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 0.0009982/0.0009982, allocations: 81.14 kB / 19.87 MB, free: 4.621 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 0.001166/0.001166, allocations: 173 kB / 23.28 MB, free: 1.223 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 1.057/1.057, allocations: 177.1 MB / 203.7 MB, free: 5.527 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 0.04946/0.04946, allocations: 9.55 MB / 269.8 MB, free: 3.797 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 1.893e-06/1.893e-06, allocations: 0 / 343.3 MB, free: 7.527 MB / 314.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.05e-05/2.239e-05, allocations: 2.312 kB / 343.3 MB, free: 7.523 MB / 314.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.00498/0.005003, allocations: 4.461 MB / 347.8 MB, free: 3.043 MB / 314.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0004594/0.005462, allocations: 303.3 kB / 348.1 MB, free: 2.746 MB / 314.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.966e-05/0.005562, allocations: 16 kB / 348.1 MB, free: 2.73 MB / 314.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001032/0.005665, allocations: 59.53 kB / 348.2 MB, free: 2.672 MB / 314.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001949/0.00586, allocations: 75.22 kB / 348.2 MB, free: 2.598 MB / 314.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002254/0.006085, allocations: 71.83 kB / 348.3 MB, free: 2.527 MB / 314.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0002469/0.006332, allocations: 303.1 kB / 348.6 MB, free: 2.23 MB / 314.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002264/0.006558, allocations: 117 kB / 348.7 MB, free: 2.125 MB / 314.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001791/0.006738, allocations: 199.6 kB / 348.9 MB, free: 1.93 MB / 314.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001359/0.006873, allocations: 115.7 kB / 349 MB, free: 1.816 MB / 314.7 MB
Notification: Performance of NFPackage.collectConstants: time 3.739e-05/0.006911, allocations: 32 kB / 349.1 MB, free: 1.785 MB / 314.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.286e-05/0.006944, allocations: 32 kB / 349.1 MB, free: 1.754 MB / 314.7 MB
Notification: Performance of NFScalarize.scalarize: time 4.842e-05/0.006992, allocations: 75.72 kB / 349.2 MB, free: 1.68 MB / 314.7 MB
Notification: Performance of NFVerifyModel.verify: time 7.519e-05/0.007067, allocations: 107.8 kB / 349.3 MB, free: 1.574 MB / 314.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002281/0.007295, allocations: 239 kB / 349.5 MB, free: 1.34 MB / 314.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.216e-06/0.007299, allocations: 0 / 349.5 MB, free: 1.34 MB / 314.7 MB
Notification: Performance of FrontEnd: time 8.31e-07/0.007299, allocations: 0 / 349.5 MB, free: 1.34 MB / 314.7 MB
Notification: Performance of Transformations before backend: time 6.382e-06/0.007306, allocations: 0 / 349.5 MB, free: 1.34 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 0.0005974/0.007903, allocations: 0.6407 MB / 350.1 MB, free: 0.6562 MB / 314.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.919e-05/0.007942, allocations: 8.031 kB / 350.1 MB, free: 0.6484 MB / 314.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.368e-05/0.008016, allocations: 68.7 kB / 350.2 MB, free: 0.582 MB / 314.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001017/0.008118, allocations: 148.2 kB / 350.4 MB, free: 420 kB / 314.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.027e-05/0.008138, allocations: 33.31 kB / 350.4 MB, free: 388 kB / 314.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.302e-05/0.008181, allocations: 44.36 kB / 350.4 MB, free: 344 kB / 314.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002384/0.008419, allocations: 215.1 kB / 350.6 MB, free: 120 kB / 314.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.353e-05/0.008433, allocations: 4.188 kB / 350.7 MB, free: 116 kB / 314.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.856e-05/0.008451, allocations: 12.38 kB / 350.7 MB, free: 104 kB / 314.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.081e-05/0.008462, allocations: 12.38 kB / 350.7 MB, free: 92 kB / 314.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001339/0.008596, allocations: 114.8 kB / 350.8 MB, free: 15.98 MB / 330.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001085/0.009681, allocations: 0.8749 MB / 351.7 MB, free: 15.07 MB / 330.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000179/0.00986, allocations: 145.9 kB / 351.8 MB, free: 14.92 MB / 330.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 8.15e-05/0.009942, allocations: 71.66 kB / 351.9 MB, free: 14.84 MB / 330.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.221e-05/0.009954, allocations: 4 kB / 351.9 MB, free: 14.84 MB / 330.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.201e-05/0.009976, allocations: 41.33 kB / 351.9 MB, free: 14.79 MB / 330.7 MB
Notification: Performance of pre-optimization done (n=22): time 1.813e-06/0.009978, allocations: 0 / 351.9 MB, free: 14.79 MB / 330.7 MB
Notification: Performance of matching and sorting (n=26): time 0.0009093/0.01089, allocations: 0.6489 MB / 352.6 MB, free: 14.11 MB / 330.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.584e-05/0.01091, allocations: 55.41 kB / 352.6 MB, free: 14.04 MB / 330.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000117/0.01103, allocations: 238.3 kB / 352.9 MB, free: 13.79 MB / 330.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.584e-05/0.01105, allocations: 29.7 kB / 352.9 MB, free: 13.75 MB / 330.7 MB
Notification: Performance of collectInitialEqns (initialization): time 9.567e-05/0.01114, allocations: 258.8 kB / 353.1 MB, free: 13.49 MB / 330.7 MB
