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 0.001244/0.001244, allocations: 90.52 kB / 15.36 MB, free: 0.7383 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.01345/0.01345, allocations: 171.1 kB / 16.26 MB, free: 6.613 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.528/1.528, allocations: 223.3 MB / 240.3 MB, free: 5.324 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2598/0.2598, allocations: 12.25 MB / 303.7 MB, free: 2 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0004015/0.0004015, allocations: 8 kB / 367.5 MB, free: 9.449 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1299/0.1303, allocations: 53.09 MB / 420.6 MB, free: 4.25 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005897/0.1363, allocations: 3.975 MB / 424.6 MB, free: 264 kB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.2123/0.3486, allocations: 307.6 kB / 424.9 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002831/0.3489, allocations: 17.47 kB / 424.9 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001416/0.3491, allocations: 39.67 kB / 425 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002155/0.3493, allocations: 55.39 kB / 425 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002157/0.3495, allocations: 62.31 kB / 425.1 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002545/0.3498, allocations: 287.8 kB / 425.4 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002472/0.35, allocations: 136.5 kB / 425.5 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000103/0.3501, allocations: 100.5 kB / 425.6 MB, free: 35.09 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001745/0.3503, allocations: 126.5 kB / 425.7 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.478e-05/0.3504, allocations: 17.22 kB / 425.7 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.888e-05/0.3504, allocations: 12.94 kB / 425.7 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.651e-05/0.3504, allocations: 51.61 kB / 425.8 MB, free: 35.05 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001254/0.3506, allocations: 165.6 kB / 426 MB, free: 34.98 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.000294/0.3509, allocations: 329 kB / 426.3 MB, free: 34.93 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.877e-06/0.3509, allocations: 0.9688 kB / 426.3 MB, free: 34.93 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.723e-06/0.3509, allocations: 1.156 kB / 426.3 MB, free: 34.93 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 7.303e-06/0.3509, allocations: 0 / 426.3 MB, free: 34.93 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 0.0006704/0.3516, allocations: 0.545 MB / 426.8 MB, free: 34.5 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.533e-05/0.3516, allocations: 10 kB / 426.8 MB, free: 34.5 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.127e-05/0.3517, allocations: 33.59 kB / 426.9 MB, free: 34.48 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 9.119e-05/0.3518, allocations: 204.8 kB / 427.1 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.751e-05/0.3518, allocations: 28.41 kB / 427.1 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.837e-05/0.3519, allocations: 41.09 kB / 427.1 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004493/0.3524, allocations: 306.8 kB / 427.4 MB, free: 34.23 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.63e-05/0.3524, allocations: 3.094 kB / 427.4 MB, free: 34.23 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.991e-05/0.3524, allocations: 21.03 kB / 427.5 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.045e-05/0.3524, allocations: 9.5 kB / 427.5 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003211/0.3528, allocations: 238.6 kB / 427.7 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001482/0.3543, allocations: 1.045 MB / 428.7 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002732/0.3545, allocations: 178 kB / 428.9 MB, free: 33.85 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001543/0.3547, allocations: 123.4 kB / 429 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.114e-05/0.3547, allocations: 5.469 kB / 429 MB, free: 33.84 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.082e-05/0.3548, allocations: 38.83 kB / 429.1 MB, free: 33.8 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.593e-06/0.3548, allocations: 0 / 429.1 MB, free: 33.8 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001785/0.3566, allocations: 0.8889 MB / 430 MB, free: 33.5 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.627e-05/0.3566, allocations: 59.66 kB / 430 MB, free: 33.43 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001055/0.3567, allocations: 165.2 kB / 430.2 MB, free: 33.32 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.757e-05/0.3567, allocations: 31.55 kB / 430.2 MB, free: 33.29 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 7.569e-05/0.3568, allocations: 207.9 kB / 430.4 MB, free: 33.14 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 5e-05/0.3569, allocations: 101.4 kB / 430.5 MB, free: 33.07 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 3.875e-05/0.3569, allocations: 35.92 kB / 430.6 MB, free: 33.06 