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 0.00106/0.00106, allocations: 92.22 kB / 19.65 MB, free: 276 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 0.001256/0.001256, allocations: 173 kB / 23.02 MB, free: 1.547 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 0.9743/0.9743, allocations: 177.1 MB / 203.4 MB, free: 5.633 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 0.1024/0.1024, allocations: 17.45 MB / 277.4 MB, free: 11.56 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 1.433e-06/1.433e-06, allocations: 3.938 kB / 353.6 MB, free: 9.805 MB / 282.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.969e-05/3.112e-05, allocations: 6.25 kB / 353.6 MB, free: 9.797 MB / 282.7 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 0.04461/0.04465, allocations: 53.89 MB / 407.5 MB, free: 3.953 MB / 330.7 MB
Notification: Performance of NFInst.instExpressions: time 0.2237/0.2684, allocations: 122.8 MB / 0.5178 GB, free: 8.996 MB / 394.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.005061/0.2735, allocations: 95.25 kB / 0.5179 GB, free: 8.902 MB / 394.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.005574/0.279, allocations: 2.194 MB / 0.5201 GB, free: 6.699 MB / 394.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.02641/0.3054, allocations: 10.54 MB / 0.5304 GB, free: 12.21 MB / 410.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0332/0.3386, allocations: 16.25 MB / 0.5462 GB, free: 11.98 MB / 426.7 MB
Notification: Performance of NFFlatten.flatten: time 0.01186/0.3505, allocations: 10.9 MB / 0.5569 GB, free: 1.039 MB / 426.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.1781/0.5286, allocations: 4.797 MB / 0.5616 GB, free: 11.21 MB / 426.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.01384/0.5424, allocations: 7.392 MB / 0.5688 GB, free: 11.21 MB / 426.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.01062/0.553, allocations: 4.901 MB / 0.5736 GB, free: 11.21 MB / 426.7 MB
Notification: Performance of NFPackage.collectConstants: time 0.004175/0.5572, allocations: 0.8903 MB / 0.5744 GB, free: 11.21 MB / 426.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.03209/0.5893, allocations: 13.15 MB / 0.5873 GB, free: 11.18 MB / 426.7 MB
Notification: Performance of NFScalarize.scalarize: time 0.004168/0.5935, allocations: 2.159 MB / 0.5894 GB, free: 11.18 MB / 426.7 MB
Notification: Performance of NFVerifyModel.verify: time 0.007107/0.6006, allocations: 3.371 MB / 0.5927 GB, free: 11.18 MB / 426.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.05773/0.6583, allocations: 23.33 MB / 0.6155 GB, free: 8.57 MB / 426.7 MB
Notification: Performance of FrontEnd - DAE generated: time 8.296e-06/0.6583, allocations: 0.5938 kB / 0.6155 GB, free: 8.57 MB / 426.7 MB
Notification: Performance of FrontEnd: time 1.714e-06/0.6583, allocations: 0 / 0.6155 GB, free: 8.57 MB / 426.7 MB
Notification: Performance of Transformations before backend: time 0.0003639/0.6587, allocations: 0.5 kB / 0.6155 GB, free: 8.57 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 0.02378/0.6825, allocations: 10.77 MB / 0.626 GB, free: 3.516 MB / 426.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.349e-05/0.6825, allocations: 8.031 kB / 0.626 GB, free: 3.508 MB / 426.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.009656/0.6922, allocations: 3.215 MB / 0.6291 GB, free: 0.5586 MB / 426.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.007338/0.6995, allocations: 3.561 MB / 0.6326 GB, free: 13.82 MB / 442.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004931/0.7, allocations: 0.5806 MB / 0.6332 GB, free: 13.23 MB / 442.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.00245/0.7024, allocations: 0.7381 MB / 0.6339 GB, free: 12.5 MB / 442.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01452/0.717, allocations: 7.319 MB / 0.641 GB, free: 5.344 MB / 442.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.000109/0.7171, allocations: 192 / 0.641 GB, free: 5.344 MB / 442.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0007388/0.7178, allocations: 289.5 kB / 0.6413 GB, free: 5.062 MB / 442.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.544e-05/0.7179, allocations: 173.4 kB / 0.6415 GB, free: 4.895 MB / 442.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.01389/0.7318, allocations: 8.431 MB / 0.6497 GB, free: 12.47 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 0.0461/0.7779, allocations: 23.65 MB / 0.6728 GB, free: 5.223 MB / 474.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03325/0.8111, allocations: 20.49 MB / 0.6928 GB, free: 0.7148 MB / 490.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.006557/0.8177, allocations: 2.67 MB / 0.6954 GB, free: 14.03 MB / 0.4948 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.03608/0.8538, allocations: 18.54 MB / 0.7135 GB, free: 11.77 MB / 0.5105 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 6.873e-05/0.8539, allocations: 94.83 kB / 0.7136 GB, free: 11.66 MB / 0.5105 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.001783/0.8556, allocations: 0.6314 MB / 0.7142 GB, free: 11.04 MB / 0.5105 GB
Notification: Performance of pre-optimization done (n=581): time 1.781e-05/0.8557, allocations: 0 / 0.7142 GB, free: 11.04 MB / 0.5105 GB
