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 0.001472/0.001472, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 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 0.001511/0.001511, allocations: 165 kB / 23.01 MB, free: 1.555 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 0.9817/0.9817, allocations: 177.1 MB / 203.4 MB, free: 5.637 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 0.102/0.102, allocations: 17.38 MB / 277.3 MB, free: 11.64 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 1.503e-06/1.503e-06, allocations: 0 / 353.5 MB, free: 9.941 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.882e-05/2.032e-05, allocations: 2.312 kB / 353.5 MB, free: 9.938 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 0.04455/0.04457, allocations: 53.88 MB / 407.4 MB, free: 4.086 MB / 330.7 MB
Notification: Performance of NFInst.instExpressions: time 0.2457/0.2903, allocations: 122.8 MB / 0.5177 GB, free: 9.188 MB / 394.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.003949/0.2942, allocations: 97.91 kB / 0.5178 GB, free: 9.094 MB / 394.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.004126/0.2983, allocations: 2.186 MB / 0.5199 GB, free: 6.898 MB / 394.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.02349/0.3218, allocations: 10.55 MB / 0.5302 GB, free: 12.41 MB / 410.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.03815/0.36, allocations: 16.25 MB / 0.5461 GB, free: 12.18 MB / 426.7 MB
Notification: Performance of NFFlatten.flatten: time 0.03242/0.3924, allocations: 10.89 MB / 0.5568 GB, free: 1.242 MB / 426.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.1788/0.5712, allocations: 4.8 MB / 0.5614 GB, free: 10.25 MB / 426.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.01337/0.5846, allocations: 7.401 MB / 0.5687 GB, free: 10.25 MB / 426.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.009776/0.5944, allocations: 4.898 MB / 0.5734 GB, free: 10.25 MB / 426.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.00259/0.597, allocations: 0.8869 MB / 0.5743 GB, free: 10.25 MB / 426.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.03028/0.6272, allocations: 13.15 MB / 0.5872 GB, free: 10.21 MB / 426.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.003262/0.6305, allocations: 2.163 MB / 0.5893 GB, free: 10.21 MB / 426.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.006343/0.6368, allocations: 3.369 MB / 0.5926 GB, free: 10.21 MB / 426.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.05111/0.6879, allocations: 23.32 MB / 0.6153 GB, free: 7.605 MB / 426.7 MB
Notification: Performance of FrontEnd - DAE generated: time 5.971e-06/0.688, allocations: 0.9375 kB / 0.6153 GB, free: 7.605 MB / 426.7 MB
Notification: Performance of FrontEnd: time 2.234e-06/0.688, allocations: 0 / 0.6153 GB, free: 7.605 MB / 426.7 MB
Notification: Performance of Transformations before backend: time 0.0003392/0.6883, allocations: 3.938 kB / 0.6153 GB, free: 7.605 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 0.01754/0.7058, allocations: 10.77 MB / 0.6259 GB, free: 2.602 MB / 426.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.341e-05/0.7059, allocations: 16.03 kB / 0.6259 GB, free: 2.586 MB / 426.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.008423/0.7143, allocations: 3.238 MB / 0.629 GB, free: 15.71 MB / 442.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.006255/0.7206, allocations: 3.56 MB / 0.6325 GB, free: 12.98 MB / 442.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0003956/0.7209, allocations: 0.5782 MB / 0.6331 GB, free: 12.39 MB / 442.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.00126/0.7222, allocations: 0.7312 MB / 0.6338 GB, free: 11.67 MB / 442.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01044/0.7327, allocations: 7.327 MB / 0.6409 GB, free: 4.312 MB / 442.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 8.557e-05/0.7327, allocations: 7.75 kB / 0.641 GB, free: 4.309 MB / 442.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0005482/0.7333, allocations: 288.4 kB / 0.6412 GB, free: 4.027 MB / 442.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.94e-05/0.7334, allocations: 175.9 kB / 0.6414 GB, free: 3.855 MB / 442.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01157/0.7449, allocations: 8.424 MB / 0.6496 GB, free: 11.44 MB / 458.7 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 0.0333/0.7783, allocations: 23.65 MB / 0.6727 GB, free: 4.191 MB / 474.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.02327/0.8015, allocations: 20.48 MB / 0.6927 GB, free: 15.68 MB / 0.4948 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.004978/0.8065, allocations: 2.666 MB / 0.6953 GB, free: 13 MB / 0.4948 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.03137/0.8379, allocations: 18.55 MB / 0.7134 GB, free: 10.73 MB / 0.5105 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.841e-05/0.8379, allocations: 93.95 kB / 0.7135 GB, free: 10.63 MB / 0.5105 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.001859/0.8398, allocations: 0.6275 MB / 0.7141 GB, free: 10 MB / 0.5105 GB
Notification: Performance of pre-optimization done (n=581): time 1.317e-05/0.8398, allocations: 4 kB / 0.7141 GB, free: 10 MB / 0.5105 GB
