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 0.0009235/0.0009235, allocations: 81.17 kB / 19.87 MB, free: 4.621 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 0.0009587/0.0009587, allocations: 169 kB / 23.27 MB, free: 1.223 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 1.029/1.029, allocations: 177.2 MB / 203.7 MB, free: 5.52 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 0.08517/0.08517, allocations: 17.46 MB / 277.7 MB, free: 11.41 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 1.302e-06/1.302e-06, allocations: 0 / 354.1 MB, free: 10.56 MB / 330.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.52e-05/1.65e-05, allocations: 2.312 kB / 354.1 MB, free: 10.56 MB / 330.7 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 0.07045/0.07046, allocations: 53.16 MB / 407.2 MB, free: 5.41 MB / 378.7 MB
Notification: Performance of NFInst.instExpressions: time 0.2064/0.2769, allocations: 118.7 MB / 0.5136 GB, free: 37.18 MB / 410.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.004511/0.2814, allocations: 101.7 kB / 0.5137 GB, free: 37.13 MB / 410.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.005448/0.2868, allocations: 2.18 MB / 0.5158 GB, free: 36 MB / 410.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.02238/0.3092, allocations: 10.55 MB / 0.5261 GB, free: 29.68 MB / 410.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.03167/0.3409, allocations: 16.25 MB / 0.542 GB, free: 18.93 MB / 410.7 MB
Notification: Performance of NFFlatten.flatten: time 0.01073/0.3516, allocations: 10.89 MB / 0.5526 GB, free: 11.34 MB / 410.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.004889/0.3565, allocations: 4.808 MB / 0.5573 GB, free: 6.473 MB / 410.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.006967/0.3635, allocations: 7.401 MB / 0.5645 GB, free: 15.06 MB / 426.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.006408/0.3699, allocations: 4.906 MB / 0.5693 GB, free: 10.15 MB / 426.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.002619/0.3725, allocations: 0.8828 MB / 0.5702 GB, free: 9.266 MB / 426.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.03294/0.4054, allocations: 13.14 MB / 0.583 GB, free: 12.1 MB / 442.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.003154/0.4086, allocations: 2.165 MB / 0.5851 GB, free: 9.926 MB / 442.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.005749/0.4143, allocations: 3.368 MB / 0.5884 GB, free: 6.551 MB / 442.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.2212/0.6356, allocations: 23.32 MB / 0.6112 GB, free: 28.59 MB / 442.7 MB
Notification: Performance of FrontEnd - DAE generated: time 7.404e-06/0.6356, allocations: 0 / 0.6112 GB, free: 28.59 MB / 442.7 MB
Notification: Performance of FrontEnd: time 1.163e-06/0.6356, allocations: 0 / 0.6112 GB, free: 28.59 MB / 442.7 MB
Notification: Performance of Transformations before backend: time 0.0003401/0.6359, allocations: 3.5 kB / 0.6112 GB, free: 28.59 MB / 442.7 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 0.01639/0.6523, allocations: 10.83 MB / 0.6218 GB, free: 24.06 MB / 442.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.587e-05/0.6523, allocations: 12.11 kB / 0.6218 GB, free: 24.06 MB / 442.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.008746/0.6611, allocations: 3.211 MB / 0.6249 GB, free: 22.98 MB / 442.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.006077/0.6672, allocations: 3.555 MB / 0.6284 GB, free: 22.18 MB / 442.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0003732/0.6675, allocations: 0.5754 MB / 0.6289 GB, free: 22.1 MB / 442.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.001314/0.6688, allocations: 0.7351 MB / 0.6297 GB, free: 22.08 MB / 442.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.007898/0.6767, allocations: 6.616 MB / 0.6361 GB, free: 21.39 MB / 442.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 9.94e-05/0.6768, allocations: 4.875 kB / 0.6361 GB, free: 21.39 MB / 442.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0005162/0.6774, allocations: 288 kB / 0.6364 GB, free: 21.39 MB / 442.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0001032/0.6775, allocations: 179.3 kB / 0.6366 GB, free: 21.39 MB / 442.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.008579/0.686, allocations: 7.199 MB / 0.6436 GB, free: 21.21 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 0.02859/0.7146, allocations: 23.09 MB / 0.6662 GB, free: 14.92 MB / 442.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.02104/0.7357, allocations: 20.17 MB / 0.6859 GB, free: 15.58 MB / 458.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.003739/0.7394, allocations: 2.261 MB / 0.6881 GB, free: 13.36 MB / 458.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.02996/0.7694, allocations: 18.82 MB / 0.7064 GB, free: 11.31 MB / 474.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.395e-05/0.7694, allocations: 93.95 kB / 0.7065 GB, free: 11.2 MB / 474.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.001721/0.7711, allocations: 0.6273 MB / 0.7071 GB, free: 10.58 MB / 474.7 MB
Notification: Performance of pre-optimization done (n=581): time 1.61e-05/0.7712, allocations: 0 / 0.7071 GB, free: 10.58 MB / 474.7 MB
Notification: Performance of matching and sorting (n=757): time 0.05659/0.8278, allocations: 23.37 MB / 0.73 GB, free: 3.285 MB / 490.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 9.519e-05/0.8279, allocations: 129.3 kB / 0.7301 GB, free: 3.145 MB / 490.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.003924/0.8318, allocations: 3.248 MB / 0.7333 GB, free: 488 kB / 490.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0007391/0.8325, allocations: 149.7 kB / 0.7334 GB, free: 332 kB / 490.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.002055/0.8346, allocations: 3.368 MB / 0.7367 GB, free: 13.13 MB / 0.4948 GB
