[0;36mThank you for using runBioSimulations![0m

[0;36m================================================ Loading Singularity ================================================[0m

[0;36m=================================================== Set up storage ==================================================[0m

[0;36m========================================== Downloading COMBINE/OMEX archive =========================================[0m
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[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================[0m
INFO:    Using cached SIF image
10:45:17 [main] WARN  cbit.vcell.resource.PropertyLoader - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory
ServerID=7.3.0.16, SoftwareVersion=unknown
VCell CLI input archive /root/archive.omex
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TempPath Created: /tmp/vcell_temp_73ade664-50b8-4883-8312-371a941355c05535249475297990719
Python 3.8.10
utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils
cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils
cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py
statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)

Successful translation of SED-ML file : biomodel_95676312.sedml
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name:  biomodel_95676312
sedml_name:  biomodel_95676312
content.location:  ./biomodel_95676312.sedml
content_filename:  /root/outputs/temp/./biomodel_95676312.sedml
Starting simulate all tasks... 
Model [id=ode, name=ode, language=urn:sedml:language:sbml, src=biomodel_95676312_ode.xml]
There are 0 changes.
UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Simulation0]
Task [modelReference=ode, name=Simulation0, simulationReference=Simulation0, getId()=tsk_0_0]
DataGenerator [math=org.jmathml.ASTRootNode@34f22f9d, name=time_tsk_0_0, getId()=time_tsk_0_0]
DataGenerator [math=org.jmathml.ASTRootNode@3d1848cc, name=dataGen_tsk_0_0_PDE_cAMP, getId()=dataGen_tsk_0_0_PDE_cAMP]
DataGenerator [math=org.jmathml.ASTRootNode@7dda48d9, name=dataGen_tsk_0_0_PDE_Cyto, getId()=dataGen_tsk_0_0_PDE_Cyto]
DataGenerator [math=org.jmathml.ASTRootNode@6e4566f1, name=dataGen_tsk_0_0_cAMP_best, getId()=dataGen_tsk_0_0_cAMP_best]
DataGenerator [math=org.jmathml.ASTRootNode@4b6e2263, name=dataGen_tsk_0_0_s0, getId()=dataGen_tsk_0_0_s0]
Plot2D [listOfCurves=[Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_cAMP, logX=false, logY=false, name=dataGen_tsk_0_0_PDE_cAMP, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PDE_cAMP], Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_PDE_Cyto, logX=false, logY=false, name=dataGen_tsk_0_0_PDE_Cyto, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PDE_Cyto], Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_cAMP_best, logX=false, logY=false, name=dataGen_tsk_0_0_cAMP_best, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_cAMP_best], Curve [id=curve_plot2d_Simulation0_dataGen_tsk_0_0_s0, logX=false, logY=false, name=dataGen_tsk_0_0_s0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_s0]], name=ode_Simulation0_plot]
org.jlibsedml.Report@958bc87d
org.jlibsedml.Report@5ce30dfd
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
new symbol is uM,   old symbol is umol.l-1
Succesful model import: SBML file /tmp/temp1054764690439584488.xml
10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique
10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique
10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique
10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique
10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique
10:45:25 [main] WARN  cbit.vcell.mapping.AbstractMathMapping - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique
/root/outputs/biomodel_95676312.sedml
false
cbit.vcell.solver.ode.CVodeSolverStandalone@3b4d50b
Finished: SOLVER_FINISHED:completed
Succesful execution: Model 'archive__ode' Task 'Simulation0'.
Running simulation tsk_0_0_Simulation0, 332 ms
-----------------------------------------------------------------------------------------------------
Ran 1 simulations for 1 biomodels.
Ignoring unsupported output `plot2d_Simulation0` while CSV generation.
Generating report `report_Simulation0`.
Generating report `__plot__plot2d_Simulation0`.
Ignoring unsupported output `plot2d_Simulation0` while generating idNamePlotsMap.
{'report_Simulation0': 'ode_Simulation0_plot', '__plot__plot2d_Simulation0': 'ode_Simulation0_plot', 'plot2d_Simulation0': 'ode_Simulation0_plot'}
__plot__plot2d_Simulation0
report   :  /root/outputs/./biomodel_95676312.sedml/report_Simulation0.csv
report_Simulation0
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.

[0;36m===================================================== Saving log ====================================================[0m
Completed 6.4 KiB/6.4 KiB (42.7 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/rawLog.txt
Completed 1.7 KiB/1.7 KiB (8.7 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/62a215894ffe186f420c45bb/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
