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)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false)
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.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0059/0.005906, allocations: 102.7 kB / 15.73 MB, free: 6.047 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001153/0.001153, allocations: 189.1 kB / 16.67 MB, free: 5.969 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.414/1.414, allocations: 222.9 MB / 240.4 MB, free: 15.14 MB / 206.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.06346/0.06346, allocations: 12.29 MB / 302.8 MB, free: 3.215 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001108/0.001108, allocations: 60.12 kB / 420 MB, free: 17.03 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1112/0.1123, allocations: 52.08 MB / 472.1 MB, free: 12.95 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.004558/0.1169, allocations: 2.816 MB / 474.9 MB, free: 10.12 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0002689/0.1172, allocations: 195.2 kB / 475.1 MB, free: 9.93 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 8.419e-05/0.1173, allocations: 8 kB / 475.1 MB, free: 9.922 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 9.787e-05/0.1174, allocations: 31.67 kB / 475.1 MB, free: 9.891 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001388/0.1176, allocations: 47.58 kB / 475.2 MB, free: 9.844 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002274/0.1179, allocations: 51.88 kB / 475.2 MB, free: 9.793 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002013/0.1181, allocations: 187.2 kB / 475.4 MB, free: 9.609 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002363/0.1183, allocations: 103.6 kB / 475.5 MB, free: 9.504 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 8.18e-05/0.1184, allocations: 79.66 kB / 475.6 MB, free: 9.426 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001481/0.1186, allocations: 103.5 kB / 475.7 MB, free: 9.324 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 3.423e-05/0.1186, allocations: 20 kB / 475.7 MB, free: 9.305 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 3.471e-05/0.1186, allocations: 24 kB / 475.8 MB, free: 9.281 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 4.827e-05/0.1187, allocations: 51.77 kB / 475.8 MB, free: 9.23 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 9.594e-05/0.1188, allocations: 103.5 kB / 475.9 MB, free: 9.129 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002335/0.119, allocations: 231.2 kB / 476.1 MB, free: 8.902 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.901e-06/0.119, allocations: 0 / 476.1 MB, free: 8.902 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.342e-06/0.119, allocations: 3.938 kB / 476.1 MB, free: 8.898 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 8.155e-06/0.1191, allocations: 0 / 476.1 MB, free: 8.898 MB / 350.1 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 0.0007438/0.1198, allocations: 0.5032 MB / 476.6 MB, free: 8.344 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.377e-05/0.1199, allocations: 12.03 kB / 476.6 MB, free: 8.332 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.316e-05/0.1199, allocations: 16.75 kB / 476.7 MB, free: 8.316 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001593/0.1201, allocations: 192 kB / 476.9 MB, free: 8.09 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.04e-05/0.1201, allocations: 20.94 kB / 476.9 MB, free: 8.07 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.242e-05/0.1202, allocations: 28.28 kB / 476.9 MB, free: 8.043 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003584/0.1205, allocations: 209.4 kB / 477.1 MB, free: 7.836 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.525e-05/0.1206, allocations: 192 / 477.1 MB, free: 7.836 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.283e-05/0.1206, allocations: 11.94 kB / 477.1 MB, free: 7.824 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.989e-06/0.1206, allocations: 8 kB / 477.1 MB, free: 7.816 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002419/0.1208, allocations: 138.1 kB / 477.3 MB, free: 7.68 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001311/0.1222, allocations: 0.7554 MB / 478 MB, free: 6.863 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001697/0.1223, allocations: 106.5 kB / 478.1 MB, free: 6.75 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000245/0.1226, allocations: 96.78 kB / 478.2 MB, free: 6.652 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 1.815e-05/0.1226, allocations: 288 / 478.2 MB, free: 6.652 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.166e-05/0.1227, allocations: 38.56 kB / 478.3 MB, free: 6.605 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 1.222e-06/0.1227, allocations: 0 / 478.3 MB, free: 6.605 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.00122/0.1239, allocations: 0.5815 MB / 478.8 MB, free: 5.973 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.035e-05/0.1239, allocations: 55.41 kB / 478.9 MB, free: 5.906 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001209/0.1241, allocations: 154.4 kB / 479 MB, free: 5.738 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.16e-05/0.1241, allocations: 25.7 kB / 479.1 MB, free: 5.707 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 8.534e-05/0.1242, allocations: 155.9 kB / 479.2 MB, free: 5.551 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 4.43e-05/0.1242, allocations: 63.11 kB / 479.3 MB, free: 5.488 