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Submit Smoldyn 2.74 #713

Open
ssandrews opened this issue Jan 22, 2025 · 7 comments
Open

Submit Smoldyn 2.74 #713

ssandrews opened this issue Jan 22, 2025 · 7 comments
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Invalid This doesn't seem right Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry

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@ssandrews
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id: smoldyn
version: "2.74"
specificationsUrl: https://raw.githubusercontent.com/ssandrews/Smoldyn/0a1d577ac153fad15fee91722db72ef260139877/biosimulators.json
specificationsPatch:
version: "2.74"
image:
url: ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74
digest: "sha256:6b4a481f03f45da027f39bafc362315308794a4ff5229755edaf0dfe37af56cf"
validateImage: true
commitSimulator: true
@ssandrews ssandrews added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Jan 22, 2025
@biosimulators-daemon
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Thank you @ssandrews for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

@biosimulators-daemon
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The specifications of your simulator is valid!

@biosimulators-daemon
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Summary of tests

  • Executed 74 test cases

  • Passed 7 test cases:

    • cli.CliDescribesSupportedEnvironmentVariablesInline
    • cli.CliDisplaysHelpInline
    • cli.CliDisplaysVersionInformationInline
    • docker_image.DeclaresSupportedEnvironmentVariables
    • docker_image.DefaultUserIsRoot
    • docker_image.HasBioContainersLabels
    • docker_image.HasOciLabels

  • Failed 19 test cases:

    • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
    • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
    • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
    • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
    • docker_image.SingularityImageExecutesSimulationsSuccessfully
    • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
    • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
    • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
    • results_report.SimulatorGeneratesReportsOfSimulationResults
    • sedml.SimulatorProducesLinear2DPlots
    • sedml.SimulatorProducesLogarithmic2DPlots
    • sedml.SimulatorProducesMultiplePlots
    • sedml.SimulatorSupportsAlgorithmParameters
    • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
    • sedml.SimulatorSupportsMultipleReportsPerSedDocument
    • sedml.SimulatorSupportsMultipleTasksPerSedDocument
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

  • Skipped 48 test cases:

    • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
    • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
    • published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
    • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
    • published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
    • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
    • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
    • published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
    • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
    • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
    • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
    • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
    • published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
    • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
    • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
    • sedml.SimulatorProducesLinear3DPlots
    • sedml.SimulatorProducesLogarithmic3DPlots
    • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
    • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
    • sedml.SimulatorSupportsComputeModelChanges
    • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
    • sedml.SimulatorSupportsDataSetsWithDifferentShapes
    • sedml.SimulatorSupportsModelAttributeChanges
    • sedml.SimulatorSupportsRepeatedTasksWithChanges
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
    • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
    • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
    • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
    • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
    • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
    • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
    • sedml.SimulatorSupportsSubstitutingAlgorithms
    • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

@biosimulators-daemon
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Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (4.0 s)

Test that SED documents in nested directories can be executed

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

�[31mlist index out of range�[0m
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (4.0 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

�[31mlist index out of range�[0m
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (125.7 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp8xhu59l_/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp8xhu59l_/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp8xhu59l_/model.txt

 starting clock time: Wed Jan 22 20:34:34 2025

 3 dimensions

 Random number seed: 1737578074

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

simulation__copy.sedml

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp8xhu59l_/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp8xhu59l_/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp8xhu59l_/model.txt

 starting clock time: Wed Jan 22 20:36:03 2025

 3 dimensions

 Random number seed: 1737578163

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmp8xhu59l_/modelout.txt'.�[0m
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (115.2 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpm7ui1j7y/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpm7ui1j7y/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpm7ui1j7y/model.txt

 starting clock time: Wed Jan 22 20:36:40 2025

 3 dimensions

 Random number seed: 1737578200

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

simulation__copy.sedml

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpm7ui1j7y/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpm7ui1j7y/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpm7ui1j7y/model.txt

 starting clock time: Wed Jan 22 20:38:00 2025

 3 dimensions

 Random number seed: 1737578280

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpm7ui1j7y/modelout.txt'.�[0m
docker_image.SingularityImageExecutesSimulationsSuccessfully (125.5 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

