Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.CaOscillations.Cytosol.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 0.001293/0.001293, allocations: 107.2 kB / 16.45 MB, free: 6.508 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 0.00154/0.00154, allocations: 196.6 kB / 19.41 MB, free: 3.672 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 1.452/1.452, allocations: 225.6 MB / 247.8 MB, free: 13.97 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 0.07185/0.07185, allocations: 12.41 MB / 315.1 MB, free: 14.14 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: "" <> buildModelFMU(BioChem.Examples.CaOscillations.Cytosol,fileNamePrefix="BioChem_BioChem_Examples_CaOscillations_Cytosol",fmuType="me",version="2.0",platforms={"static"}) "" <> buildModelFMU(BioChem.Examples.CaOscillations.Cytosol,fileNamePrefix="BioChem_BioChem_Examples_CaOscillations_Cytosol",fmuType="me",version="2.0",platforms={"static"}) [Timeout 660] "Warning: Ignoring unknown experiment annotation option: Algorithm = \"dassl\" Notification: Performance of FrontEnd - loaded program: time 0.001941/0.001941, allocations: 67.23 kB / 439.5 MB, free: 8.145 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1084/0.1103, allocations: 54.91 MB / 494.4 MB, free: 1.172 MB / 350.1 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.004793/0.1151, allocations: 2.84 MB / 497.3 MB, free: 14.32 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.0002951/0.1154, allocations: 191.2 kB / 497.5 MB, free: 14.13 MB / 366.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 7.731e-05/0.1155, allocations: 12 kB / 497.5 MB, free: 14.12 MB / 366.1 MB Notification: Performance of NFTyping.typeComponents: time 8.556e-05/0.1156, allocations: 31.73 kB / 497.5 MB, free: 14.09 MB / 366.1 MB Notification: Performance of NFTyping.typeBindings: time 0.0001649/0.1157, allocations: 47.52 kB / 497.6 MB, free: 14.04 MB / 366.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.000189/0.1159, allocations: 47.92 kB / 497.6 MB, free: 13.99 MB / 366.1 MB Notification: Performance of NFFlatten.flatten: time 0.0002743/0.1162, allocations: 183.2 kB / 497.8 MB, free: 13.81 MB / 366.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0002073/0.1164, allocations: 71.61 kB / 497.8 MB, free: 13.74 MB / 366.1 MB Notification: Performance of NFEvalConstants.evaluate: time 9.72e-05/0.1165, allocations: 79.66 kB / 497.9 MB, free: 13.66 MB / 366.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0001604/0.1167, allocations: 99.55 kB / 498 MB, free: 13.56 MB / 366.1 MB Notification: Performance of NFPackage.collectConstants: time 4.244e-05/0.1167, allocations: 24 kB / 498 MB, free: 13.54 MB / 366.1 MB Notification: Performance of NFFlatten.collectFunctions: time 3.344e-05/0.1167, allocations: 20 kB / 498.1 MB, free: 13.52 MB / 366.1 MB Notification: Performance of NFScalarize.scalarize: time 5.882e-05/0.1168, allocations: 55.81 kB / 498.1 MB, free: 13.46 MB / 366.1 MB Notification: Performance of NFVerifyModel.verify: time 0.0001105/0.1169, allocations: 99.47 kB / 498.2 MB, free: 13.37 MB / 366.1 MB Notification: Performance of NFConvertDAE.convert: time 0.0003128/0.1172, allocations: 238.9 kB / 498.4 MB, free: 13.13 MB / 366.1 MB Notification: Performance of FrontEnd - DAE generated: time 5.189e-06/0.1172, allocations: 0 / 498.4 MB, free: 13.13 MB / 366.1 MB Notification: Performance of FrontEnd: time 4.187e-06/0.1172, allocations: 7.984 kB / 498.5 MB, free: 13.12 MB / 366.1 MB Notification: Performance of Transformations before backend: time 7.084e-06/0.1172, allocations: 0 / 498.5 MB, free: 13.12 MB / 366.1 MB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 60 * Number of variables: 60 Notification: Performance of Generate backend data structure: time 0.0008456/0.1181, allocations: 0.4952 MB / 499 MB, free: 12.58 MB / 366.1 MB Notification: Performance of prepare preOptimizeDAE: time 4.153e-05/0.1181, allocations: 8.031 kB / 499 MB, free: 12.57 MB / 366.1 MB Notification: Performance of preOpt introduceOutputAliases (simulation): time 8.293e-05/0.1182, allocations: 62.72 kB / 499 MB, free: 12.5 MB / 366.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 5.669e-05/0.1183, allocations: 28.75 kB / 499 MB, free: 12.47 MB / 366.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001916/0.1185, allocations: 192 kB / 499.2 MB, free: 12.25 MB / 366.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.203e-05/0.1185, allocations: 16.94 kB / 499.3 MB, free: 12.23 MB / 366.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 5.326e-05/0.1185, allocations: 24.38 kB / 499.3 MB, free: 12.21 MB / 366.