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 0.001251/0.001251, allocations: 80.94 kB / 19.94 MB, free: 4.543 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 0.004676/0.004676, allocations: 177.4 kB / 23.36 MB, free: 1.129 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 0.9316/0.9316, allocations: 177.2 MB / 203.8 MB, free: 5.477 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 0.03877/0.03877, allocations: 9.558 MB / 269.8 MB, free: 3.824 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 9.12e-07/9.12e-07, allocations: 0 / 290.1 MB, free: 16.81 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.281e-05/1.373e-05, allocations: 2.312 kB / 290.1 MB, free: 16.81 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.004552/0.004566, allocations: 4.484 MB / 294.6 MB, free: 15.25 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0003981/0.004964, allocations: 313 kB / 294.9 MB, free: 15.14 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.125e-05/0.005055, allocations: 15.66 kB / 294.9 MB, free: 15.14 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 9.16e-05/0.005147, allocations: 54.75 kB / 294.9 MB, free: 15.11 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.00015/0.005297, allocations: 78.19 kB / 295 MB, free: 15.05 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001726/0.005469, allocations: 69.58 kB / 295.1 MB, free: 15.05 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0002464/0.005716, allocations: 310.4 kB / 295.4 MB, free: 14.96 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001824/0.005898, allocations: 120.6 kB / 295.5 MB, free: 14.94 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001673/0.006065, allocations: 198.6 kB / 295.7 MB, free: 14.92 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001583/0.006224, allocations: 109.6 kB / 295.8 MB, free: 14.9 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 4.308e-05/0.006267, allocations: 33.41 kB / 295.8 MB, free: 14.9 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.793e-05/0.006305, allocations: 33.94 kB / 295.9 MB, free: 14.9 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 4.769e-05/0.006352, allocations: 74.48 kB / 295.9 MB, free: 14.88 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 8.618e-05/0.006438, allocations: 110.9 kB / 296.1 MB, free: 14.86 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002279/0.006666, allocations: 238.8 kB / 296.3 MB, free: 14.8 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.396e-06/0.00667, allocations: 2.953 kB / 296.3 MB, free: 14.8 MB / 266.7 MB
Notification: Performance of FrontEnd: time 7.32e-07/0.006671, allocations: 0 / 296.3 MB, free: 14.8 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 5.541e-06/0.006676, allocations: 0 / 296.3 MB, free: 14.8 MB / 266.7 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 0.0005715/0.007248, allocations: 0.5167 MB / 296.8 MB, free: 14.46 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.329e-05/0.007281, allocations: 9.641 kB / 296.8 MB, free: 14.46 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.386e-05/0.007355, allocations: 53.88 kB / 296.9 MB, free: 14.46 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 9.145e-05/0.007446, allocations: 145.5 kB / 297 MB, free: 14.31 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.372e-05/0.00747, allocations: 29.41 kB / 297 MB, free: 14.31 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.871e-05/0.007519, allocations: 40.22 kB / 297.1 MB, free: 14.31 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002759/0.007794, allocations: 225.6 kB / 297.3 MB, free: 14.26 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.534e-05/0.00781, allocations: 10.56 kB / 297.3 MB, free: 14.25 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.871e-05/0.007829, allocations: 14.59 kB / 297.3 MB, free: 14.25 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.156e-05/0.00784, allocations: 9.094 kB / 297.3 MB, free: 14.25 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001305/0.007971, allocations: 102.2 kB / 297.4 MB, free: 14.24 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001013/0.008984, allocations: 0.7232 MB / 298.2 MB, free: 13.96 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001861/0.00917, allocations: 121.8 kB / 298.3 MB, free: 13.93 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 7.662e-05/0.009246, allocations: 71 kB / 298.3 MB, free: 13.92 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.232e-05/0.009259, allocations: 8.281 kB / 298.4 MB, free: 13.92 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.612e-05/0.009275, allocations: 36.12 kB / 298.4 MB, free: 13.88 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=22): time 1.773e-06/0.009277, allocations: 0 / 298.4 MB, free: 13.88 MB / 266.7 MB
Notification: Performance of matching and sorting (n=26): time 0.0008943/0.01017, allocations: 0.6098 MB / 299 MB, free: 13.67 MB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.363e-05/0.01019, allocations: 55.36 kB / 299.1 MB, free: 13.61 MB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.26e-05/0.01028, allocations: 174.7 kB / 299.2 MB, free: 13.47 MB / 266.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.137e-05/0.01029, allocations: 30.3 kB / 299.3 MB, free: 13.44 MB / 266.7 MB
Notification: Performance of collectInitialEqns (initialization): time 7.258e-05/0.01036, allocations: 213.5 kB / 299.5 MB, free: 13.27 MB / 266.7 MB
Notification: Performance of collectInitialBindings (initialization): time 5.259e-05/0.01041, allocations: 102.1 kB / 299.6 MB, free: 13.19 MB / 266.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.951e-05/0.01047, allocations: 68.39 kB / 299.6 MB, free: 13.15 MB / 266.7 MB