The Docker image could not be successfully executed as a Singularity image (error code 1:
  --------------------------------------------------------------
  Running Smoldyn 2.74
  
  CONFIGURATION FILE
   Path: '/tmp/tmpkdptvst2/'
   Name: 'model.txt'
   Reading file: '/tmp/tmpkdptvst2/model.txt'
   Loaded file successfully
   setting up molecules
   setting up virtual boxes
   setting up reactions
   setting up graphics
  
  SIMULATION PARAMETERS
   file: /tmp/tmpkdptvst2/model.txt
   starting clock time: Wed Jan 22 20:32:11 2025
   3 dimensions
   Random number seed: 1737577931
   Time from 0 to 20 step 0.001
  
  GRAPHICS PARAMETERS
   No graphical output
  
  WALL PARAMETERS
   wall 0: dimension x, at -100, periodic
   wall 1: dimension x, at 100, periodic
   wall 2: dimension y, at -100, periodic
   wall 3: dimension y, at 100, periodic
   wall 4: dimension z, at -10, periodic
   wall 5: dimension z, at 10, periodic
   system volume: 800000
   system corners : (-100,-100,-10) and (100,100,10)
  
  MOLECULE PARAMETERS
   3 molecule lists:
    rlist, flist, unassignedlist
   2 species defined:
   rabbit:
    solution: difc=100, rms step=0.447214, list=rlist, number=1000
    solution: color= 1,0,0, display size= 2
   fox:
    solution: difc=100, rms step=0.447214, list=flist, number=1000
    solution: color= 0,0.5,0, display size= 3
   Overall spatial resolution: 0.447214
  
  SURFACE PARAMETERS
   No internal surfaces
  
  RUNTIME COMMAND INTERPRETER
   No output files
   No output data tables
   No commands
  
  VIRTUAL BOX PARAMETERS
   2352 boxes
   Number of boxes on each side: 28 28 3
   Requested molecules per box: 1
   Box dimensions:  7.14286 7.14286 6.66667
   Box volumes: 340.136
   Molecules per box= 0.85034
  
  ORDER 0 REACTION PARAMETERS
   No reactions of order 0
  
  ORDER 1 REACTION PARAMETERS
   2 reactions defined
   Reactive molecule lists: rlist flist
   Reactants, sorted by molecule species:
    rabbit : r1
    fox : r3
   Reaction details:
    Reaction r1: rabbit -> rabbit + rabbit
     requested and actual rate constants : 10, 10
     characteristic time: 0.1
     conditional reaction probability per time step: 0.00995017
     unbinding radius: 0
    Reaction r3: fox -> 0
     requested and actual rate constants : 10, 10
     characteristic time: 0.1
     conditional reaction probability per time step: 0.00995017
  
  ORDER 2 REACTION PARAMETERS
   1 reactions defined
   Reactive molecule lists: flist+rlist rlist+flist
   Reactants, sorted by molecule species:
    rabbit+fox : r2
   Reaction details:
    Reaction r2: rabbit + fox -> fox + fox
     requested and actual rate constants : 8000, 8000.09
     characteristic time: 0.199998
     binding radius: 3.55359
     unbinding radius: 0
  
  RULES:
   none
  
  PARAMETER CHECK
   WARNING: reactive volume of rabbit is 23.4963 % of total volume
   WARNING: reactive volume of fox is 23.4963 % of total volume
   WARNING: total reactive volume is a large fraction of total volume
   No errors
   3 total warnings
  
  Simulating
  --------------------------------------------------------------
  Running Smoldyn 2.74
  
  CONFIGURATION FILE
   Path: '/tmp/tmpkdptvst2/'
   Name: 'model.txt'
   Reading file: '/tmp/tmpkdptvst2/model.txt'
   Loaded file successfully
   setting up molecules
   setting up virtual boxes
   setting up reactions
   setting up graphics
  
  SIMULATION PARAMETERS
   file: /tmp/tmpkdptvst2/model.txt
   starting clock time: Wed Jan 22 20:33:27 2025
   3 dimensions
   Random number seed: 1737578007
   Time from 0 to 20 step 0.001
  
