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 0.001741/0.001741, allocations: 100.1 kB / 15.88 MB, free: 12 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.002176/0.002176, allocations: 200 kB / 16.79 MB, free: 6.809 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 2.321/2.321, allocations: 222.9 MB / 240.5 MB, free: 4.617 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.3283/0.3283, allocations: 12.27 MB / 302.9 MB, free: 1.363 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.002584/0.002584, allocations: 67.89 kB / 365.8 MB, free: 10.28 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1674/0.17, allocations: 52.08 MB / 417.8 MB, free: 6.09 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.01095/0.181, allocations: 4.399 MB / 422.2 MB, free: 1.668 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0009798/0.182, allocations: 315.2 kB / 422.5 MB, free: 1.355 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003477/0.1824, allocations: 19.94 kB / 422.6 MB, free: 1.336 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002643/0.1827, allocations: 35.8 kB / 422.6 MB, free: 1.301 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004768/0.1832, allocations: 55.48 kB / 422.6 MB, free: 1.246 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003864/0.1836, allocations: 63.92 kB / 422.7 MB, free: 1.184 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0006832/0.1843, allocations: 287.2 kB / 423 MB, free: 0.9023 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004572/0.1848, allocations: 140.9 kB / 423.1 MB, free: 0.7656 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002456/0.1851, allocations: 123.6 kB / 423.2 MB, free: 0.6445 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003672/0.1855, allocations: 155.3 kB / 423.4 MB, free: 0.4922 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 9.545e-05/0.1856, allocations: 24 kB / 423.4 MB, free: 480 kB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001019/0.1857, allocations: 28 kB / 423.5 MB, free: 452 kB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001056/0.1858, allocations: 67.7 kB / 423.5 MB, free: 384 kB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002815/0.1861, allocations: 155.2 kB / 423.7 MB, free: 228 kB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.318/0.5042, allocations: 264.5 kB / 423.9 MB, free: 36.83 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.985e-06/0.5042, allocations: 2.188 kB / 423.9 MB, free: 36.83 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.473e-06/0.5042, allocations: 0 / 423.9 MB, free: 36.83 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 3.87e-05/0.5043, allocations: 1.656 kB / 423.9 MB, free: 36.83 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 0.001418/0.5057, allocations: 0.6021 MB / 424.5 MB, free: 36.42 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.037e-05/0.5058, allocations: 8.719 kB / 424.5 MB, free: 36.42 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 9.912e-05/0.5059, allocations: 32.03 kB / 424.6 MB, free: 36.4 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001586/0.5061, allocations: 214.5 kB / 424.8 MB, free: 36.18 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.401e-05/0.5061, allocations: 23.91 kB / 424.8 MB, free: 36.18 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.767e-05/0.5063, allocations: 39.34 kB / 424.8 MB, free: 36.18 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0008187/0.5071, allocations: 306 kB / 425.1 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.891e-05/0.5071, allocations: 6.906 kB / 425.1 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 5.081e-05/0.5072, allocations: 19.12 kB / 425.2 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.773e-05/0.5072, allocations: 10.12 kB / 425.2 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0007358/0.508, allocations: 237.2 kB / 425.4 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002842/0.5108, allocations: 1.042 MB / 426.5 MB, free: 35.79 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000521/0.5114, allocations: 183.1 kB / 426.6 MB, free: 35.77 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002843/0.5117, allocations: 120.7 kB / 426.7 MB, free: 35.76 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.457e-05/0.5117, allocations: 4.906 kB / 426.8 MB, free: 35.76 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.229e-05/0.5118, allocations: 38.72 kB / 426.8 MB, free: 35.72 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 2.515e-06/0.5118, allocations: 2.938 kB / 426.8 MB, free: 35.72 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.003205/0.515, allocations: 0.8918 MB / 427.7 MB, free: 35.41 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.218e-05/0.515, allocations: 55.5 kB / 427.7 MB, free: 35.35 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001834/0.5152, allocations: 165.8 kB / 427.9 MB, free: 35.24 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.725e-05/0.5153, allocations: 33.33 kB / 427.9 MB, free: 35.21 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001101/0.5154, allocations: 212.8 kB / 428.1 MB, free: 