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 0.007009/0.007009, allocations: 99.31 kB / 15.73 MB, free: 6.047 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001439/0.00144, allocations: 187.7 kB / 16.67 MB, free: 5.977 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.454/1.454, allocations: 222.9 MB / 240.4 MB, free: 4.312 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2667/0.2667, allocations: 12.27 MB / 302.8 MB, free: 1.184 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001296/0.001296, allocations: 64.14 kB / 420 MB, free: 3.477 MB / 350.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.3168/0.3181, allocations: 52.08 MB / 472.1 MB, free: 16.67 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.00578/0.3239, allocations: 4.312 MB / 476.4 MB, free: 13.64 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003255/0.3243, allocations: 292.3 kB / 476.7 MB, free: 13.39 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001261/0.3244, allocations: 15.94 kB / 476.7 MB, free: 13.39 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001054/0.3246, allocations: 56.47 kB / 476.8 MB, free: 13.34 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001719/0.3247, allocations: 71.75 kB / 476.9 MB, free: 13.28 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.000196/0.3249, allocations: 70.44 kB / 476.9 MB, free: 13.22 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002758/0.3252, allocations: 302 kB / 477.2 MB, free: 13.04 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003067/0.3255, allocations: 157.7 kB / 477.4 MB, free: 12.95 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001255/0.3257, allocations: 131 kB / 477.5 MB, free: 12.87 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001787/0.3259, allocations: 161.7 kB / 477.7 MB, free: 12.75 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 5.839e-05/0.3259, allocations: 32.97 kB / 477.7 MB, free: 12.75 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 5.833e-05/0.326, allocations: 32.81 kB / 477.7 MB, free: 12.75 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 5.729e-05/0.3261, allocations: 76.88 kB / 477.8 MB, free: 12.68 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001388/0.3262, allocations: 161.1 kB / 478 MB, free: 12.57 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0003144/0.3265, allocations: 361.9 kB / 478.3 MB, free: 12.3 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.629e-06/0.3265, allocations: 0 / 478.3 MB, free: 12.3 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.124e-06/0.3265, allocations: 0 / 478.3 MB, free: 12.3 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 7.805e-06/0.3265, allocations: 0 / 478.3 MB, free: 12.3 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 0.0008408/0.3274, allocations: 0.6051 MB / 478.9 MB, free: 11.76 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.024e-05/0.3274, allocations: 8.688 kB / 478.9 MB, free: 11.76 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.558e-05/0.3275, allocations: 38.5 kB / 479 MB, free: 11.74 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001248/0.3276, allocations: 204.9 kB / 479.2 MB, free: 11.51 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.921e-05/0.3277, allocations: 28.81 kB / 479.2 MB, free: 11.5 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.723e-05/0.3278, allocations: 41.19 kB / 479.2 MB, free: 11.48 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004763/0.3282, allocations: 303.8 kB / 479.5 MB, free: 11.31 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.742e-05/0.3283, allocations: 192 / 479.5 MB, free: 11.31 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.958e-05/0.3283, allocations: 19.72 kB / 479.5 MB, free: 11.29 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.558e-05/0.3283, allocations: 12.84 kB / 479.6 MB, free: 11.29 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003658/0.3287, allocations: 243.6 kB / 479.8 MB, free: 11.18 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001609/0.3303, allocations: 1.032 MB / 480.8 MB, free: 10.39 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003185/0.3306, allocations: 177.3 kB / 481 MB, free: 10.29 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001739/0.3308, allocations: 128.5 kB / 481.1 MB, free: 10.23 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.761e-05/0.3308, allocations: 2.156 kB / 481.1 MB, free: 10.23 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.627e-05/0.3309, allocations: 36.19 kB / 481.2 MB, free: 10.18 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.323e-06/0.3309, allocations: 1.125 kB / 481.2 MB, free: 10.18 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001801/0.3327, allocations: 0.9084 MB / 482.1 MB, free: 9.582 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.473e-05/0.3327, allocations: 54.38 kB / 482.1 MB, free: 9.52 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001116/0.3328, allocations: 168.2 kB / 482.3 MB, free: 9.375 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.562e-05/0.3329, allocations: 30.8 kB / 482.3 MB, free: 9.34 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 7.328e-05/0.3329, allocations: 210 kB / 482.5 MB, free: 9.148 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.399e-05/0.333, allocations: 93.75 kB / 482.6 MB, free: 9.066 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.11e-05/0.3331, allocations: 