Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.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 0.0008468/0.0008468, allocations: 80.81 kB / 19.94 MB, free: 4.543 MB / 18.57 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 0.001355/0.001355, allocations: 173 kB / 23.36 MB, free: 1.129 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 0.938/0.938, allocations: 177.1 MB / 203.8 MB, free: 5.484 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/package.mo): time 0.09624/0.09624, allocations: 17.47 MB / 277.7 MB, free: 11.43 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/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(Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane")
translateModel(Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.713e-06/1.713e-06, allocations: 0 / 300.8 MB, free: 1.742 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.623e-05/1.794e-05, allocations: 2.312 kB / 300.8 MB, free: 1.738 MB / 266.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical master/Obsolete.mo:14335:7-14335:66: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 master/Obsolete.mo:14335:7-14335:66: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.Obsolete.Examples.AcidBase.Dev.RedCellMembrane): time 0.04586/0.04588, allocations: 59 MB / 359.8 MB, free: 9.246 MB / 330.7 MB
Notification: Performance of NFInst.instExpressions: time 0.2388/0.2847, allocations: 120.4 MB / 480.2 MB, free: 28.08 MB / 410.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.003978/0.2887, allocations: 103.3 kB / 480.3 MB, free: 28.08 MB / 410.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.004325/0.293, allocations: 2.214 MB / 482.5 MB, free: 28.08 MB / 410.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.02103/0.314, allocations: 10.66 MB / 493.2 MB, free: 25.71 MB / 410.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.02998/0.344, allocations: 16.4 MB / 0.4976 GB, free: 21.18 MB / 410.7 MB
Notification: Performance of NFFlatten.flatten: time 0.01018/0.3542, allocations: 10.87 MB / 0.5082 GB, free: 16.69 MB / 410.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004923/0.3591, allocations: 4.878 MB / 0.513 GB, free: 13.39 MB / 410.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.008161/0.3673, allocations: 7.394 MB / 0.5202 GB, free: 9.691 MB / 410.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.00665/0.3739, allocations: 4.841 MB / 0.525 GB, free: 7.637 MB / 410.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.002184/0.3761, allocations: 0.8909 MB / 0.5258 GB, free: 7.062 MB / 410.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.02821/0.4043, allocations: 13.14 MB / 0.5387 GB, free: 10.51 MB / 426.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.002884/0.4072, allocations: 2.17 MB / 0.5408 GB, free: 8.52 MB / 426.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.005451/0.4126, allocations: 3.368 MB / 0.5441 GB, free: 5.34 MB / 426.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.04624/0.4589, allocations: 23.32 MB / 0.5668 GB, free: 15.84 MB / 458.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.962e-06/0.4589, allocations: 0 / 0.5668 GB, free: 15.84 MB / 458.7 MB
Notification: Performance of FrontEnd: time 1.443e-06/0.4589, allocations: 0 / 0.5668 GB, free: 15.84 MB / 458.7 MB
Notification: Performance of Transformations before backend: time 0.0002552/0.4591, allocations: 0 / 0.5668 GB, free: 15.84 MB / 458.7 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 0.01454/0.4737, allocations: 10.59 MB / 0.5772 GB, free: 5.656 MB / 458.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.477e-05/0.4737, allocations: 8.031 kB / 0.5772 GB, free: 5.648 MB / 458.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.006294/0.48, allocations: 3.089 MB / 0.5802 GB, free: 2.605 MB / 458.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.004371/0.4844, allocations: 2.678 MB / 0.5828 GB, free: 15.94 MB / 474.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0002986/0.4847, allocations: 0.579 MB / 0.5834 GB, free: 15.35 MB / 474.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0008459/0.4855, allocations: 0.7398 MB / 0.5841 GB, free: 14.62 MB / 474.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.006619/0.4921, allocations: 6.655 MB / 0.5906 GB, free: 8.113 MB / 474.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 8.588e-05/0.4922, allocations: 4.125 kB / 0.5906 GB, free: 8.109 MB / 474.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0004577/0.4927, allocations: 291.1 kB / 0.5909 GB, free: 7.828 MB / 474.