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.841e-05/0.1243, allocations: 45.61 kB / 479.3 MB, free: 5.438 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001112/0.1244, allocations: 326.8 kB / 479.6 MB, free: 5.109 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.994e-05/0.1245, allocations: 44.2 kB / 479.7 MB, free: 5.066 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001194/0.1246, allocations: 94.44 kB / 479.8 MB, free: 4.953 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001233/0.1259, allocations: 392.5 kB / 480.2 MB, free: 4.547 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.282e-06/0.1259, allocations: 0 / 480.2 MB, free: 4.547 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002923/0.1262, allocations: 208.5 kB / 480.4 MB, free: 4.34 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.55e-05/0.1262, allocations: 11.94 kB / 480.4 MB, free: 4.328 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.791e-06/0.1262, allocations: 0 / 480.4 MB, free: 4.328 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.033e-05/0.1263, allocations: 7.938 kB / 480.4 MB, free: 4.32 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001965/0.1265, allocations: 55.91 kB / 480.4 MB, free: 4.266 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.063e-06/0.1265, allocations: 0 / 480.4 MB, free: 4.266 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.815e-05/0.1266, allocations: 8 kB / 480.4 MB, free: 4.258 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.464e-05/0.1266, allocations: 12.19 kB / 480.5 MB, free: 4.246 MB / 350.1 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 0.0002425/0.1268, allocations: 155.3 kB / 480.6 MB, free: 4.086 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.793e-05/0.1269, allocations: 15.81 kB / 480.6 MB, free: 4.07 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002826/0.1272, allocations: 180.6 kB / 480.8 MB, free: 3.891 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.375e-06/0.1272, allocations: 0 / 480.8 MB, free: 3.891 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.819e-06/0.1272, allocations: 0 / 480.8 MB, free: 3.891 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.122e-06/0.1272, allocations: 3.984 kB / 480.8 MB, free: 3.887 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007077/0.1279, allocations: 0.518 MB / 481.3 MB, free: 3.312 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.683e-06/0.1279, allocations: 0 / 481.3 MB, free: 3.312 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000182/0.1281, allocations: 31.92 kB / 481.4 MB, free: 3.281 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 2.354e-06/0.1281, allocations: 0 / 481.4 MB, free: 3.281 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.888e-05/0.1282, allocations: 8 kB / 481.4 MB, free: 3.273 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.603e-06/0.1282, allocations: 4 kB / 481.4 MB, free: 3.27 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.183e-06/0.1282, allocations: 0 / 481.4 MB, free: 3.27 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000375/0.1286, allocations: 309.8 kB / 481.7 MB, free: 2.953 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.126e-05/0.1286, allocations: 92.91 kB / 481.8 MB, free: 2.844 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.246e-05/0.1286, allocations: 0 / 481.8 MB, free: 2.844 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.734e-05/0.1287, allocations: 8.062 kB / 481.8 MB, free: 2.836 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.056e-05/0.1288, allocations: 11.92 kB / 481.8 MB, free: 2.824 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.286e-05/0.1288, allocations: 8 kB / 481.8 MB, free: 2.816 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 6.905e-05/0.1289, allocations: 111.2 kB / 481.9 MB, free: 2.707 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.1289, allocations: 4 kB / 481.9 MB, free: 2.703 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0002759/0.1292, allocations: 36 kB / 481.9 MB, free: 2.668 MB / 350.1 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 9.195e-05/0.1293, allocations: 95.78 kB / 482 MB, free: 2.566 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0002748/0.1295, allocations: 143.7 kB / 482.2 MB, free: 2.426 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.695e-06/0.1296, allocations: 3.938 kB / 482.2 MB, free: 2.422 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 8.65e-05/0.1296, allocations: 70.31 kB / 482.2 MB, free: 2.355 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002687/0.1299, allocations: 16 kB / 482.3 MB, free: 2.34 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0007978/0.1307, allocations: 0.5086 MB / 482.8 MB, free: 1.805 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002924/0.131, allocations: 0.7397 MB / 483.5 MB, free: 1.039 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 6.725e-05/0.1311, allocations: 17.36 kB / 483.5 MB, free: 1.016 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.188e-05/0.1312, allocations: 19.44 kB / 483.5 MB, free: 1 MB / 350.1 MB
Notification: Performance of SimCode: time 2.31e-07/0.1312, allocations: 0 / 483.5 MB, free: 1 MB / 350.1 MB
Notification: Performance of Templates: time 0.004325/0.1355, allocations: 1.444 MB / 485 MB, free: 15.57 MB / 366.1 MB
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile
(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 & ./BioChem_BioChem.Examples.CaOscillations.Cytosol  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1)