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 0.001009/0.001009, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 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 0.001111/0.001111, allocations: 173.3 kB / 23.02 MB, free: 1.551 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 0.9971/0.9971, allocations: 177.2 MB / 203.4 MB, free: 5.629 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 0.04213/0.04213, allocations: 9.551 MB / 269.5 MB, free: 3.934 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 2.374e-06/2.374e-06, allocations: 0 / 342.9 MB, free: 6.746 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.117e-05/3.354e-05, allocations: 2.312 kB / 342.9 MB, free: 6.742 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003704/0.003738, allocations: 2.435 MB / 345.3 MB, free: 4.297 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0003563/0.004094, allocations: 195.2 kB / 345.5 MB, free: 4.105 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.087e-05/0.004185, allocations: 12 kB / 345.5 MB, free: 4.094 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 8.131e-05/0.004266, allocations: 35.67 kB / 345.6 MB, free: 4.059 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001584/0.004425, allocations: 43.58 kB / 345.6 MB, free: 4.016 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002097/0.004634, allocations: 51.86 kB / 345.7 MB, free: 3.965 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.000197/0.004831, allocations: 191.1 kB / 345.8 MB, free: 3.777 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001963/0.005028, allocations: 68.86 kB / 345.9 MB, free: 3.711 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001291/0.005157, allocations: 119.8 kB / 346 MB, free: 3.594 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001563/0.005313, allocations: 83.69 kB / 346.1 MB, free: 3.512 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 4.144e-05/0.005355, allocations: 24 kB / 346.1 MB, free: 3.488 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.954e-05/0.005384, allocations: 20 kB / 346.1 MB, free: 3.469 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 3.887e-05/0.005423, allocations: 47.83 kB / 346.2 MB, free: 3.422 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 6.872e-05/0.005492, allocations: 71.83 kB / 346.3 MB, free: 3.352 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002156/0.005707, allocations: 147.3 kB / 346.4 MB, free: 3.207 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 2.655e-06/0.00571, allocations: 0 / 346.4 MB, free: 3.207 MB / 266.7 MB
Notification: Performance of FrontEnd: time 7.11e-07/0.005711, allocations: 0 / 346.4 MB, free: 3.207 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 5.53e-06/0.005716, allocations: 0 / 346.4 MB, free: 3.207 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 0.0006098/0.006326, allocations: 0.5275 MB / 346.9 MB, free: 2.641 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.162e-05/0.006368, allocations: 12.03 kB / 346.9 MB, free: 2.629 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.879e-05/0.006446, allocations: 44.8 kB / 347 MB, free: 2.586 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 9.106e-05/0.006538, allocations: 132.4 kB / 347.1 MB, free: 2.43 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.189e-05/0.006559, allocations: 16.88 kB / 347.1 MB, free: 2.41 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.416e-05/0.006604, allocations: 24.38 kB / 347.2 MB, free: 2.387 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003188/0.006922, allocations: 204.7 kB / 347.4 MB, free: 2.172 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.525e-05/0.006938, allocations: 192 / 347.4 MB, free: 2.172 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.975e-05/0.006957, allocations: 12.38 kB / 347.4 MB, free: 2.16 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.015e-05/0.006968, allocations: 8.375 kB / 347.4 MB, free: 2.152 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001494/0.007117, allocations: 88.75 kB / 347.5 MB, free: 2.066 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001097/0.008214, allocations: 0.7969 MB / 348.3 MB, free: 1.215 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001775/0.008391, allocations: 114 kB / 348.4 MB, free: 1.082 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002119/0.008603, allocations: 99.45 kB / 348.5 MB, free: 0.9766 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.216e-05/0.008625, allocations: 4 kB / 348.5 MB, free: 0.9727 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.518e-05/0.008651, allocations: 45.27 kB / 348.5 MB, free: 0.918 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=15): time 2.815e-06/0.008653, allocations: 3.984 kB / 348.5 MB, free: 0.9141 MB / 266.7 MB
Notification: Performance of matching and sorting (n=17): time 0.00114/0.009793, allocations: 0.5943 MB / 349.1 MB, free: 260 kB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.88e-05/0.009822, allocations: 77.11 kB / 349.2 MB, free: 164 kB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001142/0.009936, allocations: 197.9 kB / 349.4 MB, free: 15.95 MB / 282.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.846e-05/0.009955, allocations: 29.7 kB / 349.4 MB, free: 15.91 MB / 282.7 MB
Notification: Performance of collectInitialEqns (initialization): time 8.861e-05/0.01004, allocations: 210.8 kB / 349.6 MB, free: 15.7 MB / 282.7 MB