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.954e-05/0.4928, allocations: 175.9 kB / 0.5911 GB, free: 7.656 MB / 474.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.007168/0.4999, allocations: 6.327 MB / 0.5972 GB, free: 1.312 MB / 474.7 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 0.3351/0.8351, allocations: 18.29 MB / 0.6151 GB, free: 80.93 MB / 490.8 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.02037/0.8555, allocations: 19.05 MB / 0.6337 GB, free: 79.87 MB / 490.8 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.003176/0.8586, allocations: 1.957 MB / 0.6356 GB, free: 79.81 MB / 490.8 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.02681/0.8854, allocations: 16.83 MB / 0.6521 GB, free: 79.19 MB / 490.8 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.08e-05/0.8855, allocations: 90.22 kB / 0.6521 GB, free: 79.14 MB / 490.8 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.001506/0.887, allocations: 0.6182 MB / 0.6527 GB, free: 79.14 MB / 490.8 MB
Notification: Performance of pre-optimization done (n=581): time 1.277e-05/0.887, allocations: 1.125 kB / 0.6527 GB, free: 79.14 MB / 490.8 MB
Notification: Performance of matching and sorting (n=757): time 0.05079/0.9378, allocations: 23.98 MB / 0.6762 GB, free: 71.15 MB / 490.8 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.639e-05/0.9379, allocations: 129.3 kB / 0.6763 GB, free: 71.01 MB / 490.8 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001916/0.9398, allocations: 2.995 MB / 0.6792 GB, free: 69.3 MB / 490.8 MB
Notification: Performance of collectPreVariables (initialization): time 0.0004411/0.9402, allocations: 149.6 kB / 0.6794 GB, free: 69.25 MB / 490.8 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0009439/0.9412, allocations: 2.777 MB / 0.6821 GB, free: 67.54 MB / 490.8 MB
Notification: Performance of collectInitialBindings (initialization): time 0.001417/0.9426, allocations: 2.713 MB / 0.6847 GB, free: 65.79 MB / 490.8 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.001323/0.9439, allocations: 1.696 MB / 0.6864 GB, free: 64.95 MB / 490.8 MB
Notification: Performance of setup shared object (initialization): time 2.829e-05/0.9439, allocations: 311.7 kB / 0.6867 GB, free: 64.65 MB / 490.8 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001215/0.9452, allocations: 1.135 MB / 0.6878 GB, free: 63.66 MB / 490.8 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001836/0.947, allocations: 4.066 MB / 0.6917 GB, free: 58.93 MB / 490.8 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.004271/0.9513, allocations: 6.629 MB / 0.6982 GB, free: 52.64 MB / 490.8 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.986e-05/0.9513, allocations: 24 kB / 0.6982 GB, free: 52.62 MB / 490.8 MB
Notification: Performance of matching and sorting (n=1205) (initialization): time 0.007335/0.9586, allocations: 6.161 MB / 0.7043 GB, free: 48.48 MB / 490.8 MB
Notification: Performance of prepare postOptimizeDAE: time 4.177e-05/0.9587, allocations: 47.19 kB / 0.7043 GB, free: 48.44 MB / 490.8 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.701e-05/0.9587, allocations: 92 kB / 0.7044 GB, free: 48.35 MB / 490.8 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.004608/0.9633, allocations: 1.857 MB / 0.7062 GB, free: 46.68 MB / 490.8 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.004807/0.9681, allocations: 2.224 MB / 0.7084 GB, free: 44.69 MB / 490.8 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.0064/0.9745, allocations: 9.26 MB / 0.7174 GB, free: 35.68 MB / 490.8 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003514/0.978, allocations: 297.6 kB / 0.7177 GB, free: 35.55 MB / 490.8 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0004943/0.9785, allocations: 441.7 kB / 0.7181 GB, free: 35.2 MB / 490.8 MB
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 (1143):
 * Single equations (assignments): 1137
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 6
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 3 systems
   {(2,20,100.0%), (1,3,100.0%), (1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 3 systems
   {(3,27), (1,3), (1,3)}
