Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.AcidBase.Dev.RedCellMembrane.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/Chemical 1.4.0/package.mo", uses=false)
Using package Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0/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(Chemical.Examples.AcidBase.Dev.RedCellMembrane,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.AcidBase.Dev.RedCellMembrane")
translateModel(Chemical.Examples.AcidBase.Dev.RedCellMembrane,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.AcidBase.Dev.RedCellMembrane")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001069/0.001068, allocations: 102.4 kB / 15.71 MB, free: 440 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001047/0.001047, allocations: 174.4 kB / 16.58 MB, free: 6.418 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.544/1.544, allocations: 223.2 MB / 240.6 MB, free: 5.34 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0/package.mo): time 0.315/0.315, allocations: 15.27 MB / 307 MB, free: 15.8 MB / 254.1 MB
Notification: Performance of FrontEnd - loaded program: time 0.0003396/0.0003396, allocations: 8 kB / 372.1 MB, free: 3.98 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.4607/0.4611, allocations: 54.63 MB / 426.7 MB, free: 39.93 MB / 350.1 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0/package.mo:3011:6-3011:65:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0/package.mo:3011:6-3011:65:writable] Notification: The diagnostics message for the missing inner is: 
Your model is using an outer "system" component but
an inner "system" component is not defined.
For simulation drag Modelica.Fluid.System into your model
to specify system properties.
Notification: Performance of NFInst.instantiate(Chemical.Examples.AcidBase.Dev.RedCellMembrane): time 0.02763/0.4888, allocations: 31.46 MB / 458.2 MB, free: 20.7 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.136/0.6248, allocations: 109.8 MB / 0.5547 GB, free: 8.594 MB / 430.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.008898/0.6337, allocations: 142.9 kB / 0.5548 GB, free: 8.453 MB / 430.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.008176/0.6419, allocations: 2.165 MB / 0.5569 GB, free: 6.273 MB / 430.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.03411/0.6761, allocations: 8.624 MB / 0.5654 GB, free: 13.59 MB / 446.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.04814/0.7243, allocations: 12.6 MB / 0.5777 GB, free: 0.918 MB / 446.1 MB
Notification: Performance of NFFlatten.flatten: time 0.3491/1.073, allocations: 9.596 MB / 0.587 GB, free: 9.066 MB / 446.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.009156/1.083, allocations: 4.37 MB / 0.5913 GB, free: 8.609 MB / 446.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.01273/1.095, allocations: 4.191 MB / 0.5954 GB, free: 8.609 MB / 446.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.01493/1.11, allocations: 5.325 MB / 0.6006 GB, free: 8.605 MB / 446.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.00567/1.116, allocations: 475 kB / 0.601 GB, free: 8.605 MB / 446.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.06081/1.177, allocations: 12.53 MB / 0.6133 GB, free: 8.602 MB / 446.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.008238/1.185, allocations: 1.64 MB / 0.6149 GB, free: 8.602 MB / 446.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.009293/1.195, allocations: 1.381 MB / 0.6162 GB, free: 8.57 MB / 446.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.04518/1.24, allocations: 17.98 MB / 0.6338 GB, free: 5.125 MB / 446.1 MB
Notification: Performance of FrontEnd - DAE generated: time 9.888e-06/1.24, allocations: 0 / 0.6338 GB, free: 5.125 MB / 446.1 MB
Notification: Performance of FrontEnd: time 3.867e-06/1.24, allocations: 0 / 0.6338 GB, free: 5.125 MB / 446.1 MB
Notification: Performance of Transformations before backend: time 0.0007742/1.241, allocations: 0 / 0.6338 GB, free: 5.125 MB / 446.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 1818
 * Number of variables: 1818
Notification: Performance of Generate backend data structure: time 0.03324/1.274, allocations: 8.599 MB / 0.6422 GB, free: 13.2 MB / 462.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.108e-05/1.274, allocations: 8.031 kB / 0.6422 GB, free: 13.19 MB / 462.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.01223/1.286, allocations: 1.907 MB / 0.6441 GB, free: 11.38 MB / 462.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.01118/1.297, allocations: 3.186 MB / 0.6472 GB, free: 9.16 MB / 462.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0009089/1.298, allocations: 0.5555 MB / 0.6477 GB, free: 8.824 MB / 462.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.004248/1.303, allocations: 0.733 MB / 0.6484 GB, free: 8.332 MB / 462.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.03399/1.337, allocations: 9.123 MB / 0.6573 GB, free: 2.051 MB / 462.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0006176/1.337, allocations: 3.281 kB / 0.6573 GB, free: 2.051 MB / 462.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.004122/1.342, allocations: 289.1 kB / 0.6576 GB, free: 1.992 MB / 462.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002848/1.342, allocations: 176 kB / 0.6578 GB, free: 1.82 MB / 462.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.03504/1.377, allocations: 12.62 MB / 0.6701 GB, free: 8.801 MB / 478.1 MB
Warning: The model contains alias variables with redundant start and/or conflicting nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts.
