Submit BioNetGen 2.5.2

[biosimulators-daemon]

---

id: bionetgen version: 2.5.2 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BioNetGen/51e87c41eeec5a818410d3a917249a85cde72da1/biosimulators.json specificationsPatch: version: 2.5.2 image: url: ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2 validateImage: true commitSimulator: true

---

[biosimulators-daemon]

Thank you @biosimulators-daemon 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 is available here.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 35 test cases

• Passed 26 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels
  • exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • results_report.SimulatorGeneratesReportsOfSimultionResults
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Failed 0 test cases

• Skipped 9 test cases:

  • 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
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • 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-fbc/Escherichia-coli-core-metabolism

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (11.0 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

  The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

  If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

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

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.0 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'

  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:

sedml.SimulatorProducesLinear2DPlots (7.8 s)

Test that a simulator produces linear 2D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 3 curves

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmpplat2whd/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmpplat2whd/task.xml.
  Running NFsim on 8e7ff88f34cb
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpplat2whd/task.xml -o /tmp/tmpplat2whd/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpplat2whd/task.species -cb -seed 1663454709
  [simulation PID is: 14]
  starting NFsim v1.12.1...

  Seeding random number generator with: 1663454709
  reading xml file (/tmp/tmpplat2whd/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 3.380000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 4.648000e-03s  events (step): 141
  Sim time: 2.000000e+00    CPU time (total): 8.954000e-03s  events (step): 146
  Sim time: 3.000000e+00    CPU time (total): 1.311500e-02s  events (step): 155
  Sim time: 4.000000e+00    CPU time (total): 1.825600e-02s  events (step): 183
  Sim time: 5.000000e+00    CPU time (total): 2.198800e-02s  events (step): 130
  Sim time: 6.000000e+00    CPU time (total): 2.601800e-02s  events (step): 150
  Sim time: 7.000000e+00    CPU time (total): 3.014500e-02s  events (step): 149
  Sim time: 8.000000e+00    CPU time (total): 3.485000e-02s  events (step): 171
  Sim time: 9.000000e+00    CPU time (total): 3.893600e-02s  events (step): 155
  Sim time: 1.000000e+01    CPU time (total): 4.279400e-02s  events (step): 148
  Sim time: 1.100000e+01    CPU time (total): 4.698900e-02s  events (step): 150
  Sim time: 1.200000e+01    CPU time (total): 5.225200e-02s  events (step): 203
  Sim time: 1.300000e+01    CPU time (total): 5.698600e-02s  events (step): 182
  Sim time: 1.400000e+01    CPU time (total): 6.025600e-02s  events (step): 123
  Sim time: 1.500000e+01    CPU time (total): 6.453100e-02s  events (step): 160
  Sim time: 1.600000e+01    CPU time (total): 7.030100e-02s  events (step): 215
  Sim time: 1.700000e+01    CPU time (total): 7.546400e-02s  events (step): 195
  Sim time: 1.800000e+01    CPU time (total): 7.944200e-02s  events (step): 148
  Sim time: 1.900000e+01    CPU time (total): 8.372600e-02s  events (step): 162
  Sim time: 2.000000e+01    CPU time (total): 8.785700e-02s  events (step): 153
  Sim time: 2.100000e+01    CPU time (total): 9.223900e-02s  events (step): 164
  Sim time: 2.200000e+01    CPU time (total): 9.569400e-02s  events (step): 132
  Sim time: 2.300000e+01    CPU time (total): 1.009200e-01s  events (step): 190
  Sim time: 2.400000e+01    CPU time (total): 1.051460e-01s  events (step): 157
  Sim time: 2.500000e+01    CPU time (total): 1.093940e-01s  events (step): 158
  Sim time: 2.600000e+01    CPU time (total): 1.130410e-01s  events (step): 136
  Sim time: 2.700000e+01    CPU time (total): 1.169490e-01s  events (step): 146
  Sim time: 2.800000e+01    CPU time (total): 1.204020e-01s  events (step): 126
  Sim time: 2.900000e+01    CPU time (total): 1.247310e-01s  events (step): 159
  Sim time: 3.000000e+01    CPU time (total): 1.292100e-01s  events (step): 162
  Sim time: 3.100000e+01    CPU time (total): 1.333060e-01s  events (step): 157
  Sim time: 3.200000e+01    CPU time (total): 1.385060e-01s  events (step): 195
  Sim time: 3.300000e+01    CPU time (total): 1.425560e-01s  events (step): 153
  Sim time: 3.400000e+01    CPU time (total): 1.466800e-01s  events (step): 146
  Sim time: 3.500000e+01    CPU time (total): 1.515620e-01s  events (step): 180
  Sim time: 3.600000e+01    CPU time (total): 1.564140e-01s  events (step): 177
  Sim time: 3.700000e+01    CPU time (total): 1.600350e-01s  events (step): 131
  Sim time: 3.800000e+01    CPU time (total): 1.636450e-01s  events (step): 130
  Sim time: 3.900000e+01    CPU time (total): 1.672550e-01s  events (step): 136
  Sim time: 4.000000e+01    CPU time (total): 1.708910e-01s  events (step): 135
  Sim time: 4.100000e+01    CPU time (total): 1.755590e-01s  events (step): 169
  Sim time: 4.200000e+01    CPU time (total): 1.796970e-01s  events (step): 156
  Sim time: 4.300000e+01    CPU time (total): 1.837610e-01s  events (step): 144
  Sim time: 4.400000e+01    CPU time (total): 1.890740e-01s  events (step): 198
  Sim time: 4.500000e+01    CPU time (total): 1.934860e-01s  events (step): 166
  Sim time: 4.600000e+01    CPU time (total): 1.981390e-01s  events (step): 167
  Sim time: 4.700000e+01    CPU time (total): 2.034390e-01s  events (step): 191
  Sim time: 4.800000e+01    CPU time (total): 2.076870e-01s  events (step): 157
  Sim time: 4.900000e+01    CPU time (total): 2.118250e-01s  events (step): 149
  Sim time: 5.000000e+01    CPU time (total): 2.173100e-01s  events (step): 206
  Sim time: 5.100000e+01    CPU time (total): 2.215630e-01s  events (step): 154
  Sim time: 5.200000e+01    CPU time (total): 2.256520e-01s  events (step): 148
  Sim time: 5.300000e+01    CPU time (total): 2.298520e-01s  events (step): 161
  Sim time: 5.400000e+01    CPU time (total): 2.346250e-01s  events (step): 175
  Sim time: 5.500000e+01    CPU time (total): 2.397320e-01s  events (step): 181
  Sim time: 5.600000e+01    CPU time (total): 2.439500e-01s  events (step): 159
  Sim time: 5.700000e+01    CPU time (total): 2.471920e-01s  events (step): 120
  Sim time: 5.800000e+01    CPU time (total): 2.516460e-01s  events (step): 163
  Sim time: 5.900000e+01    CPU time (total): 2.563270e-01s  events (step): 175
  Sim time: 6.000000e+01    CPU time (total): 2.612840e-01s  events (step): 184
  Sim time: 6.100000e+01    CPU time (total): 2.651550e-01s  events (step): 145
  Sim time: 6.200000e+01    CPU time (total): 2.697740e-01s  events (step): 167
  Sim time: 6.300000e+01    CPU time (total): 2.735210e-01s  events (step): 133
  Sim time: 6.400000e+01    CPU time (total): 2.778960e-01s  events (step): 158
  Sim time: 6.500000e+01    CPU time (total): 2.825900e-01s  events (step): 176
  Sim time: 6.600000e+01    CPU time (total): 2.869510e-01s  events (step): 160
  Sim time: 6.700000e+01    CPU time (total): 2.912660e-01s  events (step): 157
  Sim time: 6.800000e+01    CPU time (total): 2.956110e-01s  events (step): 152
  Sim time: 6.900000e+01    CPU time (total): 2.991800e-01s  events (step): 135
  Sim time: 7.000000e+01    CPU time (total): 3.035380e-01s  events (step): 153
  Sim time: 7.100000e+01    CPU time (total): 3.081170e-01s  events (step): 166
  Sim time: 7.200000e+01    CPU time (total): 3.124180e-01s  events (step): 162
  Sim time: 7.300000e+01    CPU time (total): 3.160920e-01s  events (step): 131
  Sim time: 7.400000e+01    CPU time (total): 3.202030e-01s  events (step): 144
  Sim time: 7.500000e+01    CPU time (total): 3.251720e-01s  events (step): 183
  Sim time: 7.600000e+01    CPU time (total): 3.298550e-01s  events (step): 172
  Sim time: 7.700000e+01    CPU time (total): 3.347390e-01s  events (step): 182
  Sim time: 7.800000e+01    CPU time (total): 3.387080e-01s  events (step): 144
  Sim time: 7.900000e+01    CPU time (total): 3.432840e-01s  events (step): 167
  Sim time: 8.000000e+01    CPU time (total): 3.476060e-01s  events (step): 159
  Sim time: 8.100000e+01    CPU time (total): 3.518920e-01s  events (step): 158
  Sim time: 8.200000e+01    CPU time (total): 3.566220e-01s  events (step): 171
  Sim time: 8.300000e+01    CPU time (total): 3.610330e-01s  events (step): 166
  Sim time: 8.400000e+01    CPU time (total): 3.661130e-01s  events (step): 186
  Sim time: 8.500000e+01    CPU time (total): 3.711780e-01s  events (step): 194
  Sim time: 8.600000e+01    CPU time (total): 3.753130e-01s  events (step): 150
  Sim time: 8.700000e+01    CPU time (total): 3.783090e-01s  events (step): 107
  Sim time: 8.800000e+01    CPU time (total): 3.821340e-01s  events (step): 135
  Sim time: 8.900000e+01    CPU time (total): 3.858490e-01s  events (step): 142
  Sim time: 9.000000e+01    CPU time (total): 3.890870e-01s  events (step): 113
  Sim time: 9.100000e+01    CPU time (total): 3.928910e-01s  events (step): 135
  Sim time: 9.200000e+01    CPU time (total): 3.987810e-01s  events (step): 213
  Sim time: 9.300000e+01    CPU time (total): 4.039540e-01s  events (step): 184
  Sim time: 9.400000e+01    CPU time (total): 4.083200e-01s  events (step): 155
  Sim time: 9.500000e+01    CPU time (total): 4.125360e-01s  events (step): 150
  Sim time: 9.600000e+01    CPU time (total): 4.174400e-01s  events (step): 182
  Sim time: 9.700000e+01    CPU time (total): 4.213680e-01s  events (step): 140
  Sim time: 9.800000e+01    CPU time (total): 4.263270e-01s  events (step): 182
  Sim time: 9.900000e+01    CPU time (total): 4.304330e-01s  events (step): 149
  Sim time: 1.000000e+02    CPU time (total): 4.342100e-01s  events (step): 140

     You just simulated 15911 reactions in 4.343500e-01s
     ( 3.663175e+04 reactions/sec, 2.729872e-05 CPU seconds/event )
     Null events: 0   (2.729872e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 0.913542s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmpplat2whd/task.species
  Read 0 unique species of 73 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 1.28 s.
  Finished processing file /tmp/tmpplat2whd/task.bngl.
  CPU TIME: total 5.77 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (10.4 s)

Test that a simulator produces linear 3D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 3 surfaces

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmp5gc0bcda/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmp5gc0bcda/task.xml.
  Running NFsim on 539fa4d1fc33
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp5gc0bcda/task.xml -o /tmp/tmp5gc0bcda/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmp5gc0bcda/task.species -seed 795663570 -cb
  [simulation PID is: 15]
  starting NFsim v1.12.1...

