Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.CellDivison.cell.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0008335/0.0008335, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.001001/0.001001, allocations: 165 kB / 23.02 MB, free: 1.551 MB / 18.57 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 1.03/1.03, allocations: 177.1 MB / 203.4 MB, free: 5.188 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo): time 0.03911/0.03911, allocations: 9.541 MB / 269.5 MB, free: 3.82 MB / 250.7 MB
"
[Timeout remaining time 180]
Using package BioChem with version 1.1.3 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CellDivison.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CellDivison.cell")
translateModel(BioChem.Examples.CellDivison.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CellDivison.cell") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.202e-06/1.202e-06, allocations: 0 / 342.9 MB, free: 7.773 MB / 314.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.463e-05/2.583e-05, allocations: 4.984 kB / 342.9 MB, free: 7.77 MB / 314.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CellDivison.cell): time 0.00699/0.007016, allocations: 6.085 MB / 349 MB, free: 1.656 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0006825/0.007698, allocations: 466.9 kB / 349.4 MB, free: 1.199 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001741/0.007872, allocations: 28 kB / 349.5 MB, free: 1.172 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001568/0.008029, allocations: 83.33 kB / 349.5 MB, free: 1.09 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0002681/0.008297, allocations: 130.7 kB / 349.7 MB, free: 0.9609 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002611/0.008558, allocations: 95.84 kB / 349.8 MB, free: 0.8672 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0004533/0.009012, allocations: 470.4 kB / 350.2 MB, free: 416 kB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003557/0.009367, allocations: 170.4 kB / 350.4 MB, free: 240 kB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003582/0.009725, allocations: 295.4 kB / 350.7 MB, free: 15.95 MB / 330.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003081/0.01003, allocations: 159.5 kB / 350.8 MB, free: 15.79 MB / 330.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001107/0.01014, allocations: 52 kB / 350.9 MB, free: 15.74 MB / 330.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 7.13e-05/0.01022, allocations: 48 kB / 350.9 MB, free: 15.69 MB / 330.7 MB
Notification: Performance of NFScalarize.scalarize: time 6.425e-05/0.01028, allocations: 111.6 kB / 351 MB, free: 15.58 MB / 330.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001306/0.01041, allocations: 163.7 kB / 351.2 MB, free: 15.42 MB / 330.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0003733/0.01078, allocations: 358.6 kB / 351.6 MB, free: 15.07 MB / 330.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.899e-06/0.01079, allocations: 0 / 351.6 MB, free: 15.07 MB / 330.7 MB
Notification: Performance of FrontEnd: time 1.794e-06/0.01079, allocations: 0 / 351.6 MB, free: 15.07 MB / 330.7 MB
Notification: Performance of Transformations before backend: time 6.802e-06/0.0108, allocations: 0 / 351.6 MB, free: 15.07 MB / 330.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 148
 * Number of variables: 148
Notification: Performance of Generate backend data structure: time 0.0007075/0.0115, allocations: 0.7654 MB / 352.3 MB, free: 14.27 MB / 330.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.173e-05/0.01155, allocations: 12.03 kB / 352.3 MB, free: 14.25 MB / 330.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001133/0.01166, allocations: 100.6 kB / 352.4 MB, free: 14.16 MB / 330.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001334/0.01179, allocations: 160 kB / 352.6 MB, free: 13.97 MB / 330.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.555e-05/0.01183, allocations: 49.69 kB / 352.6 MB, free: 13.92 MB / 330.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.914e-05/0.0119, allocations: 60.38 kB / 352.7 MB, free: 13.86 MB / 330.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004812/0.01238, allocations: 440.6 kB / 353.1 MB, free: 13.41 MB / 330.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.673e-05/0.0124, allocations: 8.141 kB / 353.1 MB, free: 13.41 MB / 330.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.035e-05/0.01243, allocations: 24.36 kB / 353.2 MB, free: 13.38 MB / 330.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.496e-05/0.01244, allocations: 16.38 kB / 353.2 MB, free: 13.37 MB / 330.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002828/0.01272, allocations: 223.7 kB / 353.4 MB, free: 13.15 MB / 330.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001581/0.01431, allocations: 1.475 MB / 354.9 MB, free: 11.63 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000342/0.01465, allocations: 246.8 kB / 355.1 MB, free: 11.38 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001536/0.0148, allocations: 127.1 kB / 355.2 MB, free: 11.25 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.169e-05/0.01482, allocations: 11.94 kB / 355.2 MB, free: 11.24 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.538e-05/0.01485, allocations: 37.39 kB / 355.3 MB, free: 11.19 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=35): time 1.363e-06/0.01485, allocations: 4 kB / 355.3 MB, free: 11.19 MB / 330.7 MB
Notification: Performance of matching and sorting (n=42): time 0.001535/0.01638, allocations: 1.073 MB / 356.4 MB, free: 10.08 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.845e-05/0.01641, allocations: 55.41 kB / 356.4 MB, free: 10.02 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001316/0.01654, allocations: 255.3 kB / 356.7 MB, free: 9.746 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.727e-05/0.01656, allocations: 33.7 kB / 356.7 MB, free: 9.707 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001222/0.01668, allocations: 327.1 kB / 357 MB, free: 9.383 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 7.736e-05/0.01676, allocations: 162.6 kB / 357.2 MB, free: 9.223 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.793e-05/0.01685, allocations: 104 kB / 357.3 MB, free: 9.113 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.000133/0.01698, allocations: 0.5078 MB / 357.8 MB, free: 8.594 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001152/0.0171, allocations: 97.19 kB / 357.9 MB, free: 8.5 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002276/0.01732, allocations: 343.2 kB / 358.2 MB, free: 8.059 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005201/0.01784, allocations: 0.5678 MB / 358.8 MB, free: 7.379 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.214e-06/0.01785, allocations: 0 / 358.8 MB, free: 7.379 MB / 330.7 MB