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.08401/1.461, allocations: 29.78 MB / 0.6992 GB, free: 2.605 MB / 494.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.04107/1.502, allocations: 20.37 MB / 0.7191 GB, free: 2.496 MB / 0.4981 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01173/1.514, allocations: 4.682 MB / 0.7237 GB, free: 15.93 MB / 0.5137 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.06687/1.581, allocations: 35.69 MB / 0.7585 GB, free: 14.18 MB / 0.545 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 7.927e-05/1.581, allocations: 91.12 kB / 0.7586 GB, free: 14.07 MB / 0.545 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003176/1.584, allocations: 0.5851 MB / 0.7592 GB, free: 13.49 MB / 0.545 GB
Notification: Performance of pre-optimization done (n=581): time 1.71e-05/1.584, allocations: 3.984 kB / 0.7592 GB, free: 13.48 MB / 0.545 GB
Notification: Performance of matching and sorting (n=754): time 0.7382/2.322, allocations: 36.25 MB / 0.7946 GB, free: 199.5 MB / 0.545 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001246/2.323, allocations: 131.9 kB / 0.7947 GB, free: 199.4 MB / 0.545 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.006118/2.329, allocations: 3.343 MB / 0.798 GB, free: 198.2 MB / 0.545 GB
Notification: Performance of collectPreVariables (initialization): time 0.001811/2.331, allocations: 146.8 kB / 0.7981 GB, free: 198.1 MB / 0.545 GB
Notification: Performance of collectInitialEqns (initialization): time 0.002287/2.333, allocations: 3.148 MB / 0.8012 GB, free: 195.6 MB / 0.545 GB
Notification: Performance of collectInitialBindings (initialization): time 0.003602/2.336, allocations: 2.577 MB / 0.8037 GB, free: 193.6 MB / 0.545 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0004882/2.337, allocations: 190.2 kB / 0.8039 GB, free: 193.4 MB / 0.545 GB
Notification: Performance of setup shared object (initialization): time 0.0004749/2.337, allocations: 0.6497 MB / 0.8045 GB, free: 193 MB / 0.545 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.005596/2.343, allocations: 2.853 MB / 0.8073 GB, free: 191.8 MB / 0.545 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.008054/2.351, allocations: 5.736 MB / 0.8129 GB, free: 187.1 MB / 0.545 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.008426/2.36, allocations: 3.666 MB / 0.8165 GB, free: 185.4 MB / 0.545 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.029e-05/2.36, allocations: 27.19 kB / 0.8165 GB, free: 185.4 MB / 0.545 GB
Notification: Performance of matching and sorting (n=1202) (initialization): time 0.03093/2.391, allocations: 10.72 MB / 0.827 GB, free: 181.1 MB / 0.545 GB
Notification: Performance of prepare postOptimizeDAE: time 0.0002496/2.391, allocations: 44.72 kB / 0.827 GB, free: 181.1 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002987/2.391, allocations: 88.06 kB / 0.8271 GB, free: 181.1 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01084/2.402, allocations: 1.881 MB / 0.8289 GB, free: 180.7 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01706/2.419, allocations: 2.317 MB / 0.8312 GB, free: 180.5 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02499/2.444, allocations: 11.81 MB / 0.8427 GB, free: 171.1 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.009365/2.454, allocations: 465.4 kB / 0.8432 GB, free: 171 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.002792/2.457, allocations: 0.5199 MB / 0.8437 GB, free: 170.9 MB / 0.545 GB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 413
 * 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 (1140):
 * Single equations (assignments): 1134
 * 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: 6
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 3 {(2,100.0%) 20,(1,100.0%) 3,(1,100.0%) 3}
 * Non-linear torn systems: 3 {3 27,1 3,1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.006914/2.463, allocations: 1.192 MB / 0.8448 GB, free: 170 MB / 0.545 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00259/2.466, allocations: 0.576 MB / 0.8454 GB, free: 169.7 MB / 0.545 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.03652/2.503, allocations: 10.19 MB / 0.8554 GB, free: 165.3 MB / 0.545 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.791e-05/2.503, allocations: 76 kB / 0.8554 GB, free: 165.2 MB / 0.545 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.4e-05/2.503, allocations: 13.41 kB / 0.8554 GB, free: 165.2 MB / 0.545 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0003077/2.503, allocations: 38.81 kB / 0.8555 GB, free: 165.2 MB / 0.545 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.05167/2.555, allocations: 