70.25 kB / 482.7 MB, free: 9.016 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 5.575e-05/0.3331, allocations: 327 kB / 483 MB, free: 8.691 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001267/0.3333, allocations: 82.5 kB / 483.1 MB, free: 8.648 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001743/0.3334, allocations: 190.6 kB / 483.3 MB, free: 8.469 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002644/0.3361, allocations: 0.8332 MB / 484.1 MB, free: 7.973 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.685e-06/0.3361, allocations: 1.094 kB / 484.1 MB, free: 7.973 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004499/0.3366, allocations: 341.7 kB / 484.4 MB, free: 7.797 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.664e-05/0.3366, allocations: 9.844 kB / 484.4 MB, free: 7.793 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.817e-06/0.3366, allocations: 4.594 kB / 484.5 MB, free: 7.793 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.819e-05/0.3366, allocations: 6 kB / 484.5 MB, free: 7.793 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002808/0.3369, allocations: 81.03 kB / 484.5 MB, free: 7.773 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.191e-05/0.3369, allocations: 6.469 kB / 484.5 MB, free: 7.773 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000134/0.3371, allocations: 11.77 kB / 484.6 MB, free: 7.766 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.315e-05/0.3371, allocations: 17.19 kB / 484.6 MB, free: 7.762 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 0.0002197/0.3373, allocations: 173 kB / 484.7 MB, free: 7.605 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.089e-05/0.3374, allocations: 20.19 kB / 484.8 MB, free: 7.594 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.764e-05/0.3374, allocations: 37.12 kB / 484.8 MB, free: 7.559 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.466e-06/0.3375, allocations: 2.188 kB / 484.8 MB, free: 7.559 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.363e-06/0.3375, allocations: 1.094 kB / 484.8 MB, free: 7.559 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.548e-06/0.3375, allocations: 8 kB / 484.8 MB, free: 7.551 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003766/0.3379, allocations: 369.2 kB / 485.2 MB, free: 7.227 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.224e-06/0.3379, allocations: 1.25 kB / 485.2 MB, free: 7.227 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002403/0.3381, allocations: 46.84 kB / 485.2 MB, free: 7.215 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.935e-06/0.3381, allocations: 1.031 kB / 485.2 MB, free: 7.215 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.758e-05/0.3381, allocations: 6.094 kB / 485.2 MB, free: 7.211 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.384e-06/0.3382, allocations: 0.8125 kB / 485.2 MB, free: 7.211 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.423e-06/0.3382, allocations: 5.141 kB / 485.2 MB, free: 7.207 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004626/0.3386, allocations: 438.7 kB / 485.7 MB, free: 6.918 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.931e-05/0.3387, allocations: 89.48 kB / 485.7 MB, free: 6.816 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.759e-05/0.3387, allocations: 9.484 kB / 485.8 MB, free: 6.809 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001213/0.3388, allocations: 5.344 kB / 485.8 MB, free: 6.805 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.757e-05/0.3389, allocations: 12.14 kB / 485.8 MB, free: 6.801 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.361e-05/0.3389, allocations: 12.05 kB / 485.8 MB, free: 6.793 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.569e-05/0.3389, allocations: 113.9 kB / 485.9 MB, free: 6.703 MB / 350.1 MB
Notification: Performance of sort global known variables: time 6.81e-07/0.339, allocations: 0 / 485.9 MB, free: 6.703 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.000323/0.3393, allocations: 70.94 kB / 486 MB, free: 6.688 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 8.502e-05/0.3394, allocations: 95.62 kB / 486.1 MB, free: 6.594 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003517/0.3397, allocations: 244 kB / 486.3 MB, free: 6.492 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.244e-06/0.3397, allocations: 1.438 kB / 486.3 MB, free: 6.492 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001245/0.3399, allocations: 107.4 kB / 486.4 MB, free: 6.445 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002889/0.3402, allocations: 29.92 kB / 486.4 MB, free: 6.426 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001065/0.3412, allocations: 0.7277 MB / 487.2 MB, free: 5.895 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001806/0.3414, allocations: 0.7695 MB / 487.9 MB, free: 5.16 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 9.071e-05/0.3415, allocations: 29.12 kB / 488 MB, free: 5.145 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.519e-05/0.3416, allocations: 20.56 kB / 488 MB, free: 5.141 MB / 350.1 MB
Notification: Performance of SimCode: time 3.31e-07/0.3416, allocations: 0 / 488 MB, free: 5.141 MB / 350.1 MB
Notification: Performance of Templates: time 0.004549/0.3462, allocations: 2.131 MB / 490.1 MB, free: 4.078 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)