Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.GMO.cell.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 0.0009482/0.0009482, allocations: 80.94 kB / 19.94 MB, free: 4.547 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 0.001132/0.001132, allocations: 173.4 kB / 23.36 MB, free: 1.133 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 1.003/1.003, allocations: 177.1 MB / 203.8 MB, free: 5.469 MB / 186.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo): time 0.04036/0.04036, allocations: 9.56 MB / 269.8 MB, free: 3.809 MB / 250.7 MB
"
[Timeout remaining time 180]
Using package BioChem with version 1.1.3 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/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(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell")
translateModel(BioChem.Examples.GMO.cell,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.453e-06/1.453e-06, allocations: 0 / 290.1 MB, free: 18.42 MB / 266.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.358e-05/1.503e-05, allocations: 5.75 kB / 290.1 MB, free: 18.41 MB / 266.7 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.00581/0.005825, allocations: 4.525 MB / 294.7 MB, free: 16.52 MB / 266.7 MB
Notification: Performance of NFInst.instExpressions: time 0.0005123/0.006338, allocations: 318.5 kB / 295 MB, free: 16.29 MB / 266.7 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001214/0.006459, allocations: 15.31 kB / 295 MB, free: 16.29 MB / 266.7 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001008/0.00656, allocations: 54.55 kB / 295 MB, free: 16.25 MB / 266.7 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001824/0.006742, allocations: 79.81 kB / 295.1 MB, free: 16.19 MB / 266.7 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0001881/0.00693, allocations: 67.95 kB / 295.2 MB, free: 16.16 MB / 266.7 MB
Notification: Performance of NFFlatten.flatten: time 0.0002808/0.007211, allocations: 311.6 kB / 295.5 MB, free: 16 MB / 266.7 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002119/0.007423, allocations: 122.8 kB / 295.6 MB, free: 15.94 MB / 266.7 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002086/0.007632, allocations: 195.6 kB / 295.8 MB, free: 15.86 MB / 266.7 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001852/0.007817, allocations: 111.1 kB / 295.9 MB, free: 15.82 MB / 266.7 MB
Notification: Performance of NFPackage.collectConstants: time 5.256e-05/0.007869, allocations: 34.97 kB / 295.9 MB, free: 15.82 MB / 266.7 MB
Notification: Performance of NFFlatten.collectFunctions: time 4.362e-05/0.007913, allocations: 32.16 kB / 296 MB, free: 15.82 MB / 266.7 MB
Notification: Performance of NFScalarize.scalarize: time 5.191e-05/0.007965, allocations: 74.78 kB / 296 MB, free: 15.77 MB / 266.7 MB
Notification: Performance of NFVerifyModel.verify: time 9.651e-05/0.008061, allocations: 114.2 kB / 296.2 MB, free: 15.72 MB / 266.7 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002717/0.008333, allocations: 236.4 kB / 296.4 MB, free: 15.6 MB / 266.7 MB
Notification: Performance of FrontEnd - DAE generated: time 3.346e-06/0.008336, allocations: 0 / 296.4 MB, free: 15.6 MB / 266.7 MB
Notification: Performance of FrontEnd: time 1.002e-06/0.008337, allocations: 0 / 296.4 MB, free: 15.6 MB / 266.7 MB
Notification: Performance of Transformations before backend: time 6.101e-06/0.008344, allocations: 0.5 kB / 296.4 MB, free: 15.6 MB / 266.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 96
 * Number of variables: 96
Notification: Performance of Generate backend data structure: time 0.0006109/0.008955, allocations: 0.5198 MB / 296.9 MB, free: 15.21 MB / 266.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.217e-05/0.008987, allocations: 9.938 kB / 296.9 MB, free: 15.21 MB / 266.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.153e-05/0.009068, allocations: 56.02 kB / 297 MB, free: 15.2 MB / 266.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 9.034e-05/0.009159, allocations: 143.7 kB / 297.1 MB, free: 15.05 MB / 266.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.479e-05/0.009183, allocations: 29.47 kB / 297.1 MB, free: 15.04 MB / 266.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.779e-05/0.009231, allocations: 38.03 kB / 297.2 MB, free: 15.03 MB / 266.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002789/0.00951, allocations: 228.3 kB / 297.4 MB, free: 14.94 MB / 266.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.605e-05/0.009526, allocations: 7.719 kB / 297.4 MB, free: 14.94 MB / 266.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.029e-05/0.009546, allocations: 15.12 kB / 297.4 MB, free: 14.93 MB / 266.