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 5.573e-05/0.357, allocations: 331 kB / 430.9 MB, free: 32.75 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001132/0.3571, allocations: 85 kB / 431 MB, free: 32.74 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001462/0.3572, allocations: 192.6 kB / 431.1 MB, free: 32.62 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003107/0.3604, allocations: 0.8623 MB / 432 MB, free: 32.48 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.584e-06/0.3604, allocations: 0 / 432 MB, free: 32.48 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004219/0.3608, allocations: 344.1 kB / 432.3 MB, free: 32.43 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.673e-05/0.3608, allocations: 9.719 kB / 432.4 MB, free: 32.43 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.053e-06/0.3608, allocations: 6.562 kB / 432.4 MB, free: 32.43 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.572e-05/0.3609, allocations: 4.312 kB / 432.4 MB, free: 32.43 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002818/0.3612, allocations: 78.06 kB / 432.4 MB, free: 32.43 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.237e-05/0.3612, allocations: 9.703 kB / 432.5 MB, free: 32.43 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001699/0.3613, allocations: 14.06 kB / 432.5 MB, free: 32.43 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.048e-05/0.3614, allocations: 16.56 kB / 432.5 MB, free: 32.43 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 0.0002402/0.3616, allocations: 172.7 kB / 432.7 MB, free: 32.31 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.073e-05/0.3617, allocations: 22.91 kB / 432.7 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 8.373e-05/0.3618, allocations: 32.09 kB / 432.7 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.32e-06/0.3618, allocations: 5.312 kB / 432.7 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.917e-06/0.3618, allocations: 0.7969 kB / 432.7 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.21e-06/0.3618, allocations: 1.734 kB / 432.7 MB, free: 32.29 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004032/0.3622, allocations: 362.2 kB / 433.1 MB, free: 32.09 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.134e-06/0.3622, allocations: 0 / 433.1 MB, free: 32.09 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002409/0.3625, allocations: 54.2 kB / 433.1 MB, free: 32.09 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.374e-06/0.3625, allocations: 0 / 433.1 MB, free: 32.09 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.713e-05/0.3625, allocations: 3.5 kB / 433.1 MB, free: 32.09 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.425e-06/0.3625, allocations: 8.562 kB / 433.1 MB, free: 32.09 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.333e-06/0.3625, allocations: 0.5625 kB / 433.1 MB, free: 32.09 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004782/0.363, allocations: 431.4 kB / 433.6 MB, free: 31.94 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.857e-05/0.363, allocations: 88.48 kB / 433.6 MB, free: 31.84 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.912e-05/0.3631, allocations: 3.875 kB / 433.6 MB, free: 31.84 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001504/0.3632, allocations: 13.72 kB / 433.7 MB, free: 31.83 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.174e-05/0.3633, allocations: 22.48 kB / 433.7 MB, free: 31.83 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.304e-05/0.3633, allocations: 6.75 kB / 433.7 MB, free: 31.83 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.901e-05/0.3633, allocations: 125.1 kB / 433.8 MB, free: 31.75 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.3633, allocations: 0 / 433.8 MB, free: 31.75 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.000317/0.3637, allocations: 64.03 kB / 433.9 MB, free: 31.75 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 7.885e-05/0.3638, allocations: 97.3 kB / 434 MB, free: 31.66 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003413/0.3641, allocations: 250.1 kB / 434.2 MB, free: 31.64 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.124e-06/0.3641, allocations: 0 / 434.2 MB, free: 31.64 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001285/0.3642, allocations: 112.3 kB / 434.3 MB, free: 31.63 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004067/0.3647, allocations: 27.14 kB / 434.3 MB, free: 31.62 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001228/0.3659, allocations: 0.9539 MB / 435.3 MB, free: 31.04 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000162/0.3661, allocations: 0.7706 MB / 436.1 MB, free: 30.33 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0001157/0.3662, allocations: 22.61 kB / 436.1 MB, free: 30.33 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.428e-05/0.3663, allocations: 24.11 kB / 436.1 MB, free: 30.32 MB / 350.1 MB
Notification: Performance of SimCode: time 3.71e-07/0.3663, allocations: 0 / 436.1 MB, free: 30.32 MB / 350.1 MB
Notification: Performance of Templates: time 0.004087/0.3704, allocations: 1.915 MB / 438 MB, free: 30.24 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)