Notification: Performance of prepare postOptimizeDAE: time 0.001828/0.9804, allocations: 0.6987 MB / 0.7188 GB, free: 34.96 MB / 490.8 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0008382/0.9812, allocations: 0.5596 MB / 0.7194 GB, free: 34.49 MB / 490.8 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.007403/0.9886, allocations: 6.06 MB / 0.7253 GB, free: 29.42 MB / 490.8 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.624e-05/0.9886, allocations: 76 kB / 0.7253 GB, free: 29.35 MB / 490.8 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.857e-06/0.9886, allocations: 4 kB / 0.7253 GB, free: 29.34 MB / 490.8 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.658e-05/0.9887, allocations: 42.53 kB / 0.7254 GB, free: 29.3 MB / 490.8 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01064/0.9993, allocations: 8.327 MB / 0.7335 GB, free: 21.52 MB / 490.8 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.176e-05/0.9993, allocations: 4 kB / 0.7335 GB, free: 21.52 MB / 490.8 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.003142/1.002, allocations: 1.437 MB / 0.7349 GB, free: 20.15 MB / 490.8 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.003933/1.006, allocations: 1.657 MB / 0.7365 GB, free: 18.51 MB / 490.8 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0003899/1.007, allocations: 251.9 kB / 0.7368 GB, free: 18.26 MB / 490.8 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.00553/1.012, allocations: 8.855 MB / 0.7454 GB, free: 9.102 MB / 490.8 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.746e-06/1.012, allocations: 4 kB / 0.7454 GB, free: 9.098 MB / 490.8 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.007545/1.02, allocations: 6.841 MB / 0.7521 GB, free: 2.262 MB / 490.8 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001817/1.022, allocations: 0.8 MB / 0.7529 GB, free: 1.469 MB / 490.8 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0005388/1.022, allocations: 144 kB / 0.753 GB, free: 1.328 MB / 490.8 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001388/1.024, allocations: 152 kB / 0.7532 GB, free: 1.18 MB / 490.8 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0005459/1.024, allocations: 0.5987 MB / 0.7538 GB, free: 0.582 MB / 490.8 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003139/1.024, allocations: 247.9 kB / 0.754 GB, free: 348 kB / 490.8 MB
Notification: Performance of sorting global known variables: time 0.001111/1.026, allocations: 1.381 MB / 0.7554 GB, free: 15.12 MB / 0.4949 GB
Notification: Performance of sort global known variables: time 1.8e-07/1.026, allocations: 0 / 0.7554 GB, free: 15.12 MB / 0.4949 GB
Notification: Performance of remove unused functions: time 0.01135/1.037, allocations: 5.101 MB / 0.7603 GB, free: 10.7 MB / 0.4949 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 (761):
 * Single equations (assignments): 755
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 6
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems (#iteration vars, #inner vars, density): 3 systems
   {(2,20,100.0%), (1,3,100.0%), (1,3,100.0%)}
 * Non-linear torn systems (#iteration vars, #inner vars): 3 systems
   {(4,33), (1,3), (1,3)}
Notification: Performance of Backend phase and start with SimCode phase: time 0.009761/1.047, allocations: 6.301 MB / 0.7665 GB, free: 5.27 MB / 0.4949 GB
Notification: Performance of simCode: created initialization part: time 0.007602/1.054, allocations: 5.558 MB / 0.7719 GB, free: 48 kB / 0.4949 GB
Notification: Performance of simCode: created event and clocks part: time 0.0001487/1.054, allocations: 71.98 kB / 0.772 GB, free: 15.97 MB / 0.5105 GB
Notification: Performance of simCode: created simulation system equations: time 0.003623/1.058, allocations: 3.107 MB / 0.775 GB, free: 13.02 MB / 0.5105 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003471/1.062, allocations: 1.314 MB / 0.7763 GB, free: 11.82 MB / 0.5105 GB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0135/1.075, allocations: 11.15 MB / 0.7872 GB, free: 0.6992 MB / 0.5105 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001127/1.076, allocations: 1.079 MB / 0.7882 GB, free: 15.59 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 0.004558/1.081, allocations: 1.642 MB / 0.7898 GB, free: 14.05 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.003467/1.084, allocations: 1.982 MB / 0.7918 GB, free: 12.05 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.894e-06/1.084, allocations: 3.094 kB / 0.7918 GB, free: 12.05 MB / 0.5262 GB
Notification: Performance of Templates: time 0.304/1.388, allocations: 190.9 MB / 0.9782 GB, free: 6.445 MB / 0.5418 GB
"
[Timeout remaining time 659]
make -j1 -f Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.makefile [Timeout 660]
(rm -f Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.pipe ; mkfifo Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.pipe ; head -c 1048576 < Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.pipe >> ../files/Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.sim & ./Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_master_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 8.58864681608975]