Notification: Performance of matching and sorting (n=74) (initialization): time 0.0004746/0.01832, allocations: 473.4 kB / 359.2 MB, free: 6.914 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.893e-05/0.01834, allocations: 8 kB / 359.2 MB, free: 6.906 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.122e-05/0.01835, allocations: 11.98 kB / 359.3 MB, free: 6.895 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.016e-05/0.01837, allocations: 8 kB / 359.3 MB, free: 6.887 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000268/0.01864, allocations: 139.8 kB / 359.4 MB, free: 6.75 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.414e-05/0.01865, allocations: 11.94 kB / 359.4 MB, free: 6.738 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.91e-05/0.01875, allocations: 23.94 kB / 359.4 MB, free: 6.715 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.133e-05/0.01877, allocations: 24 kB / 359.5 MB, free: 6.691 MB / 330.7 MB
Warning: Assuming fixed start value for the following 8 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         EmptySet.c:VARIABLE(min = 0.0 start = 0.0 unit = \"mol/l\" fixed = true stateSelect=StateSelect.prefer )  \"Current concentration of substance (mM)\" type: Real
         YP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         Y.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         pM.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
         CP.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         C2.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: 25
 * 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 (74):
 * Single equations (assignments): 74
 * 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 0.0001951/0.01897, allocations: 214.8 kB / 359.7 MB, free: 6.473 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.851e-05/0.01902, allocations: 43.81 kB / 359.7 MB, free: 6.43 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.333e-05/0.01907, allocations: 42.98 kB / 359.8 MB, free: 6.391 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.156e-06/0.01907, allocations: 4 kB / 359.8 MB, free: 6.387 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.728e-06/0.01908, allocations: 0 / 359.8 MB, free: 6.387 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.551e-06/0.01908, allocations: 3.984 kB / 359.8 MB, free: 6.383 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007861/0.01987, allocations: 0.7428 MB / 360.5 MB, free: 5.594 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.465e-06/0.01987, allocations: 0 / 360.5 MB, free: 5.594 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002313/0.0201, allocations: 99.89 kB / 360.6 MB, free: 5.496 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.475e-06/0.02011, allocations: 0 / 360.6 MB, free: 5.496 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.033e-05/0.02013, allocations: 15.98 kB / 360.6 MB, free: 5.48 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 6.261e-06/0.02013, allocations: 11.92 kB / 360.6 MB, free: 5.469 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.021e-06/0.02013, allocations: 0 / 360.6 MB, free: 5.469 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000483/0.02062, allocations: 0.5555 MB / 361.2 MB, free: 4.883 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.952e-05/0.02064, allocations: 19.86 kB / 361.2 MB, free: 4.863 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.592e-05/0.02066, allocations: 11.94 kB / 361.2 MB, free: 4.852 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.794e-05/0.02074, allocations: 16 kB / 361.2 MB, free: 4.836 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.556e-05/0.02078, allocations: 31.94 kB / 361.3 MB, free: 4.805 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.185e-05/0.02079, allocations: 8 kB / 361.3 MB, free: 4.797 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 6.813e-05/0.02086, allocations: 161.1 kB / 361.4 MB, free: 4.641 MB / 330.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.02086, allocations: 0 / 361.4 MB, free: 4.641 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.0002585/0.02112, allocations: 100 kB / 361.5 MB, free: 4.543 MB / 330.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 2
 * Number of states: 8 (V,EmptySet.c,C2.n,CP.n,M.n,pM.n,Y.n,YP.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 (42):
 * Single equations (assignments): 42
 * 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 0.0001024/0.02122, allocations: 107.2 kB / 361.6 MB, free: 4.43 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.0003537/0.02157, allocations: 320.2 kB / 361.9 MB, free: 4.117 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.714e-06/0.02157, allocations: 0 / 361.9 MB, free: 4.117 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001312/0.0217, allocations: 147.5 kB / 362.1 MB, free: 3.969 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002622/0.02197, allocations: 44.66 kB / 362.1 MB, free: 3.926 MB / 330.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001067/0.02303, allocations: 0.9881 MB / 363.1 MB, free: 2.898 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 6.729e-05/0.0231, allocations: 113.1 kB / 363.2 MB, free: 2.77 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 9.699e-05/0.0232, allocations: 34.97 kB / 363.3 MB, free: 2.734 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 7.782e-05/0.02328, allocations: 36.48 kB / 363.3 MB, free: 2.699 MB / 330.7 MB
Notification: Performance of SimCode: time 7.62e-07/0.02328, allocations: 0 / 363.3 MB, free: 2.699 MB / 330.7 MB
Notification: Performance of Templates: time 0.004992/0.02827, allocations: 3.249 MB / 366.5 MB, free: 15.52 MB / 346.7 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.CellDivison.cell.makefile [Timeout 660]
(rm -f BioChem_BioChem.Examples.CellDivison.cell.pipe ; mkfifo BioChem_BioChem.Examples.CellDivison.cell.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CellDivison.cell.pipe >> ../files/BioChem_BioChem.Examples.CellDivison.cell.sim & ./BioChem_BioChem.Examples.CellDivison.cell -abortSlowSimulation -alarm=240  -lv LOG_STATS > BioChem_BioChem.Examples.CellDivison.cell.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 3.027787803206593]