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 0.0008552/0.0008552, allocations: 92.2 kB / 20.19 MB, free: 4.363 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 0.000882/0.000882, allocations: 173 kB / 23.49 MB, free: 1.059 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 0.9705/0.9705, allocations: 177.1 MB / 203.8 MB, free: 5.625 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 0.04007/0.04007, allocations: 9.553 MB / 269.8 MB, free: 4.008 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 1.503e-06/1.503e-06, allocations: 0 / 342.9 MB, free: 7.09 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.113e-05/2.263e-05, allocations: 5.406 kB / 342.9 MB, free: 7.086 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.002287/0.00231, allocations: 2.432 MB / 345.3 MB, free: 4.645 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0002624/0.002572, allocations: 199.2 kB / 345.5 MB, free: 4.449 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 7.373e-05/0.002646, allocations: 8 kB / 345.5 MB, free: 4.441 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 5.1e-05/0.002697, allocations: 31.69 kB / 345.6 MB, free: 4.41 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001059/0.002803, allocations: 47.56 kB / 345.6 MB, free: 4.363 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001527/0.002955, allocations: 47.88 kB / 345.7 MB, free: 4.316 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0001199/0.003075, allocations: 191.1 kB / 345.8 MB, free: 4.129 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001446/0.00322, allocations: 68.84 kB / 345.9 MB, free: 4.062 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 8.403e-05/0.003304, allocations: 123.8 kB / 346 MB, free: 3.941 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001068/0.003411, allocations: 79.72 kB / 346.1 MB, free: 3.863 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 2.783e-05/0.003439, allocations: 20 kB / 346.1 MB, free: 3.844 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 1.818e-05/0.003457, allocations: 20 kB / 346.1 MB, free: 3.824 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 2.618e-05/0.003483, allocations: 47.83 kB / 346.2 MB, free: 3.777 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 4.812e-05/0.003531, allocations: 67.83 kB / 346.3 MB, free: 3.711 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001538/0.003685, allocations: 155.3 kB / 346.4 MB, free: 3.559 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.024e-06/0.003687, allocations: 0 / 346.4 MB, free: 3.559 MB / 266.7 MB
Notification: Performance of FrontEnd: time 8.01e-07/0.003688, allocations: 0 / 346.4 MB, free: 3.559 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 4.939e-06/0.003693, allocations: 0 / 346.4 MB, free: 3.559 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 0.0004486/0.004141, allocations: 0.5353 MB / 346.9 MB, free: 2.984 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.513e-05/0.004176, allocations: 8.031 kB / 347 MB, free: 2.977 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.023e-05/0.004237, allocations: 44.8 kB / 347 MB, free: 2.934 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 7.996e-05/0.004317, allocations: 128.4 kB / 347.1 MB, free: 2.781 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.69e-05/0.004333, allocations: 16.88 kB / 347.1 MB, free: 2.762 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.429e-05/0.004368, allocations: 24.38 kB / 347.2 MB, free: 2.738 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002214/0.004589, allocations: 204.7 kB / 347.4 MB, free: 2.523 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.216e-05/0.004601, allocations: 192 / 347.4 MB, free: 2.523 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.754e-05/0.004619, allocations: 16.38 kB / 347.4 MB, free: 2.508 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.806e-06/0.004628, allocations: 4.375 kB / 347.4 MB, free: 2.504 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001231/0.004751, allocations: 88.75 kB / 347.5 MB, free: 2.418 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008053/0.005556, allocations: 0.8047 MB / 348.3 MB, free: 1.559 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000126/0.005682, allocations: 110.1 kB / 348.4 MB, free: 1.426 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001557/0.005838, allocations: 91.31 kB / 348.5 MB, free: 1.328 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.515e-05/0.005853, allocations: 4 kB / 348.5 MB, free: 1.324 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.714e-05/0.00587, allocations: 45.25 kB / 348.5 MB, free: 1.27 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=15): time 1.322e-06/0.005871, allocations: 0 / 348.5 MB, free: 1.27 MB / 266.7 MB
Notification: Performance of matching and sorting (n=17): time 0.0008047/0.006676, allocations: 0.5988 MB / 349.1 MB, free: 0.6055 MB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.483e-05/0.006701, allocations: 85.05 kB / 349.2 MB, free: 0.5039 MB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 7.033e-05/0.006771, allocations: 189.9 kB / 349.4 MB, free: 308 kB / 266.7 MB
Notification: Performance of collectPreVariables (initialization): time 9.067e-06/0.00678, allocations: 29.7 kB / 349.4 MB, free: 272 kB / 266.7 MB
Notification: Performance of collectInitialEqns (initialization): time 4.888e-05/0.006829, allocations: 218.8 kB / 349.6 MB, free: 48 kB / 266.7 MB
