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 4.1.0+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 0.001401/0.001401, allocations: 73.88 kB / 20.66 MB, free: 3.844 MB / 18.57 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 0.001038/0.001038, allocations: 169 kB / 24.06 MB, free: 456 kB / 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 1.018/1.018, allocations: 177.1 MB / 204.5 MB, free: 5.508 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 0.04025/0.04025, allocations: 9.548 MB / 270.6 MB, free: 3.793 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.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.262e-06/1.262e-06, allocations: 0 / 344.1 MB, free: 7.527 MB / 314.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.214e-05/2.34e-05, allocations: 4.844 kB / 344.1 MB, free: 7.523 MB / 314.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.004374/0.004398, allocations: 4.453 MB / 348.6 MB, free: 3.051 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0003046/0.004702, allocations: 311.2 kB / 348.9 MB, free: 2.746 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 8.587e-05/0.004788, allocations: 16 kB / 348.9 MB, free: 2.73 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 7.823e-05/0.004866, allocations: 59.53 kB / 349 MB, free: 2.672 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.000139/0.005006, allocations: 75.22 kB / 349 MB, free: 2.598 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.000149/0.005155, allocations: 67.89 kB / 349.1 MB, free: 2.531 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0002082/0.005363, allocations: 307 kB / 349.4 MB, free: 2.23 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001782/0.005541, allocations: 117 kB / 349.5 MB, free: 2.125 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001404/0.005681, allocations: 195.6 kB / 349.7 MB, free: 1.934 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000125/0.005806, allocations: 111.7 kB / 349.8 MB, free: 1.824 MB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 3.661e-05/0.005843, allocations: 32 kB / 349.8 MB, free: 1.793 MB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.364e-05/0.005876, allocations: 39.94 kB / 349.9 MB, free: 1.754 MB / 314.7 MB
Notification: Performance of NFScalarize.scalarize: time 4.44e-05/0.005921, allocations: 75.72 kB / 350 MB, free: 1.68 MB / 314.7 MB
Notification: Performance of NFVerifyModel.verify: time 7.629e-05/0.005997, allocations: 115.7 kB / 350.1 MB, free: 1.566 MB / 314.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002052/0.006202, allocations: 227.1 kB / 350.3 MB, free: 1.344 MB / 314.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.254e-06/0.006205, allocations: 0 / 350.3 MB, free: 1.344 MB / 314.7 MB
Notification: Performance of FrontEnd: time 8.42e-07/0.006205, allocations: 0 / 350.3 MB, free: 1.344 MB / 314.7 MB
Notification: Performance of Transformations before backend: time 4.068e-06/0.006209, allocations: 0 / 350.3 MB, free: 1.344 MB / 314.7 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 0.0005672/0.006777, allocations: 0.6407 MB / 350.9 MB, free: 0.6602 MB / 314.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.178e-05/0.006808, allocations: 8.031 kB / 350.9 MB, free: 0.6523 MB / 314.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.533e-05/0.006884, allocations: 68.7 kB / 351 MB, free: 0.5859 MB / 314.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001044/0.006988, allocations: 148.1 kB / 351.1 MB, free: 424 kB / 314.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.149e-05/0.00701, allocations: 33.38 kB / 351.2 MB, free: 392 kB / 314.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.164e-05/0.007051, allocations: 36.38 kB / 351.2 MB, free: 356 kB / 314.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002132/0.007264, allocations: 219.1 kB / 351.4 MB, free: 128 kB / 314.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.257e-05/0.007277, allocations: 192 / 351.4 MB, free: 128 kB / 314.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.967e-05/0.007307, allocations: 16.38 kB / 351.4 MB, free: 112 kB / 314.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.005e-05/0.007317, allocations: 8.375 kB / 351.5 MB, free: 104 kB / 314.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001362/0.007453, allocations: 122.8 kB / 351.6 MB, free: 15.98 MB / 330.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001003/0.008456, allocations: 0.8748 MB / 352.4 MB, free: 15.07 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002026/0.008659, allocations: 142.9 kB / 352.6 MB, free: 14.92 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 7.767e-05/0.008736, allocations: 79.64 kB / 352.7 MB, free: 14.84 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.183e-05/0.008748, allocations: 4 kB / 352.7 MB, free: 14.84 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.869e-05/0.008767, allocations: 37.39 kB / 352.7 MB, free: 14.79 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=22): time 1.532e-06/0.008768, allocations: 0 / 352.7 MB, free: 14.79 MB / 330.7 MB
