Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.CircadianOscillator.Container.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001318/0.001318, allocations: 112.7 kB / 18.94 MB, free: 2.93 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001456/0.001456, allocations: 189.4 kB / 22.22 MB, free: 5.105 MB / 14.72 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.461/1.461, allocations: 225.6 MB / 251 MB, free: 13.02 MB / 206.1 MB
"
[Timeout remaining time 178]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.07044/0.07044, allocations: 12.43 MB / 318.7 MB, free: 12.95 MB / 254.1 MB
"
[Timeout remaining time 180]
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-1,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") [Timeout 660]
"Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\"
Notification: Performance of FrontEnd - loaded program: time 0.002055/0.002055, allocations: 69.64 kB / 445.3 MB, free: 3.973 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1307/0.1327, allocations: 54.96 MB / 0.4885 GB, free: 12.94 MB / 366.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01405/0.1468, allocations: 8.568 MB / 0.4969 GB, free: 4.328 MB / 366.1 MB
Notification: Performance of NFInst.instExpressions: time 0.002028/0.1488, allocations: 0.8146 MB / 0.4977 GB, free: 3.512 MB / 366.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0007286/0.1495, allocations: 40 kB / 0.4977 GB, free: 3.473 MB / 366.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0004992/0.15, allocations: 146.8 kB / 0.4979 GB, free: 3.328 MB / 366.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0006604/0.1507, allocations: 206 kB / 0.4981 GB, free: 3.125 MB / 366.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0004542/0.1512, allocations: 199.8 kB / 0.4983 GB, free: 2.93 MB / 366.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0009062/0.1521, allocations: 0.8414 MB / 0.4991 GB, free: 2.086 MB / 366.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006344/0.1527, allocations: 375 kB / 0.4995 GB, free: 1.691 MB / 366.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003935/0.1531, allocations: 374.7 kB / 0.4998 GB, free: 1.324 MB / 366.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004847/0.1536, allocations: 438 kB / 0.5002 GB, free: 0.8945 MB / 366.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001457/0.1537, allocations: 116 kB / 0.5003 GB, free: 0.7812 MB / 366.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001376/0.1539, allocations: 116 kB / 0.5005 GB, free: 0.668 MB / 366.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001949/0.1541, allocations: 223.2 kB / 0.5007 GB, free: 460 kB / 366.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0004383/0.1545, allocations: 485.8 kB / 0.5011 GB, free: 15.97 MB / 382.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.001219/0.1557, allocations: 1.163 MB / 0.5023 GB, free: 14.8 MB / 382.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.32e-06/0.1557, allocations: 7.938 kB / 0.5023 GB, free: 14.79 MB / 382.1 MB
Notification: Performance of FrontEnd: time 1.393e-06/0.1557, allocations: 0 / 0.5023 GB, free: 14.79 MB / 382.1 MB
Notification: Performance of Transformations before backend: time 2.086e-05/0.1557, allocations: 0 / 0.5023 GB, free: 14.79 MB / 382.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
* Number of equations: 252
* Number of variables: 252
Notification: Performance of Generate backend data structure: time 0.001716/0.1575, allocations: 1.074 MB / 0.5033 GB, free: 13.68 MB / 382.1 MB
Notification: Performance of prepare preOptimizeDAE: time 2.881e-05/0.1575, allocations: 11.97 kB / 0.5033 GB, free: 13.67 MB / 382.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001594/0.1576, allocations: 100.3 kB / 0.5034 GB, free: 13.57 MB / 382.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003304/0.158, allocations: 252.7 kB / 0.5037 GB, free: 13.3 MB / 382.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.041e-05/0.158, allocations: 74.38 kB / 0.5037 GB, free: 13.22 MB / 382.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001494/0.1582, allocations: 100.3 kB / 0.5038 GB, free: 13.12 MB / 382.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001514/0.1597, allocations: 0.8764 MB / 0.5047 GB, free: 12.24 MB / 382.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.324e-05/0.1597, allocations: 4.188 kB / 0.5047 GB, free: 12.23 MB / 382.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.864e-05/0.1598, allocations: 43.94 kB / 0.5047 GB, free: 12.19 MB / 382.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.142e-05/0.1598, allocations: 24 kB / 0.5048 GB, free: 12.17 MB / 382.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001163/0.161, allocations: 0.6208 MB / 0.5054 GB, free: 11.54 MB / 382.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004587/0.1656, allocations: 2.774 MB / 0.5081 GB, free: 8.695 MB / 382.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001045/0.1666, allocations: 0.4947 MB / 0.5086 GB, free: 8.184 MB / 382.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004297/0.1671, allocations: 271 kB / 0.5088 GB, free: 7.914 MB / 382.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.073e-05/0.1671, allocations: 12.44 kB / 0.5088 GB, free: 7.902 MB / 382.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 4.482e-05/0.1671, allocations: 35 kB / 0.5089 GB, free: 7.855 MB / 382.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.684e-06/0.1671, allocations: 0 / 0.5089 GB, free: 7.855 MB / 382.1 MB