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.09e-05/0.009557, allocations: 9.875 kB / 297.4 MB, free: 14.93 MB / 266.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001589/0.009716, allocations: 105.1 kB / 297.5 MB, free: 14.91 MB / 266.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001166/0.01088, allocations: 0.7203 MB / 298.3 MB, free: 14.55 MB / 266.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001984/0.01108, allocations: 131 kB / 298.4 MB, free: 14.5 MB / 266.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 8.854e-05/0.01117, allocations: 60.66 kB / 298.4 MB, free: 14.48 MB / 266.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.356e-05/0.01118, allocations: 5.812 kB / 298.4 MB, free: 14.48 MB / 266.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.888e-05/0.0112, allocations: 37.78 kB / 298.5 MB, free: 14.44 MB / 266.7 MB
Notification: Performance of pre-optimization done (n=22): time 1.153e-06/0.0112, allocations: 3.938 kB / 298.5 MB, free: 14.44 MB / 266.7 MB
Notification: Performance of matching and sorting (n=26): time 0.001078/0.01228, allocations: 0.6058 MB / 299.1 MB, free: 14.2 MB / 266.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 1.979e-05/0.0123, allocations: 60.44 kB / 299.1 MB, free: 14.13 MB / 266.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.783e-05/0.01239, allocations: 172.6 kB / 299.3 MB, free: 13.99 MB / 266.7 MB
Notification: Performance of collectPreVariables (initialization): time 1.037e-05/0.0124, allocations: 29.7 kB / 299.3 MB, free: 13.96 MB / 266.7 MB
Notification: Performance of collectInitialEqns (initialization): time 6.434e-05/0.01246, allocations: 212.2 kB / 299.6 MB, free: 13.78 MB / 266.7 MB
Notification: Performance of collectInitialBindings (initialization): time 4.567e-05/0.01251, allocations: 98.33 kB / 299.6 MB, free: 13.7 MB / 266.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.334e-05/0.01258, allocations: 68.05 kB / 299.7 MB, free: 13.66 MB / 266.7 MB
Notification: Performance of setup shared object (initialization): time 3.528e-05/0.01262, allocations: 335.3 kB / 300 MB, free: 13.34 MB / 266.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 5.192e-05/0.01267, allocations: 34.53 kB / 300.1 MB, free: 13.34 MB / 266.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.472e-05/0.01276, allocations: 155.5 kB / 300.2 MB, free: 13.19 MB / 266.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002692/0.01303, allocations: 275.1 kB / 300.5 MB, free: 13.04 MB / 266.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.385e-06/0.01304, allocations: 5.438 kB / 300.5 MB, free: 13.04 MB / 266.7 MB
Notification: Performance of matching and sorting (n=46) (initialization): time 0.0002671/0.0133, allocations: 221 kB / 300.7 MB, free: 12.96 MB / 266.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.361e-05/0.01332, allocations: 8.156 kB / 300.7 MB, free: 12.96 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.424e-06/0.01332, allocations: 5.656 kB / 300.7 MB, free: 12.96 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.753e-05/0.01334, allocations: 5.812 kB / 300.7 MB, free: 12.96 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002494/0.01359, allocations: 84.08 kB / 300.8 MB, free: 12.96 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.947e-06/0.0136, allocations: 10.73 kB / 300.8 MB, free: 12.95 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001039/0.0137, allocations: 21.67 kB / 300.9 MB, free: 12.94 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.839e-05/0.01372, allocations: 10.36 kB / 300.9 MB, free: 12.94 MB / 266.7 MB
Warning: Assuming fixed start value for the following 5 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  \"Compartment volume\" type: Real
         ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         X.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         M.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer )  \"Number of moles of substance in pool (mol)\" type: Real
         C.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: 16
 * 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 (46):
 * Single equations (assignments): 46