Notification: Performance of matching and sorting (n=26): time 0.0009159/0.009684, allocations: 0.6452 MB / 353.3 MB, free: 14.11 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.632e-05/0.009711, allocations: 55.41 kB / 353.4 MB, free: 14.04 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.433e-05/0.009805, allocations: 234.3 kB / 353.6 MB, free: 13.79 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.389e-05/0.009819, allocations: 29.7 kB / 353.7 MB, free: 13.76 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001412/0.00996, allocations: 262.8 kB / 353.9 MB, free: 13.5 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 4.715e-05/0.01001, allocations: 103.1 kB / 354 MB, free: 13.39 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.26e-05/0.01007, allocations: 67.33 kB / 354.1 MB, free: 13.32 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001148/0.01018, allocations: 0.5001 MB / 354.6 MB, free: 12.81 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 5.138e-05/0.01024, allocations: 44.34 kB / 354.6 MB, free: 12.76 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001138/0.01035, allocations: 211.3 kB / 354.8 MB, free: 12.49 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000234/0.01058, allocations: 331.2 kB / 355.2 MB, free: 12.1 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.633e-06/0.01059, allocations: 0 / 355.2 MB, free: 12.1 MB / 330.7 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0002449/0.01083, allocations: 277.5 kB / 355.4 MB, free: 11.82 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.411e-05/0.01084, allocations: 8 kB / 355.4 MB, free: 11.81 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.524e-06/0.01085, allocations: 11.88 kB / 355.4 MB, free: 11.8 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 9.137e-06/0.01086, allocations: 4 kB / 355.5 MB, free: 11.8 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002742/0.01114, allocations: 87.83 kB / 355.5 MB, free: 11.71 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.581e-06/0.01114, allocations: 4 kB / 355.5 MB, free: 11.71 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.329e-05/0.01121, allocations: 12 kB / 355.6 MB, free: 11.7 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.273e-05/0.01123, allocations: 12 kB / 355.6 MB, free: 11.68 MB / 330.7 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 0.000132/0.01136, allocations: 197.5 kB / 355.8 MB, free: 11.48 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.696e-05/0.0114, allocations: 31.86 kB / 355.8 MB, free: 11.45 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.939e-05/0.01144, allocations: 33.91 kB / 355.8 MB, free: 11.43 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.745e-06/0.01144, allocations: 3.984 kB / 355.8 MB, free: 11.42 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.124e-06/0.01144, allocations: 0 / 355.8 MB, free: 11.42 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.917e-06/0.01144, allocations: 7.984 kB / 355.8 MB, free: 11.41 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002226/0.01167, allocations: 209.1 kB / 356 MB, free: 11.18 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.543e-06/0.01167, allocations: 0 / 356 MB, free: 11.18 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001283/0.0118, allocations: 47.97 kB / 356.1 MB, free: 11.14 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.014e-06/0.0118, allocations: 0 / 356.1 MB, free: 11.14 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.224e-05/0.01181, allocations: 4 kB / 356.1 MB, free: 11.13 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.343e-06/0.01181, allocations: 4 kB / 356.1 MB, free: 11.13 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.106e-06/0.01182, allocations: 7.875 kB / 356.1 MB, free: 11.12 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003008/0.01212, allocations: 379.6 kB / 356.5 MB, free: 10.73 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.458e-05/0.01213, allocations: 19.91 kB / 356.5 MB, free: 10.71 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.766e-05/0.01215, allocations: 64 / 356.5 MB, free: 10.71 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.706e-05/0.01222, allocations: 16 kB / 356.5 MB, free: 10.7 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.377e-05/0.01224, allocations: 23.89 kB / 356.5 MB, free: 10.67 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.615e-06/0.01225, allocations: 4 kB / 356.5 MB, free: 10.67 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 4.89e-05/0.0123, allocations: 151.8 kB / 356.7 MB, free: 10.52 MB / 330.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.0123, allocations: 0 / 356.7 MB, free: 10.52 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.0002025/0.0125, allocations: 67.94 kB / 356.7 MB, free: 10.45 MB / 330.7 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 7.647e-05/0.01257, allocations: 99.19 kB / 356.8 MB, free: 10.34 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.0001798/0.01275, allocations: 184.1 kB / 357 MB, free: 10.16 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.974e-06/0.01276, allocations: 0 / 357 MB, free: 10.16 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 6.574e-05/0.01282, allocations: 87.45 kB / 357.1 MB, free: 10.07 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0001952/0.01302, allocations: 19.98 kB / 357.1 MB, free: 10.05 MB / 330.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0006917/0.01371, allocations: 0.6358 MB / 357.8 MB, free: 9.383 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.144e-05/0.01376, allocations: 88.31 kB / 357.9 MB, free: 9.277 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 6.49e-05/0.01383, allocations: 29.94 kB / 357.9 MB, free: 9.25 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 9.92e-05/0.01392, allocations: 102.2 kB / 358 MB, free: 9.148 MB / 330.7 MB
Notification: Performance of SimCode: time 7.22e-07/0.01393, allocations: 0 / 358 MB, free: 9.148 MB / 330.7 MB
Notification: Performance of Templates: time 0.004045/0.01797, allocations: 2.257 MB / 360.2 MB, free: 6.93 MB / 330.7 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile [Timeout 660]
(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=240  -lv LOG_STATS > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 2.9087117817252874]