Notification: Performance of collectInitialBindings (initialization): time 0.002711/0.8373, allocations: 2.708 MB / 0.7393 GB, free: 10.58 MB / 0.4948 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002395/0.8397, allocations: 1.744 MB / 0.741 GB, free: 9.012 MB / 0.4948 GB
Notification: Performance of setup shared object (initialization): time 0.0001158/0.8398, allocations: 476.8 kB / 0.7415 GB, free: 8.543 MB / 0.4948 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002375/0.8422, allocations: 1.334 MB / 0.7428 GB, free: 7.203 MB / 0.4948 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004988/0.8472, allocations: 5.401 MB / 0.7481 GB, free: 316 kB / 0.4948 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.008266/0.8554, allocations: 7.933 MB / 0.7558 GB, free: 7.18 MB / 0.5105 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.473e-05/0.8555, allocations: 32 kB / 0.7558 GB, free: 7.148 MB / 0.5105 GB
Notification: Performance of matching and sorting (n=1205) (initialization): time 0.01453/0.87, allocations: 7.939 MB / 0.7636 GB, free: 15.75 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 5.833e-05/0.8701, allocations: 44 kB / 0.7636 GB, free: 15.71 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.983e-05/0.8702, allocations: 88 kB / 0.7637 GB, free: 15.62 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.005817/0.876, allocations: 1.861 MB / 0.7655 GB, free: 13.75 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00613/0.8821, allocations: 2.254 MB / 0.7677 GB, free: 11.64 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.2273/1.109, allocations: 13.02 MB / 0.7805 GB, free: 127.3 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005138/1.115, allocations: 289.5 kB / 0.7807 GB, free: 127.3 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00133/1.116, allocations: 454.2 kB / 0.7812 GB, free: 127.3 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 0.002825/1.119, allocations: 0.7468 MB / 0.7819 GB, free: 127.1 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.001735/1.12, allocations: 0.8075 MB / 0.7827 GB, free: 127.1 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0113/1.132, allocations: 7.343 MB / 0.7899 GB, free: 126.8 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.86e-05/1.132, allocations: 78.53 kB / 0.7899 GB, free: 126.8 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.273e-05/1.132, allocations: 8.438 kB / 0.7899 GB, free: 126.8 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.597e-05/1.132, allocations: 38.91 kB / 0.79 GB, free: 126.8 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01613/1.148, allocations: 10.73 MB / 0.8005 GB, free: 125.9 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.301e-05/1.148, allocations: 3.312 kB / 0.8005 GB, free: 125.9 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00391/1.152, allocations: 1.46 MB / 0.8019 GB, free: 125.9 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.004657/1.157, allocations: 1.644 MB / 0.8035 GB, free: 125.8 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0008498/1.157, allocations: 270.9 kB / 0.8037 GB, free: 125.8 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.007082/1.164, allocations: 12.5 MB / 0.816 GB, free: 115.4 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.158e-06/1.164, allocations: 8.281 kB / 0.816 GB, free: 115.4 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01422/1.179, allocations: 8.275 MB / 0.824 GB, free: 114.3 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.002487/1.181, allocations: 1.236 MB / 0.8253 GB, free: 114 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0008009/1.182, allocations: 149.6 kB / 0.8254 GB, free: 114 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002213/1.184, allocations: 153.4 kB / 0.8255 GB, free: 114 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0008352/1.185, allocations: 0.6125 MB / 0.8261 GB, free: 114 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0004863/1.186, allocations: 262.5 kB / 0.8264 GB, free: 114 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 0.001471/1.187, allocations: 1.512 MB / 0.8279 GB, free: 113.7 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 6e-08/1.187, allocations: 0 / 0.8279 GB, free: 113.7 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.01195/1.199, allocations: 5.106 MB / 0.8329 GB, free: 113.7 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 0.01149/1.21, allocations: 6.247 MB / 0.839 GB, free: 113.2 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.00836/1.219, allocations: 6.28 MB / 0.8451 GB, free: 109.6 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 5.821e-06/1.219, allocations: 4 kB / 0.8451 GB, free: 109.6 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.003688/1.222, allocations: 3.619 MB / 0.8486 GB, free: 106.7 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0038/1.226, allocations: 1.322 MB / 0.8499 GB, free: 106 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 0.0144/1.241, allocations: 11.33 MB / 0.861 GB, free: 96.15 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0009146/1.242, allocations: 1.081 MB / 0.862 GB, free: 95.32 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 0.005444/1.247, allocations: 1.644 MB / 0.8636 GB, free: 94 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.004184/1.251, allocations: 2.172 MB / 0.8658 GB, free: 92.33 MB / 0.5261 GB
Notification: Performance of SimCode: time 1.503e-06/1.251, allocations: 4 kB / 0.8658 GB, free: 92.33 MB / 0.5261 GB
Notification: Performance of Templates: time 0.3977/1.649, allocations: 191.3 MB / 1.053 GB, free: 108.6 MB / 0.5417 GB
"
[Timeout remaining time 658]
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: 9.217519680038095]