Notification: Performance of setup shared object (initialization): time 4.226e-05/0.01052, allocations: 333.4 kB / 300 MB, free: 12.82 MB / 266.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 4.709e-05/0.01056, allocations: 35.23 kB / 300 MB, free: 12.82 MB / 266.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.899e-05/0.01065, allocations: 152.8 kB / 300.1 MB, free: 12.68 MB / 266.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002301/0.01088, allocations: 278.5 kB / 300.4 MB, free: 12.52 MB / 266.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.154e-06/0.01088, allocations: 1.438 kB / 300.4 MB, free: 12.52 MB / 266.7 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0002355/0.01112, allocations: 227.6 kB / 300.6 MB, free: 12.45 MB / 266.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.537e-05/0.01113, allocations: 6.625 kB / 300.6 MB, free: 12.45 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.076e-06/0.01114, allocations: 5.469 kB / 300.6 MB, free: 12.45 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.735e-05/0.01116, allocations: 6.672 kB / 300.7 MB, free: 12.45 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001672/0.01133, allocations: 78.81 kB / 300.7 MB, free: 12.44 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.187e-06/0.01134, allocations: 13.66 kB / 300.7 MB, free: 12.44 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 6.745e-05/0.0114, allocations: 14.7 kB / 300.8 MB, free: 12.43 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.326e-05/0.01142, allocations: 13.25 kB / 300.8 MB, free: 12.43 MB / 266.7 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 0.0001187/0.01154, allocations: 146.3 kB / 300.9 MB, free: 12.3 MB / 266.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.224e-05/0.01157, allocations: 19.14 kB / 300.9 MB, free: 12.29 MB / 266.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.448e-05/0.0116, allocations: 30.91 kB / 301 MB, free: 12.27 MB / 266.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.118e-06/0.01161, allocations: 3.734 kB / 301 MB, free: 12.27 MB / 266.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.835e-06/0.01161, allocations: 0 / 301 MB, free: 12.27 MB / 266.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.09e-06/0.01161, allocations: 3.875 kB / 301 MB, free: 12.27 MB / 266.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002089/0.01182, allocations: 182.1 kB / 301.1 MB, free: 12.16 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.272e-06/0.01182, allocations: 3.938 kB / 301.2 MB, free: 12.15 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001312/0.01196, allocations: 43.83 kB / 301.2 MB, free: 12.15 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.554e-06/0.01196, allocations: 1.844 kB / 301.2 MB, free: 12.15 MB / 266.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.372e-05/0.01197, allocations: 6.797 kB / 301.2 MB, free: 12.15 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.583e-06/0.01197, allocations: 2.812 kB / 301.2 MB, free: 12.15 MB / 266.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.342e-06/0.01198, allocations: 5.359 kB / 301.2 MB, free: 12.14 MB / 266.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002438/0.01222, allocations: 305.9 kB / 301.5 MB, free: 11.98 MB / 266.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.363e-05/0.01223, allocations: 14.77 kB / 301.5 MB, free: 11.97 MB / 266.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.823e-05/0.01225, allocations: 6.406 kB / 301.5 MB, free: 11.97 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 5.439e-05/0.01231, allocations: 6 kB / 301.5 MB, free: 11.96 MB / 266.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.473e-05/0.01233, allocations: 15.86 kB / 301.6 MB, free: 11.96 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.434e-06/0.01234, allocations: 3.406 kB / 301.6 MB, free: 11.96 MB / 266.7 MB
Notification: Performance of sorting global known variables: time 3.177e-05/0.01237, allocations: 44.55 kB / 301.6 MB, free: 11.95 MB / 266.7 MB
Notification: Performance of sort global known variables: time 4e-08/0.01237, allocations: 0 / 301.6 MB, free: 11.95 MB / 266.7 MB
Notification: Performance of remove unused functions: time 0.0001867/0.01256, allocations: 64.41 kB / 301.7 MB, free: 11.94 MB / 266.7 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 6.895e-05/0.01262, allocations: 84.5 kB / 301.7 MB, free: 11.86 MB / 266.7 MB
Notification: Performance of simCode: created initialization part: time 0.0001724/0.0128, allocations: 164.5 kB / 301.9 MB, free: 11.82 MB / 266.7 MB
Notification: Performance of simCode: created event and clocks part: time 6.171e-06/0.0128, allocations: 3.625 kB / 301.9 MB, free: 11.82 MB / 266.7 MB
Notification: Performance of simCode: created simulation system equations: time 5.801e-05/0.01286, allocations: 75.16 kB / 302 MB, free: 11.8 MB / 266.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0001536/0.01301, allocations: 29.23 kB / 302 MB, free: 11.79 MB / 266.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0005935/0.01361, allocations: 0.5722 MB / 302.6 MB, free: 11.45 MB / 266.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.767e-05/0.01366, allocations: 89.86 kB / 302.7 MB, free: 11.38 MB / 266.7 MB
Notification: Performance of simCode: alias equations: time 6.362e-05/0.01372, allocations: 25.23 kB / 302.7 MB, free: 11.38 MB / 266.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.996e-05/0.01381, allocations: 84.44 kB / 302.8 MB, free: 11.33 MB / 266.7 MB
Notification: Performance of SimCode: time 8.32e-07/0.01381, allocations: 0 / 302.8 MB, free: 11.33 MB / 266.7 MB
Notification: Performance of Templates: time 0.003645/0.01746, allocations: 2.194 MB / 305 MB, free: 10.52 MB / 266.7 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: 2.6593208499252796]