  GRAPHICS PARAMETERS
   No graphical output
  
  WALL PARAMETERS
   wall 0: dimension x, at -100, periodic
   wall 1: dimension x, at 100, periodic
   wall 2: dimension y, at -100, periodic
   wall 3: dimension y, at 100, periodic
   wall 4: dimension z, at -10, periodic
   wall 5: dimension z, at 10, periodic
   system volume: 800000
   system corners : (-100,-100,-10) and (100,100,10)
  
  MOLECULE PARAMETERS
   3 molecule lists:
    rlist, flist, unassignedlist
   2 species defined:
   rabbit:
    solution: difc=100, rms step=0.447214, list=rlist, number=1000
    solution: color= 1,0,0, display size= 2
   fox:
    solution: difc=100, rms step=0.447214, list=flist, number=1000
    solution: color= 0,0.5,0, display size= 3
   Overall spatial resolution: 0.447214
  
  SURFACE PARAMETERS
   No internal surfaces
  
  RUNTIME COMMAND INTERPRETER
   No output files
   No output data tables
   No commands
  
  VIRTUAL BOX PARAMETERS
   2352 boxes
   Number of boxes on each side: 28 28 3
   Requested molecules per box: 1
   Box dimensions:  7.14286 7.14286 6.66667
   Box volumes: 340.136
   Molecules per box= 0.85034
  
  ORDER 0 REACTION PARAMETERS
   No reactions of order 0
  
  ORDER 1 REACTION PARAMETERS
   2 reactions defined
   Reactive molecule lists: rlist flist
   Reactants, sorted by molecule species:
    rabbit : r1
    fox : r3
   Reaction details:
    Reaction r1: rabbit -> rabbit + rabbit
     requested and actual rate constants : 10, 10
     characteristic time: 0.1
     conditional reaction probability per time step: 0.00995017
     unbinding radius: 0
    Reaction r3: fox -> 0
     requested and actual rate constants : 10, 10
     characteristic time: 0.1
     conditional reaction probability per time step: 0.00995017
  
  ORDER 2 REACTION PARAMETERS
   1 reactions defined
   Reactive molecule lists: flist+rlist rlist+flist
   Reactants, sorted by molecule species:
    rabbit+fox : r2
   Reaction details:
    Reaction r2: rabbit + fox -> fox + fox
     requested and actual rate constants : 8000, 8000.09
     characteristic time: 0.199998
     binding radius: 3.55359
     unbinding radius: 0
  
  RULES:
   none
  
  PARAMETER CHECK
   WARNING: reactive volume of rabbit is 23.4963 % of total volume
   WARNING: reactive volume of fox is 23.4963 % of total volume
   WARNING: total reactive volume is a large fraction of total volume
   No errors
   3 total warnings
  
  GENERATING A SIMULARIUM FILE ------------- 
  []
  generated polydata
  manifest.xml
  reports.h5
  expected-results.json
  metadata.rdf
  simulation.sedml
  model.txt
  Writing trajectory to VTK -------------
  Successfully wrote VTK file to /root/simulation.vtk.
  Reading Smoldyn Data -------------

Log: None

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (106.9 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpxrwb0uyt/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpxrwb0uyt/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpxrwb0uyt/model.txt

 starting clock time: Wed Jan 22 21:23:19 2025

 3 dimensions

 Random number seed: 1737580999

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpxrwb0uyt/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpxrwb0uyt/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpxrwb0uyt/model.txt

 starting clock time: Wed Jan 22 21:24:31 2025

 3 dimensions

 Random number seed: 1737581071

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

�[0m�[31m2025-01-22 21:25:01.773 ( 102.980s) [    7FA061DE4740]  vtkPolyDataWriter.cxx:102    ERR| vtkPolyDataWriter (0x563c9388b670): Ran out of disk space; deleting file: /tmp/out/simulation.vtk�[0m

