Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr BioChem_BioChem.Examples.GMO.cell.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.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008781/0.0008778, allocations: 102.7 kB / 15.71 MB, free: 460 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: 175.6 kB / 16.58 MB, free: 6.863 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.49/1.49, allocations: 223.2 MB / 240.6 MB, free: 5.316 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo): time 0.2598/0.2598, allocations: 12.21 MB / 303.9 MB, free: 1.938 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003449/0.000345, allocations: 8 kB / 367.5 MB, free: 9.664 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1372/0.1375, allocations: 53.09 MB / 420.6 MB, free: 4.488 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.005025/0.1426, allocations: 3.817 MB / 424.4 MB, free: 0.6562 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003408/0.143, allocations: 307.1 kB / 424.7 MB, free: 360 kB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 9.471e-05/0.1431, allocations: 16 kB / 424.7 MB, free: 344 kB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 7.808e-05/0.1432, allocations: 43.72 kB / 424.8 MB, free: 300 kB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001613/0.1433, allocations: 63.47 kB / 424.8 MB, free: 236 kB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001815/0.1435, allocations: 51.94 kB / 424.9 MB, free: 184 kB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.2822/0.4258, allocations: 271.4 kB / 425.2 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003466/0.4262, allocations: 124.7 kB / 425.3 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001468/0.4263, allocations: 96.61 kB / 425.4 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000175/0.4265, allocations: 121.4 kB / 425.5 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.058e-05/0.4265, allocations: 15.19 kB / 425.5 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.874e-05/0.4266, allocations: 15.41 kB / 425.5 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 6.132e-05/0.4267, allocations: 48.77 kB / 425.6 MB, free: 35.08 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 7.183e-05/0.4267, allocations: 77.23 kB / 425.6 MB, free: 35.05 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002965/0.427, allocations: 256.6 kB / 425.9 MB, free: 35.04 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.653e-06/0.4271, allocations: 0 / 425.9 MB, free: 35.04 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.934e-06/0.4271, allocations: 1.75 kB / 425.9 MB, free: 35.04 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 6.662e-06/0.4271, allocations: 0 / 425.9 MB, free: 35.04 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: 96
 * Number of variables: 96
Notification: Performance of Generate backend data structure: time 0.0007573/0.4278, allocations: 0.5473 MB / 426.4 MB, free: 34.61 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.923e-05/0.4279, allocations: 8.812 kB / 426.5 MB, free: 34.61 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.935e-05/0.428, allocations: 34.66 kB / 426.5 MB, free: 34.6 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001161/0.4281, allocations: 198 kB / 426.7 MB, free: 34.39 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.101e-05/0.4281, allocations: 27.97 kB / 426.7 MB, free: 34.39 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.751e-05/0.4282, allocations: 42.64 kB / 426.7 MB, free: 34.38 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004731/0.4287, allocations: 307.1 kB / 427 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.757e-05/0.4287, allocations: 0 / 427 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.046e-05/0.4287, allocations: 17.75 kB / 427.1 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.24e-05/0.4288, allocations: 13.48 kB / 427.1 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003591/0.4291, allocations: 237.5 kB / 427.3 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001596/0.4307, allocations: 1.039 MB / 428.3 MB, free: 33.99 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003228/0.4311, allocations: 183.1 kB / 428.5 MB, free: 33.97 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001686/0.4312, allocations: 129.7 kB / 428.7 MB, free: 33.96 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.812e-05/0.4313, allocations: 3.344 kB / 428.7 MB, free: 33.96 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.306e-05/0.4313, allocations: 35.91 kB / 428.7 MB, free: 33.92 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=22): time 1.343e-06/0.4313, allocations: 0.75 kB / 428.7 MB, free: 33.92 MB / 350.1 MB
Notification: Performance of matching and sorting (n=26): time 0.001777/0.4331, allocations: 0.8922 MB / 429.6 MB, free: 33.62 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.835e-05/0.4331, allocations: 59.2 kB / 429.6 MB, free: 33.55 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001137/0.4333, allocations: 168.6 kB / 429.8 MB, free: 33.44 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 1.727e-05/0.4333, allocations: 32.55 kB / 429.8 MB, free: 33.41 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 8.095e-05/0.4334, allocations: 213.8 kB / 430 MB, free: 33.25 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.83e-05/0.4334, allocations: 93.41 kB / 430.1 MB, free: 33.19 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 1.349e-05/0.4334, allocations: 6.75 kB / 430.1 MB, free: 33.19 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 6.982e-05/0.4335, allocations: 327.8 kB / 430.5 MB, free: 32.88 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001173/0.4336, allocations: 84.89 