  Seeding random number generator with: 795663570
  reading xml file (/tmp/tmp5gc0bcda/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 3.440000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 5.864000e-03s  events (step): 169
  Sim time: 2.000000e+00    CPU time (total): 9.855000e-03s  events (step): 146
  Sim time: 3.000000e+00    CPU time (total): 1.401300e-02s  events (step): 151
  Sim time: 4.000000e+00    CPU time (total): 1.772900e-02s  events (step): 136
  Sim time: 5.000000e+00    CPU time (total): 2.125500e-02s  events (step): 124
  Sim time: 6.000000e+00    CPU time (total): 2.592100e-02s  events (step): 176
  Sim time: 7.000000e+00    CPU time (total): 3.056700e-02s  events (step): 164
  Sim time: 8.000000e+00    CPU time (total): 3.435900e-02s  events (step): 142
  Sim time: 9.000000e+00    CPU time (total): 3.882000e-02s  events (step): 163
  Sim time: 1.000000e+01    CPU time (total): 4.453100e-02s  events (step): 207
  Sim time: 1.100000e+01    CPU time (total): 4.950800e-02s  events (step): 186
  Sim time: 1.200000e+01    CPU time (total): 5.335900e-02s  events (step): 141
  Sim time: 1.300000e+01    CPU time (total): 5.765200e-02s  events (step): 165
  Sim time: 1.400000e+01    CPU time (total): 6.172500e-02s  events (step): 151
  Sim time: 1.500000e+01    CPU time (total): 6.618900e-02s  events (step): 167
  Sim time: 1.600000e+01    CPU time (total): 7.032300e-02s  events (step): 153
  Sim time: 1.700000e+01    CPU time (total): 7.553200e-02s  events (step): 181
  Sim time: 1.800000e+01    CPU time (total): 7.980500e-02s  events (step): 148
  Sim time: 1.900000e+01    CPU time (total): 8.323500e-02s  events (step): 129
  Sim time: 2.000000e+01    CPU time (total): 8.797800e-02s  events (step): 176
  Sim time: 2.100000e+01    CPU time (total): 9.330900e-02s  events (step): 198
  Sim time: 2.200000e+01    CPU time (total): 9.645600e-02s  events (step): 120
  Sim time: 2.300000e+01    CPU time (total): 1.008400e-01s  events (step): 161
  Sim time: 2.400000e+01    CPU time (total): 1.051260e-01s  events (step): 157
  Sim time: 2.500000e+01    CPU time (total): 1.097780e-01s  events (step): 170
  Sim time: 2.600000e+01    CPU time (total): 1.142350e-01s  events (step): 166
  Sim time: 2.700000e+01    CPU time (total): 1.191250e-01s  events (step): 167
  Sim time: 2.800000e+01    CPU time (total): 1.238070e-01s  events (step): 171
  Sim time: 2.900000e+01    CPU time (total): 1.283300e-01s  events (step): 162
  Sim time: 3.000000e+01    CPU time (total): 1.320900e-01s  events (step): 134
  Sim time: 3.100000e+01    CPU time (total): 1.366360e-01s  events (step): 167
  Sim time: 3.200000e+01    CPU time (total): 1.408510e-01s  events (step): 158
  Sim time: 3.300000e+01    CPU time (total): 1.461340e-01s  events (step): 195
  Sim time: 3.400000e+01    CPU time (total): 1.511990e-01s  events (step): 188
  Sim time: 3.500000e+01    CPU time (total): 1.560420e-01s  events (step): 175
  Sim time: 3.600000e+01    CPU time (total): 1.601230e-01s  events (step): 152
  Sim time: 3.700000e+01    CPU time (total): 1.632120e-01s  events (step): 113
  Sim time: 3.800000e+01    CPU time (total): 1.671560e-01s  events (step): 146
  Sim time: 3.900000e+01    CPU time (total): 1.714030e-01s  events (step): 154
  Sim time: 4.000000e+01    CPU time (total): 1.759180e-01s  events (step): 165
  Sim time: 4.100000e+01    CPU time (total): 1.807300e-01s  events (step): 181
  Sim time: 4.200000e+01    CPU time (total): 1.856000e-01s  events (step): 178
  Sim time: 4.300000e+01    CPU time (total): 1.906080e-01s  events (step): 174
  Sim time: 4.400000e+01    CPU time (total): 1.952270e-01s  events (step): 163
  Sim time: 4.500000e+01    CPU time (total): 2.029360e-01s  events (step): 238
  Sim time: 4.600000e+01    CPU time (total): 2.164620e-01s  events (step): 483
  Sim time: 4.700000e+01    CPU time (total): 2.321210e-01s  events (step): 547
  Sim time: 4.800000e+01    CPU time (total): 2.485880e-01s  events (step): 677
  Sim time: 4.900000e+01    CPU time (total): 2.712390e-01s  events (step): 933
  Sim time: 5.000000e+01    CPU time (total): 2.935060e-01s  events (step): 928
  Sim time: 5.100000e+01    CPU time (total): 3.155750e-01s  events (step): 953
  Sim time: 5.200000e+01    CPU time (total): 3.432930e-01s  events (step): 1129
  Sim time: 5.300000e+01    CPU time (total): 3.730620e-01s  events (step): 1319
  Sim time: 5.400000e+01    CPU time (total): 4.040230e-01s  events (step): 1337
  Sim time: 5.500000e+01    CPU time (total): 4.308140e-01s  events (step): 1075
  Sim time: 5.600000e+01    CPU time (total): 4.562650e-01s  events (step): 1066
  Sim time: 5.700000e+01    CPU time (total): 4.832400e-01s  events (step): 1134
  Sim time: 5.800000e+01    CPU time (total): 5.095980e-01s  events (step): 1088
  Sim time: 5.900000e+01    CPU time (total): 5.414930e-01s  events (step): 1011
  Sim time: 6.000000e+01    CPU time (total): 6.109480e-01s  events (step): 1082
  Sim time: 6.100000e+01    CPU time (total): 6.835000e-01s  events (step): 1067
  Sim time: 6.200000e+01    CPU time (total): 7.556690e-01s  events (step): 1324
  Sim time: 6.300000e+01    CPU time (total): 8.430790e-01s  events (step): 1629
  Sim time: 6.400000e+01    CPU time (total): 9.200760e-01s  events (step): 1489
  Sim time: 6.500000e+01    CPU time (total): 9.906450e-01s  events (step): 1338
  Sim time: 6.600000e+01    CPU time (total): 1.051513e+00s  events (step): 1106
  Sim time: 6.700000e+01    CPU time (total): 1.117577e+00s  events (step): 1210
  Sim time: 6.800000e+01    CPU time (total): 1.190263e+00s  events (step): 1316
  Sim time: 6.900000e+01    CPU time (total): 1.260466e+00s  events (step): 1260
  Sim time: 7.000000e+01    CPU time (total): 1.331441e+00s  events (step): 1355
  Sim time: 7.100000e+01    CPU time (total): 1.402312e+00s  events (step): 1353
  Sim time: 7.200000e+01    CPU time (total): 1.465406e+00s  events (step): 1204
  Sim time: 7.300000e+01    CPU time (total): 1.539044e+00s  events (step): 1389
  Sim time: 7.400000e+01    CPU time (total): 1.611427e+00s  events (step): 1363
  Sim time: 7.500000e+01    CPU time (total): 1.684535e+00s  events (step): 1548
  Sim time: 7.600000e+01    CPU time (total): 1.750243e+00s  events (step): 1432
  Sim time: 7.700000e+01    CPU time (total): 1.818260e+00s  events (step): 1409
  Sim time: 7.800000e+01    CPU time (total): 1.872888e+00s  events (step): 1333
  Sim time: 7.900000e+01    CPU time (total): 1.928268e+00s  events (step): 1345
  Sim time: 8.000000e+01    CPU time (total): 1.985843e+00s  events (step): 1303
  Sim time: 8.100000e+01    CPU time (total): 2.037984e+00s  events (step): 1270
  Sim time: 8.200000e+01    CPU time (total): 2.096257e+00s  events (step): 1483
  Sim time: 8.300000e+01    CPU time (total): 2.149638e+00s  events (step): 1275
  Sim time: 8.400000e+01    CPU time (total): 2.204022e+00s  events (step): 1334
  Sim time: 8.500000e+01    CPU time (total): 2.256980e+00s  events (step): 1286
  Sim time: 8.600000e+01    CPU time (total): 2.315993e+00s  events (step): 1444
  Sim time: 8.700000e+01    CPU time (total): 2.369162e+00s  events (step): 1313
  Sim time: 8.800000e+01    CPU time (total): 2.423987e+00s  events (step): 1323
  Sim time: 8.900000e+01    CPU time (total): 2.483455e+00s  events (step): 1425
  Sim time: 9.000000e+01    CPU time (total): 2.540716e+00s  events (step): 1354
  Sim time: 9.100000e+01    CPU time (total): 2.600216e+00s  events (step): 1391
  Sim time: 9.200000e+01    CPU time (total): 2.653766e+00s  events (step): 1179
  Sim time: 9.300000e+01    CPU time (total): 2.707705e+00s  events (step): 1295
  Sim time: 9.400000e+01    CPU time (total): 2.764830e+00s  events (step): 1331
  Sim time: 9.500000e+01    CPU time (total): 2.819786e+00s  events (step): 1386
  Sim time: 9.600000e+01    CPU time (total): 2.871749e+00s  events (step): 1440
  Sim time: 9.700000e+01    CPU time (total): 2.925987e+00s  events (step): 1499
  Sim time: 9.800000e+01    CPU time (total): 2.973024e+00s  events (step): 1252
  Sim time: 9.900000e+01    CPU time (total): 3.022710e+00s  events (step): 1358
  Sim time: 1.000000e+02    CPU time (total): 3.075207e+00s  events (step): 1557

     You just simulated 76059 reactions in 3.075436e+00s
     ( 2.473113e+04 reactions/sec, 4.043487e-05 CPU seconds/event )
     Null events: 0   (4.043487e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 3.56203s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmp5gc0bcda/task.species
  Read 4 unique species of 75 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 3.92 s.
  Finished processing file /tmp/tmp5gc0bcda/task.bngl.
  CPU TIME: total 8.31 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (7.9 s)

Test that a simulator produces logarithmic 2D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 3 curves

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmpu7bbfvj6/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmpu7bbfvj6/task.xml.
  Running NFsim on d3f29cf17e8d
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpu7bbfvj6/task.xml -o /tmp/tmpu7bbfvj6/task.gdat -sim 100 -oSteps 100 -cb -ss /tmp/tmpu7bbfvj6/task.species -seed 1404860826
  [simulation PID is: 14]
  starting NFsim v1.12.1...

  Seeding random number generator with: 1404860826
  reading xml file (/tmp/tmpu7bbfvj6/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 3.200000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 4.267000e-03s  events (step): 116
  Sim time: 2.000000e+00    CPU time (total): 9.066000e-03s  events (step): 167
  Sim time: 3.000000e+00    CPU time (total): 1.352000e-02s  events (step): 162
  Sim time: 4.000000e+00    CPU time (total): 1.717700e-02s  events (step): 133
  Sim time: 5.000000e+00    CPU time (total): 2.192000e-02s  events (step): 172
  Sim time: 6.000000e+00    CPU time (total): 2.629200e-02s  events (step): 164
  Sim time: 7.000000e+00    CPU time (total): 3.149900e-02s  events (step): 189
  Sim time: 8.000000e+00    CPU time (total): 3.674800e-02s  events (step): 194
  Sim time: 9.000000e+00    CPU time (total): 4.139100e-02s  events (step): 162
  Sim time: 1.000000e+01    CPU time (total): 4.577400e-02s  events (step): 157
  Sim time: 1.100000e+01    CPU time (total): 5.050700e-02s  events (step): 170
  Sim time: 1.200000e+01    CPU time (total): 5.501600e-02s  events (step): 168
  Sim time: 1.300000e+01    CPU time (total): 5.978300e-02s  events (step): 159
  Sim time: 1.400000e+01    CPU time (total): 6.321600e-02s  events (step): 128
  Sim time: 1.500000e+01    CPU time (total): 6.701900e-02s  events (step): 139
  Sim time: 1.600000e+01    CPU time (total): 7.049200e-02s  events (step): 123
  Sim time: 1.700000e+01    CPU time (total): 7.513200e-02s  events (step): 167
  Sim time: 1.800000e+01    CPU time (total): 7.878300e-02s  events (step): 133
  Sim time: 1.900000e+01    CPU time (total): 8.377600e-02s  events (step): 186
  Sim time: 2.000000e+01    CPU time (total): 8.896200e-02s  events (step): 184
  Sim time: 2.100000e+01    CPU time (total): 9.349900e-02s  events (step): 166
  Sim time: 2.200000e+01    CPU time (total): 9.779500e-02s  events (step): 156
  Sim time: 2.300000e+01    CPU time (total): 1.019840e-01s  events (step): 148
  Sim time: 2.400000e+01    CPU time (total): 1.071010e-01s  events (step): 183
  Sim time: 2.500000e+01    CPU time (total): 1.120740e-01s  events (step): 181
  Sim time: 2.600000e+01    CPU time (total): 1.162190e-01s  events (step): 151
  Sim time: 2.700000e+01    CPU time (total): 1.212700e-01s  events (step): 182
  Sim time: 2.800000e+01    CPU time (total): 1.256060e-01s  events (step): 157
  Sim time: 2.900000e+01    CPU time (total): 1.302140e-01s  events (step): 166
  Sim time: 3.000000e+01    CPU time (total): 1.356690e-01s  events (step): 199
  Sim time: 3.100000e+01    CPU time (total): 1.397140e-01s  events (step): 150
  Sim time: 3.200000e+01    CPU time (total): 1.443220e-01s  events (step): 164
  Sim time: 3.300000e+01    CPU time (total): 1.492910e-01s  events (step): 180
  Sim time: 3.400000e+01    CPU time (total): 1.542680e-01s  events (step): 182
  Sim time: 3.500000e+01    CPU time (total): 1.601350e-01s  events (step): 213
  Sim time: 3.600000e+01    CPU time (total): 1.646710e-01s  events (step): 169
  Sim time: 3.700000e+01    CPU time (total): 1.685590e-01s  events (step): 139
  Sim time: 3.800000e+01    CPU time (total): 1.741950e-01s  events (step): 199
  Sim time: 3.900000e+01    CPU time (total): 1.787880e-01s  events (step): 163
  Sim time: 4.000000e+01    CPU time (total): 1.836000e-01s  events (step): 175
  Sim time: 4.100000e+01    CPU time (total): 1.877620e-01s  events (step): 154
  Sim time: 4.200000e+01    CPU time (total): 1.911870e-01s  events (step): 122
  Sim time: 4.300000e+01    CPU time (total): 1.960430e-01s  events (step): 181
  Sim time: 4.400000e+01    CPU time (total): 2.003810e-01s  events (step): 162
  Sim time: 4.500000e+01    CPU time (total): 2.035570e-01s  events (step): 114
  Sim time: 4.600000e+01    CPU time (total): 2.078410e-01s  events (step): 150
  Sim time: 4.700000e+01    CPU time (total): 2.128570e-01s  events (step): 186
  Sim time: 4.800000e+01    CPU time (total): 2.165430e-01s  events (step): 129
  Sim time: 4.900000e+01    CPU time (total): 2.202650e-01s  events (step): 136
  Sim time: 5.000000e+01    CPU time (total): 2.247750e-01s  events (step): 159
  Sim time: 5.100000e+01    CPU time (total): 2.297300e-01s  events (step): 181
  Sim time: 5.200000e+01    CPU time (total): 2.343100e-01s  events (step): 159
  Sim time: 5.300000e+01    CPU time (total): 2.392860e-01s  events (step): 172
  Sim time: 5.400000e+01    CPU time (total): 2.443150e-01s  events (step): 185
  Sim time: 5.500000e+01    CPU time (total): 2.482600e-01s  events (step): 140
  Sim time: 5.600000e+01    CPU time (total): 2.514900e-01s  events (step): 116
  Sim time: 5.700000e+01    CPU time (total): 2.563890e-01s  events (step): 175
  Sim time: 5.800000e+01    CPU time (total): 2.600050e-01s  events (step): 129
  Sim time: 5.900000e+01    CPU time (total): 2.646570e-01s  events (step): 164
  Sim time: 6.000000e+01    CPU time (total): 2.690280e-01s  events (step): 159
  Sim time: 6.100000e+01    CPU time (total): 2.727230e-01s  events (step): 129
  Sim time: 6.200000e+01    CPU time (total): 2.770090e-01s  events (step): 156
  Sim time: 6.300000e+01    CPU time (total): 2.820710e-01s  events (step): 174
  Sim time: 6.400000e+01    CPU time (total): 2.869100e-01s  events (step): 169
  Sim time: 6.500000e+01    CPU time (total): 2.919760e-01s  events (step): 188
  Sim time: 6.600000e+01    CPU time (total): 2.966520e-01s  events (step): 171
  Sim time: 6.700000e+01    CPU time (total): 3.016410e-01s  events (step): 177
  Sim time: 6.800000e+01    CPU time (total): 3.056530e-01s  events (step): 140
  Sim time: 6.900000e+01    CPU time (total): 3.100760e-01s  events (step): 152
  Sim time: 7.000000e+01    CPU time (total): 3.142890e-01s  events (step): 147
  Sim time: 7.100000e+01    CPU time (total): 3.185830e-01s  events (step): 152
  Sim time: 7.200000e+01    CPU time (total): 3.242140e-01s  events (step): 205
  Sim time: 7.300000e+01    CPU time (total): 3.274320e-01s  events (step): 120
  Sim time: 7.400000e+01    CPU time (total): 3.331320e-01s  events (step): 196
  Sim time: 7.500000e+01    CPU time (total): 3.373950e-01s  events (step): 152
  Sim time: 7.600000e+01    CPU time (total): 3.418610e-01s  events (step): 160
  Sim time: 7.700000e+01    CPU time (total): 3.456350e-01s  events (step): 131
  Sim time: 7.800000e+01    CPU time (total): 3.510470e-01s  events (step): 192
  Sim time: 7.900000e+01    CPU time (total): 3.561230e-01s  events (step): 183
  Sim time: 8.000000e+01    CPU time (total): 3.607990e-01s  events (step): 156
  Sim time: 8.100000e+01    CPU time (total): 3.657030e-01s  events (step): 179
  Sim time: 8.200000e+01    CPU time (total): 3.693570e-01s  events (step): 128
  Sim time: 8.300000e+01    CPU time (total): 3.740010e-01s  events (step): 162
  Sim time: 8.400000e+01    CPU time (total): 3.780170e-01s  events (step): 145
  Sim time: 8.500000e+01    CPU time (total): 3.830580e-01s  events (step): 178
  Sim time: 8.600000e+01    CPU time (total): 3.883580e-01s  events (step): 190
  Sim time: 8.700000e+01    CPU time (total): 3.932100e-01s  events (step): 168
  Sim time: 8.800000e+01    CPU time (total): 3.980320e-01s  events (step): 176
  Sim time: 8.900000e+01    CPU time (total): 4.023590e-01s  events (step): 152
  Sim time: 9.000000e+01    CPU time (total): 4.073280e-01s  events (step): 178
  Sim time: 9.100000e+01    CPU time (total): 4.120750e-01s  events (step): 168
  Sim time: 9.200000e+01    CPU time (total): 4.164300e-01s  events (step): 156
  Sim time: 9.300000e+01    CPU time (total): 4.205320e-01s  events (step): 147
  Sim time: 9.400000e+01    CPU time (total): 4.242300e-01s  events (step): 131
  Sim time: 9.500000e+01    CPU time (total): 4.284890e-01s  events (step): 150
  Sim time: 9.600000e+01    CPU time (total): 4.330820e-01s  events (step): 166
  Sim time: 9.700000e+01    CPU time (total): 4.386260e-01s  events (step): 192
  Sim time: 9.800000e+01    CPU time (total): 4.423440e-01s  events (step): 133
  Sim time: 9.900000e+01    CPU time (total): 4.475750e-01s  events (step): 185
  Sim time: 1.000000e+02    CPU time (total): 4.516120e-01s  events (step): 140