ERROR:root:Ran out of disk space; deleting file: /tmp/out/simulation.vtk

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpxrwb0uyt/modelout.txt'.�[0m
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (95.8 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpme3vyu4b/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpme3vyu4b/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpme3vyu4b/model.txt

 starting clock time: Wed Jan 22 21:25:06 2025

 3 dimensions

 Random number seed: 1737581106

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

/xvfb-startup.sh: line 10:    18 Killed                  "$@"
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (180.2 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpbchg8esa/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpbchg8esa/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpbchg8esa/model.txt

 starting clock time: Wed Jan 22 21:26:43 2025

 3 dimensions

 Random number seed: 1737581203

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpbchg8esa/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpbchg8esa/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpbchg8esa/model.txt

 starting clock time: Wed Jan 22 21:29:02 2025

 3 dimensions

 Random number seed: 1737581342

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

�[0m�[31m2025-01-22 21:29:36.805 ( 173.959s) [    7FB12D2B5740]  vtkPolyDataWriter.cxx:102    ERR| vtkPolyDataWriter (0x55b35a2e67d0): Ran out of disk space; deleting file: /tmp/out/simulation.vtk�[0m

ERROR:root:Ran out of disk space; deleting file: /tmp/out/simulation.vtk

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpbchg8esa/modelout.txt'.�[0m
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (122.2 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp1j6l0kvo/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp1j6l0kvo/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp1j6l0kvo/model.txt

 starting clock time: Wed Jan 22 21:29:43 2025

 3 dimensions

 Random number seed: 1737581383

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp1j6l0kvo/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp1j6l0kvo/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp1j6l0kvo/model.txt

 starting clock time: Wed Jan 22 21:31:11 2025

 3 dimensions

 Random number seed: 1737581471

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

�[0m�[31m2025-01-22 21:31:40.009 ( 116.797s) [    7FACED7EC740]  vtkPolyDataWriter.cxx:102    ERR| vtkPolyDataWriter (0x55d993bd6920): Ran out of disk space; deleting file: /tmp/out/simulation.vtk�[0m

ERROR:root:Ran out of disk space; deleting file: /tmp/out/simulation.vtk

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmp1j6l0kvo/modelout.txt'.�[0m
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (125.5 s)

Required model formats and simulation algorithms for SED tasks:

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpv0grqdfw/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpv0grqdfw/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpv0grqdfw/model.txt

 starting clock time: Wed Jan 22 21:31:45 2025

 3 dimensions

 Random number seed: 1737581505

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpv0grqdfw/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpv0grqdfw/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpv0grqdfw/model.txt

 starting clock time: Wed Jan 22 21:33:16 2025

 3 dimensions

 Random number seed: 1737581596

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

�[0m�[31m2025-01-22 21:33:46.466 ( 121.478s) [    7FDFCD30F740]  vtkPolyDataWriter.cxx:102    ERR| vtkPolyDataWriter (0x55fa71573c70): Ran out of disk space; deleting file: /tmp/out/simulation.vtk�[0m

ERROR:root:Ran out of disk space; deleting file: /tmp/out/simulation.vtk

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpv0grqdfw/modelout.txt'.�[0m
results_report.SimulatorGeneratesReportsOfSimulationResults (111.0 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpk6x0n4qn/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpk6x0n4qn/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpk6x0n4qn/model.txt

 starting clock time: Wed Jan 22 21:21:28 2025

 3 dimensions

 Random number seed: 1737580888

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpk6x0n4qn/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpk6x0n4qn/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpk6x0n4qn/model.txt

 starting clock time: Wed Jan 22 21:22:43 2025

 3 dimensions

 Random number seed: 1737580963

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

�[0m�[31m2025-01-22 21:23:14.868 ( 107.089s) [    7F2A25078740]  vtkPolyDataWriter.cxx:102    ERR| vtkPolyDataWriter (0x5587368cd850): Ran out of disk space; deleting file: /tmp/out/simulation.vtk�[0m

ERROR:root:Ran out of disk space; deleting file: /tmp/out/simulation.vtk

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpk6x0n4qn/modelout.txt'.�[0m
sedml.SimulatorProducesLinear2DPlots (114.6 s)

Test that a simulator produces linear 2D plots

Exception:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpkvlgq9ep/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpkvlgq9ep/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpkvlgq9ep/model.txt

 starting clock time: Wed Jan 22 20:42:41 2025

 3 dimensions

 Random number seed: 1737578561

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, period ...