Notification: Performance of matching and sorting (n=757): time 0.05959/0.9152, allocations: 26.4 MB / 0.74 GB, free: 0.5391 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 9.464e-05/0.9153, allocations: 129.3 kB / 0.7401 GB, free: 408 kB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.2082/1.123, allocations: 3.269 MB / 0.7433 GB, free: 129.4 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 0.00126/1.125, allocations: 153.8 kB / 0.7435 GB, free: 129.4 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 0.001716/1.126, allocations: 3.326 MB / 0.7467 GB, free: 128.7 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 0.002721/1.129, allocations: 2.68 MB / 0.7493 GB, free: 127.3 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002797/1.132, allocations: 1.709 MB / 0.751 GB, free: 127.2 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 5.374e-05/1.132, allocations: 478.2 kB / 0.7515 GB, free: 126.7 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.00356/1.136, allocations: 1.73 MB / 0.7532 GB, free: 126.7 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.004742/1.14, allocations: 5.758 MB / 0.7588 GB, free: 121.7 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.01005/1.15, allocations: 8.624 MB / 0.7672 GB, free: 116.7 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001269/1.151, allocations: 26.25 kB / 0.7672 GB, free: 116.7 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=1205) (initialization): time 0.01661/1.167, allocations: 8.781 MB / 0.7758 GB, free: 116 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 7.371e-05/1.167, allocations: 43.53 kB / 0.7758 GB, free: 116 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.482e-05/1.167, allocations: 90.78 kB / 0.7759 GB, free: 116 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.005467/1.173, allocations: 1.881 MB / 0.7778 GB, free: 116 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.006368/1.179, allocations: 2.328 MB / 0.78 GB, free: 116 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.009464/1.189, allocations: 13.26 MB / 0.793 GB, free: 105.3 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.005752/1.194, allocations: 289.7 kB / 0.7933 GB, free: 105.3 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.001761/1.196, allocations: 0.5198 MB / 0.7938 GB, free: 105.3 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 0.002975/1.199, allocations: 0.7376 MB / 0.7945 GB, free: 105.1 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.002064/1.201, allocations: 0.8087 MB / 0.7953 GB, free: 104.8 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01383/1.215, allocations: 8.036 MB / 0.8031 GB, free: 104.3 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.194e-05/1.215, allocations: 76.31 kB / 0.8032 GB, free: 104.3 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.176e-05/1.215, allocations: 7.922 kB / 0.8032 GB, free: 104.3 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.529e-05/1.215, allocations: 38.86 kB / 0.8032 GB, free: 104.3 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02287/1.238, allocations: 12.02 MB / 0.815 GB, free: 103.2 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.595e-05/1.238, allocations: 7.625 kB / 0.815 GB, free: 103.2 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.004149/1.242, allocations: 1.536 MB / 0.8165 GB, free: 103.2 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.004935/1.247, allocations: 1.67 MB / 0.8181 GB, free: 103.1 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.001148/1.248, allocations: 262.6 kB / 0.8184 GB, free: 103.1 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.008369/1.257, allocations: 12.73 MB / 0.8308 GB, free: 90.56 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.997e-06/1.257, allocations: 4 kB / 0.8308 GB, free: 90.56 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01556/1.272, allocations: 9.31 MB / 0.8399 GB, free: 82.04 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.003436/1.276, allocations: 1.24 MB / 0.8411 GB, free: 81.04 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.001171/1.277, allocations: 151.9 kB / 0.8412 GB, free: 80.89 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.002379/1.279, allocations: 147.7 kB / 0.8414 GB, free: 80.75 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0007628/1.28, allocations: 0.6084 MB / 0.842 GB, free: 80.24 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0005092/1.28, allocations: 322.5 kB / 0.8423 GB, free: 79.93 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 0.001978/1.282, allocations: 1.633 MB / 0.8439 GB, free: 78.29 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 2.4e-07/1.282, allocations: 0 / 0.8439 GB, free: 78.29 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.01522/1.298, allocations: 5.104 MB / 0.8489 GB, free: 73.82 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 0.01411/1.312, allocations: 5.93 MB / 0.8547 GB, free: 68.75 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0128/1.325, allocations: 6.992 MB / 0.8615 GB, free: 61.96 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 8.166e-06/1.325, allocations: 4 kB / 0.8615 GB, free: 61.96 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.00643/1.331, allocations: 3.951 MB / 0.8654 GB, free: 58.07 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.006296/1.337, allocations: 1.317 MB / 0.8666 GB, free: 56.83 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 0.01868/1.356, allocations: 11.57 MB / 0.8779 GB, free: 45.14 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001181/1.357, allocations: 1.082 MB / 0.879 GB, free: 44.02 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 0.005997/1.363, allocations: 1.654 MB / 0.8806 GB, free: 42.48 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0023/1.365, allocations: 1.127 MB / 0.8817 GB, free: 41.36 MB / 0.5261 GB
Notification: Performance of SimCode: time 2.795e-06/1.365, allocations: 0 / 0.8817 GB, free: 41.36 MB / 0.5261 GB
Notification: Performance of Templates: time 0.3667/1.732, allocations: 187.1 MB / 1.064 GB, free: 18.11 MB / 0.5261 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: 9.352672699838877]