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 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008247/0.000825, allocations: 100.5 kB / 15.71 MB, free: 452 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001036/0.001036, allocations: 175.7 kB / 16.58 MB, free: 6.879 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.454/1.454, allocations: 223.3 MB / 240.6 MB, free: 5.418 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo): time 0.2455/0.2455, allocations: 12.21 MB / 303.9 MB, free: 1.855 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003372/0.0003372, allocations: 8 kB / 367.5 MB, free: 9.652 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1305/0.1309, allocations: 53.09 MB / 420.6 MB, free: 4.473 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.003371/0.1343, allocations: 2.398 MB / 423 MB, free: 2.062 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0002646/0.1346, allocations: 183.3 kB / 423.2 MB, free: 1.883 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 7.11e-05/0.1347, allocations: 8 kB / 423.2 MB, free: 1.875 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 5.933e-05/0.1348, allocations: 23.86 kB / 423.2 MB, free: 1.852 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.000134/0.1349, allocations: 39.64 kB / 423.2 MB, free: 1.812 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001809/0.1351, allocations: 35.95 kB / 423.3 MB, free: 1.777 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002037/0.1353, allocations: 163.3 kB / 423.4 MB, free: 1.617 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002039/0.1355, allocations: 77.36 kB / 423.5 MB, free: 1.539 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 6.727e-05/0.1356, allocations: 59.78 kB / 423.6 MB, free: 1.48 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001364/0.1357, allocations: 83.5 kB / 423.7 MB, free: 1.398 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 2.711e-05/0.1358, allocations: 8 kB / 423.7 MB, free: 1.391 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 2.744e-05/0.1358, allocations: 12 kB / 423.7 MB, free: 1.379 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 3.424e-05/0.1358, allocations: 31.84 kB / 423.7 MB, free: 1.348 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 4.736e-05/0.1359, allocations: 61.58 kB / 423.8 MB, free: 1.281 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0001887/0.1361, allocations: 175.8 kB / 423.9 MB, free: 1.109 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.394e-06/0.1361, allocations: 0 / 423.9 MB, free: 1.109 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.044e-06/0.1361, allocations: 0 / 423.9 MB, free: 1.109 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 8.166e-06/0.1361, allocations: 0 / 423.9 MB, free: 1.109 MB / 350.1 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 0.0007864/0.1369, allocations: 467.3 kB / 424.4 MB, free: 0.6055 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.07e-05/0.137, allocations: 15.97 kB / 424.4 MB, free: 0.5898 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.364e-05/0.1371, allocations: 23.72 kB / 424.4 MB, free: 0.5664 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001977/0.1373, allocations: 190.7 kB / 424.6 MB, free: 348 kB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.752e-05/0.1373, allocations: 16.56 kB / 424.6 MB, free: 332 kB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.706e-05/0.1374, allocations: 24 kB / 424.7 MB, free: 308 kB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004338/0.1378, allocations: 208.8 kB / 424.9 MB, free: 92 kB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.107e-05/0.1378, allocations: 0 / 424.9 MB, free: 92 kB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.103e-05/0.1379, allocations: 12 kB / 424.9 MB, free: 80 kB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.075e-05/0.1379, allocations: 4 kB / 424.9 MB, free: 76 kB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.2571/0.395, allocations: 135.4 kB / 425 MB, free: 38.46 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001573/0.3966, allocations: 0.7554 MB / 425.8 MB, free: 38.16 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.000208/0.3969, allocations: 103.4 kB / 425.9 MB, free: 38.14 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002376/0.3971, allocations: 103.3 kB / 426 MB, free: 38.13 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.318e-05/0.3971, allocations: 3.906 kB / 426 MB, free: 38.13 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.449e-05/0.3972, allocations: 31.62 kB / 426 MB, free: 38.09 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.934e-06/0.3972, allocations: 0.625 kB / 426 MB, free: 38.09 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.001296/0.3985, allocations: 0.5823 MB / 426.6 MB, free: 37.79 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.322e-05/0.3985, allocations: 53.94 kB / 426.6 MB, free: 37.73 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001326/0.3987, allocations: 142.7 kB / 426.8 MB, free: 37.62 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.522e-05/0.3987, allocations: 31.73 kB / 426.8 MB, free: 37.59 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001032/0.3988, allocations: 153.8 kB / 427 MB, free: 37.47 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 5.013e-05/0.3988, allocations: 68.8 kB / 427 MB, free: 37.43 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.047e-05/0.3989, allocations: 6.5 kB / 427 MB, free: 37.43 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 9.641e-05/0.399, allocations: 325 kB / 427.4 MB, free: 37.12 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.008e-05/0.3991, allocations: 39.41 kB / 427.4 MB, free: 37.12 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001134/0.3992, allocations: 94.84 kB / 427.5 MB, free: 37.07 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001242/0.3993, allocations: 