@biosimulators-daemon
Copy link

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.2 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

@biosimulators-daemon
Copy link

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_3240 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000086

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000027

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log: None

published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9000 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (128.4 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp4ljfhq8t/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp4ljfhq8t/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp4ljfhq8t/model.txt

 starting clock time: Wed Jan 22 20:38:36 2025

 3 dimensions

 Random number seed: 1737578316

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp4ljfhq8t/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp4ljfhq8t/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp4ljfhq8t/model.txt

 starting clock time: Wed Jan 22 20:40:04 2025

 3 dimensions

 Random number seed: 1737578404

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmp4ljfhq8t/modelout.txt'.�[0m
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (116.3 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.

Reason for skip:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmplbzo0gka/'

 Name: 'model.txt'

 Reading file: '/tmp/tmplbzo0gka/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmplbzo0gka/model.txt

 starting clock time: Wed Jan 22 20:40:44 2025

 3 dimensions

 Random number seed: 1737578444

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmplbzo0gka/'

 Name: 'model.txt'

 Reading file: '/tmp/tmplbzo0gka/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmplbzo0gka/model.txt

 starting clock time: Wed Jan 22 20:42:04 2025

 3 dimensions

 Random number seed: 1737578524

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmplbzo0gka/modelout.txt'.�[0m
sedml.SimulatorProducesLinear3DPlots (0.1 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.1 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.1 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsComputeModelChanges (0.1 s)

Test that a simulator supports compute model changes

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (133.4 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp8hk37_47/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp8hk37_47/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp8hk37_47/model.txt

 starting clock time: Wed Jan 22 20:50:35 2025

 3 dimensions

 Random number seed: 1737579035

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp8hk37_47/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp8hk37_47/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp8hk37_47/model.txt

 starting clock time: Wed Jan 22 20:52:08 2025

 3 dimensions

 Random number seed: 1737579128

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmp8hk37_47/modelout.txt'.�[0m
sedml.SimulatorSupportsDataSetsWithDifferentShapes (134.9 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpuos14j30/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpuos14j30/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpuos14j30/model.txt

 starting clock time: Wed Jan 22 20:52:47 2025

 3 dimensions

 Random number seed: 1737579167

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpuos14j30/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpuos14j30/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpuos14j30/model.txt

 starting clock time: Wed Jan 22 20:54:22 2025

 3 dimensions

 Random number seed: 1737579262

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpuos14j30/modelout.txt'.�[0m
sedml.SimulatorSupportsModelAttributeChanges (0.1 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.1 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.1 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

This test is only implemented for XML-based model languages. Please contact the BioSimulators Team to discuss implementing tests for additional languages.

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (110.8 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp8zyjg6sa/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp8zyjg6sa/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp8zyjg6sa/model.txt

 starting clock time: Wed Jan 22 21:01:02 2025

 3 dimensions

 Random number seed: 1737579662

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmp8zyjg6sa/'

 Name: 'model.txt'

 Reading file: '/tmp/tmp8zyjg6sa/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmp8zyjg6sa/model.txt

 starting clock time: Wed Jan 22 21:02:17 2025

 3 dimensions

 Random number seed: 1737579737

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

�[0m�[31m2025-01-22 21:02:48.210 ( 106.723s) [    7F7BBF72E740]  vtkPolyDataWriter.cxx:102    ERR| vtkPolyDataWriter (0x559b6dfeca70): Ran out of disk space; deleting file: /tmp/out/simulation.vtk�[0m

ERROR:root:Ran out of disk space; deleting file: /tmp/out/simulation.vtk

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmp8zyjg6sa/modelout.txt'.�[0m
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (176.3 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpc9dx2khb/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpc9dx2khb/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpc9dx2khb/model.txt

 starting clock time: Wed Jan 22 21:02:52 2025

 3 dimensions

 Random number seed: 1737579772

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Simulating

Libsmoldyn notification from smolRunSim: Simulation complete

[]

generated polydata

manifest.xml

expected-results.json

reports.h5

model.txt

simulation.sedml

metadata.rdf

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmpc9dx2khb/'

 Name: 'model.txt'