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004001/0.1189, allocations: 209.5 kB / 499.5 MB, free: 12 MB / 366.1 MB Notification: Performance of preOpt findStateOrder (simulation): time 1.947e-05/0.119, allocations: 3.938 kB / 499.5 MB, free: 12 MB / 366.1 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.377e-05/0.119, allocations: 8 kB / 499.5 MB, free: 11.99 MB / 366.1 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.015e-05/0.119, allocations: 7.938 kB / 499.5 MB, free: 11.98 MB / 366.1 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002713/0.1193, allocations: 134.2 kB / 499.6 MB, free: 11.85 MB / 366.1 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001492/0.1208, allocations: 0.7673 MB / 0.4887 GB, free: 11.02 MB / 366.1 MB Notification: Performance of preOpt comSubExp (simulation): time 0.000204/0.121, allocations: 102.4 kB / 0.4888 GB, free: 10.91 MB / 366.1 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0002898/0.1212, allocations: 104.7 kB / 0.4889 GB, free: 10.8 MB / 366.1 MB Notification: Performance of preOpt evalFunc (simulation): time 2.008e-05/0.1213, allocations: 4 kB / 0.4889 GB, free: 10.8 MB / 366.1 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.674e-05/0.1213, allocations: 30.56 kB / 0.4889 GB, free: 10.76 MB / 366.1 MB Notification: Performance of pre-optimization done (n=15): time 1.442e-06/0.1213, allocations: 0 / 0.4889 GB, free: 10.76 MB / 366.1 MB Notification: Performance of matching and sorting (n=17): time 0.001329/0.1226, allocations: 0.5751 MB / 0.4895 GB, free: 10.14 MB / 366.1 MB Notification: Performance of inlineWhenForInitialization (initialization): time 5.546e-05/0.1227, allocations: 55.41 kB / 0.4895 GB, free: 10.07 MB / 366.1 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001393/0.1228, allocations: 153.4 kB / 0.4897 GB, free: 9.906 MB / 366.1 MB Notification: Performance of collectPreVariables (initialization): time 2.858e-05/0.1228, allocations: 29.7 kB / 0.4897 GB, free: 9.871 MB / 366.1 MB Notification: Performance of collectInitialEqns (initialization): time 0.000103/0.123, allocations: 156.2 kB / 0.4898 GB, free: 9.715 MB / 366.1 MB Notification: Performance of collectInitialBindings (initialization): time 6.093e-05/0.123, allocations: 67.44 kB / 0.4899 GB, free: 9.648 MB / 366.1 MB Notification: Performance of simplifyInitialFunctions (initialization): time 7.229e-05/0.1231, allocations: 49.66 kB / 0.49 GB, free: 9.594 MB / 366.1 MB Notification: Performance of setup shared object (initialization): time 0.0001484/0.1232, allocations: 326.8 kB / 0.4903 GB, free: 9.266 MB / 366.1 MB Notification: Performance of preBalanceInitialSystem (initialization): time 8.681e-05/0.1233, allocations: 40.2 kB / 0.4903 GB, free: 9.227 MB / 366.1 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.000137/0.1235, allocations: 101.2 kB / 0.4904 GB, free: 9.109 MB / 366.1 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.001527/0.125, allocations: 388.9 kB / 0.4908 GB, free: 8.707 MB / 366.1 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.353e-06/0.125, allocations: 4 kB / 0.4908 GB, free: 8.703 MB / 366.1 MB Notification: Performance of matching and sorting (n=28) (initialization): time 0.0003641/0.1253, allocations: 205.3 kB / 0.491 GB, free: 8.496 MB / 366.1 MB Notification: Performance of prepare postOptimizeDAE: time 2.515e-05/0.1254, allocations: 7.438 kB / 0.491 GB, free: 8.492 MB / 366.1 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.904e-06/0.1254, allocations: 7.938 kB / 0.491 GB, free: 8.484 MB / 366.1 MB Notification: Performance of postOpt tearingSystem (initialization): time 1.835e-05/0.1254, allocations: 4 kB / 0.491 GB, free: 8.48 MB / 366.1 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002178/0.1256, allocations: 51.91 kB / 0.491 GB, free: 8.43 MB / 366.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.092e-05/0.1256, allocations: 4 kB / 0.491 GB, free: 8.426 MB / 366.1 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.085e-05/0.1257, allocations: 12.19 kB / 0.4911 GB, free: 8.414 MB / 366.1 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.822e-05/0.1257, allocations: 8 kB / 0.4911 GB, free: 8.406 MB / 366.1 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 endoplasmicReticulum.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real p3_sbml:VARIABLE(start = 0.95 fixed = true ) type: Real Ca_Cyt.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real endoplasmicReticulum.CaER.