67.89 kB / 427.5 MB, free: 37.06 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.203e-06/0.3993, allocations: 0 / 427.5 MB, free: 37.06 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003254/0.3996, allocations: 205.6 kB / 427.7 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.315e-05/0.3997, allocations: 12.75 kB / 427.8 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.177e-06/0.3997, allocations: 2 kB / 427.8 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.794e-05/0.3997, allocations: 4.469 kB / 427.8 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001992/0.3999, allocations: 53.34 kB / 427.8 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.021e-05/0.3999, allocations: 6.875 kB / 427.8 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.215e-05/0.4, allocations: 13.03 kB / 427.8 MB, free: 37.02 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.657e-05/0.4001, allocations: 9.375 kB / 427.8 MB, free: 37.02 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         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
         endoplasmicReticulum.CaER.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         endoplasmicReticulum.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 7
 * 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 (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0002212/0.4003, allocations: 149.8 kB / 428 MB, free: 36.9 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.257e-05/0.4003, allocations: 9.844 kB / 428 MB, free: 36.89 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000325/0.4007, allocations: 178.8 kB / 428.2 MB, free: 36.86 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.272e-06/0.4007, allocations: 3.828 kB / 428.2 MB, free: 36.86 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.302e-06/0.4007, allocations: 3.281 kB / 428.2 MB, free: 36.86 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.388e-06/0.4007, allocations: 0 / 428.2 MB, free: 36.86 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006199/0.4013, allocations: 0.517 MB / 428.7 MB, free: 36.55 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.114e-06/0.4013, allocations: 0 / 428.7 MB, free: 36.55 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001784/0.4015, allocations: 35.23 kB / 428.7 MB, free: 36.55 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.497e-06/0.4015, allocations: 6.672 kB / 428.7 MB, free: 36.55 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.631e-05/0.4016, allocations: 2.562 kB / 428.7 MB, free: 36.55 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.673e-06/0.4016, allocations: 3.125 kB / 428.7 MB, free: 36.55 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.22e-07/0.4016, allocations: 3.406 kB / 428.8 MB, free: 36.55 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003385/0.4019, allocations: 308.3 kB / 429.1 MB, free: 36.41 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.09e-05/0.402, allocations: 87.89 kB / 429.1 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.633e-05/0.402, allocations: 7.391 kB / 429.1 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001031/0.4021, allocations: 10.08 kB / 429.2 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.796e-05/0.4021, allocations: 14.92 kB / 429.2 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.077e-05/0.4022, allocations: 7.438 kB / 429.2 MB, free: 36.3 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 5.577e-05/0.4022, allocations: 107.8 kB / 429.3 MB, free: 36.23 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1e-07/0.4022, allocations: 0 / 429.3 MB, free: 36.23 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002673/0.4025, allocations: 41.69 kB / 429.3 MB, free: 36.23 MB / 350.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,endoplasmicReticulum.V,endoplasmicReticulum.CaER.n,Ca_Cyt.n,p3_sbml)
 * 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 (linear and non-linear blocks): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 8.729e-05/0.4026, allocations: 96.66 kB / 429.4 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002401/0.4028, allocations: 135 kB / 429.6 MB, free: 36.13 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.044e-06/0.4028, allocations: 0 / 429.6 MB, free: 36.13 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 8.547e-05/0.4029, allocations: 70.12 kB / 429.6 MB, free: 36.12 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002811/0.4032, allocations: 13.38 kB / 429.6 MB, free: 36.12 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0008551/0.4041, allocations: 0.6539 MB / 430.3 MB, free: 35.76 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000168/0.4043, allocations: 0.7368 MB / 431 MB, free: 35.07 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.762e-05/0.4043, allocations: 19.91 kB / 431 MB, free: 35.06 MB / 350.1 MB
Notification: Performance of SimCode: time 9.02e-07/0.4043, allocations: 4 kB / 431 MB, free: 35.05 MB / 350.1 MB
Notification: Performance of Templates: time 0.003594/0.4079, allocations: 1.984 MB / 433 MB, free: 34.96 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile clang++  NOTFOUND  -Winvalid-pch -O0 -g -DNDEBUG -fPIC   -std=c++11 -DBOOST_ALL_DYN_LINK   -DUSE_DGESV -DUSE_LOGGER -DOMC_BUILD -DUSE_THREAD -DSUNDIALS_MAJOR_VERSION=5 -DSUNDIALS_MINOR_VERSION=4 -DPMC_USE_SUNDIALS -I"." -I"/var/lib/jenkins1/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/bin/../include/omc/cpp/" -I.  -I"." -I"." -I"/var/lib/jenkins1/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/include/omc/c/sundials"     -DMEASURETIME_PROFILEBLOCKS -DUSE_LOGGER  -c -o OMCppBioChem_BioChem.Examples.CaOscillations.CytosolCalcHelperMain.o OMCppBioChem_BioChem.Examples.CaOscillations.CytosolCalcHelperMain.cpp
clang: error: no such file or directory: 'NOTFOUND'
make: *** [<builtin>: OMCppBioChem_BioChem.Examples.CaOscillations.CytosolCalcHelperMain.o] Error 1