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 0.001197/0.001197, allocations: 92.22 kB / 19.65 MB, free: 276 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 0.001869/0.001869, allocations: 169 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 0.9671/0.9671, allocations: 177.1 MB / 203.4 MB, free: 5.652 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 0.05291/0.05291, allocations: 9.548 MB / 269.5 MB, free: 3.961 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 1.923e-06/1.923e-06, allocations: 0 / 342.9 MB, free: 6.77 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.732e-05/2.924e-05, allocations: 2.312 kB / 342.9 MB, free: 6.766 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.006045/0.006075, allocations: 2.439 MB / 345.3 MB, free: 4.316 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0003273/0.006402, allocations: 195.2 kB / 345.5 MB, free: 4.125 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 8.393e-05/0.006486, allocations: 12 kB / 345.5 MB, free: 4.113 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 7.532e-05/0.006561, allocations: 35.67 kB / 345.6 MB, free: 4.078 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001327/0.006694, allocations: 39.58 kB / 345.6 MB, free: 4.039 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001985/0.006892, allocations: 51.86 kB / 345.6 MB, free: 3.988 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0001634/0.007056, allocations: 195.1 kB / 345.8 MB, free: 3.797 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001814/0.007237, allocations: 64.86 kB / 345.9 MB, free: 3.734 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001067/0.007344, allocations: 123.8 kB / 346 MB, free: 3.613 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.003158/0.0105, allocations: 83.7 kB / 346.1 MB, free: 3.531 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 3.498e-05/0.01054, allocations: 20 kB / 346.1 MB, free: 3.512 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.554e-05/0.01056, allocations: 20 kB / 346.1 MB, free: 3.492 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 3.349e-05/0.0106, allocations: 47.83 kB / 346.2 MB, free: 3.445 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 5.85e-05/0.01065, allocations: 67.83 kB / 346.3 MB, free: 3.379 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001967/0.01085, allocations: 155.3 kB / 346.4 MB, free: 3.227 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.396e-06/0.01085, allocations: 0 / 346.4 MB, free: 3.227 MB / 266.7 MB
Notification: Performance of FrontEnd: time 1.262e-06/0.01086, allocations: 0 / 346.4 MB, free: 3.227 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 5.911e-06/0.01086, allocations: 0 / 346.4 MB, free: 3.227 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 0.0005342/0.0114, allocations: 0.5275 MB / 346.9 MB, free: 2.66 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.964e-05/0.01144, allocations: 12.03 kB / 346.9 MB, free: 2.648 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.275e-05/0.01151, allocations: 44.8 kB / 347 MB, free: 2.605 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 7.836e-05/0.01159, allocations: 132.4 kB / 347.1 MB, free: 2.449 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.027e-05/0.01161, allocations: 16.88 kB / 347.1 MB, free: 2.43 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.576e-05/0.01165, allocations: 24.38 kB / 347.2 MB, free: 2.406 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002708/0.01192, allocations: 200.7 kB / 347.4 MB, free: 2.195 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.351e-05/0.01194, allocations: 192 / 347.4 MB, free: 2.195 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.112e-05/0.01196, allocations: 16.38 kB / 347.4 MB, free: 2.18 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.008e-05/0.01197, allocations: 4.375 kB / 347.4 MB, free: 2.176 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001594/0.01213, allocations: 92.75 kB / 347.5 MB, free: 2.086 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009413/0.01307, allocations: 0.793 MB / 348.3 MB, free: 1.238 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001483/0.01322, allocations: 114.1 kB / 348.4 MB, free: 1.102 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.003207/0.01642, allocations: 95.31 kB / 348.5 MB, free: 1 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.445e-05/0.01645, allocations: 7.984 kB / 348.5 MB, free: 0.9922 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.993e-05/0.01647, allocations: 41.27 kB / 348.5 MB, free: 0.9414 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=15): time 1.563e-06/0.01647, allocations: 0 / 348.5 MB, free: 0.9414 MB / 266.7 MB
Notification: Performance of matching and sorting (n=17): time 0.0009832/0.01745, allocations: 0.5945 MB / 349.1 MB, free: 288 kB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.419e-05/0.01748, allocations: 81.05 kB / 349.2 MB, free: 188 kB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001134/0.01759, allocations: 201.9 kB / 349.4 MB, free: 15.97 MB / 282.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.709e-05/0.01761, allocations: 25.7 kB / 349.4 MB, free: 15.94 MB / 282.7 MB
Notification: Performance of collectInitialEqns (initialization): time 9.794e-05/0.01771, allocations: 214.8 kB / 349.6 MB, free: 15.72 MB / 282.7 MB
Notification: Performance of collectInitialBindings (initialization): time 4.831e-05/0.01775, allocations: 71.44 kB / 349.7 MB, free: 15.65 MB / 282.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.966e-05/0.01782, allocations: 55.17 kB / 349.7 MB, free: 15.59 MB / 282.7 MB
