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 0.001066/0.001066, allocations: 111.3 kB / 15.23 MB, free: 0.6602 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001195/0.001196, allocations: 197.9 kB / 16.14 MB, free: 6.66 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.25/1.25, allocations: 222.9 MB / 239.8 MB, free: 4.57 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.3033/0.3033, allocations: 12.27 MB / 302.2 MB, free: 1.344 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001753/0.001753, allocations: 60.14 kB / 365.1 MB, free: 10.26 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09572/0.09749, allocations: 52.09 MB / 417.2 MB, free: 6.059 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005588/0.1031, allocations: 4.399 MB / 421.6 MB, free: 1.637 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003272/0.1035, allocations: 311.1 kB / 421.9 MB, free: 1.328 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.25e-05/0.1036, allocations: 16 kB / 421.9 MB, free: 1.312 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001017/0.1037, allocations: 47.72 kB / 421.9 MB, free: 1.266 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001508/0.1039, allocations: 55.53 kB / 422 MB, free: 1.211 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001715/0.104, allocations: 59.94 kB / 422.1 MB, free: 1.152 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002331/0.1043, allocations: 283.2 kB / 422.3 MB, free: 0.875 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002329/0.1045, allocations: 148.8 kB / 422.5 MB, free: 0.7305 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001001/0.1046, allocations: 123.6 kB / 422.6 MB, free: 0.6094 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001602/0.1048, allocations: 151.3 kB / 422.7 MB, free: 472 kB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.011e-05/0.1048, allocations: 24 kB / 422.8 MB, free: 448 kB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 4.871e-05/0.1049, allocations: 28 kB / 422.8 MB, free: 420 kB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 5.514e-05/0.1049, allocations: 71.73 kB / 422.9 MB, free: 348 kB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001204/0.1051, allocations: 151.2 kB / 423 MB, free: 196 kB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.153/0.2581, allocations: 345.4 kB / 423.3 MB, free: 36.94 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.353e-06/0.2581, allocations: 0.5 kB / 423.3 MB, free: 36.94 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.793e-06/0.2581, allocations: 0 / 423.3 MB, free: 36.94 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.449e-05/0.2581, allocations: 0.75 kB / 423.3 MB, free: 36.94 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 0.0008974/0.259, allocations: 0.6023 MB / 424 MB, free: 36.53 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.631e-05/0.2591, allocations: 9.156 kB / 424 MB, free: 36.53 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.716e-05/0.2592, allocations: 35.28 kB / 424 MB, free: 36.51 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 9.817e-05/0.2593, allocations: 208.1 kB / 424.2 MB, free: 36.29 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.452e-05/0.2593, allocations: 27.06 kB / 424.2 MB, free: 36.29 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.453e-05/0.2594, allocations: 39.69 kB / 424.3 MB, free: 36.29 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004859/0.2598, allocations: 308.2 kB / 424.6 MB, free: 36.25 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.012e-05/0.2599, allocations: 4.891 kB / 424.6 MB, free: 36.25 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.506e-05/0.2599, allocations: 19.53 kB / 424.6 MB, free: 36.25 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.188e-05/0.2599, allocations: 8.625 kB / 424.6 MB, free: 36.25 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003868/0.2603, allocations: 237.8 kB / 424.8 MB, free: 36.25 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001631/0.262, allocations: 1.042 MB / 425.9 MB, free: 35.9 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002854/0.2623, allocations: 180.6 kB / 426 MB, free: 35.88 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001529/0.2624, allocations: 124.9 kB / 426.2 MB, free: 35.87 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.015e-05/0.2625, allocations: 2.531 kB / 426.2 MB, free: 35.87 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.49e-05/0.2625, allocations: 36.81 kB / 426.2 MB, free: 35.83 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.333e-06/0.2625, allocations: 0 / 426.2 MB, free: 35.83 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.00172/0.2642, allocations: 0.896 MB / 427.1 MB, free: 35.52 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.158e-05/0.2642, allocations: 54.88 kB / 427.2 MB, free: 35.46 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.846e-05/0.2643, allocations: 166.7 kB / 427.3 MB, free: 35.35 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.51e-05/0.2644, allocations: 32.86 kB / 427.4 MB, free: 35.32 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 5.778e-05/0.2644, allocations: 210.3 kB / 427.6 MB, free: 35.16 