16.43 MB / 0.8715 GB, free: 151.5 MB / 0.545 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.43e-05/2.555, allocations: 7.953 kB / 0.8715 GB, free: 151.5 MB / 0.545 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.008358/2.563, allocations: 1.534 MB / 0.873 GB, free: 150 MB / 0.545 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.008578/2.572, allocations: 1.684 MB / 0.8747 GB, free: 148.3 MB / 0.545 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.002591/2.575, allocations: 259.9 kB / 0.8749 GB, free: 148 MB / 0.545 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01476/2.589, allocations: 11.1 MB / 0.8858 GB, free: 136.3 MB / 0.545 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.558e-06/2.59, allocations: 7.938 kB / 0.8858 GB, free: 136.3 MB / 0.545 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.03371/2.623, allocations: 13.03 MB / 0.8985 GB, free: 123.1 MB / 0.545 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.005017/2.628, allocations: 1.254 MB / 0.8997 GB, free: 121.8 MB / 0.545 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.002775/2.631, allocations: 148 kB / 0.8999 GB, free: 121.7 MB / 0.545 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.005961/2.637, allocations: 295.4 kB / 0.9001 GB, free: 121.4 MB / 0.545 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.001868/2.639, allocations: 0.5857 MB / 0.9007 GB, free: 120.8 MB / 0.545 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.001402/2.64, allocations: 311.9 kB / 0.901 GB, free: 120.5 MB / 0.545 GB
Notification: Performance of sorting global known variables: time 0.00413/2.645, allocations: 2.008 MB / 0.903 GB, free: 118.5 MB / 0.545 GB
Notification: Performance of sort global known variables: time 2.91e-07/2.645, allocations: 0 / 0.903 GB, free: 118.5 MB / 0.545 GB
Notification: Performance of remove unused functions: time 0.02119/2.666, allocations: 4.908 MB / 0.9078 GB, free: 114.1 MB / 0.545 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 16
 * Number of states: 34 (blood_erythrocytes.temperature,blood_erythrocytes.mass,blood_plasma.temperature,HCO3.logn,H2O.logn,HCO3_E.logn,H2O_E.logn,Cl_E.logn,Cl.logn,albumin.logn,permeableUncharged.logn,permeableUncharged_E.logn,chargedImpermeable_E.logn,Lac_E.logn,Lac.logn,H_E.logn,H.logn,CO2.logn,CO2_E.logn,O2.logn,O2_E.logn,K.logn,Na.logn,Na_E.logn,K_E.logn,H2PO4_E.logn,ADP_E.logn,ATP_E.logn,HPO4_E.logn,globulins.logn,Ca.logn,Mg.logn,DPG.logn,GSH.logn)
 * 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 (758):
 * Single equations (assignments): 752
 * 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: 6
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 3 {(2,100.0%) 20,(1,100.0%) 3,(1,100.0%) 3}
 * Non-linear torn systems: 3 {4 33,1 3,1 3}
Notification: Performance of Backend phase and start with SimCode phase: time 0.01848/2.684, allocations: 5.387 MB / 0.913 GB, free: 110 MB / 0.545 GB
Notification: Performance of simCode: created initialization part: time 0.01996/2.704, allocations: 9.012 MB / 0.9218 GB, free: 100.9 MB / 0.545 GB
Notification: Performance of simCode: created event and clocks part: time 1.045e-05/2.704, allocations: 0 / 0.9218 GB, free: 100.9 MB / 0.545 GB
Notification: Performance of simCode: created simulation system equations: time 0.009925/2.714, allocations: 4.911 MB / 0.9266 GB, free: 95.96 MB / 0.545 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.009953/2.724, allocations: 1.11 MB / 0.9277 GB, free: 94.86 MB / 0.545 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.03205/2.756, allocations: 15.55 MB / 0.9429 GB, free: 79.25 MB / 0.545 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00462/2.761, allocations: 3.172 MB / 0.946 GB, free: 76.04 MB / 0.545 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.004578/2.766, allocations: 1.454 MB / 0.9474 GB, free: 74.59 MB / 0.545 GB
Notification: Performance of SimCode: time 2.275e-06/2.766, allocations: 1.969 kB / 0.9474 GB, free: 74.59 MB / 0.545 GB
Notification: Performance of Templates: time 0.9649/3.731, allocations: 280.6 MB / 1.221 GB, free: 171.9 MB / 0.545 GB
make -j1 -f Chemical_Chemical.Examples.AcidBase.Dev.RedCellMembrane.makefile
make -j1 -f Chemical_Chemical.Examples.AcidBase.Dev.RedCellMembrane.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 OMCppChemical_Chemical.Examples.AcidBase.Dev.RedCellMembraneCalcHelperMain.o OMCppChemical_Chemical.Examples.AcidBase.Dev.RedCellMembraneCalcHelperMain.cpp
clang: error: no such file or directory: 'NOTFOUND'
make: *** [<builtin>: OMCppChemical_Chemical.Examples.AcidBase.Dev.RedCellMembraneCalcHelperMain.o] Error 1