     You just simulated 16144 reactions in 4.517380e-01s
     ( 3.573753e+04 reactions/sec, 2.798179e-05 CPU seconds/event )
     Null events: 0   (2.798179e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 0.932214s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmpu7bbfvj6/task.species
  Read 1 unique species of 74 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 1.31 s.
  Finished processing file /tmp/tmpu7bbfvj6/task.bngl.
  CPU TIME: total 5.83 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (10.2 s)

Test that a simulator produces logarithmic 3D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 3 surfaces

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmprexly4jw/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmprexly4jw/task.xml.
  Running NFsim on 1332acbb4f3b
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmprexly4jw/task.xml -o /tmp/tmprexly4jw/task.gdat -sim 100 -oSteps 100 -seed 1641808642 -ss /tmp/tmprexly4jw/task.species -cb
  [simulation PID is: 15]
  starting NFsim v1.12.1...

  Seeding random number generator with: 1641808642
  reading xml file (/tmp/tmprexly4jw/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 3.360000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 4.572000e-03s  events (step): 128
  Sim time: 2.000000e+00    CPU time (total): 9.568000e-03s  events (step): 180
  Sim time: 3.000000e+00    CPU time (total): 1.363900e-02s  events (step): 151
  Sim time: 4.000000e+00    CPU time (total): 1.788600e-02s  events (step): 155
  Sim time: 5.000000e+00    CPU time (total): 2.217400e-02s  events (step): 158
  Sim time: 6.000000e+00    CPU time (total): 2.562500e-02s  events (step): 132
  Sim time: 7.000000e+00    CPU time (total): 2.957100e-02s  events (step): 144
  Sim time: 8.000000e+00    CPU time (total): 3.359200e-02s  events (step): 152
  Sim time: 9.000000e+00    CPU time (total): 3.896900e-02s  events (step): 193
  Sim time: 1.000000e+01    CPU time (total): 4.375700e-02s  events (step): 171
  Sim time: 1.100000e+01    CPU time (total): 4.838200e-02s  events (step): 172
  Sim time: 1.200000e+01    CPU time (total): 5.247100e-02s  events (step): 152
  Sim time: 1.300000e+01    CPU time (total): 5.617500e-02s  events (step): 137
  Sim time: 1.400000e+01    CPU time (total): 6.027700e-02s  events (step): 152
  Sim time: 1.500000e+01    CPU time (total): 6.540300e-02s  events (step): 190
  Sim time: 1.600000e+01    CPU time (total): 6.886100e-02s  events (step): 126
  Sim time: 1.700000e+01    CPU time (total): 7.305000e-02s  events (step): 153
  Sim time: 1.800000e+01    CPU time (total): 7.752500e-02s  events (step): 169
  Sim time: 1.900000e+01    CPU time (total): 8.230700e-02s  events (step): 176
  Sim time: 2.000000e+01    CPU time (total): 8.674800e-02s  events (step): 164
  Sim time: 2.100000e+01    CPU time (total): 9.082900e-02s  events (step): 153
  Sim time: 2.200000e+01    CPU time (total): 9.536400e-02s  events (step): 170
  Sim time: 2.300000e+01    CPU time (total): 1.001570e-01s  events (step): 178
  Sim time: 2.400000e+01    CPU time (total): 1.040470e-01s  events (step): 146
  Sim time: 2.500000e+01    CPU time (total): 1.092400e-01s  events (step): 195
  Sim time: 2.600000e+01    CPU time (total): 1.134910e-01s  events (step): 156
  Sim time: 2.700000e+01    CPU time (total): 1.172510e-01s  events (step): 134
  Sim time: 2.800000e+01    CPU time (total): 1.210010e-01s  events (step): 142
  Sim time: 2.900000e+01    CPU time (total): 1.261760e-01s  events (step): 188
  Sim time: 3.000000e+01    CPU time (total): 1.319800e-01s  events (step): 216
  Sim time: 3.100000e+01    CPU time (total): 1.372280e-01s  events (step): 185
  Sim time: 3.200000e+01    CPU time (total): 1.412600e-01s  events (step): 154
  Sim time: 3.300000e+01    CPU time (total): 1.459680e-01s  events (step): 169
  Sim time: 3.400000e+01    CPU time (total): 1.500790e-01s  events (step): 150
  Sim time: 3.500000e+01    CPU time (total): 1.544970e-01s  events (step): 164
  Sim time: 3.600000e+01    CPU time (total): 1.575400e-01s  events (step): 104
  Sim time: 3.700000e+01    CPU time (total): 1.621820e-01s  events (step): 173
  Sim time: 3.800000e+01    CPU time (total): 1.664670e-01s  events (step): 153
  Sim time: 3.900000e+01    CPU time (total): 1.698830e-01s  events (step): 123
  Sim time: 4.000000e+01    CPU time (total): 1.747520e-01s  events (step): 170
  Sim time: 4.100000e+01    CPU time (total): 1.785780e-01s  events (step): 141
  Sim time: 4.200000e+01    CPU time (total): 1.827390e-01s  events (step): 157
  Sim time: 4.300000e+01    CPU time (total): 1.873910e-01s  events (step): 166
  Sim time: 4.400000e+01    CPU time (total): 1.922530e-01s  events (step): 177
  Sim time: 4.500000e+01    CPU time (total): 1.972100e-01s  events (step): 181
  Sim time: 4.600000e+01    CPU time (total): 2.017150e-01s  events (step): 167
  Sim time: 4.700000e+01    CPU time (total): 2.060560e-01s  events (step): 161
  Sim time: 4.800000e+01    CPU time (total): 2.099840e-01s  events (step): 142
  Sim time: 4.900000e+01    CPU time (total): 2.152520e-01s  events (step): 198
  Sim time: 5.000000e+01    CPU time (total): 2.198900e-01s  events (step): 165
  Sim time: 5.100000e+01    CPU time (total): 2.241600e-01s  events (step): 159
  Sim time: 5.200000e+01    CPU time (total): 2.277720e-01s  events (step): 130
  Sim time: 5.300000e+01    CPU time (total): 2.314130e-01s  events (step): 131
  Sim time: 5.400000e+01    CPU time (total): 2.357360e-01s  events (step): 163
  Sim time: 5.500000e+01    CPU time (total): 2.395870e-01s  events (step): 136
  Sim time: 5.600000e+01    CPU time (total): 2.432670e-01s  events (step): 129
  Sim time: 5.700000e+01    CPU time (total): 2.480010e-01s  events (step): 166
  Sim time: 5.800000e+01    CPU time (total): 2.522530e-01s  events (step): 151
  Sim time: 5.900000e+01    CPU time (total): 2.619490e-01s  events (step): 376
  Sim time: 6.000000e+01    CPU time (total): 2.944840e-01s  events (step): 1479
  Sim time: 6.100000e+01    CPU time (total): 3.234150e-01s  events (step): 1371
  Sim time: 6.200000e+01    CPU time (total): 3.545450e-01s  events (step): 1422
  Sim time: 6.300000e+01    CPU time (total): 3.888800e-01s  events (step): 1603
  Sim time: 6.400000e+01    CPU time (total): 4.219880e-01s  events (step): 1542
  Sim time: 6.500000e+01    CPU time (total): 4.611480e-01s  events (step): 1858
  Sim time: 6.600000e+01    CPU time (total): 5.006910e-01s  events (step): 1922
  Sim time: 6.700000e+01    CPU time (total): 5.393220e-01s  events (step): 1795
  Sim time: 6.800000e+01    CPU time (total): 5.793080e-01s  events (step): 1845
  Sim time: 6.900000e+01    CPU time (total): 6.239000e-01s  events (step): 1975
  Sim time: 7.000000e+01    CPU time (total): 6.657440e-01s  events (step): 1844
  Sim time: 7.100000e+01    CPU time (total): 7.073000e-01s  events (step): 1785
  Sim time: 7.200000e+01    CPU time (total): 7.521620e-01s  events (step): 2009
  Sim time: 7.300000e+01    CPU time (total): 7.980690e-01s  events (step): 2060
  Sim time: 7.400000e+01    CPU time (total): 8.445240e-01s  events (step): 2077
  Sim time: 7.500000e+01    CPU time (total): 8.916490e-01s  events (step): 2019
  Sim time: 7.600000e+01    CPU time (total): 9.356900e-01s  events (step): 1983
  Sim time: 7.700000e+01    CPU time (total): 9.767350e-01s  events (step): 1799
  Sim time: 7.800000e+01    CPU time (total): 1.028508e+00s  events (step): 1931
  Sim time: 7.900000e+01    CPU time (total): 1.085698e+00s  events (step): 1833
  Sim time: 8.000000e+01    CPU time (total): 1.139428e+00s  events (step): 1827
  Sim time: 8.100000e+01    CPU time (total): 1.183040e+00s  events (step): 1951
  Sim time: 8.200000e+01    CPU time (total): 1.229832e+00s  events (step): 2062
  Sim time: 8.300000e+01    CPU time (total): 1.285355e+00s  events (step): 2263
  Sim time: 8.400000e+01    CPU time (total): 1.341296e+00s  events (step): 2044
  Sim time: 8.500000e+01    CPU time (total): 1.403074e+00s  events (step): 2041
  Sim time: 8.600000e+01    CPU time (total): 1.459375e+00s  events (step): 1764
  Sim time: 8.700000e+01    CPU time (total): 1.518756e+00s  events (step): 1828
  Sim time: 8.800000e+01    CPU time (total): 1.596243e+00s  events (step): 2195
  Sim time: 8.900000e+01    CPU time (total): 1.686295e+00s  events (step): 2104
  Sim time: 9.000000e+01    CPU time (total): 1.780820e+00s  events (step): 2062
  Sim time: 9.100000e+01    CPU time (total): 1.867943e+00s  events (step): 1941
  Sim time: 9.200000e+01    CPU time (total): 1.955037e+00s  events (step): 1989
  Sim time: 9.300000e+01    CPU time (total): 2.032671e+00s  events (step): 1897
  Sim time: 9.400000e+01    CPU time (total): 2.121102e+00s  events (step): 2162
  Sim time: 9.500000e+01    CPU time (total): 2.210394e+00s  events (step): 2202
  Sim time: 9.600000e+01    CPU time (total): 2.298128e+00s  events (step): 2160
  Sim time: 9.700000e+01    CPU time (total): 2.385971e+00s  events (step): 2167
  Sim time: 9.800000e+01    CPU time (total): 2.484903e+00s  events (step): 2428
  Sim time: 9.900000e+01    CPU time (total): 2.584723e+00s  events (step): 2318
  Sim time: 1.000000e+02    CPU time (total): 2.684576e+00s  events (step): 2417