 * 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 0.0001339/0.01386, allocations: 149.2 kB / 301 MB, free: 12.81 MB / 266.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.204e-05/0.0139, allocations: 20.02 kB / 301 MB, free: 12.8 MB / 266.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.683e-05/0.01394, allocations: 31.55 kB / 301.1 MB, free: 12.78 MB / 266.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.925e-06/0.01395, allocations: 4.312 kB / 301.1 MB, free: 12.78 MB / 266.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.657e-06/0.01395, allocations: 1.062 kB / 301.1 MB, free: 12.78 MB / 266.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.05e-06/0.01396, allocations: 1.359 kB / 301.1 MB, free: 12.78 MB / 266.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002688/0.01423, allocations: 179 kB / 301.2 MB, free: 12.67 MB / 266.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.623e-06/0.01423, allocations: 4.641 kB / 301.2 MB, free: 12.67 MB / 266.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001905/0.01442, allocations: 60.14 kB / 301.3 MB, free: 12.66 MB / 266.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.206e-06/0.01442, allocations: 2.016 kB / 301.3 MB, free: 12.66 MB / 266.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.564e-05/0.01444, allocations: 6.828 kB / 301.3 MB, free: 12.66 MB / 266.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.487e-06/0.01444, allocations: 3.719 kB / 301.3 MB, free: 12.66 MB / 266.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.232e-06/0.01444, allocations: 0.8438 kB / 301.3 MB, free: 12.66 MB / 266.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002791/0.01472, allocations: 302.4 kB / 301.6 MB, free: 12.5 MB / 266.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 1.583e-05/0.01474, allocations: 14.52 kB / 301.6 MB, free: 12.49 MB / 266.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.23e-05/0.01476, allocations: 5.719 kB / 301.6 MB, free: 12.48 MB / 266.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.993e-05/0.01485, allocations: 10.28 kB / 301.6 MB, free: 12.48 MB / 266.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 2.984e-05/0.01488, allocations: 14.75 kB / 301.7 MB, free: 12.48 MB / 266.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0003121/0.01519, allocations: 9.719 kB / 301.7 MB, free: 12.48 MB / 266.7 MB
Notification: Performance of sorting global known variables: time 3.761e-05/0.01523, allocations: 38.97 kB / 301.7 MB, free: 12.46 MB / 266.7 MB
Notification: Performance of sort global known variables: time 9e-08/0.01523, allocations: 0 / 301.7 MB, free: 12.46 MB / 266.7 MB
Notification: Performance of remove unused functions: time 0.0002961/0.01552, allocations: 67.41 kB / 301.8 MB, free: 12.45 MB / 266.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,C.n,M.n,X.n,ambientSubstance.n)
 * 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 (26):
 * Single equations (assignments): 26
 * 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 6.894e-05/0.01559, allocations: 78.34 kB / 301.8 MB, free: 12.38 MB / 266.7 MB
Notification: Performance of simCode: created initialization part: time 0.0002044/0.0158, allocations: 171.4 kB / 302 MB, free: 12.34 MB / 266.7 MB
Notification: Performance of simCode: created event and clocks part: time 6.863e-06/0.0158, allocations: 1.312 kB / 302 MB, free: 12.34 MB / 266.7 MB
Notification: Performance of simCode: created simulation system equations: time 8.049e-05/0.01588, allocations: 71.78 kB / 302.1 MB, free: 12.32 MB / 266.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002057/0.01609, allocations: 31.05 kB / 302.1 MB, free: 12.3 MB / 266.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007255/0.01682, allocations: 0.5769 MB / 302.7 MB, free: 11.95 MB / 266.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.487e-05/0.01687, allocations: 90.61 kB / 302.8 MB, free: 11.88 MB / 266.7 MB
Notification: Performance of simCode: alias equations: time 0.0001158/0.01699, allocations: 23.02 kB / 302.8 MB, free: 11.88 MB / 266.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001269/0.01711, allocations: 84.11 kB / 302.9 MB, free: 11.83 MB / 266.7 MB
Notification: Performance of SimCode: time 6.51e-07/0.01711, allocations: 0 / 302.9 MB, free: 11.83 MB / 266.7 MB
Notification: Performance of Templates: time 0.004396/0.02151, allocations: 2.193 MB / 305.1 MB, free: 10.92 MB / 266.7 MB
"
[Timeout remaining time 660]
make -j1 -f BioChem_BioChem.Examples.GMO.cell.makefile [Timeout 660]
(rm -f BioChem_BioChem.Examples.GMO.cell.pipe ; mkfifo BioChem_BioChem.Examples.GMO.cell.pipe ; head -c 1048576 < BioChem_BioChem.Examples.GMO.cell.pipe >> ../files/BioChem_BioChem.Examples.GMO.cell.sim & ./BioChem_BioChem.Examples.GMO.cell -abortSlowSimulation -alarm=240 -s gbode -gbm=radauIIA3 -lv LOG_STATS > BioChem_BioChem.Examples.GMO.cell.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 2.7694095708429813]