Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.CaOscillations.Cytosol.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 0.0008585/0.0008585, allocations: 80.94 kB / 19.94 MB, free: 4.547 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 0.0008651/0.0008651, allocations: 177 kB / 23.36 MB, free: 1.133 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 0.9518/0.9518, allocations: 177.1 MB / 203.8 MB, free: 5.488 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 0.04477/0.04477, allocations: 9.554 MB / 269.8 MB, free: 3.836 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.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2400,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2400,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.413e-06/1.413e-06, allocations: 0 / 290.1 MB, free: 18.03 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.538e-05/1.679e-05, allocations: 3.406 kB / 290.1 MB, free: 18.03 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003032/0.003048, allocations: 2.425 MB / 292.5 MB, free: 17.39 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0004859/0.003534, allocations: 202.8 kB / 292.7 MB, free: 17.32 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 8.113e-05/0.003616, allocations: 8.375 kB / 292.7 MB, free: 17.32 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 6.674e-05/0.003682, allocations: 31.34 kB / 292.7 MB, free: 17.3 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001338/0.003816, allocations: 52.02 kB / 292.8 MB, free: 17.27 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001853/0.004001, allocations: 46.09 kB / 292.8 MB, free: 17.26 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0001743/0.004176, allocations: 190 kB / 293 MB, free: 17.21 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001482/0.004324, allocations: 73.67 kB / 293.1 MB, free: 17.2 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001307/0.004454, allocations: 125.2 kB / 293.2 MB, free: 17.18 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001481/0.004603, allocations: 76.56 kB / 293.3 MB, free: 17.17 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 3.709e-05/0.00464, allocations: 22.06 kB / 293.3 MB, free: 17.17 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.809e-05/0.004668, allocations: 22.09 kB / 293.3 MB, free: 17.17 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 3.59e-05/0.004704, allocations: 49.69 kB / 293.4 MB, free: 17.16 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 6.251e-05/0.004766, allocations: 70.38 kB / 293.4 MB, free: 17.14 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001831/0.004949, allocations: 152.2 kB / 293.6 MB, free: 17.1 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.495e-06/0.004952, allocations: 2.109 kB / 293.6 MB, free: 17.1 MB / 266.7 MB
Notification: Performance of FrontEnd: time 6.31e-07/0.004952, allocations: 0 / 293.6 MB, free: 17.1 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 6.011e-06/0.004958, allocations: 0 / 293.6 MB, free: 17.1 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: 60
 * Number of variables: 60
Notification: Performance of Generate backend data structure: time 0.0004434/0.005402, allocations: 419.5 kB / 294 MB, free: 16.8 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.303e-05/0.005435, allocations: 9.219 kB / 294 MB, free: 16.8 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.106e-05/0.005496, allocations: 36.22 kB / 294 MB, free: 16.8 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 7.056e-05/0.005566, allocations: 133.1 kB / 294.2 MB, free: 16.66 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.75e-05/0.005584, allocations: 16.66 kB / 294.2 MB, free: 16.65 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.907e-05/0.005623, allocations: 24.56 kB / 294.2 MB, free: 16.65 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002119/0.005835, allocations: 188.3 kB / 294.4 MB, free: 16.57 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.065e-05/0.005846, allocations: 5.828 kB / 294.4 MB, free: 16.57 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.324e-05/0.005859, allocations: 11.78 kB / 294.4 MB, free: 16.56 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.808e-06/0.005869, allocations: 7.359 kB / 294.4 MB, free: 16.56 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 8.675e-05/0.005955, allocations: 64.3 kB / 294.5 MB, free: 