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 0.0009773/0.0009773, allocations: 81.17 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 0.001444/0.001444, allocations: 169 kB / 23.27 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 0.9648/0.9648, allocations: 177.2 MB / 203.7 MB, free: 5.516 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 0.04037/0.04037, allocations: 9.547 MB / 269.8 MB, free: 3.809 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 1.512e-06/1.512e-06, allocations: 0 / 343.3 MB, free: 6.484 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.197e-05/1.349e-05, allocations: 2.312 kB / 343.3 MB, free: 6.48 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.0028/0.002813, allocations: 2.424 MB / 345.8 MB, free: 4.047 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0003141/0.003128, allocations: 195.2 kB / 345.9 MB, free: 3.855 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.605e-05/0.003224, allocations: 8 kB / 346 MB, free: 3.848 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 7.143e-05/0.003295, allocations: 31.73 kB / 346 MB, free: 3.816 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001498/0.003445, allocations: 47.52 kB / 346 MB, free: 3.77 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001842/0.003629, allocations: 43.92 kB / 346.1 MB, free: 3.727 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0001628/0.003792, allocations: 195.1 kB / 346.3 MB, free: 3.535 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001692/0.003961, allocations: 72.86 kB / 346.3 MB, free: 3.465 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.000117/0.004078, allocations: 119.8 kB / 346.5 MB, free: 3.348 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001427/0.004221, allocations: 75.72 kB / 346.5 MB, free: 3.273 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 3.388e-05/0.004255, allocations: 24 kB / 346.6 MB, free: 3.25 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.83e-05/0.004283, allocations: 20 kB / 346.6 MB, free: 3.23 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 3.525e-05/0.004318, allocations: 43.83 kB / 346.6 MB, free: 3.188 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 5.764e-05/0.004376, allocations: 67.83 kB / 346.7 MB, free: 3.121 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001786/0.004554, allocations: 163.3 kB / 346.8 MB, free: 2.961 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 1.704e-06/0.004556, allocations: 0 / 346.8 MB, free: 2.961 MB / 266.7 MB
Notification: Performance of FrontEnd: time 6.42e-07/0.004557, allocations: 0 / 346.8 MB, free: 2.961 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 3.887e-06/0.004561, allocations: 4 kB / 346.8 MB, free: 2.957 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 0.0004961/0.005057, allocations: 0.5274 MB / 347.4 MB, free: 2.391 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.814e-05/0.005095, allocations: 8.031 kB / 347.4 MB, free: 2.383 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.464e-05/0.00516, allocations: 44.8 kB / 347.4 MB, free: 2.34 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 6.791e-05/0.005227, allocations: 132.3 kB / 347.6 MB, free: 2.184 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.893e-05/0.005246, allocations: 20.88 kB / 347.6 MB, free: 2.16 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.628e-05/0.005283, allocations: 24.38 kB / 347.6 MB, free: 2.137 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002185/0.005501, allocations: 192.7 kB / 347.8 MB, free: 1.934 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.401e-05/0.005515, allocations: 192 / 347.8 MB, free: 1.934 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.818e-05/0.005533, allocations: 8.375 kB / 347.8 MB, free: 1.926 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.03e-05/0.005544, allocations: 8.375 kB / 347.8 MB, free: 1.918 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001077/0.005651, allocations: 79.06 kB / 347.9 MB, free: 1.844 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008888/0.00654, allocations: 0.7585 MB / 348.6 MB, free: 1.039 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001188/0.006659, allocations: 110.1 kB / 348.7 MB, free: 0.9062 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001496/0.006809, allocations: 87.47 kB / 348.8 MB, free: 0.8125 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.024e-05/0.006829, allocations: 4 kB / 348.8 MB, free: 0.8086 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.893e-05/0.006848, allocations: 41.39 kB / 348.9 MB, free: 0.7578 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=15): time 1.613e-06/0.006849, allocations: 4 kB / 348.9 MB, free: 0.7539 MB / 266.7 MB
Notification: Performance of matching and sorting (n=17): time 0.0007694/0.007619, allocations: 0.5209 MB / 349.4 MB, free: 168 kB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.085e-05/0.00764, allocations: 85.05 kB / 349.5 MB, free: 64 kB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001177/0.007757, allocations: 204.2 kB / 349.7 MB, free: 15.85 MB / 282.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.703e-05/0.007774, allocations: 29.7 kB / 349.7 MB, free: 15.81 MB / 282.7 MB
Notification: Performance of collectInitialEqns (initialization): time 9.492e-05/0.007869, allocations: 214.8 kB / 349.9 MB, free: 15.6 MB / 282.7 MB