Notification: Performance of collectInitialBindings (initialization): time 3.946e-05/0.01008, allocations: 71.42 kB / 349.7 MB, free: 15.63 MB / 282.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.883e-05/0.01014, allocations: 59.17 kB / 349.8 MB, free: 15.57 MB / 282.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001882/0.01033, allocations: 0.4884 MB / 350.2 MB, free: 15.07 MB / 282.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 4.719e-05/0.01038, allocations: 28.22 kB / 350.3 MB, free: 15.04 MB / 282.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.341e-05/0.01046, allocations: 115 kB / 350.4 MB, free: 14.9 MB / 282.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002021/0.01066, allocations: 196.4 kB / 350.6 MB, free: 14.68 MB / 282.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.212e-06/0.01066, allocations: 4 kB / 350.6 MB, free: 14.67 MB / 282.7 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002064/0.01087, allocations: 181.3 kB / 350.8 MB, free: 14.49 MB / 282.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.746e-05/0.01089, allocations: 8 kB / 350.8 MB, free: 14.48 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.621e-06/0.01089, allocations: 3.938 kB / 350.8 MB, free: 14.48 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.682e-05/0.01091, allocations: 4 kB / 350.8 MB, free: 14.47 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001467/0.01106, allocations: 51.97 kB / 350.8 MB, free: 14.42 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.188e-06/0.01107, allocations: 3.938 kB / 350.8 MB, free: 14.42 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 6.923e-05/0.01113, allocations: 12.19 kB / 350.8 MB, free: 14.41 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.844e-05/0.01115, allocations: 15.98 kB / 350.8 MB, free: 14.39 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 0.0001753/0.01133, allocations: 178.8 kB / 351 MB, free: 14.2 MB / 282.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.645e-05/0.01137, allocations: 15.89 kB / 351 MB, free: 14.19 MB / 282.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000176/0.01154, allocations: 130.4 kB / 351.2 MB, free: 14.06 MB / 282.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.474e-06/0.01154, allocations: 4 kB / 351.2 MB, free: 14.05 MB / 282.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.486e-06/0.01155, allocations: 0 / 351.2 MB, free: 14.05 MB / 282.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.487e-06/0.01155, allocations: 0 / 351.2 MB, free: 14.05 MB / 282.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007099/0.01226, allocations: 0.5941 MB / 351.8 MB, free: 13.41 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.335e-06/0.01226, allocations: 4 kB / 351.8 MB, free: 13.41 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001171/0.01238, allocations: 43.91 kB / 351.8 MB, free: 13.37 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.118e-06/0.01238, allocations: 0 / 351.8 MB, free: 13.37 MB / 282.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.548e-05/0.0124, allocations: 4 kB / 351.8 MB, free: 13.36 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.165e-06/0.0124, allocations: 4.031 kB / 351.8 MB, free: 13.36 MB / 282.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.827e-06/0.01241, allocations: 3.984 kB / 351.8 MB, free: 13.36 MB / 282.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003222/0.01273, allocations: 462.1 kB / 352.3 MB, free: 12.88 MB / 282.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.207e-05/0.01274, allocations: 11.95 kB / 352.3 MB, free: 12.87 MB / 282.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 1.779e-05/0.01276, allocations: 4 kB / 352.3 MB, free: 12.87 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.693e-05/0.01282, allocations: 4 kB / 352.3 MB, free: 12.86 MB / 282.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.767e-05/0.01285, allocations: 15.97 kB / 352.3 MB, free: 12.85 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.155e-06/0.01286, allocations: 4 kB / 352.3 MB, free: 12.84 MB / 282.7 MB
Notification: Performance of sorting global known variables: time 5.3e-05/0.01291, allocations: 153.1 kB / 352.5 MB, free: 12.7 MB / 282.7 MB
Notification: Performance of sort global known variables: time 6e-08/0.01291, allocations: 0 / 352.5 MB, free: 12.7 MB / 282.7 MB
Notification: Performance of remove unused functions: time 0.0002054/0.01312, allocations: 40 kB / 352.5 MB, free: 12.66 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 8.828e-05/0.01321, allocations: 103.2 kB / 352.6 MB, free: 12.54 MB / 282.7 MB
Notification: Performance of simCode: created initialization part: time 0.0001945/0.0134, allocations: 122.2 kB / 352.7 MB, free: 12.42 MB / 282.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.964e-06/0.0134, allocations: 0 / 352.7 MB, free: 12.42 MB / 282.7 MB
Notification: Performance of simCode: created simulation system equations: time 5.727e-05/0.01346, allocations: 59.59 kB / 352.8 MB, free: 12.36 MB / 282.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002932/0.01375, allocations: 20.42 kB / 352.8 MB, free: 12.34 MB / 282.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0006372/0.01439, allocations: 474.1 kB / 353.3 MB, free: 11.84 MB / 282.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.729e-05/0.01445, allocations: 79.83 kB / 353.3 MB, free: 11.74 MB / 282.7 MB
Notification: Performance of simCode: alias equations: time 4.902e-05/0.0145, allocations: 17.48 kB / 353.4 MB, free: 11.72 MB / 282.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.914e-05/0.01455, allocations: 24.48 kB / 353.4 MB, free: 11.7 MB / 282.7 MB
Notification: Performance of SimCode: time 7.22e-07/0.01455, allocations: 0 / 353.4 MB, free: 11.7 MB / 282.7 MB
Notification: Performance of Templates: time 0.00353/0.01808, allocations: 1.335 MB / 354.7 MB, free: 10.39 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: 2.8740681330673397]