Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_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 0.001335/0.001335, allocations: 73.09 kB / 20.66 MB, free: 3.84 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 0.001377/0.001377, allocations: 169 kB / 24.05 MB, free: 456 kB / 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 0.9634/0.9634, allocations: 177.1 MB / 204.5 MB, free: 5.504 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/package.mo): time 0.08065/0.08065, allocations: 17.39 MB / 278.4 MB, free: 11.48 MB / 266.7 MB
"
[Timeout remaining time 180]
Using package Chemical with version 2.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/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_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane")
translateModel(Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.305e-06/2.305e-06, allocations: 3.984 kB / 354.7 MB, free: 9.668 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.081e-05/1.312e-05, allocations: 5.688 kB / 354.7 MB, free: 9.664 MB / 282.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 2.0.0/Obsolete.mo:14337:7-14337:66: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 2.0.0/Obsolete.mo:14337:7-14337:66: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 0.03942/0.03944, allocations: 53.14 MB / 407.9 MB, free: 4.555 MB / 330.7 MB
Notification: Performance of NFInst.instExpressions: time 0.2089/0.2484, allocations: 118.7 MB / 0.5142 GB, free: 13.45 MB / 394.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.005494/0.2539, allocations: 99.25 kB / 0.5143 GB, free: 13.36 MB / 394.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.006323/0.2602, allocations: 2.192 MB / 0.5164 GB, free: 11.16 MB / 394.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.02441/0.2846, allocations: 10.54 MB / 0.5267 GB, free: 0.668 MB / 394.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.03521/0.3198, allocations: 16.26 MB / 0.5426 GB, free: 452 kB / 410.7 MB
Notification: Performance of NFFlatten.flatten: time 0.01332/0.3331, allocations: 10.89 MB / 0.5532 GB, free: 5.512 MB / 426.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.007101/0.3402, allocations: 4.811 MB / 0.5579 GB, free: 0.6211 MB / 426.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.1935/0.5337, allocations: 7.386 MB / 0.5651 GB, free: 12.18 MB / 426.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.01052/0.5442, allocations: 4.903 MB / 0.5699 GB, free: 12.18 MB / 426.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.003312/0.5476, allocations: 0.8872 MB / 0.5708 GB, free: 12.18 MB / 426.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.03349/0.581, allocations: 13.15 MB / 0.5836 GB, free: 12.18 MB / 426.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.003566/0.5846, allocations: 2.163 MB / 0.5857 GB, free: 12.18 MB / 426.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.006178/0.5908, allocations: 3.372 MB / 0.589 GB, free: 12.18 MB / 426.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0509/0.6417, allocations: 23.33 MB / 0.6118 GB, free: 9.609 MB / 426.7 MB
Notification: Performance of FrontEnd - DAE generated: time 4.548e-06/0.6417, allocations: 0.9375 kB / 0.6118 GB, free: 9.609 MB / 426.7 MB
Notification: Performance of FrontEnd: time 1.152e-06/0.6417, allocations: 0 / 0.6118 GB, free: 9.609 MB / 426.7 MB
Notification: Performance of Transformations before backend: time 0.0004629/0.6422, allocations: 0 / 0.6118 GB, free: 9.609 MB / 426.7 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 0.01875/0.6609, allocations: 10.84 MB / 0.6224 GB, free: 2.332 MB / 426.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.34e-05/0.6609, allocations: 8.031 kB / 0.6224 GB, free: 2.324 MB / 426.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.008804/0.6697, allocations: 3.243 MB / 0.6256 GB, free: 15.79 MB / 442.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.006343/0.6761, allocations: 3.544 MB / 0.629 GB, free: 13.88 MB / 442.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004486/0.6765, allocations: 0.5783 MB / 0.6296 GB, free: 13.51 MB / 442.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001695/0.6782, allocations: 0.7467 MB / 0.6303 GB, free: 13.02 MB / 442.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.009779/0.688, allocations: 6.621 MB / 0.6368 GB, free: 7.98 MB / 442.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0001356/0.6881, allocations: 2.906 kB / 0.6368 GB, free: 7.98 MB / 442.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0006366/0.6888, allocations: 287.8 kB / 0.6371 GB, free: 7.922 MB / 442.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001193/0.6889, allocations: 172 kB / 0.6372 GB, free: 7.754 MB / 442.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01027/0.6992, allocations: 7.201 MB / 0.6443 GB, free: 0.9766 MB / 442.7 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 0.04111/0.7403, allocations: 23.09 MB / 0.6668 GB, free: 10.81 MB / 474.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0239/0.7642, allocations: 19.92 MB / 0.6863 GB, free: 7 MB / 490.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.004482/0.7687, allocations: 2.255 MB / 0.6885 GB, free: 4.789 MB / 490.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.03335/0.802, allocations: 18.55 MB / 0.7066 GB, free: 2.676 MB / 0.4948 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 7.01e-05/0.8021, allocations: 97.89 kB / 0.7067 GB, free: 2.566 MB / 0.4948 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.001863/0.8039, allocations: 0.6267 MB / 0.7073 GB, free: 1.941 MB / 0.4948 GB
Notification: Performance of pre-optimization done (n=581): time 2.065e-05/0.804, allocations: 0 / 0.7073 GB, free: 1.941 MB / 0.4948 GB