Notification: Performance of matching and sorting (n=59): time 0.00519/0.1723, allocations: 2.118 MB / 0.5109 GB, free: 5.715 MB / 382.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.962e-05/0.1724, allocations: 85.61 kB / 0.511 GB, free: 5.613 MB / 382.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004415/0.1728, allocations: 361.5 kB / 0.5114 GB, free: 5.254 MB / 382.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.697e-05/0.1729, allocations: 37.73 kB / 0.5114 GB, free: 5.211 MB / 382.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003269/0.1732, allocations: 467.6 kB / 0.5118 GB, free: 4.746 MB / 382.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001838/0.1734, allocations: 230.1 kB / 0.5121 GB, free: 4.52 MB / 382.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001967/0.1736, allocations: 138.6 kB / 0.5122 GB, free: 4.379 MB / 382.1 MB
Notification: Performance of setup shared object (initialization): time 0.0002/0.1738, allocations: 358.8 kB / 0.5125 GB, free: 4.02 MB / 382.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003931/0.1742, allocations: 252.7 kB / 0.5128 GB, free: 3.77 MB / 382.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0006014/0.1748, allocations: 484.8 kB / 0.5132 GB, free: 3.176 MB / 382.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005757/0.1805, allocations: 1.693 MB / 0.5149 GB, free: 1.363 MB / 382.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.781e-06/0.1805, allocations: 7.938 kB / 0.5149 GB, free: 1.355 MB / 382.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.00136/0.1819, allocations: 0.8013 MB / 0.5157 GB, free: 0.5469 MB / 382.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.116e-05/0.1819, allocations: 13.23 kB / 0.5157 GB, free: 0.5352 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.899e-05/0.1819, allocations: 12 kB / 0.5157 GB, free: 0.5234 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 3.317e-05/0.182, allocations: 12 kB / 0.5157 GB, free: 0.5117 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006571/0.1826, allocations: 180.4 kB / 0.5159 GB, free: 344 kB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.974e-05/0.1826, allocations: 15.94 kB / 0.5159 GB, free: 328 kB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003271/0.183, allocations: 32 kB / 0.5159 GB, free: 296 kB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.409e-05/0.183, allocations: 32 kB / 0.516 GB, free: 264 kB / 382.1 MB
Warning: Assuming fixed start value for the following 12 variables:
V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real
nucleus.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real
cytoplasm.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real
cytoplasm.ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
cytoplasm.y5.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
cytoplasm.y4.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
cytoplasm.y2.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
cytoplasm.y1.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
nucleus.ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
nucleus.y7.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
nucleus.y6.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
nucleus.y3.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real
Notification: Model statistics after passing the back-end for initialization:
* Number of independent subsystems: 39
* 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 (107):
* Single equations (assignments): 107
* Array equations: 0
* Algorithm blocks: 0
* Record equations: 0
* When equations: 0
* If-equations: 0
* Equation systems (not torn): 0
* Torn equation systems: 0
* Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.2401/0.4231, allocations: 288.2 kB / 0.5162 GB, free: 29.18 MB / 382.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001828/0.4232, allocations: 48.3 kB / 0.5163 GB, free: 29.18 MB / 382.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001776/0.4234, allocations: 69.05 kB / 0.5164 GB, free: 29.18 MB / 382.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 9.557e-06/0.4234, allocations: 5.875 kB / 0.5164 GB, free: 29.18 MB / 382.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.155e-05/0.4234, allocations: 4.531 kB / 0.5164 GB, free: 29.18 MB / 382.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.989e-06/0.4235, allocations: 8.828 kB / 0.5164 GB, free: 29.18 MB / 382.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.00118/0.4246, allocations: 0.7299 MB / 0.5171 GB, free: 29.02 MB / 382.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.158e-06/0.4246, allocations: 1.688 kB / 0.5171 GB, free: 29.02 MB / 382.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005236/0.4252, allocations: 107.3 kB / 0.5172 GB, free: 29.02 MB / 382.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 7.754e-06/0.4252, allocations: 4.844 kB / 0.5172 GB, free: 29.02 MB / 382.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.737e-05/0.4252, allocations: 18.11 kB / 0.5172 GB, free: 29.02 MB / 382.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.12e-06/0.4252, allocations: 2.906 kB / 0.5172 GB, free: 29.02 MB / 382.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.633e-06/0.4252, allocations: 3.469 kB / 0.5172 GB, free: 29.02 MB / 382.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001078/0.4263, allocations: 0.9308 MB / 0.5181 GB, free: 28.81 MB / 382.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.399e-05/0.4264, allocations: 46.02 kB / 0.5182 GB, free: 28.81 MB / 382.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.466e-05/0.4264, allocations: 15.91 kB / 0.5182 GB, free: 28.81 MB / 382.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002548/0.4267, allocations: 9.406 kB / 0.5182 GB, free: 28.81 MB / 382.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.408e-05/0.4267, allocations: 46.08 kB / 0.5182 GB, free: 28.81 MB / 382.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.48e-05/0.4268, allocations: 16.31 kB / 0.5183 GB, free: 28.81 MB / 382.1 MB
Notification: Performance of sorting global known variables: time 0.0002046/0.427, allocations: 239 kB / 0.5185 GB, free: 28.72 MB / 382.1 MB
Notification: Performance of sort global known variables: time 7e-08/0.427, allocations: 0 / 0.5185 GB, free: 28.72 MB / 382.1 MB
Notification: Performance of remove unused functions: time 0.000613/0.4276, allocations: 157.3 kB / 0.5186 GB, free: 28.72 MB / 382.1 MB
Notification: Model statistics after passing the back-end for simulation:
* Number of independent subsystems: 2
* Number of states: 12 (nucleus.V,nucleus.y3.n,nucleus.y6.n,nucleus.y7.n,nucleus.ambientSubstance.n,cytoplasm.V,cytoplasm.y1.n,cytoplasm.y2.n,cytoplasm.y4.n,cytoplasm.y5.n,cytoplasm.ambientSubstance.n,V)
* 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 (59):
* Single equations (assignments): 59
* Array equations: 0
* Algorithm blocks: 0
* Record equations: 0
* When equations: 0
* If-equations: 0
* Equation systems (not torn): 0
* Torn equation systems: 0
* Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.0001286/0.4277, allocations: 115.3 kB / 0.5187 GB, free: 28.64 MB / 382.1 MB
Notification: Performance of simCode: created initialization part: time 0.0008898/0.4286, allocations: 0.5536 MB / 0.5193 GB, free: 28.63 MB / 382.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.906e-06/0.4286, allocations: 0.9062 kB / 0.5193 GB, free: 28.63 MB / 382.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003379/0.4289, allocations: 247.9 kB / 0.5195 GB, free: 28.62 MB / 382.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005238/0.4295, allocations: 68.89 kB / 0.5196 GB, free: 28.62 MB / 382.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002863/0.4323, allocations: 1.822 MB / 0.5214 GB, free: 27.77 MB / 382.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005107/0.4328, allocations: 0.9414 MB / 0.5223 GB, free: 27.06 MB / 382.1 MB
Notification: Performance of simCode: alias equations: time 0.0002876/0.4331, allocations: 62.38 kB / 0.5223 GB, free: 27.04 MB / 382.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00015/0.4333, allocations: 44.56 kB / 0.5224 GB, free: 27.04 MB / 382.1 MB
Notification: Performance of SimCode: time 1.002e-06/0.4333, allocations: 4 kB / 0.5224 GB, free: 27.03 MB / 382.1 MB
Notification: Performance of Templates: time 0.01417/0.4475, allocations: 6.045 MB / 0.5283 GB, free: 26.6 MB / 382.1 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile [Timeout 660]
(rm -f BioChem_BioChem.Examples.CircadianOscillator.Container.pipe ; mkfifo BioChem_BioChem.Examples.CircadianOscillator.Container.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CircadianOscillator.Container.pipe >> ../files/BioChem_BioChem.Examples.CircadianOscillator.Container.sim & ./BioChem_BioChem.Examples.CircadianOscillator.Container -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1) [Timeout 480]
[Calling sys.exit(0), Time elapsed: 5.08396050799638]
Failed to read output from testmodel.py, exit status != 0:
0.45578564144670963 0.46695273800000003 0.30893126000000004
Calling exit ...
<OMPython.OMCSessionZMQ object at 0x7f75e74397b0>