     You just simulated 89549 reactions in 2.684766e+00s
     ( 3.335449e+04 reactions/sec, 2.998097e-05 CPU seconds/event )
     Null events: 0   (2.998097e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 3.16551s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmprexly4jw/task.species
  Read 9 unique species of 78 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 3.54 s.
  Finished processing file /tmp/tmprexly4jw/task.bngl.
  CPU TIME: total 8.04 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (12.5 s)

Test that a simulator produces multiple plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (2):
        plot_0: 2 curves
        plot_1: 1 curves

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmpw02cb8g_/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmpw02cb8g_/task.xml.
  Running NFsim on 8135a10f9025
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpw02cb8g_/task.xml -o /tmp/tmpw02cb8g_/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpw02cb8g_/task.species -cb -seed 909892705
  [simulation PID is: 15]
  starting NFsim v1.12.1...

  Seeding random number generator with: 909892705
  reading xml file (/tmp/tmpw02cb8g_/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 3.390000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 4.270000e-03s  events (step): 123
  Sim time: 2.000000e+00    CPU time (total): 9.332000e-03s  events (step): 185
  Sim time: 3.000000e+00    CPU time (total): 1.420400e-02s  events (step): 176
  Sim time: 4.000000e+00    CPU time (total): 1.857900e-02s  events (step): 166
  Sim time: 5.000000e+00    CPU time (total): 2.298600e-02s  events (step): 143
  Sim time: 6.000000e+00    CPU time (total): 2.813200e-02s  events (step): 178
  Sim time: 7.000000e+00    CPU time (total): 3.332000e-02s  events (step): 184
  Sim time: 8.000000e+00    CPU time (total): 4.512300e-02s  events (step): 458
  Sim time: 9.000000e+00    CPU time (total): 6.313000e-02s  events (step): 765
  Sim time: 1.000000e+01    CPU time (total): 8.912500e-02s  events (step): 1068
  Sim time: 1.100000e+01    CPU time (total): 1.118340e-01s  events (step): 967
  Sim time: 1.200000e+01    CPU time (total): 1.369170e-01s  events (step): 1083
  Sim time: 1.300000e+01    CPU time (total): 1.617620e-01s  events (step): 1077
  Sim time: 1.400000e+01    CPU time (total): 1.876320e-01s  events (step): 1143
  Sim time: 1.500000e+01    CPU time (total): 2.182130e-01s  events (step): 1356
  Sim time: 1.600000e+01    CPU time (total): 2.532730e-01s  events (step): 1580
  Sim time: 1.700000e+01    CPU time (total): 2.852790e-01s  events (step): 1422
  Sim time: 1.800000e+01    CPU time (total): 3.192230e-01s  events (step): 1534
  Sim time: 1.900000e+01    CPU time (total): 3.537650e-01s  events (step): 1552
  Sim time: 2.000000e+01    CPU time (total): 3.868900e-01s  events (step): 1535
  Sim time: 2.100000e+01    CPU time (total): 4.272480e-01s  events (step): 1814
  Sim time: 2.200000e+01    CPU time (total): 4.643930e-01s  events (step): 1741
  Sim time: 2.300000e+01    CPU time (total): 4.991830e-01s  events (step): 1630
  Sim time: 2.400000e+01    CPU time (total): 5.654050e-01s  events (step): 1801
  Sim time: 2.500000e+01    CPU time (total): 6.389380e-01s  events (step): 2018
  Sim time: 2.600000e+01    CPU time (total): 7.167650e-01s  events (step): 2157
  Sim time: 2.700000e+01    CPU time (total): 8.039150e-01s  events (step): 2291
  Sim time: 2.800000e+01    CPU time (total): 8.787230e-01s  events (step): 2081
  Sim time: 2.900000e+01    CPU time (total): 9.490950e-01s  events (step): 1988
  Sim time: 3.000000e+01    CPU time (total): 1.021328e+00s  events (step): 1992
  Sim time: 3.100000e+01    CPU time (total): 1.086641e+00s  events (step): 1940
  Sim time: 3.200000e+01    CPU time (total): 1.141282e+00s  events (step): 1913
  Sim time: 3.300000e+01    CPU time (total): 1.200135e+00s  events (step): 1906
  Sim time: 3.400000e+01    CPU time (total): 1.265265e+00s  events (step): 2241
  Sim time: 3.500000e+01    CPU time (total): 1.329778e+00s  events (step): 2530
  Sim time: 3.600000e+01    CPU time (total): 1.380765e+00s  events (step): 2393
  Sim time: 3.700000e+01    CPU time (total): 1.449085e+00s  events (step): 2688
  Sim time: 3.800000e+01    CPU time (total): 1.531671e+00s  events (step): 2513
  Sim time: 3.900000e+01    CPU time (total): 1.615445e+00s  events (step): 2598
  Sim time: 4.000000e+01    CPU time (total): 1.699973e+00s  events (step): 2513
  Sim time: 4.100000e+01    CPU time (total): 1.778754e+00s  events (step): 2507
  Sim time: 4.200000e+01    CPU time (total): 1.856612e+00s  events (step): 2578
  Sim time: 4.300000e+01    CPU time (total): 1.934884e+00s  events (step): 2540
  Sim time: 4.400000e+01    CPU time (total): 2.008563e+00s  events (step): 2381
  Sim time: 4.500000e+01    CPU time (total): 2.080616e+00s  events (step): 2347
  Sim time: 4.600000e+01    CPU time (total): 2.151955e+00s  events (step): 2240
  Sim time: 4.700000e+01    CPU time (total): 2.221271e+00s  events (step): 2244
  Sim time: 4.800000e+01    CPU time (total): 2.292744e+00s  events (step): 2388
  Sim time: 4.900000e+01    CPU time (total): 2.367038e+00s  events (step): 2418
  Sim time: 5.000000e+01    CPU time (total): 2.441635e+00s  events (step): 2441
  Sim time: 5.100000e+01    CPU time (total): 2.514287e+00s  events (step): 2296
  Sim time: 5.200000e+01    CPU time (total): 2.583635e+00s  events (step): 2337
  Sim time: 5.300000e+01    CPU time (total): 2.629797e+00s  events (step): 2183
  Sim time: 5.400000e+01    CPU time (total): 2.675307e+00s  events (step): 2094
  Sim time: 5.500000e+01    CPU time (total): 2.720894e+00s  events (step): 2090
  Sim time: 5.600000e+01    CPU time (total): 2.763801e+00s  events (step): 1928
  Sim time: 5.700000e+01    CPU time (total): 2.802236e+00s  events (step): 1789
  Sim time: 5.800000e+01    CPU time (total): 2.847118e+00s  events (step): 2068
  Sim time: 5.900000e+01    CPU time (total): 2.893215e+00s  events (step): 2158
  Sim time: 6.000000e+01    CPU time (total): 2.937614e+00s  events (step): 2082
  Sim time: 6.100000e+01    CPU time (total): 2.995812e+00s  events (step): 2058
  Sim time: 6.200000e+01    CPU time (total): 3.057602e+00s  events (step): 2142
  Sim time: 6.300000e+01    CPU time (total): 3.118373e+00s  events (step): 2076
  Sim time: 6.400000e+01    CPU time (total): 3.179146e+00s  events (step): 2134
  Sim time: 6.500000e+01    CPU time (total): 3.239144e+00s  events (step): 1884
  Sim time: 6.600000e+01    CPU time (total): 3.299325e+00s  events (step): 1780
  Sim time: 6.700000e+01    CPU time (total): 3.350982e+00s  events (step): 1560
  Sim time: 6.800000e+01    CPU time (total): 3.404921e+00s  events (step): 1599
  Sim time: 6.900000e+01    CPU time (total): 3.462692e+00s  events (step): 1708
  Sim time: 7.000000e+01    CPU time (total): 3.520772e+00s  events (step): 1698
  Sim time: 7.100000e+01    CPU time (total): 3.581179e+00s  events (step): 1745
  Sim time: 7.200000e+01    CPU time (total): 3.637840e+00s  events (step): 1611
  Sim time: 7.300000e+01    CPU time (total): 3.690843e+00s  events (step): 1557
  Sim time: 7.400000e+01    CPU time (total): 3.733125e+00s  events (step): 1205
  Sim time: 7.500000e+01    CPU time (total): 3.784284e+00s  events (step): 1477
  Sim time: 7.600000e+01    CPU time (total): 3.832275e+00s  events (step): 1363
  Sim time: 7.700000e+01    CPU time (total): 3.873228e+00s  events (step): 1330
  Sim time: 7.800000e+01    CPU time (total): 3.918855e+00s  events (step): 1387
  Sim time: 7.900000e+01    CPU time (total): 3.965790e+00s  events (step): 1503
  Sim time: 8.000000e+01    CPU time (total): 4.019697e+00s  events (step): 1759
  Sim time: 8.100000e+01    CPU time (total): 4.081565e+00s  events (step): 1894
  Sim time: 8.200000e+01    CPU time (total): 4.140844e+00s  events (step): 1866
  Sim time: 8.300000e+01    CPU time (total): 4.193427e+00s  events (step): 1710
  Sim time: 8.400000e+01    CPU time (total): 4.250818e+00s  events (step): 1829
  Sim time: 8.500000e+01    CPU time (total): 4.306921e+00s  events (step): 1736
  Sim time: 8.600000e+01    CPU time (total): 4.360100e+00s  events (step): 1683
  Sim time: 8.700000e+01    CPU time (total): 4.417783e+00s  events (step): 1910
  Sim time: 8.800000e+01    CPU time (total): 4.471717e+00s  events (step): 1766
  Sim time: 8.900000e+01    CPU time (total): 4.525250e+00s  events (step): 1659
  Sim time: 9.000000e+01    CPU time (total): 4.580494e+00s  events (step): 1797
  Sim time: 9.100000e+01    CPU time (total): 4.636047e+00s  events (step): 1651
  Sim time: 9.200000e+01    CPU time (total): 4.693117e+00s  events (step): 1781
  Sim time: 9.300000e+01    CPU time (total): 4.752783e+00s  events (step): 1834
  Sim time: 9.400000e+01    CPU time (total): 4.807844e+00s  events (step): 1683
  Sim time: 9.500000e+01    CPU time (total): 4.863123e+00s  events (step): 1810
  Sim time: 9.600000e+01    CPU time (total): 4.921285e+00s  events (step): 1865
  Sim time: 9.700000e+01    CPU time (total): 4.973556e+00s  events (step): 1777
  Sim time: 9.800000e+01    CPU time (total): 5.029942e+00s  events (step): 1907
  Sim time: 9.900000e+01    CPU time (total): 5.089112e+00s  events (step): 1991
  Sim time: 1.000000e+02    CPU time (total): 5.148053e+00s  events (step): 2083

     You just simulated 174361 reactions in 5.148270e+00s
     ( 3.386788e+04 reactions/sec, 2.952650e-05 CPU seconds/event )
     Null events: 0   (2.952650e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 5.62757s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmpw02cb8g_/task.species
  Read 4 unique species of 75 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 6.00 s.
  Finished processing file /tmp/tmpw02cb8g_/task.bngl.
  CPU TIME: total 10.45 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (1.8 s)

Test that a simulator supports multiple time courses with non-zero initial times

Warnings:

  The image 'ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2' could not execute the archive:

    Unknown error

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        report: 3 data sets

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  The initial time of a network free simulation (KISAO_0000263) must be 0.

[biosimulators-daemon]

The image for your simulator is valid!

[biosimulators-daemon]

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.

[biosimulators-daemon]

Thank you @biosimulators-daemon 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 is available here.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 35 test cases

• Passed 26 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels
  • exec_status_report.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • results_report.SimulatorGeneratesReportsOfSimultionResults
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

• Failed 0 test cases

• Skipped 9 test cases:

  • 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
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • 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-fbc/Escherichia-coli-core-metabolism

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (10.6 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

  The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

  The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
    - 'ALGORITHM_SUBSTITUTION_POLICY'

  If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

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

Log:

docker_image.DeclaresSupportedEnvironmentVariables (1.7 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'

  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:

sedml.SimulatorProducesLinear2DPlots (10.9 s)

Test that a simulator produces linear 2D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 3 curves

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmp71tebu76/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmp71tebu76/task.xml.
  Running NFsim on 4670f4541e83
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp71tebu76/task.xml -o /tmp/tmp71tebu76/task.gdat -sim 100 -oSteps 100 -seed 1053331894 -cb -ss /tmp/tmp71tebu76/task.species
  [simulation PID is: 14]
  starting NFsim v1.12.1...