Notification: Performance of matching and sorting (n=757): time 0.05202/0.856, allocations: 23.33 MB / 0.7301 GB, free: 10.68 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.174e-05/0.856, allocations: 125.3 kB / 0.7302 GB, free: 10.55 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003064/0.8591, allocations: 3.253 MB / 0.7334 GB, free: 7.871 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 0.0008478/0.86, allocations: 149.7 kB / 0.7335 GB, free: 7.719 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001644/0.8616, allocations: 3.369 MB / 0.7368 GB, free: 4.527 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 0.002382/0.864, allocations: 2.7 MB / 0.7394 GB, free: 1.98 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002276/0.8663, allocations: 1.746 MB / 0.7412 GB, free: 420 kB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 0.178/1.044, allocations: 488.7 kB / 0.7416 GB, free: 130.1 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.003398/1.048, allocations: 1.328 MB / 0.7429 GB, free: 130.1 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004291/1.052, allocations: 5.4 MB / 0.7482 GB, free: 125.1 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.009921/1.062, allocations: 7.934 MB / 0.7559 GB, free: 120.1 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001011/1.062, allocations: 31.56 kB / 0.756 GB, free: 120.1 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=1205) (initialization): time 0.0139/1.076, allocations: 7.919 MB / 0.7637 GB, free: 119.8 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 5.673e-05/1.076, allocations: 46.34 kB / 0.7637 GB, free: 119.8 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.285e-05/1.076, allocations: 90.19 kB / 0.7638 GB, free: 119.8 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.005218/1.081, allocations: 1.852 MB / 0.7656 GB, free: 119.7 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00595/1.087, allocations: 2.255 MB / 0.7678 GB, free: 119.7 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.008542/1.096, allocations: 13.01 MB / 0.7806 GB, free: 109.2 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00486/1.101, allocations: 292.5 kB / 0.7808 GB, free: 109.2 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0008244/1.101, allocations: 454.5 kB / 0.7813 GB, free: 109.2 MB / 0.5261 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 (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 0.002031/1.103, allocations: 0.7419 MB / 0.782 GB, free: 109.1 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001404/1.105, allocations: 0.8143 MB / 0.7828 GB, free: 109 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01082/1.116, allocations: 7.313 MB / 0.7899 GB, free: 108.5 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.227e-05/1.116, allocations: 77.19 kB / 0.79 GB, free: 108.5 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.349e-05/1.116, allocations: 3.938 kB / 0.79 GB, free: 108.5 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.971e-05/1.116, allocations: 38.62 kB / 0.79 GB, free: 108.5 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01731/1.133, allocations: 10.7 MB / 0.8005 GB, free: 107.5 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.484e-05/1.133, allocations: 4.25 kB / 0.8005 GB, free: 107.5 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004027/1.137, allocations: 1.467 MB / 0.8019 GB, free: 107.5 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.005035/1.142, allocations: 1.643 MB / 0.8035 GB, free: 107.3 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0007291/1.143, allocations: 265.9 kB / 0.8038 GB, free: 107.3 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.007398/1.15, allocations: 12.49 MB / 0.816 GB, free: 96.85 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.068e-06/1.15, allocations: 11.62 kB / 0.816 GB, free: 96.85 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01322/1.163, allocations: 8.252 MB / 0.824 GB, free: 93.88 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003278/1.167, allocations: 1.242 MB / 0.8253 GB, free: 93.22 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001012/1.168, allocations: 145.1 kB / 0.8254 GB, free: 93.19 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002249/1.17, allocations: 146.9 kB / 0.8255 GB, free: 93.15 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0007416/1.171, allocations: 0.6182 MB / 0.8261 GB, free: 92.9 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0005094/1.171, allocations: 262.6 kB / 0.8264 GB, free: 92.73 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 0.00149/1.173, allocations: 1.513 MB / 0.8279 GB, free: 91.8 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 2e-07/1.173, allocations: 0 / 0.8279 GB, free: 91.8 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.01292/1.186, allocations: 5.102 MB / 0.8329 GB, free: 88.21 MB / 0.5261 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 0.01243/1.198, allocations: 6.249 MB / 0.839 GB, free: 84.27 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.01038/1.208, allocations: 6.286 MB / 0.8451 GB, free: 79.21 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 6.983e-06/1.208, allocations: 0 / 0.8451 GB, free: 79.21 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.004469/1.213, allocations: 3.621 MB / 0.8486 GB, free: 75.87 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.004664/1.218, allocations: 1.32 MB / 0.8499 GB, free: 75.01 MB / 0.5261 GB
Error: Error parsing unit kDa: Unit not found
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.01482/1.232, allocations: 11.33 MB / 0.861 GB, free: 64.07 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0009544/1.233, allocations: 1.085 MB / 0.862 GB, free: 62.96 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 0.00521/1.239, allocations: 1.632 MB / 0.8636 GB, free: 61.43 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00364/1.242, allocations: 2.161 MB / 0.8657 GB, free: 59.27 MB / 0.5261 GB
Notification: Performance of SimCode: time 1.874e-06/1.242, allocations: 0 / 0.8657 GB, free: 59.27 MB / 0.5261 GB
Notification: Performance of Templates: time 0.3543/1.597, allocations: 193.6 MB / 1.055 GB, free: 31.66 MB / 0.5261 GB
"
[Timeout remaining time 658]
make -j1 -f Chemical_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.makefile [Timeout 660]
(rm -f Chemical_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.pipe ; mkfifo Chemical_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.pipe ; head -c 1048576 < Chemical_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.pipe >> ../files/Chemical_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.sim & ./Chemical_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane -abortSlowSimulation -alarm=240  -lv LOG_STATS > Chemical_Chemical.Obsolete.Examples.AcidBase.Dev.RedCellMembrane.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 9.279684646986425]