35.05 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 9.446e-05/0.5155, allocations: 98.69 kB / 428.2 MB, free: 34.99 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001305/0.5157, allocations: 67.45 kB / 428.3 MB, free: 34.97 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 6.848e-05/0.5157, allocations: 327 kB / 428.6 MB, free: 34.66 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002109/0.516, allocations: 85.22 kB / 428.7 MB, free: 34.66 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002717/0.5162, allocations: 190.9 kB / 428.9 MB, free: 34.53 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005114/0.5214, allocations: 0.8217 MB / 429.7 MB, free: 34.39 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.038e-06/0.5214, allocations: 2.562 kB / 429.7 MB, free: 34.39 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0008319/0.5223, allocations: 348 kB / 430.1 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.375e-05/0.5223, allocations: 5.125 kB / 430.1 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.168e-05/0.5223, allocations: 5.75 kB / 430.1 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.597e-05/0.5224, allocations: 6.469 kB / 430.1 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005195/0.5229, allocations: 79.95 kB / 430.2 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.733e-05/0.5229, allocations: 10.16 kB / 430.2 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003209/0.5233, allocations: 14.88 kB / 430.2 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.294e-05/0.5233, allocations: 15.81 kB / 430.2 MB, free: 34.36 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 0.0004145/0.5237, allocations: 179.7 kB / 430.4 MB, free: 34.23 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.845e-05/0.5238, allocations: 24.66 kB / 430.4 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 9.535e-05/0.5239, allocations: 27.41 kB / 430.4 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.672e-06/0.5239, allocations: 2.75 kB / 430.4 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.749e-06/0.524, allocations: 3.5 kB / 430.4 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.967e-06/0.524, allocations: 3.75 kB / 430.4 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000758/0.5247, allocations: 365.1 kB / 430.8 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.168e-06/0.5248, allocations: 0.5 kB / 430.8 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004431/0.5252, allocations: 44.89 kB / 430.8 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 5.189e-06/0.5252, allocations: 1.281 kB / 430.8 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.103e-05/0.5253, allocations: 7.844 kB / 430.8 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.22e-06/0.5253, allocations: 0.625 kB / 430.8 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.308e-06/0.5253, allocations: 9.188 kB / 430.8 MB, free: 34.03 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0008647/0.5262, allocations: 426.9 kB / 431.3 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.366e-05/0.5263, allocations: 99.52 kB / 431.4 MB, free: 33.77 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.059e-05/0.5263, allocations: 7.656 kB / 431.4 MB, free: 33.77 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002777/0.5266, allocations: 11.22 kB / 431.4 MB, free: 33.77 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.176e-05/0.5267, allocations: 16 kB / 431.4 MB, free: 33.77 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.564e-05/0.5267, allocations: 9.672 kB / 431.4 MB, free: 33.77 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001136/0.5269, allocations: 119.6 kB / 431.5 MB, free: 33.7 MB / 350.1 MB
Notification: Performance of sort global known variables: time 2.91e-07/0.5269, allocations: 0 / 431.5 MB, free: 33.7 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0006324/0.5275, allocations: 67.91 kB / 431.6 MB, free: 33.7 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 0.0001242/0.5277, allocations: 103.6 kB / 431.7 MB, free: 33.61 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0005801/0.5283, allocations: 246.6 kB / 431.9 MB, free: 33.61 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.955e-06/0.5283, allocations: 0 / 431.9 MB, free: 33.61 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002276/0.5285, allocations: 111.5 kB / 432 MB, free: 33.61 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005362/0.5291, allocations: 30.41 kB / 432.1 MB, free: 33.61 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00205/0.5311, allocations: 0.9086 MB / 433 MB, free: 33.02 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002631/0.5314, allocations: 0.7642 MB / 433.7 MB, free: 32.32 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000151/0.5316, allocations: 27.73 kB / 433.8 MB, free: 32.31 MB / 350.1 MB
Notification: Performance of SimCode: time 4.61e-07/0.5316, allocations: 4 kB / 433.8 MB, free: 32.31 MB / 350.1 MB
Notification: Performance of Templates: time 0.007189/0.5388, allocations: 2.823 MB / 436.6 MB, free: 32.17 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)