  Seeding random number generator with: 1053331894
  reading xml file (/tmp/tmp71tebu76/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 2.630000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 5.172000e-03s  events (step): 138
  Sim time: 2.000000e+00    CPU time (total): 1.111500e-02s  events (step): 184
  Sim time: 3.000000e+00    CPU time (total): 1.694500e-02s  events (step): 201
  Sim time: 4.000000e+00    CPU time (total): 2.263300e-02s  events (step): 173
  Sim time: 5.000000e+00    CPU time (total): 2.614900e-02s  events (step): 128
  Sim time: 6.000000e+00    CPU time (total): 3.004800e-02s  events (step): 129
  Sim time: 7.000000e+00    CPU time (total): 3.549900e-02s  events (step): 177
  Sim time: 8.000000e+00    CPU time (total): 4.106500e-02s  events (step): 180
  Sim time: 9.000000e+00    CPU time (total): 4.604500e-02s  events (step): 173
  Sim time: 1.000000e+01    CPU time (total): 4.986100e-02s  events (step): 131
  Sim time: 1.100000e+01    CPU time (total): 5.527300e-02s  events (step): 192
  Sim time: 1.200000e+01    CPU time (total): 5.987900e-02s  events (step): 170
  Sim time: 1.300000e+01    CPU time (total): 6.483600e-02s  events (step): 162
  Sim time: 1.400000e+01    CPU time (total): 6.934600e-02s  events (step): 137
  Sim time: 1.500000e+01    CPU time (total): 7.390800e-02s  events (step): 171
  Sim time: 1.600000e+01    CPU time (total): 7.888300e-02s  events (step): 176
  Sim time: 1.700000e+01    CPU time (total): 8.326100e-02s  events (step): 165
  Sim time: 1.800000e+01    CPU time (total): 8.670200e-02s  events (step): 122
  Sim time: 1.900000e+01    CPU time (total): 9.168500e-02s  events (step): 161
  Sim time: 2.000000e+01    CPU time (total): 9.597900e-02s  events (step): 155
  Sim time: 2.100000e+01    CPU time (total): 1.013650e-01s  events (step): 191
  Sim time: 2.200000e+01    CPU time (total): 1.067910e-01s  events (step): 173
  Sim time: 2.300000e+01    CPU time (total): 1.112750e-01s  events (step): 160
  Sim time: 2.400000e+01    CPU time (total): 1.161560e-01s  events (step): 174
  Sim time: 2.500000e+01    CPU time (total): 1.212270e-01s  events (step): 190
  Sim time: 2.600000e+01    CPU time (total): 1.258670e-01s  events (step): 164
  Sim time: 2.700000e+01    CPU time (total): 1.307410e-01s  events (step): 154
  Sim time: 2.800000e+01    CPU time (total): 1.349980e-01s  events (step): 153
  Sim time: 2.900000e+01    CPU time (total): 1.402370e-01s  events (step): 175
  Sim time: 3.000000e+01    CPU time (total): 1.452590e-01s  events (step): 184
  Sim time: 3.100000e+01    CPU time (total): 1.508000e-01s  events (step): 181
  Sim time: 3.200000e+01    CPU time (total): 1.557510e-01s  events (step): 164
  Sim time: 3.300000e+01    CPU time (total): 1.617180e-01s  events (step): 183
  Sim time: 3.400000e+01    CPU time (total): 1.672400e-01s  events (step): 169
  Sim time: 3.500000e+01    CPU time (total): 1.715180e-01s  events (step): 145
  Sim time: 3.600000e+01    CPU time (total): 1.752370e-01s  events (step): 123
  Sim time: 3.700000e+01    CPU time (total): 1.826930e-01s  events (step): 145
  Sim time: 3.800000e+01    CPU time (total): 1.880300e-01s  events (step): 191
  Sim time: 3.900000e+01    CPU time (total): 1.928610e-01s  events (step): 164
  Sim time: 4.000000e+01    CPU time (total): 1.978930e-01s  events (step): 169
  Sim time: 4.100000e+01    CPU time (total): 2.022960e-01s  events (step): 147
  Sim time: 4.200000e+01    CPU time (total): 2.072840e-01s  events (step): 162
  Sim time: 4.300000e+01    CPU time (total): 2.127030e-01s  events (step): 175
  Sim time: 4.400000e+01    CPU time (total): 2.175240e-01s  events (step): 163
  Sim time: 4.500000e+01    CPU time (total): 2.232830e-01s  events (step): 194
  Sim time: 4.600000e+01    CPU time (total): 2.278090e-01s  events (step): 149
  Sim time: 4.700000e+01    CPU time (total): 2.319370e-01s  events (step): 145
  Sim time: 4.800000e+01    CPU time (total): 2.368120e-01s  events (step): 156
  Sim time: 4.900000e+01    CPU time (total): 2.412430e-01s  events (step): 140
  Sim time: 5.000000e+01    CPU time (total): 2.462550e-01s  events (step): 174
  Sim time: 5.100000e+01    CPU time (total): 2.510560e-01s  events (step): 174
  Sim time: 5.200000e+01    CPU time (total): 2.559160e-01s  events (step): 180
  Sim time: 5.300000e+01    CPU time (total): 2.607080e-01s  events (step): 165
  Sim time: 5.400000e+01    CPU time (total): 2.652370e-01s  events (step): 166
  Sim time: 5.500000e+01    CPU time (total): 2.701560e-01s  events (step): 190
  Sim time: 5.600000e+01    CPU time (total): 2.756200e-01s  events (step): 184
  Sim time: 5.700000e+01    CPU time (total): 2.795520e-01s  events (step): 138
  Sim time: 5.800000e+01    CPU time (total): 2.842050e-01s  events (step): 179
  Sim time: 5.900000e+01    CPU time (total): 2.881400e-01s  events (step): 122
  Sim time: 6.000000e+01    CPU time (total): 2.919390e-01s  events (step): 143
  Sim time: 6.100000e+01    CPU time (total): 2.979300e-01s  events (step): 202
  Sim time: 6.200000e+01    CPU time (total): 3.018260e-01s  events (step): 147
  Sim time: 6.300000e+01    CPU time (total): 3.068410e-01s  events (step): 169
  Sim time: 6.400000e+01    CPU time (total): 3.128160e-01s  events (step): 187
  Sim time: 6.500000e+01    CPU time (total): 3.174940e-01s  events (step): 178
  Sim time: 6.600000e+01    CPU time (total): 3.214900e-01s  events (step): 139
  Sim time: 6.700000e+01    CPU time (total): 3.261370e-01s  events (step): 153
  Sim time: 6.800000e+01    CPU time (total): 3.305490e-01s  events (step): 161
  Sim time: 6.900000e+01    CPU time (total): 3.351110e-01s  events (step): 152
  Sim time: 7.000000e+01    CPU time (total): 3.386900e-01s  events (step): 132
  Sim time: 7.100000e+01    CPU time (total): 3.435180e-01s  events (step): 174
  Sim time: 7.200000e+01    CPU time (total): 3.506350e-01s  events (step): 197
  Sim time: 7.300000e+01    CPU time (total): 3.555480e-01s  events (step): 159
  Sim time: 7.400000e+01    CPU time (total): 3.597220e-01s  events (step): 136
  Sim time: 7.500000e+01    CPU time (total): 3.643490e-01s  events (step): 148
  Sim time: 7.600000e+01    CPU time (total): 3.689640e-01s  events (step): 148
  Sim time: 7.700000e+01    CPU time (total): 3.733380e-01s  events (step): 132
  Sim time: 7.800000e+01    CPU time (total): 3.798360e-01s  events (step): 196
  Sim time: 7.900000e+01    CPU time (total): 3.857600e-01s  events (step): 191
  Sim time: 8.000000e+01    CPU time (total): 3.911480e-01s  events (step): 177
  Sim time: 8.100000e+01    CPU time (total): 3.970640e-01s  events (step): 171
  Sim time: 8.200000e+01    CPU time (total): 4.026500e-01s  events (step): 174
  Sim time: 8.300000e+01    CPU time (total): 4.076610e-01s  events (step): 159
  Sim time: 8.400000e+01    CPU time (total): 4.127060e-01s  events (step): 162
  Sim time: 8.500000e+01    CPU time (total): 4.188080e-01s  events (step): 186
  Sim time: 8.600000e+01    CPU time (total): 4.253290e-01s  events (step): 179
  Sim time: 8.700000e+01    CPU time (total): 4.306300e-01s  events (step): 170
  Sim time: 8.800000e+01    CPU time (total): 4.364850e-01s  events (step): 189
  Sim time: 8.900000e+01    CPU time (total): 4.419970e-01s  events (step): 170
  Sim time: 9.000000e+01    CPU time (total): 4.474670e-01s  events (step): 158
  Sim time: 9.100000e+01    CPU time (total): 4.533550e-01s  events (step): 188
  Sim time: 9.200000e+01    CPU time (total): 4.584810e-01s  events (step): 161
  Sim time: 9.300000e+01    CPU time (total): 4.647850e-01s  events (step): 188
  Sim time: 9.400000e+01    CPU time (total): 4.699400e-01s  events (step): 162
  Sim time: 9.500000e+01    CPU time (total): 4.733370e-01s  events (step): 117
  Sim time: 9.600000e+01    CPU time (total): 4.789170e-01s  events (step): 182
  Sim time: 9.700000e+01    CPU time (total): 4.842890e-01s  events (step): 195
  Sim time: 9.800000e+01    CPU time (total): 4.880980e-01s  events (step): 137
  Sim time: 9.900000e+01    CPU time (total): 4.928220e-01s  events (step): 140
  Sim time: 1.000000e+02    CPU time (total): 4.996690e-01s  events (step): 191

     You just simulated 16481 reactions in 4.998590e-01s
     ( 3.297130e+04 reactions/sec, 3.032941e-05 CPU seconds/event )
     Null events: 0   (3.032941e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 1.09648s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmp71tebu76/task.species
  Read 0 unique species of 73 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 1.68 s.
  Finished processing file /tmp/tmp71tebu76/task.bngl.
  CPU TIME: total 7.74 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLinear3DPlots (10.8 s)

Test that a simulator produces linear 3D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 3 surfaces

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmpvcz2dw_z/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmpvcz2dw_z/task.xml.
  Running NFsim on 3badd09216ff
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpvcz2dw_z/task.xml -o /tmp/tmpvcz2dw_z/task.gdat -sim 100 -oSteps 100 -ss /tmp/tmpvcz2dw_z/task.species -cb -seed 72033610
  [simulation PID is: 14]
  starting NFsim v1.12.1...