Notification: Performance of collectInitialBindings (initialization): time 5.826e-05/0.0112, allocations: 103.1 kB / 353.2 MB, free: 13.39 MB / 330.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.579e-05/0.01128, allocations: 67.33 kB / 353.3 MB, free: 13.32 MB / 330.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001414/0.01142, allocations: 0.504 MB / 353.8 MB, free: 12.8 MB / 330.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 5.368e-05/0.01147, allocations: 40.34 kB / 353.8 MB, free: 12.76 MB / 330.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001245/0.01159, allocations: 205.9 kB / 354 MB, free: 12.49 MB / 330.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002424/0.01184, allocations: 331.1 kB / 354.4 MB, free: 12.1 MB / 330.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.633e-06/0.01184, allocations: 0 / 354.4 MB, free: 12.1 MB / 330.7 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0002562/0.0121, allocations: 281.5 kB / 354.6 MB, free: 11.82 MB / 330.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.289e-05/0.01211, allocations: 4 kB / 354.6 MB, free: 11.82 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.306e-06/0.01212, allocations: 7.938 kB / 354.7 MB, free: 11.81 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.34e-05/0.01213, allocations: 8 kB / 354.7 MB, free: 11.8 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001684/0.0123, allocations: 79.89 kB / 354.7 MB, free: 11.72 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.874e-06/0.01231, allocations: 11.94 kB / 354.8 MB, free: 11.71 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 6.816e-05/0.01237, allocations: 8 kB / 354.8 MB, free: 11.7 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.329e-05/0.01239, allocations: 12 kB / 354.8 MB, free: 11.69 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 0.0001519/0.01254, allocations: 203.6 kB / 355 MB, free: 11.49 MB / 330.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.529e-05/0.01257, allocations: 27.86 kB / 355 MB, free: 11.46 MB / 330.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.556e-05/0.01262, allocations: 33.91 kB / 355 MB, free: 11.43 MB / 330.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.146e-06/0.01262, allocations: 4 kB / 355 MB, free: 11.43 MB / 330.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.994e-06/0.01263, allocations: 0 / 355 MB, free: 11.43 MB / 330.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.288e-06/0.01263, allocations: 7.984 kB / 355 MB, free: 11.42 MB / 330.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002493/0.01288, allocations: 213.1 kB / 355.3 MB, free: 11.19 MB / 330.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.054e-06/0.01288, allocations: 0 / 355.3 MB, free: 11.19 MB / 330.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001248/0.01301, allocations: 47.91 kB / 355.3 MB, free: 11.14 MB / 330.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.697e-06/0.01301, allocations: 4 kB / 355.3 MB, free: 11.14 MB / 330.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.465e-05/0.01302, allocations: 4 kB / 355.3 MB, free: 11.13 MB / 330.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.154e-06/0.01303, allocations: 0 / 355.3 MB, free: 11.13 MB / 330.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.166e-06/0.01303, allocations: 7.922 kB / 355.3 MB, free: 11.12 MB / 330.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003399/0.01337, allocations: 387.6 kB / 355.7 MB, free: 10.73 MB / 330.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.522e-05/0.01338, allocations: 11.91 kB / 355.7 MB, free: 10.71 MB / 330.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.043e-05/0.01341, allocations: 12 kB / 355.7 MB, free: 10.7 MB / 330.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.458e-05/0.01347, allocations: 4 kB / 355.7 MB, free: 10.7 MB / 330.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.827e-05/0.0135, allocations: 23.89 kB / 355.7 MB, free: 10.68 MB / 330.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.055e-06/0.01351, allocations: 4 kB / 355.7 MB, free: 10.67 MB / 330.7 MB
Notification: Performance of sorting global known variables: time 6.44e-05/0.01357, allocations: 155.8 kB / 355.9 MB, free: 10.52 MB / 330.7 MB
Notification: Performance of sort global known variables: time 4.1e-08/0.01357, allocations: 0 / 355.9 MB, free: 10.52 MB / 330.7 MB
Notification: Performance of remove unused functions: time 0.0002261/0.0138, allocations: 60 kB / 356 MB, free: 10.46 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 0.0001173/0.01391, allocations: 99.19 kB / 356.1 MB, free: 10.35 MB / 330.7 MB
Notification: Performance of simCode: created initialization part: time 0.000225/0.01414, allocations: 187.9 kB / 356.2 MB, free: 10.16 MB / 330.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.227e-06/0.01414, allocations: 0 / 356.2 MB, free: 10.16 MB / 330.7 MB
Notification: Performance of simCode: created simulation system equations: time 7.284e-05/0.01421, allocations: 83.52 kB / 356.3 MB, free: 10.08 MB / 330.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002385/0.01445, allocations: 28.05 kB / 356.3 MB, free: 10.05 MB / 330.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007679/0.01522, allocations: 0.6398 MB / 357 MB, free: 9.379 MB / 330.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.428e-05/0.01528, allocations: 92.31 kB / 357.1 MB, free: 9.27 MB / 330.7 MB
Notification: Performance of simCode: alias equations: time 7.03e-05/0.01535, allocations: 25.94 kB / 357.1 MB, free: 9.246 MB / 330.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001081/0.01545, allocations: 102.2 kB / 357.2 MB, free: 9.145 MB / 330.7 MB
Notification: Performance of SimCode: time 9.72e-07/0.01545, allocations: 0 / 357.2 MB, free: 9.145 MB / 330.7 MB
Notification: Performance of Templates: time 0.004046/0.0195, allocations: 2.186 MB / 359.4 MB, free: 6.984 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: 2.8666054671630263]