Notification: Performance of collectInitialBindings (initialization): time 4.978e-05/0.007919, allocations: 67.42 kB / 350 MB, free: 15.53 MB / 282.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.479e-05/0.007994, allocations: 51.2 kB / 350 MB, free: 15.47 MB / 282.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001523/0.008146, allocations: 0.4962 MB / 350.5 MB, free: 14.96 MB / 282.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 4.198e-05/0.008188, allocations: 20.22 kB / 350.6 MB, free: 14.95 MB / 282.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.745e-05/0.008276, allocations: 107 kB / 350.7 MB, free: 14.81 MB / 282.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002359/0.008511, allocations: 177.3 kB / 350.8 MB, free: 14.61 MB / 282.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.443e-06/0.008513, allocations: 0 / 350.8 MB, free: 14.61 MB / 282.7 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002302/0.008743, allocations: 172.7 kB / 351 MB, free: 14.43 MB / 282.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.64e-05/0.00876, allocations: 7.938 kB / 351 MB, free: 14.43 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.764e-06/0.008767, allocations: 8.062 kB / 351 MB, free: 14.42 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.355e-05/0.008781, allocations: 192 / 351 MB, free: 14.42 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001724/0.008953, allocations: 59.91 kB / 351.1 MB, free: 14.36 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.851e-06/0.008959, allocations: 4 kB / 351.1 MB, free: 14.36 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.762e-05/0.009047, allocations: 4 kB / 351.1 MB, free: 14.35 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.33e-05/0.00906, allocations: 15.98 kB / 351.1 MB, free: 14.34 MB / 282.7 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 0.0001265/0.009186, allocations: 174.5 kB / 351.3 MB, free: 14.15 MB / 282.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.873e-05/0.009225, allocations: 23.84 kB / 351.3 MB, free: 14.13 MB / 282.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001419/0.009367, allocations: 130.1 kB / 351.4 MB, free: 14 MB / 282.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.763e-06/0.009369, allocations: 0 / 351.4 MB, free: 14 MB / 282.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.495e-06/0.009371, allocations: 4 kB / 351.4 MB, free: 14 MB / 282.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.406e-06/0.009375, allocations: 0 / 351.4 MB, free: 14 MB / 282.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004588/0.009834, allocations: 0.5398 MB / 352 MB, free: 13.42 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.906e-06/0.009836, allocations: 7.938 kB / 352 MB, free: 13.41 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001108/0.009947, allocations: 36.02 kB / 352 MB, free: 13.38 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.535e-06/0.00995, allocations: 3.938 kB / 352 MB, free: 13.38 MB / 282.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.256e-05/0.009962, allocations: 8 kB / 352 MB, free: 13.37 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.683e-06/0.009964, allocations: 0 / 352 MB, free: 13.37 MB / 282.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.755e-06/0.009967, allocations: 7.969 kB / 352 MB, free: 13.36 MB / 282.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002382/0.01021, allocations: 434.6 kB / 352.4 MB, free: 12.91 MB / 282.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.237e-05/0.01022, allocations: 19.83 kB / 352.5 MB, free: 12.89 MB / 282.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.42e-05/0.01023, allocations: 4 kB / 352.5 MB, free: 12.89 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.553e-05/0.0103, allocations: 4 kB / 352.5 MB, free: 12.88 MB / 282.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.109e-05/0.01032, allocations: 15.92 kB / 352.5 MB, free: 12.87 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 6.121e-06/0.01032, allocations: 7.984 kB / 352.5 MB, free: 12.86 MB / 282.7 MB
Notification: Performance of sorting global known variables: time 3.838e-05/0.01036, allocations: 143.1 kB / 352.6 MB, free: 12.72 MB / 282.7 MB
Notification: Performance of sort global known variables: time 5e-08/0.01036, allocations: 0 / 352.6 MB, free: 12.72 MB / 282.7 MB
Notification: Performance of remove unused functions: time 0.0001974/0.01056, allocations: 40 kB / 352.7 MB, free: 12.68 MB / 282.7 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 6.749e-05/0.01063, allocations: 95.25 kB / 352.8 MB, free: 12.57 MB / 282.7 MB
Notification: Performance of simCode: created initialization part: time 0.0001274/0.01076, allocations: 108.7 kB / 352.9 MB, free: 12.46 MB / 282.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.353e-06/0.01076, allocations: 0 / 352.9 MB, free: 12.46 MB / 282.7 MB
Notification: Performance of simCode: created simulation system equations: time 4.511e-05/0.0108, allocations: 51.97 kB / 352.9 MB, free: 12.41 MB / 282.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002293/0.01103, allocations: 32.17 kB / 353 MB, free: 12.38 MB / 282.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0004982/0.01153, allocations: 473.9 kB / 353.4 MB, free: 11.88 MB / 282.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.65e-05/0.01158, allocations: 83.75 kB / 353.5 MB, free: 11.77 MB / 282.7 MB
Notification: Performance of simCode: alias equations: time 4.446e-05/0.01162, allocations: 17.48 kB / 353.5 MB, free: 11.76 MB / 282.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 7.565e-05/0.0117, allocations: 90.19 kB / 353.6 MB, free: 11.67 MB / 282.7 MB
Notification: Performance of SimCode: time 5.91e-07/0.0117, allocations: 0 / 353.6 MB, free: 11.67 MB / 282.7 MB
Notification: Performance of Templates: time 0.002997/0.01469, allocations: 1.404 MB / 355 MB, free: 10.29 MB / 282.7 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: 2.5966948023997247]