  Seeding random number generator with: 72033610
  reading xml file (/tmp/tmpvcz2dw_z/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 2.240000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 5.654000e-03s  events (step): 155
  Sim time: 2.000000e+00    CPU time (total): 1.004700e-02s  events (step): 145
  Sim time: 3.000000e+00    CPU time (total): 1.485600e-02s  events (step): 169
  Sim time: 4.000000e+00    CPU time (total): 1.977300e-02s  events (step): 155
  Sim time: 5.000000e+00    CPU time (total): 2.478100e-02s  events (step): 173
  Sim time: 6.000000e+00    CPU time (total): 3.042400e-02s  events (step): 200
  Sim time: 7.000000e+00    CPU time (total): 3.547700e-02s  events (step): 167
  Sim time: 8.000000e+00    CPU time (total): 4.045300e-02s  events (step): 165
  Sim time: 9.000000e+00    CPU time (total): 4.642100e-02s  events (step): 176
  Sim time: 1.000000e+01    CPU time (total): 5.221300e-02s  events (step): 173
  Sim time: 1.100000e+01    CPU time (total): 5.645200e-02s  events (step): 133
  Sim time: 1.200000e+01    CPU time (total): 6.038800e-02s  events (step): 135
  Sim time: 1.300000e+01    CPU time (total): 6.517300e-02s  events (step): 136
  Sim time: 1.400000e+01    CPU time (total): 6.941700e-02s  events (step): 139
  Sim time: 1.500000e+01    CPU time (total): 7.613800e-02s  events (step): 226
  Sim time: 1.600000e+01    CPU time (total): 8.062000e-02s  events (step): 153
  Sim time: 1.700000e+01    CPU time (total): 8.514300e-02s  events (step): 147
  Sim time: 1.800000e+01    CPU time (total): 8.972900e-02s  events (step): 159
  Sim time: 1.900000e+01    CPU time (total): 9.423700e-02s  events (step): 143
  Sim time: 2.000000e+01    CPU time (total): 9.889500e-02s  events (step): 154
  Sim time: 2.100000e+01    CPU time (total): 1.047220e-01s  events (step): 189
  Sim time: 2.200000e+01    CPU time (total): 1.099950e-01s  events (step): 173
  Sim time: 2.300000e+01    CPU time (total): 1.182930e-01s  events (step): 189
  Sim time: 2.400000e+01    CPU time (total): 1.221140e-01s  events (step): 139
  Sim time: 2.500000e+01    CPU time (total): 1.264380e-01s  events (step): 133
  Sim time: 2.600000e+01    CPU time (total): 1.316800e-01s  events (step): 183
  Sim time: 2.700000e+01    CPU time (total): 1.363440e-01s  events (step): 155
  Sim time: 2.800000e+01    CPU time (total): 1.399670e-01s  events (step): 116
  Sim time: 2.900000e+01    CPU time (total): 1.445450e-01s  events (step): 144
  Sim time: 3.000000e+01    CPU time (total): 1.492640e-01s  events (step): 151
  Sim time: 3.100000e+01    CPU time (total): 1.544980e-01s  events (step): 168
  Sim time: 3.200000e+01    CPU time (total): 1.590300e-01s  events (step): 150
  Sim time: 3.300000e+01    CPU time (total): 1.632460e-01s  events (step): 137
  Sim time: 3.400000e+01    CPU time (total): 1.677350e-01s  events (step): 150
  Sim time: 3.500000e+01    CPU time (total): 1.731330e-01s  events (step): 173
  Sim time: 3.600000e+01    CPU time (total): 1.789300e-01s  events (step): 189
  Sim time: 3.700000e+01    CPU time (total): 1.831100e-01s  events (step): 137
  Sim time: 3.800000e+01    CPU time (total): 1.885140e-01s  events (step): 180
  Sim time: 3.900000e+01    CPU time (total): 1.934220e-01s  events (step): 158
  Sim time: 4.000000e+01    CPU time (total): 1.976220e-01s  events (step): 151
  Sim time: 4.100000e+01    CPU time (total): 2.017890e-01s  events (step): 143
  Sim time: 4.200000e+01    CPU time (total): 2.059760e-01s  events (step): 138
  Sim time: 4.300000e+01    CPU time (total): 2.097650e-01s  events (step): 131
  Sim time: 4.400000e+01    CPU time (total): 2.165380e-01s  events (step): 230
  Sim time: 4.500000e+01    CPU time (total): 2.219390e-01s  events (step): 174
  Sim time: 4.600000e+01    CPU time (total): 2.254450e-01s  events (step): 128
  Sim time: 4.700000e+01    CPU time (total): 2.307770e-01s  events (step): 179
  Sim time: 4.800000e+01    CPU time (total): 2.365960e-01s  events (step): 189
  Sim time: 4.900000e+01    CPU time (total): 2.416430e-01s  events (step): 168
  Sim time: 5.000000e+01    CPU time (total): 2.459060e-01s  events (step): 142
  Sim time: 5.100000e+01    CPU time (total): 2.510110e-01s  events (step): 167
  Sim time: 5.200000e+01    CPU time (total): 2.550210e-01s  events (step): 131
  Sim time: 5.300000e+01    CPU time (total): 2.603460e-01s  events (step): 172
  Sim time: 5.400000e+01    CPU time (total): 2.649090e-01s  events (step): 147
  Sim time: 5.500000e+01    CPU time (total): 2.690550e-01s  events (step): 125
  Sim time: 5.600000e+01    CPU time (total): 2.750500e-01s  events (step): 174
  Sim time: 5.700000e+01    CPU time (total): 2.796720e-01s  events (step): 160
  Sim time: 5.800000e+01    CPU time (total): 2.842280e-01s  events (step): 156
  Sim time: 5.900000e+01    CPU time (total): 2.888470e-01s  events (step): 156
  Sim time: 6.000000e+01    CPU time (total): 2.934430e-01s  events (step): 155
  Sim time: 6.100000e+01    CPU time (total): 2.980220e-01s  events (step): 153
  Sim time: 6.200000e+01    CPU time (total): 3.016210e-01s  events (step): 125
  Sim time: 6.300000e+01    CPU time (total): 3.052050e-01s  events (step): 134
  Sim time: 6.400000e+01    CPU time (total): 3.089550e-01s  events (step): 136
  Sim time: 6.500000e+01    CPU time (total): 3.127400e-01s  events (step): 129
  Sim time: 6.600000e+01    CPU time (total): 3.175520e-01s  events (step): 164
  Sim time: 6.700000e+01    CPU time (total): 3.221600e-01s  events (step): 158
  Sim time: 6.800000e+01    CPU time (total): 3.260740e-01s  events (step): 147
  Sim time: 6.900000e+01    CPU time (total): 3.305240e-01s  events (step): 160
  Sim time: 7.000000e+01    CPU time (total): 3.348410e-01s  events (step): 148
  Sim time: 7.100000e+01    CPU time (total): 3.388450e-01s  events (step): 123
  Sim time: 7.200000e+01    CPU time (total): 3.440640e-01s  events (step): 179
  Sim time: 7.300000e+01    CPU time (total): 3.482030e-01s  events (step): 150
  Sim time: 7.400000e+01    CPU time (total): 3.516110e-01s  events (step): 127
  Sim time: 7.500000e+01    CPU time (total): 3.558420e-01s  events (step): 141
  Sim time: 7.600000e+01    CPU time (total): 3.605040e-01s  events (step): 157
  Sim time: 7.700000e+01    CPU time (total): 3.642830e-01s  events (step): 129
  Sim time: 7.800000e+01    CPU time (total): 3.679510e-01s  events (step): 135
  Sim time: 7.900000e+01    CPU time (total): 3.721520e-01s  events (step): 150
  Sim time: 8.000000e+01    CPU time (total): 3.776220e-01s  events (step): 159
  Sim time: 8.100000e+01    CPU time (total): 3.818720e-01s  events (step): 141
  Sim time: 8.200000e+01    CPU time (total): 3.874290e-01s  events (step): 153
  Sim time: 8.300000e+01    CPU time (total): 3.945790e-01s  events (step): 201
  Sim time: 8.400000e+01    CPU time (total): 3.997060e-01s  events (step): 154
  Sim time: 8.500000e+01    CPU time (total): 4.051380e-01s  events (step): 178
  Sim time: 8.600000e+01    CPU time (total): 4.096630e-01s  events (step): 139
  Sim time: 8.700000e+01    CPU time (total): 4.130100e-01s  events (step): 115
  Sim time: 8.800000e+01    CPU time (total): 4.179330e-01s  events (step): 157
  Sim time: 8.900000e+01    CPU time (total): 4.227070e-01s  events (step): 154
  Sim time: 9.000000e+01    CPU time (total): 4.274860e-01s  events (step): 157
  Sim time: 9.100000e+01    CPU time (total): 4.318260e-01s  events (step): 130
  Sim time: 9.200000e+01    CPU time (total): 4.362890e-01s  events (step): 157
  Sim time: 9.300000e+01    CPU time (total): 4.412640e-01s  events (step): 158
  Sim time: 9.400000e+01    CPU time (total): 4.466500e-01s  events (step): 170
  Sim time: 9.500000e+01    CPU time (total): 4.514990e-01s  events (step): 169
  Sim time: 9.600000e+01    CPU time (total): 4.560200e-01s  events (step): 137
  Sim time: 9.700000e+01    CPU time (total): 4.624240e-01s  events (step): 199
  Sim time: 9.800000e+01    CPU time (total): 4.669400e-01s  events (step): 149
  Sim time: 9.900000e+01    CPU time (total): 4.713610e-01s  events (step): 145
  Sim time: 1.000000e+02    CPU time (total): 4.756020e-01s  events (step): 145

     You just simulated 15546 reactions in 4.757520e-01s
     ( 3.267669e+04 reactions/sec, 3.060286e-05 CPU seconds/event )
     Null events: 0   (3.060286e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 1.06919s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmpvcz2dw_z/task.species
  Read 1 unique species of 74 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 1.67 s.
  Finished processing file /tmp/tmpvcz2dw_z/task.bngl.
  CPU TIME: total 7.59 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic2DPlots (14.9 s)

Test that a simulator produces logarithmic 2D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 3 curves

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmpek28t6q7/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmpek28t6q7/task.xml.
  Running NFsim on 2c8ce9364d40
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpek28t6q7/task.xml -o /tmp/tmpek28t6q7/task.gdat -sim 100 -oSteps 100 -seed 193300752 -cb -ss /tmp/tmpek28t6q7/task.species
  [simulation PID is: 14]
  starting NFsim v1.12.1...

  Seeding random number generator with: 193300752
  reading xml file (/tmp/tmpek28t6q7/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 2.320000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 5.049000e-03s  events (step): 135
  Sim time: 2.000000e+00    CPU time (total): 1.111400e-02s  events (step): 200
  Sim time: 3.000000e+00    CPU time (total): 1.548700e-02s  events (step): 148
  Sim time: 4.000000e+00    CPU time (total): 2.000400e-02s  events (step): 165
  Sim time: 5.000000e+00    CPU time (total): 2.625500e-02s  events (step): 191
  Sim time: 6.000000e+00    CPU time (total): 3.109400e-02s  events (step): 176
  Sim time: 7.000000e+00    CPU time (total): 3.556800e-02s  events (step): 147
  Sim time: 8.000000e+00    CPU time (total): 3.966700e-02s  events (step): 153
  Sim time: 9.000000e+00    CPU time (total): 4.612200e-02s  events (step): 206
  Sim time: 1.000000e+01    CPU time (total): 5.080200e-02s  events (step): 174
  Sim time: 1.100000e+01    CPU time (total): 5.732600e-02s  events (step): 212
  Sim time: 1.200000e+01    CPU time (total): 6.240900e-02s  events (step): 162
  Sim time: 1.300000e+01    CPU time (total): 6.597500e-02s  events (step): 114
  Sim time: 1.400000e+01    CPU time (total): 6.991100e-02s  events (step): 143
  Sim time: 1.500000e+01    CPU time (total): 7.533700e-02s  events (step): 187
  Sim time: 1.600000e+01    CPU time (total): 7.976000e-02s  events (step): 151
  Sim time: 1.700000e+01    CPU time (total): 8.462600e-02s  events (step): 157
  Sim time: 1.800000e+01    CPU time (total): 8.929400e-02s  events (step): 155
  Sim time: 1.900000e+01    CPU time (total): 9.417200e-02s  events (step): 173
  Sim time: 2.000000e+01    CPU time (total): 9.931500e-02s  events (step): 175
  Sim time: 2.100000e+01    CPU time (total): 1.037780e-01s  events (step): 144
  Sim time: 2.200000e+01    CPU time (total): 1.075110e-01s  events (step): 132
  Sim time: 2.300000e+01    CPU time (total): 1.113310e-01s  events (step): 136
  Sim time: 2.400000e+01    CPU time (total): 1.154360e-01s  events (step): 152
  Sim time: 2.500000e+01    CPU time (total): 1.211310e-01s  events (step): 192
  Sim time: 2.600000e+01    CPU time (total): 1.265310e-01s  events (step): 179
  Sim time: 2.700000e+01    CPU time (total): 1.318380e-01s  events (step): 190
  Sim time: 2.800000e+01    CPU time (total): 1.358870e-01s  events (step): 125
  Sim time: 2.900000e+01    CPU time (total): 1.401630e-01s  events (step): 150
  Sim time: 3.000000e+01    CPU time (total): 1.446570e-01s  events (step): 149
  Sim time: 3.100000e+01    CPU time (total): 1.493550e-01s  events (step): 149
  Sim time: 3.200000e+01    CPU time (total): 1.555950e-01s  events (step): 190
  Sim time: 3.300000e+01    CPU time (total): 1.597520e-01s  events (step): 142
  Sim time: 3.400000e+01    CPU time (total): 1.662600e-01s  events (step): 175
  Sim time: 3.500000e+01    CPU time (total): 1.714540e-01s  events (step): 162
  Sim time: 3.600000e+01    CPU time (total): 1.772990e-01s  events (step): 197
  Sim time: 3.700000e+01    CPU time (total): 1.820030e-01s  events (step): 146
  Sim time: 3.800000e+01    CPU time (total): 1.870890e-01s  events (step): 181
  Sim time: 3.900000e+01    CPU time (total): 1.918140e-01s  events (step): 163
  Sim time: 4.000000e+01    CPU time (total): 1.973320e-01s  events (step): 183
  Sim time: 4.100000e+01    CPU time (total): 2.029050e-01s  events (step): 190
  Sim time: 4.200000e+01    CPU time (total): 2.065740e-01s  events (step): 114
  Sim time: 4.300000e+01    CPU time (total): 2.107510e-01s  events (step): 140
  Sim time: 4.400000e+01    CPU time (total): 2.159410e-01s  events (step): 178
  Sim time: 4.500000e+01    CPU time (total): 2.206280e-01s  events (step): 166
  Sim time: 4.600000e+01    CPU time (total): 2.261300e-01s  events (step): 162
  Sim time: 4.700000e+01    CPU time (total): 2.296310e-01s  events (step): 123
  Sim time: 4.800000e+01    CPU time (total): 2.338020e-01s  events (step): 134
  Sim time: 4.900000e+01    CPU time (total): 2.388250e-01s  events (step): 171
  Sim time: 5.000000e+01    CPU time (total): 2.445990e-01s  events (step): 189
  Sim time: 5.100000e+01    CPU time (total): 2.488710e-01s  events (step): 143
  Sim time: 5.200000e+01    CPU time (total): 2.541030e-01s  events (step): 177
  Sim time: 5.300000e+01    CPU time (total): 2.617040e-01s  events (step): 209
  Sim time: 5.400000e+01    CPU time (total): 2.824330e-01s  events (step): 506
  Sim time: 5.500000e+01    CPU time (total): 3.143270e-01s  events (step): 803
  Sim time: 5.600000e+01    CPU time (total): 3.514820e-01s  events (step): 872
  Sim time: 5.700000e+01    CPU time (total): 3.928660e-01s  events (step): 877
  Sim time: 5.800000e+01    CPU time (total): 4.348650e-01s  events (step): 991
  Sim time: 5.900000e+01    CPU time (total): 4.782090e-01s  events (step): 1003
  Sim time: 6.000000e+01    CPU time (total): 5.244870e-01s  events (step): 1057
  Sim time: 6.100000e+01    CPU time (total): 5.884150e-01s  events (step): 1050
  Sim time: 6.200000e+01    CPU time (total): 6.376990e-01s  events (step): 1144
  Sim time: 6.300000e+01    CPU time (total): 7.171550e-01s  events (step): 1511
  Sim time: 6.400000e+01    CPU time (total): 8.175590e-01s  events (step): 1607
  Sim time: 6.500000e+01    CPU time (total): 9.208640e-01s  events (step): 1786
  Sim time: 6.600000e+01    CPU time (total): 1.011848e+00s  events (step): 1636
  Sim time: 6.700000e+01    CPU time (total): 1.110126e+00s  events (step): 1730
  Sim time: 6.800000e+01    CPU time (total): 1.216182e+00s  events (step): 1983
  Sim time: 6.900000e+01    CPU time (total): 1.281969e+00s  events (step): 1523
  Sim time: 7.000000e+01    CPU time (total): 1.339797e+00s  events (step): 1380
  Sim time: 7.100000e+01    CPU time (total): 1.407188e+00s  events (step): 1551
  Sim time: 7.200000e+01    CPU time (total): 1.479442e+00s  events (step): 1441
  Sim time: 7.300000e+01    CPU time (total): 1.552739e+00s  events (step): 1260
  Sim time: 7.400000e+01    CPU time (total): 1.622551e+00s  events (step): 1282
  Sim time: 7.500000e+01    CPU time (total): 1.688176e+00s  events (step): 1223
  Sim time: 7.600000e+01    CPU time (total): 1.764282e+00s  events (step): 1471
  Sim time: 7.700000e+01    CPU time (total): 1.848083e+00s  events (step): 1600
  Sim time: 7.800000e+01    CPU time (total): 1.942778e+00s  events (step): 1795
  Sim time: 7.900000e+01    CPU time (total): 2.052510e+00s  events (step): 1934
  Sim time: 8.000000e+01    CPU time (total): 2.162890e+00s  events (step): 1868
  Sim time: 8.100000e+01    CPU time (total): 2.284457e+00s  events (step): 2023
  Sim time: 8.200000e+01    CPU time (total): 2.391894e+00s  events (step): 1994
  Sim time: 8.300000e+01    CPU time (total): 2.487382e+00s  events (step): 1903
  Sim time: 8.400000e+01    CPU time (total): 2.607512e+00s  events (step): 2013
  Sim time: 8.500000e+01    CPU time (total): 2.721172e+00s  events (step): 2194
  Sim time: 8.600000e+01    CPU time (total): 2.827981e+00s  events (step): 2101
  Sim time: 8.700000e+01    CPU time (total): 2.925573e+00s  events (step): 1836
  Sim time: 8.800000e+01    CPU time (total): 3.029056e+00s  events (step): 2039
  Sim time: 8.900000e+01    CPU time (total): 3.117488e+00s  events (step): 1870
  Sim time: 9.000000e+01    CPU time (total): 3.236930e+00s  events (step): 1896
  Sim time: 9.100000e+01    CPU time (total): 3.375179e+00s  events (step): 2005
  Sim time: 9.200000e+01    CPU time (total): 3.509718e+00s  events (step): 2312
  Sim time: 9.300000e+01    CPU time (total): 3.653688e+00s  events (step): 2497
  Sim time: 9.400000e+01    CPU time (total): 3.794758e+00s  events (step): 2319
  Sim time: 9.500000e+01    CPU time (total): 3.929520e+00s  events (step): 2395
  Sim time: 9.600000e+01    CPU time (total): 4.064745e+00s  events (step): 2403
  Sim time: 9.700000e+01    CPU time (total): 4.203431e+00s  events (step): 2239
  Sim time: 9.800000e+01    CPU time (total): 4.305390e+00s  events (step): 1952
  Sim time: 9.900000e+01    CPU time (total): 4.424864e+00s  events (step): 1911
  Sim time: 1.000000e+02    CPU time (total): 4.524790e+00s  events (step): 1777