 Reading file: '/tmp/tmpc9dx2khb/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmpc9dx2khb/model.txt

 starting clock time: Wed Jan 22 21:05:07 2025

 3 dimensions

 Random number seed: 1737579907

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, periodic

 wall 1: dimension x, at 100, periodic

 wall 2: dimension y, at -100, periodic

 wall 3: dimension y, at 100, periodic

 wall 4: dimension z, at -10, periodic

 wall 5: dimension z, at 10, periodic

 system volume: 800000

 system corners : (-100,-100,-10) and (100,100,10)



MOLECULE PARAMETERS

 3 molecule lists:

  rlist, flist, unassignedlist

 2 species defined:

 rabbit:

  solution: difc=100, rms step=0.447214, list=rlist, number=1000

  solution: color= 1,0,0, display size= 2

 fox:

  solution: difc=100, rms step=0.447214, list=flist, number=1000

  solution: color= 0,0.5,0, display size= 3

 Overall spatial resolution: 0.447214



SURFACE PARAMETERS

 No internal surfaces



RUNTIME COMMAND INTERPRETER

 No output files

 No output data tables

 No commands



VIRTUAL BOX PARAMETERS

 2352 boxes

 Number of boxes on each side: 28 28 3

 Requested molecules per box: 1

 Box dimensions:  7.14286 7.14286 6.66667

 Box volumes: 340.136

 Molecules per box= 0.85034



ORDER 0 REACTION PARAMETERS

 No reactions of order 0



ORDER 1 REACTION PARAMETERS

 2 reactions defined

 Reactive molecule lists: rlist flist

 Reactants, sorted by molecule species:

  rabbit : r1

  fox : r3

 Reaction details:

  Reaction r1: rabbit -> rabbit + rabbit

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017

   unbinding radius: 0

  Reaction r3: fox -> 0

   requested and actual rate constants : 10, 10

   characteristic time: 0.1

   conditional reaction probability per time step: 0.00995017



ORDER 2 REACTION PARAMETERS

 1 reactions defined

 Reactive molecule lists: flist+rlist rlist+flist

 Reactants, sorted by molecule species:

  rabbit+fox : r2

 Reaction details:

  Reaction r2: rabbit + fox -> fox + fox

   requested and actual rate constants : 8000, 8000.09

   characteristic time: 0.199998

   binding radius: 3.55359

   unbinding radius: 0



RULES:

 none



PARAMETER CHECK

 WARNING: reactive volume of rabbit is 23.4963 % of total volume

 WARNING: reactive volume of fox is 23.4963 % of total volume

 WARNING: total reactive volume is a large fraction of total volume

 No errors

 3 total warnings



Writing trajectory to VTK -------------

�[0m�[31m2025-01-22 21:05:43.318 ( 170.802s) [    7F91EDE3A740]  vtkPolyDataWriter.cxx:102    ERR| vtkPolyDataWriter (0x558bd8dc0b40): Ran out of disk space; deleting file: /tmp/out/simulation.vtk�[0m

ERROR:root:Ran out of disk space; deleting file: /tmp/out/simulation.vtk

Successfully wrote VTK file to /tmp/out/simulation.vtk.

Reading Smoldyn Data -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpc9dx2khb/modelout.txt'.�[0m
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (117.8 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.74' could not execute the archive:

  Unknown error

Log:

GENERATING A SIMULARIUM FILE ------------- 

--------------------------------------------------------------

Running Smoldyn 2.74



CONFIGURATION FILE

 Path: '/tmp/tmprk6d4ghv/'

 Name: 'model.txt'

 Reading file: '/tmp/tmprk6d4ghv/model.txt'

 Loaded file successfully

 setting up molecules

 setting up virtual boxes

 setting up reactions

 setting up graphics



SIMULATION PARAMETERS

 file: /tmp/tmprk6d4ghv/model.txt

 starting clock time: Wed Jan 22 21:05:50 2025

 3 dimensions

 Random number seed: 1737579950

 Time from 0 to 20 step 0.001



GRAPHICS PARAMETERS

 No graphical output



WALL PARAMETERS

 wall 0: dimension x, at -100, peri ...

@biosimulators-daemon
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- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/12916465330). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/12916465330).

@biosimulators-daemon biosimulators-daemon added the Invalid This doesn't seem right label Jan 22, 2025
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Invalid This doesn't seem right Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry
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@ssandrews @biosimulators-daemon