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: 7 * 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 (28): * Single equations (assignments): 28 * 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 0.0003346/0.1261, allocations: 143.4 kB / 0.4912 GB, free: 8.258 MB / 366.1 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.814e-05/0.1261, allocations: 15.91 kB / 0.4912 GB, free: 8.242 MB / 366.1 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0003304/0.1264, allocations: 174.6 kB / 0.4914 GB, free: 8.066 MB / 366.1 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.06e-06/0.1264, allocations: 4 kB / 0.4914 GB, free: 8.062 MB / 366.1 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 4.889e-06/0.1265, allocations: 0 / 0.4914 GB, free: 8.062 MB / 366.1 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.436e-06/0.1265, allocations: 0 / 0.4914 GB, free: 8.062 MB / 366.1 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000803/0.1273, allocations: 0.5181 MB / 0.4919 GB, free: 7.488 MB / 366.1 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.403e-06/0.1273, allocations: 3.938 kB / 0.4919 GB, free: 7.484 MB / 366.1 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002028/0.1275, allocations: 35.98 kB / 0.4919 GB, free: 7.449 MB / 366.1 MB Notification: Performance of postOpt tearingSystem (simulation): time 2.835e-06/0.1275, allocations: 0 / 0.4919 GB, free: 7.449 MB / 366.1 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.375e-05/0.1275, allocations: 7.938 kB / 0.4919 GB, free: 7.441 MB / 366.1 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.117e-06/0.1275, allocations: 4 kB / 0.4919 GB, free: 7.438 MB / 366.1 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.443e-06/0.1275, allocations: 0 / 0.4919 GB, free: 7.438 MB / 366.1 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000432/0.1279, allocations: 318.7 kB / 0.4922 GB, free: 7.113 MB / 366.1 MB Notification: Performance of postOpt removeConstants (simulation): time 7.346e-05/0.128, allocations: 101 kB / 0.4923 GB, free: 6.996 MB / 366.1 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.41e-05/0.128, allocations: 0 / 0.4923 GB, free: 6.996 MB / 366.1 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001064/0.1281, allocations: 4 kB / 0.4923 GB, free: 6.992 MB / 366.1 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 2.87e-05/0.1281, allocations: 15.98 kB / 0.4924 GB, free: 6.977 MB / 366.1 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.075e-05/0.1282, allocations: 4 kB / 0.4924 GB, free: 6.973 MB / 366.1 MB Notification: Performance of sorting global known variables: time 9.459e-05/0.1283, allocations: 112.9 kB / 0.4925 GB, free: 6.863 MB / 366.1 MB Notification: Performance of sort global known variables: time 8e-08/0.1283, allocations: 0 / 0.4925 GB, free: 6.863 MB / 366.1 MB Notification: Performance of remove unused functions: time 0.0002862/0.1285, allocations: 36 kB / 0.4925 GB, free: 6.828 MB / 366.1 MB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 5 (V,endoplasmicReticulum.V,endoplasmicReticulum.CaER.n,Ca_Cyt.n,p3_sbml) * 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 (18): * Single equations (assignments): 18 * 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 0.0007623/0.1293, allocations: 0.8377 MB / 0.4933 GB, free: 5.965 MB / 366.1 MB Notification: Performance of simCode: created initialization part: time 0.0002887/0.1296, allocations: 131.9 kB / 0.4934 GB, free: 5.836 MB / 366.1 MB Notification: Performance of simCode: created event and clocks part: time 2.034e-06/0.1296, allocations: 0 / 0.4934 GB, free: 5.836 MB / 366.1 MB Notification: Performance of simCode: created simulation system equations: time 9.641e-05/0.1297, allocations: 63.91 kB / 0.4935 GB, free: 5.773 MB / 366.1 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002711/0.13, allocations: 14.03 kB / 0.4935 GB, free: 5.762 MB / 366.1 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002647/0.1326, allocations: 2.158 MB / 0.4956 GB, free: 3.492 MB / 366.1 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004057/0.133, allocations: 0.7358 MB / 0.4963 GB, free: 2.73 MB / 366.1 MB Notification: Performance of simCode: alias equations: time 8.124e-05/0.1331, allocations: 17.42 kB / 0.4964 GB, free: 2.707 MB / 366.1 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001068/0.1332, allocations: 63.41 kB / 0.4964 GB, free: 2.648 MB / 366.1 MB Notification: Performance of SimCode: time 5.31e-07/0.1332, allocations: 0 / 0.4964 GB, free: 2.648 MB / 366.1 MB Notification: Performance of buildModelFMU: Generate the FMI files: time 0.02728/0.1605, allocations: 3.346 MB / 0.4997 GB, free: 15.38 MB / 382.1 MB Notification: Performance of buildModelFMU: Generate platform static: time 8.057/8.217, allocations: 3.375 kB / 0.4997 GB, free: 15.38 MB / 382.1 MB " [Timeout remaining time 652] (rm -f BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; mkfifo BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe >> ../files/BioChem_BioChem.Examples.CaOscillations.Cytosol.sim & /home/hudson/saved_omc/OMSimulator/install/bin/OMSimulator --tempDir=temp_BioChem_BioChem_Examples_CaOscillations_Cytosol_fmu --startTime=0 --stopTime=120 --stepSize=120 --timeout=50 --tolerance=1e-06 BioChem_BioChem_Examples_CaOscillations_Cytosol.fmu > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1) [Timeout 52.5] [Calling sys.exit(0), Time elapsed: 10.802313848864287] Failed to read output from testmodel.py, exit status != 0: 8.288231403101236 8.306493194 8.185920155 Calling exit ...