     You just simulated 87221 reactions in 4.525114e+00s
     ( 1.927487e+04 reactions/sec, 5.188101e-05 CPU seconds/event )
     Null events: 0   (5.188101e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 5.13532s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmpek28t6q7/task.species
  Read 4 unique species of 74 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 5.78 s.
  Finished processing file /tmp/tmpek28t6q7/task.bngl.
  CPU TIME: total 11.68 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesLogarithmic3DPlots (11.2 s)

Test that a simulator produces logarithmic 3D plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 1 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (1):
        plot_0: 3 surfaces

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmp8cqq0b1l/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmp8cqq0b1l/task.xml.
  Running NFsim on 93e146429b92
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmp8cqq0b1l/task.xml -o /tmp/tmp8cqq0b1l/task.gdat -sim 100 -oSteps 100 -cb -seed 109440741 -ss /tmp/tmp8cqq0b1l/task.species
  [simulation PID is: 15]
  starting NFsim v1.12.1...

  Seeding random number generator with: 109440741
  reading xml file (/tmp/tmp8cqq0b1l/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 2.240000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 5.599000e-03s  events (step): 144
  Sim time: 2.000000e+00    CPU time (total): 1.044000e-02s  events (step): 169
  Sim time: 3.000000e+00    CPU time (total): 1.550600e-02s  events (step): 176
  Sim time: 4.000000e+00    CPU time (total): 2.095100e-02s  events (step): 164
  Sim time: 5.000000e+00    CPU time (total): 2.565000e-02s  events (step): 162
  Sim time: 6.000000e+00    CPU time (total): 3.036100e-02s  events (step): 167
  Sim time: 7.000000e+00    CPU time (total): 3.646000e-02s  events (step): 190
  Sim time: 8.000000e+00    CPU time (total): 4.043200e-02s  events (step): 137
  Sim time: 9.000000e+00    CPU time (total): 4.495900e-02s  events (step): 153
  Sim time: 1.000000e+01    CPU time (total): 5.052400e-02s  events (step): 189
  Sim time: 1.100000e+01    CPU time (total): 5.477200e-02s  events (step): 147
  Sim time: 1.200000e+01    CPU time (total): 5.838500e-02s  events (step): 125
  Sim time: 1.300000e+01    CPU time (total): 6.242500e-02s  events (step): 142
  Sim time: 1.400000e+01    CPU time (total): 6.632800e-02s  events (step): 127
  Sim time: 1.500000e+01    CPU time (total): 7.030300e-02s  events (step): 142
  Sim time: 1.600000e+01    CPU time (total): 7.573900e-02s  events (step): 186
  Sim time: 1.700000e+01    CPU time (total): 8.026500e-02s  events (step): 147
  Sim time: 1.800000e+01    CPU time (total): 8.507100e-02s  events (step): 159
  Sim time: 1.900000e+01    CPU time (total): 8.953300e-02s  events (step): 154
  Sim time: 2.000000e+01    CPU time (total): 9.412300e-02s  events (step): 164
  Sim time: 2.100000e+01    CPU time (total): 9.907000e-02s  events (step): 167
  Sim time: 2.200000e+01    CPU time (total): 1.036030e-01s  events (step): 157
  Sim time: 2.300000e+01    CPU time (total): 1.080720e-01s  events (step): 143
  Sim time: 2.400000e+01    CPU time (total): 1.128960e-01s  events (step): 170
  Sim time: 2.500000e+01    CPU time (total): 1.181880e-01s  events (step): 189
  Sim time: 2.600000e+01    CPU time (total): 1.219360e-01s  events (step): 132
  Sim time: 2.700000e+01    CPU time (total): 1.263630e-01s  events (step): 155
  Sim time: 2.800000e+01    CPU time (total): 1.317940e-01s  events (step): 186
  Sim time: 2.900000e+01    CPU time (total): 1.351050e-01s  events (step): 112
  Sim time: 3.000000e+01    CPU time (total): 1.401360e-01s  events (step): 170
  Sim time: 3.100000e+01    CPU time (total): 1.452930e-01s  events (step): 173
  Sim time: 3.200000e+01    CPU time (total): 1.494140e-01s  events (step): 138
  Sim time: 3.300000e+01    CPU time (total): 1.553310e-01s  events (step): 193
  Sim time: 3.400000e+01    CPU time (total): 1.608950e-01s  events (step): 167
  Sim time: 3.500000e+01    CPU time (total): 1.653180e-01s  events (step): 128
  Sim time: 3.600000e+01    CPU time (total): 1.714840e-01s  events (step): 192
  Sim time: 3.700000e+01    CPU time (total): 1.777750e-01s  events (step): 204
  Sim time: 3.800000e+01    CPU time (total): 1.820250e-01s  events (step): 133
  Sim time: 3.900000e+01    CPU time (total): 1.871120e-01s  events (step): 161
  Sim time: 4.000000e+01    CPU time (total): 1.919820e-01s  events (step): 160
  Sim time: 4.100000e+01    CPU time (total): 1.966340e-01s  events (step): 147
  Sim time: 4.200000e+01    CPU time (total): 2.021310e-01s  events (step): 187
  Sim time: 4.300000e+01    CPU time (total): 2.087310e-01s  events (step): 203
  Sim time: 4.400000e+01    CPU time (total): 2.123990e-01s  events (step): 123
  Sim time: 4.500000e+01    CPU time (total): 2.176020e-01s  events (step): 175
  Sim time: 4.600000e+01    CPU time (total): 2.228930e-01s  events (step): 182
  Sim time: 4.700000e+01    CPU time (total): 2.284770e-01s  events (step): 179
  Sim time: 4.800000e+01    CPU time (total): 2.331600e-01s  events (step): 153
  Sim time: 4.900000e+01    CPU time (total): 2.384910e-01s  events (step): 167
  Sim time: 5.000000e+01    CPU time (total): 2.431710e-01s  events (step): 168
  Sim time: 5.100000e+01    CPU time (total): 2.472730e-01s  events (step): 134
  Sim time: 5.200000e+01    CPU time (total): 2.526540e-01s  events (step): 165
  Sim time: 5.300000e+01    CPU time (total): 2.576690e-01s  events (step): 169
  Sim time: 5.400000e+01    CPU time (total): 2.626040e-01s  events (step): 168
  Sim time: 5.500000e+01    CPU time (total): 2.669970e-01s  events (step): 148
  Sim time: 5.600000e+01    CPU time (total): 2.719880e-01s  events (step): 150
  Sim time: 5.700000e+01    CPU time (total): 2.775770e-01s  events (step): 187
  Sim time: 5.800000e+01    CPU time (total): 2.823240e-01s  events (step): 144
  Sim time: 5.900000e+01    CPU time (total): 2.893220e-01s  events (step): 228
  Sim time: 6.000000e+01    CPU time (total): 2.939480e-01s  events (step): 155
  Sim time: 6.100000e+01    CPU time (total): 2.989180e-01s  events (step): 148
  Sim time: 6.200000e+01    CPU time (total): 3.045460e-01s  events (step): 164
  Sim time: 6.300000e+01    CPU time (total): 3.100810e-01s  events (step): 173
  Sim time: 6.400000e+01    CPU time (total): 3.142720e-01s  events (step): 139
  Sim time: 6.500000e+01    CPU time (total): 3.187280e-01s  events (step): 153
  Sim time: 6.600000e+01    CPU time (total): 3.225940e-01s  events (step): 145
  Sim time: 6.700000e+01    CPU time (total): 3.267990e-01s  events (step): 141
  Sim time: 6.800000e+01    CPU time (total): 3.318790e-01s  events (step): 154
  Sim time: 6.900000e+01    CPU time (total): 3.376610e-01s  events (step): 163
  Sim time: 7.000000e+01    CPU time (total): 3.436200e-01s  events (step): 193
  Sim time: 7.100000e+01    CPU time (total): 3.506810e-01s  events (step): 225
  Sim time: 7.200000e+01    CPU time (total): 3.554010e-01s  events (step): 167
  Sim time: 7.300000e+01    CPU time (total): 3.600660e-01s  events (step): 147
  Sim time: 7.400000e+01    CPU time (total): 3.646550e-01s  events (step): 144
  Sim time: 7.500000e+01    CPU time (total): 3.691380e-01s  events (step): 146
  Sim time: 7.600000e+01    CPU time (total): 3.733790e-01s  events (step): 139
  Sim time: 7.700000e+01    CPU time (total): 3.776900e-01s  events (step): 146
  Sim time: 7.800000e+01    CPU time (total): 3.822110e-01s  events (step): 147
  Sim time: 7.900000e+01    CPU time (total): 3.865870e-01s  events (step): 148
  Sim time: 8.000000e+01    CPU time (total): 3.909480e-01s  events (step): 137
  Sim time: 8.100000e+01    CPU time (total): 3.951220e-01s  events (step): 125
  Sim time: 8.200000e+01    CPU time (total): 4.012730e-01s  events (step): 207
  Sim time: 8.300000e+01    CPU time (total): 4.069760e-01s  events (step): 185
  Sim time: 8.400000e+01    CPU time (total): 4.115790e-01s  events (step): 138
  Sim time: 8.500000e+01    CPU time (total): 4.171630e-01s  events (step): 180
  Sim time: 8.600000e+01    CPU time (total): 4.214060e-01s  events (step): 146
  Sim time: 8.700000e+01    CPU time (total): 4.263360e-01s  events (step): 155
  Sim time: 8.800000e+01    CPU time (total): 4.313100e-01s  events (step): 144
  Sim time: 8.900000e+01    CPU time (total): 4.368160e-01s  events (step): 170
  Sim time: 9.000000e+01    CPU time (total): 4.433550e-01s  events (step): 206
  Sim time: 9.100000e+01    CPU time (total): 4.491470e-01s  events (step): 164
  Sim time: 9.200000e+01    CPU time (total): 4.542120e-01s  events (step): 166
  Sim time: 9.300000e+01    CPU time (total): 4.590830e-01s  events (step): 150
  Sim time: 9.400000e+01    CPU time (total): 4.641400e-01s  events (step): 163
  Sim time: 9.500000e+01    CPU time (total): 4.700570e-01s  events (step): 203
  Sim time: 9.600000e+01    CPU time (total): 4.755200e-01s  events (step): 174
  Sim time: 9.700000e+01    CPU time (total): 4.797690e-01s  events (step): 134
  Sim time: 9.800000e+01    CPU time (total): 4.858060e-01s  events (step): 180
  Sim time: 9.900000e+01    CPU time (total): 4.907420e-01s  events (step): 165
  Sim time: 1.000000e+02    CPU time (total): 4.963040e-01s  events (step): 181

     You just simulated 16162 reactions in 4.964740e-01s
     ( 3.255357e+04 reactions/sec, 3.071860e-05 CPU seconds/event )
     Null events: 0   (3.071860e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 1.11805s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmp8cqq0b1l/task.species
  Read 0 unique species of 73 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 1.69 s.
  Finished processing file /tmp/tmp8cqq0b1l/task.bngl.
  CPU TIME: total 7.81 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:230: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot3D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorProducesMultiplePlots (16.2 s)

Test that a simulator produces multiple plots

Warnings:

  Simulator did not produce plots

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 0 reports, and 2 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Plots (2):
        plot_0: 2 curves
        plot_1: 1 curves

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  BioNetGen version 2.5.2
  Reading from file /tmp/tmpz_xo5cuu/task.bngl (level 0)
  Read 73 parameters.
  Read 74 molecule types.
  Read 75 species.
  Read 178 observable(s).
  Read 9 functions.
  Read 2339 reaction rule(s).
  ACTION: simulate( method=>"nf" )
  NetworkFree simulation using nf
  ACTION: simulate_nf( )
  Wrote model in xml format to /tmp/tmpz_xo5cuu/task.xml.
  Running NFsim on cdb9fea18a12
  full command: /opt/BioNetGen-2.5.2/bin/NFsim -xml /tmp/tmpz_xo5cuu/task.xml -o /tmp/tmpz_xo5cuu/task.gdat -sim 100 -oSteps 100 -cb -ss /tmp/tmpz_xo5cuu/task.species -seed 497220219
  [simulation PID is: 14]
  starting NFsim v1.12.1...