16.55 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007607/0.006716, allocations: 0.5912 MB / 295.1 MB, free: 16.15 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001037/0.00682, allocations: 84.81 kB / 295.2 MB, free: 16.09 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001334/0.006953, allocations: 74.7 kB / 295.2 MB, free: 16.07 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.706e-05/0.00697, allocations: 5.859 kB / 295.2 MB, free: 16.07 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.673e-05/0.006987, allocations: 37 kB / 295.3 MB, free: 16.03 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=15): time 2.004e-06/0.006989, allocations: 1.594 kB / 295.3 MB, free: 16.03 MB / 266.7 MB
Notification: Performance of matching and sorting (n=17): time 0.0007425/0.007731, allocations: 0.5123 MB / 295.8 MB, free: 15.69 MB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.214e-05/0.007754, allocations: 80.45 kB / 295.9 MB, free: 15.59 MB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 6.684e-05/0.00782, allocations: 145 kB / 296 MB, free: 15.47 MB / 266.7 MB
Notification: Performance of collectPreVariables (initialization): time 8.616e-06/0.007829, allocations: 30.73 kB / 296 MB, free: 15.44 MB / 266.7 MB
Notification: Performance of collectInitialEqns (initialization): time 4.607e-05/0.007875, allocations: 158.4 kB / 296.2 MB, free: 15.3 MB / 266.7 MB
Notification: Performance of collectInitialBindings (initialization): time 3.046e-05/0.007906, allocations: 76.95 kB / 296.3 MB, free: 15.24 MB / 266.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 4.691e-05/0.007952, allocations: 40.36 kB / 296.3 MB, free: 15.21 MB / 266.7 MB
Notification: Performance of setup shared object (initialization): time 3.724e-05/0.00799, allocations: 328.1 kB / 296.6 MB, free: 14.89 MB / 266.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 3.01e-05/0.00802, allocations: 17.98 kB / 296.6 MB, free: 14.89 MB / 266.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 4.995e-05/0.00807, allocations: 75.34 kB / 296.7 MB, free: 14.82 MB / 266.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001424/0.008212, allocations: 144.5 kB / 296.9 MB, free: 14.75 MB / 266.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.954e-06/0.008214, allocations: 3.75 kB / 296.9 MB, free: 14.75 MB / 266.7 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0001432/0.008357, allocations: 142.1 kB / 297 MB, free: 14.69 MB / 266.7 MB
Notification: Performance of prepare postOptimizeDAE: time 2.009e-05/0.008377, allocations: 10.09 kB / 297 MB, free: 14.69 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.522e-06/0.008384, allocations: 3.281 kB / 297 MB, free: 14.69 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.671e-05/0.008401, allocations: 3.531 kB / 297 MB, free: 14.69 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001384/0.008539, allocations: 53.36 kB / 297.1 MB, free: 14.68 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.039e-06/0.008544, allocations: 3.922 kB / 297.1 MB, free: 14.68 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 4.282e-05/0.008587, allocations: 8.016 kB / 297.1 MB, free: 14.68 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.057e-05/0.008598, allocations: 10.81 kB / 297.1 MB, free: 14.68 MB / 266.7 MB
Warning: Assuming fixed start value for the following 5 variables:
         endoplasmicReticulum.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         endoplasmicReticulum.CaER.c:VARIABLE(min = 0.0 start = 0.0 unit = \"mol/l\" fixed = true stateSelect=StateSelect.prefer )  \"Current concentration of substance (mM)\" type: Real
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         p3_sbml:VARIABLE(start = 0.95 fixed = true )  type: Real
         Ca_Cyt.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: 8
 * 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 (28):
 * Single equations (assignments): 28