kB / 430.5 MB, free: 32.88 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001611/0.4338, allocations: 195.3 kB / 430.7 MB, free: 32.75 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001686/0.434, allocations: 125 kB / 430.9 MB, free: 32.74 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.773e-06/0.434, allocations: 0 / 430.9 MB, free: 32.74 MB / 350.1 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0004455/0.4344, allocations: 345.4 kB / 431.2 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.907e-05/0.4345, allocations: 6.906 kB / 431.2 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.907e-06/0.4345, allocations: 9.266 kB / 431.2 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.797e-05/0.4345, allocations: 5.719 kB / 431.2 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002741/0.4348, allocations: 87.48 kB / 431.3 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.181e-05/0.4348, allocations: 5 kB / 431.3 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001419/0.435, allocations: 16.98 kB / 431.3 MB, free: 32.7 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.185e-05/0.435, allocations: 18.34 kB / 431.3 MB, free: 32.7 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         ambientSubstance.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
         C.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         M.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         X.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: 16
 * 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 (46):
 * Single equations (assignments): 46
 * 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 0.0002295/0.4352, allocations: 165.9 kB / 431.5 MB, free: 32.57 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.863e-05/0.4353, allocations: 20.33 kB / 431.5 MB, free: 32.57 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 8.037e-05/0.4353, allocations: 28.06 kB / 431.6 MB, free: 32.56 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.086e-06/0.4354, allocations: 5.25 kB / 431.6 MB, free: 32.56 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.564e-06/0.4354, allocations: 1.375 kB / 431.6 MB, free: 32.56 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.209e-06/0.4354, allocations: 3.422 kB / 431.6 MB, free: 32.56 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004087/0.4358, allocations: 363.6 kB / 431.9 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.024e-06/0.4358, allocations: 1.406 kB / 431.9 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002427/0.4361, allocations: 50.61 kB / 432 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.827e-06/0.4361, allocations: 3.625 kB / 432 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.873e-05/0.4361, allocations: 7.797 kB / 432 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.497e-06/0.4361, allocations: 4.25 kB / 432 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.583e-06/0.4361, allocations: 0.5 kB / 432 MB, free: 32.37 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004793/0.4366, allocations: 437.7 kB / 432.4 MB, free: 32.21 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 3.621e-05/0.4366, allocations: 93.88 kB / 432.5 MB, free: 32.11 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.174e-05/0.4367, allocations: 6.688 kB / 432.5 MB, free: 32.11 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000134/0.4368, allocations: 11.69 kB / 432.5 MB, free: 32.11 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.821e-05/0.4369, allocations: 13.83 kB / 432.5 MB, free: 32.11 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.338e-05/0.4369, allocations: 10.25 kB / 432.5 MB, free: 32.11 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 6.122e-05/0.4369, allocations: 116.8 kB / 432.7 MB, free: 32.04 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.4e-07/0.4369, allocations: 2.281 kB / 432.7 MB, free: 32.04 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0003088/0.4373, allocations: 62.78 kB / 432.7 MB, free: 32.04 MB / 350.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,C.n,M.n,X.n,ambientSubstance.n)
 * 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 (26):
 * Single equations (assignments): 26
 * 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 9.395e-05/0.4374, allocations: 106 kB / 432.8 MB, free: 31.95 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003407/0.4377, allocations: 247.1 kB / 433.1 MB, free: 31.94 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.285e-06/0.4377, allocations: 0 / 433.1 MB, free: 31.94 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001212/0.4378, allocations: 111 kB / 433.2 MB, free: 31.94 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002948/0.4381, allocations: 20.84 kB / 433.2 MB, free: 31.94 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00125/0.4394, allocations: 0.9534 MB / 434.2 MB, free: 31.37 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002042/0.4396, allocations: 0.767 MB / 434.9 MB, free: 30.67 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.147e-05/0.4397, allocations: 22.78 kB / 434.9 MB, free: 30.66 MB / 350.1 MB
Notification: Performance of SimCode: time 2.4e-07/0.4397, allocations: 4 kB / 434.9 MB, free: 30.66 MB / 350.1 MB
Notification: Performance of Templates: time 0.004158/0.4439, allocations: 2.807 MB / 437.8 MB, free: 30.51 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile
make -j1 -f BioChem_BioChem.Examples.GMO.cell.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.GMO.cellCalcHelperMain.o OMCppBioChem_BioChem.Examples.GMO.cellCalcHelperMain.cpp
clang: error: no such file or directory: 'NOTFOUND'
make: *** [<builtin>: OMCppBioChem_BioChem.Examples.GMO.cellCalcHelperMain.o] Error 1