  Seeding random number generator with: 497220219
  reading xml file (/tmp/tmpz_xo5cuu/task.xml)  
    [-------]
  preparing simulation...

  Equilibrating for :0s.  Please wait.

  simulating system for: 1.000000e+02 second(s).

  Sim time: 0.000000e+00    CPU time (total): 2.140000e-04s  events (step): 0
  Sim time: 1.000000e+00    CPU time (total): 1.238900e-02s  events (step): 188
  Sim time: 2.000000e+00    CPU time (total): 1.675900e-02s  events (step): 174
  Sim time: 3.000000e+00    CPU time (total): 2.115600e-02s  events (step): 170
  Sim time: 4.000000e+00    CPU time (total): 2.634300e-02s  events (step): 188
  Sim time: 5.000000e+00    CPU time (total): 3.037300e-02s  events (step): 167
  Sim time: 6.000000e+00    CPU time (total): 3.490600e-02s  events (step): 147
  Sim time: 7.000000e+00    CPU time (total): 4.007400e-02s  events (step): 188
  Sim time: 8.000000e+00    CPU time (total): 4.356800e-02s  events (step): 121
  Sim time: 9.000000e+00    CPU time (total): 4.788100e-02s  events (step): 138
  Sim time: 1.000000e+01    CPU time (total): 5.256400e-02s  events (step): 170
  Sim time: 1.100000e+01    CPU time (total): 5.651600e-02s  events (step): 132
  Sim time: 1.200000e+01    CPU time (total): 6.164200e-02s  events (step): 182
  Sim time: 1.300000e+01    CPU time (total): 6.727400e-02s  events (step): 188
  Sim time: 1.400000e+01    CPU time (total): 7.163400e-02s  events (step): 167
  Sim time: 1.500000e+01    CPU time (total): 7.542500e-02s  events (step): 148
  Sim time: 1.600000e+01    CPU time (total): 8.031500e-02s  events (step): 146
  Sim time: 1.700000e+01    CPU time (total): 8.446300e-02s  events (step): 150
  Sim time: 1.800000e+01    CPU time (total): 8.979100e-02s  events (step): 157
  Sim time: 1.900000e+01    CPU time (total): 9.517900e-02s  events (step): 165
  Sim time: 2.000000e+01    CPU time (total): 9.885100e-02s  events (step): 136
  Sim time: 2.100000e+01    CPU time (total): 1.041300e-01s  events (step): 166
  Sim time: 2.200000e+01    CPU time (total): 1.085410e-01s  events (step): 142
  Sim time: 2.300000e+01    CPU time (total): 1.135430e-01s  events (step): 154
  Sim time: 2.400000e+01    CPU time (total): 1.185680e-01s  events (step): 168
  Sim time: 2.500000e+01    CPU time (total): 1.227120e-01s  events (step): 137
  Sim time: 2.600000e+01    CPU time (total): 1.285130e-01s  events (step): 172
  Sim time: 2.700000e+01    CPU time (total): 1.335790e-01s  events (step): 175
  Sim time: 2.800000e+01    CPU time (total): 1.389730e-01s  events (step): 175
  Sim time: 2.900000e+01    CPU time (total): 1.452310e-01s  events (step): 179
  Sim time: 3.000000e+01    CPU time (total): 1.504990e-01s  events (step): 156
  Sim time: 3.100000e+01    CPU time (total): 1.556340e-01s  events (step): 156
  Sim time: 3.200000e+01    CPU time (total): 1.612280e-01s  events (step): 175
  Sim time: 3.300000e+01    CPU time (total): 1.657810e-01s  events (step): 138
  Sim time: 3.400000e+01    CPU time (total): 1.713970e-01s  events (step): 158
  Sim time: 3.500000e+01    CPU time (total): 1.767490e-01s  events (step): 156
  Sim time: 3.600000e+01    CPU time (total): 1.808110e-01s  events (step): 127
  Sim time: 3.700000e+01    CPU time (total): 1.862410e-01s  events (step): 168
  Sim time: 3.800000e+01    CPU time (total): 1.920040e-01s  events (step): 180
  Sim time: 3.900000e+01    CPU time (total): 1.978170e-01s  events (step): 187
  Sim time: 4.000000e+01    CPU time (total): 2.027770e-01s  events (step): 170
  Sim time: 4.100000e+01    CPU time (total): 2.085340e-01s  events (step): 152
  Sim time: 4.200000e+01    CPU time (total): 2.127450e-01s  events (step): 136
  Sim time: 4.300000e+01    CPU time (total): 2.179060e-01s  events (step): 163
  Sim time: 4.400000e+01    CPU time (total): 2.457780e-01s  events (step): 599
  Sim time: 4.500000e+01    CPU time (total): 3.105860e-01s  events (step): 1405
  Sim time: 4.600000e+01    CPU time (total): 3.719910e-01s  events (step): 1331
  Sim time: 4.700000e+01    CPU time (total): 4.409900e-01s  events (step): 1501
  Sim time: 4.800000e+01    CPU time (total): 5.183970e-01s  events (step): 1659
  Sim time: 4.900000e+01    CPU time (total): 5.946880e-01s  events (step): 1671
  Sim time: 5.000000e+01    CPU time (total): 6.653240e-01s  events (step): 1577
  Sim time: 5.100000e+01    CPU time (total): 7.485610e-01s  events (step): 1724
  Sim time: 5.200000e+01    CPU time (total): 8.345730e-01s  events (step): 1894
  Sim time: 5.300000e+01    CPU time (total): 9.431510e-01s  events (step): 2022
  Sim time: 5.400000e+01    CPU time (total): 1.048416e+00s  events (step): 2234
  Sim time: 5.500000e+01    CPU time (total): 1.151723e+00s  events (step): 2416
  Sim time: 5.600000e+01    CPU time (total): 1.267075e+00s  events (step): 2413
  Sim time: 5.700000e+01    CPU time (total): 1.369629e+00s  events (step): 2381
  Sim time: 5.800000e+01    CPU time (total): 1.496972e+00s  events (step): 2405
  Sim time: 5.900000e+01    CPU time (total): 1.605937e+00s  events (step): 2465
  Sim time: 6.000000e+01    CPU time (total): 1.721729e+00s  events (step): 2308
  Sim time: 6.100000e+01    CPU time (total): 1.835450e+00s  events (step): 2197
  Sim time: 6.200000e+01    CPU time (total): 1.963356e+00s  events (step): 2372
  Sim time: 6.300000e+01    CPU time (total): 2.092250e+00s  events (step): 2277
  Sim time: 6.400000e+01    CPU time (total): 2.213478e+00s  events (step): 2267
  Sim time: 6.500000e+01    CPU time (total): 2.322977e+00s  events (step): 2093
  Sim time: 6.600000e+01    CPU time (total): 2.437753e+00s  events (step): 2157
  Sim time: 6.700000e+01    CPU time (total): 2.561583e+00s  events (step): 2162
  Sim time: 6.800000e+01    CPU time (total): 2.681349e+00s  events (step): 2167
  Sim time: 6.900000e+01    CPU time (total): 2.804805e+00s  events (step): 2181
  Sim time: 7.000000e+01    CPU time (total): 2.918090e+00s  events (step): 1919
  Sim time: 7.100000e+01    CPU time (total): 3.037166e+00s  events (step): 2002
  Sim time: 7.200000e+01    CPU time (total): 3.144264e+00s  events (step): 2008
  Sim time: 7.300000e+01    CPU time (total): 3.250444e+00s  events (step): 1956
  Sim time: 7.400000e+01    CPU time (total): 3.346381e+00s  events (step): 1868
  Sim time: 7.500000e+01    CPU time (total): 3.456992e+00s  events (step): 2061
  Sim time: 7.600000e+01    CPU time (total): 3.564121e+00s  events (step): 2013
  Sim time: 7.700000e+01    CPU time (total): 3.676036e+00s  events (step): 2081
  Sim time: 7.800000e+01    CPU time (total): 3.790208e+00s  events (step): 2149
  Sim time: 7.900000e+01    CPU time (total): 3.885129e+00s  events (step): 1814
  Sim time: 8.000000e+01    CPU time (total): 3.969993e+00s  events (step): 1621
  Sim time: 8.100000e+01    CPU time (total): 4.065882e+00s  events (step): 1807
  Sim time: 8.200000e+01    CPU time (total): 4.162126e+00s  events (step): 1860
  Sim time: 8.300000e+01    CPU time (total): 4.255274e+00s  events (step): 1866
  Sim time: 8.400000e+01    CPU time (total): 4.357027e+00s  events (step): 1871
  Sim time: 8.500000e+01    CPU time (total): 4.464082e+00s  events (step): 2056
  Sim time: 8.600000e+01    CPU time (total): 4.563993e+00s  events (step): 1929
  Sim time: 8.700000e+01    CPU time (total): 4.643754e+00s  events (step): 1598
  Sim time: 8.800000e+01    CPU time (total): 4.717355e+00s  events (step): 1469
  Sim time: 8.900000e+01    CPU time (total): 4.805216e+00s  events (step): 1720
  Sim time: 9.000000e+01    CPU time (total): 4.897725e+00s  events (step): 1860
  Sim time: 9.100000e+01    CPU time (total): 4.982280e+00s  events (step): 1752
  Sim time: 9.200000e+01    CPU time (total): 5.072128e+00s  events (step): 1759
  Sim time: 9.300000e+01    CPU time (total): 5.165281e+00s  events (step): 1894
  Sim time: 9.400000e+01    CPU time (total): 5.267851e+00s  events (step): 2147
  Sim time: 9.500000e+01    CPU time (total): 5.365431e+00s  events (step): 2091
  Sim time: 9.600000e+01    CPU time (total): 5.452237e+00s  events (step): 2096
  Sim time: 9.700000e+01    CPU time (total): 5.533657e+00s  events (step): 1956
  Sim time: 9.800000e+01    CPU time (total): 5.630196e+00s  events (step): 2076
  Sim time: 9.900000e+01    CPU time (total): 5.706337e+00s  events (step): 1692
  Sim time: 1.000000e+02    CPU time (total): 5.777210e+00s  events (step): 1508

     You just simulated 117290 reactions in 5.777501e+00s
     ( 2.030116e+04 reactions/sec, 4.925826e-05 CPU seconds/event )
     Null events: 0   (4.925826e-05 CPU seconds/non-null event )

  saving list of final molecular species...

  done.  Total CPU time: 6.3467s

  SpeciesLabel max molecule threshold set to 20.
  WARNING: Species with more than 20 molecules will be labeled with the Quasi method.
  readNFspecies::Reading from file /tmp/tmpz_xo5cuu/task.species
  Read 4 unique species of 73 total.
  SpeciesLabel max molecule threshold set to 0.
    (all species will be labeled with the Auto method)
  CPU TIME: simulate 6.92 s.
  Finished processing file /tmp/tmpz_xo5cuu/task.bngl.
  CPU TIME: total 13.01 s.
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_0 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)
  /usr/local/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:217: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
    output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (3.0 s)

Test that a simulator supports multiple time courses with non-zero initial times

Warnings:

  The image 'ghcr.io/biosimulators/biosimulators_bionetgen/bionetgen:2.5.2' could not execute the archive:

    Unknown error

Log:

  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
    Dolan2015.sedml:
      Tasks (1):
        simulation_1
      Reports (1):
        report: 3 data sets

  Executing SED-ML file 0: Dolan2015.sedml
    Found 1 tasks
      simulation_1
    Executing task 1: simulation_1
  /usr/local/lib/python3.7/site-packages/biosimulators_bionetgen/core.py:98: IgnoredBnglFileContentWarning: Actions in the BNGL file were ignored.
    warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
  The initial time of a network free simulation (KISAO_0000263) must be 0.

[biosimulators-daemon]

The image for your simulator is valid!

[biosimulators-daemon]

The validation/submission of your simulator failed.

- 500 Server Error: Internal Server Error for url: https://api.biosimulators.org/simulators

The complete log of your validation/submission job, including further information about the failure, is available here.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

[jonrkarr]

Looks like there was an error with the API. I manually submitted the specs to the database.