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.141e-05/0.2645, allocations: 96.8 kB / 427.7 MB, free: 35.1 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.633e-05/0.2645, allocations: 66.84 kB / 427.7 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 4.209e-05/0.2646, allocations: 330 kB / 428 MB, free: 34.77 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001073/0.2647, allocations: 86.58 kB / 428.1 MB, free: 34.77 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001354/0.2648, allocations: 192.8 kB / 428.3 MB, free: 34.64 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002897/0.2678, allocations: 0.8258 MB / 429.1 MB, free: 34.5 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.914e-06/0.2678, allocations: 0.9844 kB / 429.1 MB, free: 34.5 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0003879/0.2682, allocations: 344.5 kB / 429.5 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.305e-05/0.2682, allocations: 9.406 kB / 429.5 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.272e-06/0.2682, allocations: 3 kB / 429.5 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.354e-05/0.2682, allocations: 6.812 kB / 429.5 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002788/0.2685, allocations: 77.62 kB / 429.6 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.478e-06/0.2685, allocations: 8.594 kB / 429.6 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001546/0.2687, allocations: 17.91 kB / 429.6 MB, free: 34.46 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.973e-05/0.2687, allocations: 17.25 kB / 429.6 MB, free: 34.46 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 0.0002209/0.2689, allocations: 175.9 kB / 429.8 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.843e-05/0.269, allocations: 17.31 kB / 429.8 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.526e-05/0.269, allocations: 31.81 kB / 429.8 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.716e-06/0.269, allocations: 6.062 kB / 429.8 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.503e-06/0.2691, allocations: 3.797 kB / 429.8 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.246e-06/0.2691, allocations: 0.75 kB / 429.8 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003452/0.2694, allocations: 361 kB / 430.2 MB, free: 34.14 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.363e-06/0.2694, allocations: 0 / 430.2 MB, free: 34.14 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002616/0.2697, allocations: 50.28 kB / 430.2 MB, free: 34.14 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.036e-06/0.2697, allocations: 2.031 kB / 430.2 MB, free: 34.14 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.001e-05/0.2697, allocations: 12.67 kB / 430.3 MB, free: 34.14 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.794e-06/0.2697, allocations: 0 / 430.3 MB, free: 34.14 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.52e-07/0.2697, allocations: 0 / 430.3 MB, free: 34.14 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004119/0.2702, allocations: 433.2 kB / 430.7 MB, free: 33.99 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 2.49e-05/0.2702, allocations: 95.67 kB / 430.8 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.932e-05/0.2702, allocations: 4.562 kB / 430.8 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001534/0.2704, allocations: 11.67 kB / 430.8 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.116e-05/0.2704, allocations: 17.64 kB / 430.8 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.254e-05/0.2704, allocations: 9.25 kB / 430.8 MB, free: 33.88 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 4.887e-05/0.2705, allocations: 116.8 kB / 430.9 MB, free: 33.81 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.2705, allocations: 2.297 kB / 430.9 MB, free: 33.81 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0003043/0.2708, allocations: 62.88 kB / 431 MB, free: 33.81 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 6.411e-05/0.2709, allocations: 107 kB / 431.1 MB, free: 33.72 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002971/0.2712, allocations: 244.1 kB / 431.3 MB, free: 33.72 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.795e-06/0.2712, allocations: 1.531 kB / 431.3 MB, free: 33.72 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001132/0.2713, allocations: 111.6 kB / 431.4 MB, free: 33.72 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002846/0.2716, allocations: 25.19 kB / 431.5 MB, free: 33.71 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001025/0.2726, allocations: 0.8954 MB / 432.4 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001377/0.2728, allocations: 0.7646 MB / 433.1 MB, free: 32.46 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0001077/0.2729, allocations: 25.67 kB / 433.2 MB, free: 32.46 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.484e-05/0.273, allocations: 24.62 kB / 433.2 MB, free: 32.45 MB / 350.1 MB
Notification: Performance of SimCode: time 2.21e-07/0.273, allocations: 0 / 433.2 MB, free: 32.45 MB / 350.1 MB
Notification: Performance of Templates: time 0.003705/0.2767, allocations: 1.94 MB / 435.1 MB, free: 32.38 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)