Notification: Performance of matching and sorting (n=757): time 0.2253/1.065, allocations: 26.39 MB / 0.7399 GB, free: 127.4 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.78e-05/1.065, allocations: 140 kB / 0.7401 GB, free: 127.3 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003461/1.069, allocations: 3.264 MB / 0.7432 GB, free: 126.9 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 0.001035/1.07, allocations: 149.9 kB / 0.7434 GB, free: 126.9 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001691/1.071, allocations: 3.332 MB / 0.7466 GB, free: 126.3 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 0.001959/1.073, allocations: 2.679 MB / 0.7493 GB, free: 124.9 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002187/1.076, allocations: 1.71 MB / 0.7509 GB, free: 124.7 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 4.28e-05/1.076, allocations: 481.8 kB / 0.7514 GB, free: 124.2 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002995/1.079, allocations: 1.725 MB / 0.7531 GB, free: 124.2 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004264/1.083, allocations: 5.759 MB / 0.7587 GB, free: 119.2 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.007722/1.091, allocations: 8.62 MB / 0.7671 GB, free: 114.2 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.343e-05/1.091, allocations: 26.56 kB / 0.7671 GB, free: 114.2 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=1205) (initialization): time 0.01309/1.104, allocations: 8.768 MB / 0.7757 GB, free: 113.6 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 4.608e-05/1.104, allocations: 48.22 kB / 0.7757 GB, free: 113.6 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.068e-05/1.104, allocations: 90.31 kB / 0.7758 GB, free: 113.6 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.005481/1.109, allocations: 1.876 MB / 0.7777 GB, free: 113.5 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.005225/1.115, allocations: 2.332 MB / 0.7799 GB, free: 113.5 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.009015/1.124, allocations: 13.27 MB / 0.7929 GB, free: 102.9 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003974/1.128, allocations: 290.7 kB / 0.7932 GB, free: 102.9 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0006764/1.128, allocations: 0.519 MB / 0.7937 GB, free: 102.9 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 0.0018/1.13, allocations: 0.7456 MB / 0.7944 GB, free: 102.7 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001221/1.131, allocations: 0.808 MB / 0.7952 GB, free: 102.4 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01256/1.144, allocations: 8.021 MB / 0.803 GB, free: 101.9 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.565e-05/1.144, allocations: 82.28 kB / 0.8031 GB, free: 101.8 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.101e-05/1.144, allocations: 8.906 kB / 0.8031 GB, free: 101.8 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.589e-05/1.144, allocations: 42.89 kB / 0.8032 GB, free: 101.8 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01694/1.161, allocations: 12.03 MB / 0.8149 GB, free: 100.8 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.498e-05/1.161, allocations: 3.969 kB / 0.8149 GB, free: 100.8 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.003691/1.165, allocations: 1.536 MB / 0.8164 GB, free: 100.8 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.004798/1.169, allocations: 1.664 MB / 0.818 GB, free: 100.5 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0004739/1.17, allocations: 269.6 kB / 0.8183 GB, free: 100.4 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.007273/1.177, allocations: 12.72 MB / 0.8307 GB, free: 88.96 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.126e-06/1.177, allocations: 7.406 kB / 0.8307 GB, free: 88.96 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01175/1.189, allocations: 9.302 MB / 0.8398 GB, free: 81.09 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.001906/1.191, allocations: 1.24 MB / 0.841 GB, free: 79.88 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0005136/1.191, allocations: 152 kB / 0.8412 GB, free: 79.73 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001521/1.193, allocations: 150.8 kB / 0.8413 GB, free: 79.58 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0006063/1.193, allocations: 0.6104 MB / 0.8419 GB, free: 78.97 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003815/1.194, allocations: 311.9 kB / 0.8422 GB, free: 78.67 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 0.001546/1.195, allocations: 1.633 MB / 0.8438 GB, free: 77.03 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 8e-08/1.195, allocations: 0 / 0.8438 GB, free: 77.03 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.009503/1.205, allocations: 5.109 MB / 0.8488 GB, free: 72.55 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 0.007582/1.212, allocations: 5.946 MB / 0.8546 GB, free: 67.48 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.007727/1.22, allocations: 6.996 MB / 0.8614 GB, free: 60.68 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 3.507e-06/1.22, allocations: 0 / 0.8614 GB, free: 60.68 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.003453/1.224, allocations: 3.95 MB / 0.8653 GB, free: 56.79 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003211/1.227, allocations: 1.314 MB / 0.8666 GB, free: 55.55 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 0.01249/1.239, allocations: 11.56 MB / 0.8778 GB, free: 43.87 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0007224/1.24, allocations: 1.082 MB / 0.8789 GB, free: 42.75 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 0.003804/1.244, allocations: 1.649 MB / 0.8805 GB, free: 41.22 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001629/1.245, allocations: 1.138 MB / 0.8816 GB, free: 40.09 MB / 0.5261 GB
Notification: Performance of SimCode: time 1.323e-06/1.245, allocations: 0 / 0.8816 GB, free: 40.09 MB / 0.5261 GB
Notification: Performance of Templates: time 0.3032/1.549, allocations: 165.7 MB / 1.043 GB, free: 38.35 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: 9.137296870350838]