Notification: Performance of collectInitialBindings (initialization): time 4.655e-05/0.006876, allocations: 63.48 kB / 349.7 MB, free: 15.98 MB / 282.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.602e-05/0.006932, allocations: 55.12 kB / 349.7 MB, free: 15.92 MB / 282.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001127/0.007044, allocations: 0.4962 MB / 350.2 MB, free: 15.41 MB / 282.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 4.896e-05/0.007093, allocations: 28.2 kB / 350.3 MB, free: 15.39 MB / 282.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.869e-05/0.007182, allocations: 115 kB / 350.4 MB, free: 15.25 MB / 282.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002165/0.007399, allocations: 192.3 kB / 350.6 MB, free: 15.03 MB / 282.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.623e-06/0.0074, allocations: 0 / 350.6 MB, free: 15.03 MB / 282.7 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002301/0.00763, allocations: 189.3 kB / 350.8 MB, free: 14.84 MB / 282.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.44e-05/0.007645, allocations: 11.12 kB / 350.8 MB, free: 14.83 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.859e-06/0.00765, allocations: 0 / 350.8 MB, free: 14.83 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.533e-05/0.007665, allocations: 7.938 kB / 350.8 MB, free: 14.82 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001508/0.007816, allocations: 51.97 kB / 350.8 MB, free: 14.77 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.215e-06/0.007824, allocations: 8.125 kB / 350.8 MB, free: 14.76 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 4.756e-05/0.007871, allocations: 8 kB / 350.8 MB, free: 14.75 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.237e-05/0.007884, allocations: 8 kB / 350.8 MB, free: 14.75 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 0.0001589/0.008043, allocations: 187.1 kB / 351 MB, free: 14.55 MB / 282.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.288e-05/0.008086, allocations: 27.89 kB / 351.1 MB, free: 14.52 MB / 282.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001742/0.00826, allocations: 122.4 kB / 351.2 MB, free: 14.4 MB / 282.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.386e-06/0.008263, allocations: 4 kB / 351.2 MB, free: 14.4 MB / 282.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.406e-06/0.008267, allocations: 0 / 351.2 MB, free: 14.4 MB / 282.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.817e-06/0.00827, allocations: 0 / 351.2 MB, free: 14.4 MB / 282.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005554/0.008826, allocations: 0.5932 MB / 351.8 MB, free: 13.76 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.406e-06/0.008829, allocations: 3.984 kB / 351.8 MB, free: 13.76 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001195/0.008949, allocations: 35.92 kB / 351.8 MB, free: 13.72 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.936e-06/0.008952, allocations: 0 / 351.8 MB, free: 13.72 MB / 282.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.556e-05/0.008967, allocations: 12.03 kB / 351.8 MB, free: 13.71 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.583e-06/0.008969, allocations: 0 / 351.8 MB, free: 13.71 MB / 282.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.735e-06/0.008972, allocations: 4 kB / 351.8 MB, free: 13.71 MB / 282.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003013/0.009273, allocations: 450.5 kB / 352.3 MB, free: 13.24 MB / 282.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.184e-05/0.009285, allocations: 11.94 kB / 352.3 MB, free: 13.23 MB / 282.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.986e-05/0.009304, allocations: 8 kB / 352.3 MB, free: 13.22 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.275e-05/0.009387, allocations: 11.94 kB / 352.3 MB, free: 13.21 MB / 282.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.279e-05/0.00941, allocations: 7.984 kB / 352.3 MB, free: 13.2 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.354e-06/0.009417, allocations: 4 kB / 352.3 MB, free: 13.2 MB / 282.7 MB
Notification: Performance of sorting global known variables: time 5.151e-05/0.009469, allocations: 149.2 kB / 352.5 MB, free: 13.05 MB / 282.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.009469, allocations: 4 kB / 352.5 MB, free: 13.05 MB / 282.7 MB
Notification: Performance of remove unused functions: time 0.0002206/0.00969, allocations: 40 kB / 352.5 MB, free: 13.01 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 8.366e-05/0.009773, allocations: 99.19 kB / 352.6 MB, free: 12.9 MB / 282.7 MB
Notification: Performance of simCode: created initialization part: time 0.0001871/0.00996, allocations: 127.4 kB / 352.7 MB, free: 12.77 MB / 282.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.552e-06/0.009962, allocations: 0 / 352.7 MB, free: 12.77 MB / 282.7 MB
Notification: Performance of simCode: created simulation system equations: time 6.014e-05/0.01002, allocations: 55.59 kB / 352.8 MB, free: 12.71 MB / 282.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002699/0.01029, allocations: 16.44 kB / 352.8 MB, free: 12.7 MB / 282.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0006375/0.01093, allocations: 478.1 kB / 353.3 MB, free: 12.19 MB / 282.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.515e-05/0.01098, allocations: 83.81 kB / 353.3 MB, free: 12.09 MB / 282.7 MB
Notification: Performance of simCode: alias equations: time 4.9e-05/0.01103, allocations: 17.48 kB / 353.4 MB, free: 12.07 MB / 282.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.167e-05/0.01108, allocations: 16.5 kB / 353.4 MB, free: 12.06 MB / 282.7 MB
Notification: Performance of SimCode: time 1.182e-06/0.01108, allocations: 0 / 353.4 MB, free: 12.06 MB / 282.7 MB
Notification: Performance of Templates: time 0.003071/0.01415, allocations: 1.31 MB / 354.7 MB, free: 10.78 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: 2.7150173680856824]