 * 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 0.0001199/0.008717, allocations: 141.4 kB / 297.2 MB, free: 14.54 MB / 266.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.533e-05/0.008753, allocations: 15.28 kB / 297.2 MB, free: 14.54 MB / 266.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001224/0.008875, allocations: 105.4 kB / 297.4 MB, free: 14.48 MB / 266.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.867e-06/0.008879, allocations: 2.094 kB / 297.4 MB, free: 14.48 MB / 266.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.905e-06/0.008882, allocations: 1.75 kB / 297.4 MB, free: 14.48 MB / 266.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.148e-06/0.008886, allocations: 1.766 kB / 297.4 MB, free: 14.48 MB / 266.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003961/0.009282, allocations: 402 kB / 297.8 MB, free: 14.18 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.818e-06/0.009286, allocations: 5.156 kB / 297.8 MB, free: 14.18 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001101/0.009396, allocations: 39.75 kB / 297.8 MB, free: 14.18 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.787e-06/0.0094, allocations: 1.438 kB / 297.8 MB, free: 14.18 MB / 266.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.229e-05/0.009412, allocations: 7.281 kB / 297.8 MB, free: 14.17 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.976e-06/0.009415, allocations: 1.094 kB / 297.8 MB, free: 14.17 MB / 266.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.294e-06/0.009417, allocations: 6.375 kB / 297.8 MB, free: 14.17 MB / 266.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0001932/0.009611, allocations: 316 kB / 298.1 MB, free: 13.94 MB / 266.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.348e-05/0.009624, allocations: 17.95 kB / 298.1 MB, free: 13.93 MB / 266.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.462e-05/0.009639, allocations: 10.12 kB / 298.1 MB, free: 13.92 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.198e-05/0.009701, allocations: 2.969 kB / 298.1 MB, free: 13.92 MB / 266.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.292e-05/0.009724, allocations: 15.59 kB / 298.2 MB, free: 13.92 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.374e-06/0.009731, allocations: 3.531 kB / 298.2 MB, free: 13.92 MB / 266.7 MB
Notification: Performance of sorting global known variables: time 2.39e-05/0.009755, allocations: 22.62 kB / 298.2 MB, free: 13.91 MB / 266.7 MB
Notification: Performance of sort global known variables: time 4e-08/0.009755, allocations: 0.6875 kB / 298.2 MB, free: 13.91 MB / 266.7 MB
Notification: Performance of remove unused functions: time 0.0001936/0.009948, allocations: 41.25 kB / 298.2 MB, free: 13.9 MB / 266.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 3
 * Number of states: 5 (V,Ca_Cyt.n,p3_sbml,endoplasmicReticulum.V,endoplasmicReticulum.CaER.c)
 * 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 (18):
 * Single equations (assignments): 18
 * 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 7.331e-05/0.01002, allocations: 79.09 kB / 298.3 MB, free: 13.83 MB / 266.7 MB
Notification: Performance of simCode: created initialization part: time 0.0001381/0.01016, allocations: 110.1 kB / 298.4 MB, free: 13.8 MB / 266.7 MB
Notification: Performance of simCode: created event and clocks part: time 4.038e-06/0.01016, allocations: 1.875 kB / 298.4 MB, free: 13.8 MB / 266.7 MB
Notification: Performance of simCode: created simulation system equations: time 4.708e-05/0.01021, allocations: 48.58 kB / 298.5 MB, free: 13.79 MB / 266.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000196/0.01041, allocations: 25.62 kB / 298.5 MB, free: 13.77 MB / 266.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0005395/0.01095, allocations: 452.2 kB / 298.9 MB, free: 13.48 MB / 266.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.792e-05/0.01099, allocations: 80.23 kB / 299 MB, free: 13.41 MB / 266.7 MB
Notification: Performance of simCode: alias equations: time 5.441e-05/0.01105, allocations: 14.58 kB / 299 MB, free: 13.41 MB / 266.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.98e-05/0.01112, allocations: 70.25 kB / 299.1 MB, free: 13.36 MB / 266.7 MB
Notification: Performance of SimCode: time 8.62e-07/0.01112, allocations: 1.438 kB / 299.1 MB, free: 13.36 MB / 266.7 MB
Notification: Performance of Templates: time 0.003697/0.01482, allocations: 1.399 MB / 300.5 MB, free: 13.2 MB / 266.7 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile [Timeout 660]
(rm -f BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; mkfifo BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe >> ../files/BioChem_BioChem.Examples.CaOscillations.Cytosol.sim & ./BioChem_BioChem.Examples.CaOscillations.Cytosol -abortSlowSimulation -alarm=240  -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 2.697759674862027]