Notification: Performance of setup shared object (initialization): time 0.0001386/0.01796, allocations: 0.4962 MB / 350.2 MB, free: 15.08 MB / 282.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 6.005e-05/0.01802, allocations: 20.22 kB / 350.3 MB, free: 15.06 MB / 282.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001097/0.01813, allocations: 115 kB / 350.4 MB, free: 14.92 MB / 282.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002706/0.0184, allocations: 200.7 kB / 350.6 MB, free: 14.7 MB / 282.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.924e-06/0.0184, allocations: 0 / 350.6 MB, free: 14.7 MB / 282.7 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002749/0.01868, allocations: 181.3 kB / 350.7 MB, free: 14.51 MB / 282.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.828e-05/0.0187, allocations: 8 kB / 350.7 MB, free: 14.5 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.472e-06/0.0187, allocations: 3.938 kB / 350.8 MB, free: 14.5 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.294e-05/0.01873, allocations: 7.984 kB / 350.8 MB, free: 14.49 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001859/0.01891, allocations: 51.98 kB / 350.8 MB, free: 14.44 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.566e-06/0.01892, allocations: 4.125 kB / 350.8 MB, free: 14.44 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 6.652e-05/0.01899, allocations: 15.98 kB / 350.8 MB, free: 14.42 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.508e-05/0.019, allocations: 8 kB / 350.8 MB, free: 14.41 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 0.0001931/0.0192, allocations: 179.2 kB / 351 MB, free: 14.23 MB / 282.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.721e-05/0.01925, allocations: 23.89 kB / 351 MB, free: 14.2 MB / 282.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002203/0.01947, allocations: 130 kB / 351.2 MB, free: 14.08 MB / 282.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.338e-06/0.01948, allocations: 4 kB / 351.2 MB, free: 14.07 MB / 282.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.068e-06/0.01948, allocations: 0 / 351.2 MB, free: 14.07 MB / 282.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.45e-06/0.01949, allocations: 3.984 kB / 351.2 MB, free: 14.07 MB / 282.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007177/0.02021, allocations: 0.5903 MB / 351.8 MB, free: 13.43 MB / 282.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.775e-06/0.02021, allocations: 0 / 351.8 MB, free: 13.43 MB / 282.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001591/0.02037, allocations: 39.91 kB / 351.8 MB, free: 13.39 MB / 282.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.749e-06/0.02037, allocations: 4.031 kB / 351.8 MB, free: 13.39 MB / 282.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.767e-05/0.02039, allocations: 8 kB / 351.8 MB, free: 13.38 MB / 282.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.685e-06/0.02039, allocations: 4.031 kB / 351.8 MB, free: 13.38 MB / 282.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.078e-06/0.0204, allocations: 7.984 kB / 351.8 MB, free: 13.37 MB / 282.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003857/0.02078, allocations: 450.5 kB / 352.3 MB, free: 12.91 MB / 282.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.097e-05/0.02079, allocations: 7.953 kB / 352.3 MB, free: 12.9 MB / 282.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.133e-05/0.02081, allocations: 8 kB / 352.3 MB, free: 12.89 MB / 282.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.892e-05/0.02088, allocations: 3.938 kB / 352.3 MB, free: 12.89 MB / 282.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.306e-05/0.02092, allocations: 19.97 kB / 352.3 MB, free: 12.87 MB / 282.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.195e-06/0.02092, allocations: 4 kB / 352.3 MB, free: 12.86 MB / 282.7 MB
Notification: Performance of sorting global known variables: time 5.706e-05/0.02098, allocations: 145.2 kB / 352.4 MB, free: 12.72 MB / 282.7 MB
Notification: Performance of sort global known variables: time 6.1e-08/0.02098, allocations: 0 / 352.4 MB, free: 12.72 MB / 282.7 MB
Notification: Performance of remove unused functions: time 0.0002249/0.02121, allocations: 47.98 kB / 352.5 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 0.0001092/0.02132, allocations: 95.19 kB / 352.6 MB, free: 12.57 MB / 282.7 MB
Notification: Performance of simCode: created initialization part: time 0.0002/0.02152, allocations: 126.2 kB / 352.7 MB, free: 12.45 MB / 282.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.016e-06/0.02152, allocations: 4 kB / 352.7 MB, free: 12.44 MB / 282.7 MB
Notification: Performance of simCode: created simulation system equations: time 5.95e-05/0.02158, allocations: 59.59 kB / 352.8 MB, free: 12.38 MB / 282.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002653/0.02184, allocations: 12.44 kB / 352.8 MB, free: 12.37 MB / 282.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0006301/0.02247, allocations: 482.1 kB / 353.3 MB, free: 11.86 MB / 282.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.168e-05/0.02253, allocations: 79.83 kB / 353.3 MB, free: 11.76 MB / 282.7 MB
Notification: Performance of simCode: alias equations: time 4.626e-05/0.02257, allocations: 17.48 kB / 353.4 MB, free: 11.74 MB / 282.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.548e-05/0.02262, allocations: 20.48 kB / 353.4 MB, free: 11.72 MB / 282.7 MB
Notification: Performance of SimCode: time 6.11e-07/0.02262, allocations: 0 / 353.4 MB, free: 11.72 MB / 282.7 MB
Notification: Performance of Templates: time 0.00353/0.02615, allocations: 1.293 MB / 354.7 MB, free: 10.45 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: 3.013972643762827]