / 430.2 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.516e-05/0.3127, allocations: 3.531 kB / 430.2 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 3.779e-05/0.3128, allocations: 6.031 kB / 430.2 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003906/0.3132, allocations: 82.84 kB / 430.3 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.595e-05/0.3132, allocations: 8.688 kB / 430.3 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002051/0.3134, allocations: 10.75 kB / 430.3 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.633e-05/0.3134, allocations: 15.75 kB / 430.3 MB, free: 34.26 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 0.0003983/0.3138, allocations: 174.7 kB / 430.5 MB, free: 34.14 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.558e-05/0.3139, allocations: 19.83 kB / 430.5 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 9.269e-05/0.314, allocations: 34.73 kB / 430.5 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.623e-06/0.314, allocations: 3 kB / 430.5 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.704e-06/0.3141, allocations: 0 / 430.5 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.492e-06/0.3141, allocations: 3.047 kB / 430.5 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005078/0.3146, allocations: 364.9 kB / 430.9 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.817e-06/0.3146, allocations: 1.625 kB / 430.9 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0003157/0.3149, allocations: 44.88 kB / 430.9 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 6.643e-06/0.3149, allocations: 0.625 kB / 430.9 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.285e-05/0.315, allocations: 6.562 kB / 430.9 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.978e-06/0.315, allocations: 4.375 kB / 430.9 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.473e-06/0.315, allocations: 2.281 kB / 430.9 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005838/0.3156, allocations: 433 kB / 431.4 MB, free: 33.79 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.837e-05/0.3156, allocations: 94.67 kB / 431.5 MB, free: 33.68 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.98e-05/0.3157, allocations: 4.312 kB / 431.5 MB, free: 33.68 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001825/0.3159, allocations: 5.875 kB / 431.5 MB, free: 33.68 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.896e-05/0.3159, allocations: 15.75 kB / 431.5 MB, free: 33.68 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.699e-05/0.3159, allocations: 7.438 kB / 431.5 MB, free: 33.68 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 7.148e-05/0.316, allocations: 122 kB / 431.6 MB, free: 33.61 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.316, allocations: 3.938 kB / 431.6 MB, free: 33.6 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0004771/0.3165, allocations: 70.19 kB / 431.7 MB, free: 33.6 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 0.0001039/0.3166, allocations: 97.28 kB / 431.8 MB, free: 33.52 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0004789/0.3171, allocations: 254.8 kB / 432 MB, free: 33.51 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.685e-06/0.3171, allocations: 3 kB / 432 MB, free: 33.51 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001631/0.3173, allocations: 112.6 kB / 432.1 MB, free: 33.51 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004291/0.3177, allocations: 24.33 kB / 432.2 MB, free: 33.51 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001404/0.3192, allocations: 0.7478 MB / 432.9 MB, free: 33.09 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002045/0.3194, allocations: 0.7687 MB / 433.7 MB, free: 32.39 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.000149/0.3195, allocations: 21.81 kB / 433.7 MB, free: 32.38 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.081e-05/0.3196, allocations: 21.77 kB / 433.7 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of SimCode: time 4.01e-07/0.3196, allocations: 0.75 kB / 433.7 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of Templates: time 0.005717/0.3253, allocations: 2.042 MB / 435.8 MB, free: 32.3 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile
(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)