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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.5.0.86-dev0 #658

Closed jcschaff closed 1 month ago

jcschaff commented 9 months ago

id: vcell version: 7.5.0.86-dev0 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.5.0.86-dev0/biosimulators.json specificationsPatch: version: 7.5.0.86-dev0 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.5.0.86-dev0 digest: "sha256:74950e33813980ea537589eb19db0d984fa4b2add884458f6b93b3177d663bcc" validateImage: true commitSimulator: true

biosimulators-daemon commented 9 months ago

The validation/submission of your simulator failed.

- expected a single document in the stream
-   in "<unicode string>", line 2, column 1:
-     id: vcell
-     ^
- but found another document
-   in "<unicode string>", line 12, column 1:
-     --- 
-     ^

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

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).

biosimulators-daemon commented 9 months ago

Thank you @jcschaff for your submission to the BioSimulators simulator validation/submission system!

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

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

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

biosimulators-daemon commented 9 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 9 months ago

Summary of tests

biosimulators-daemon commented 9 months ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (8.6 s)
Test that SED documents in nested directories can be executed Exception: ``` Simulator did not generate the following expected reports - `subdir/BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:93) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:115) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:509) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:477) - TempPath Created: /tmp/vcell_temp_6b871b72-6b4d-482d-a14a-ab3633e25e111259423783103065015 []{} INFO (SedmlJob:107) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:183) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 ERROR (Executable:165) - Command "/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64" ecountered a problem: : /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) []{} java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (Executable:439) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more ERROR (AbstractSolver:175) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more INFO (SolverHandler:425) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@299b9851 []{} INFO (SolverHandler:426) - Status: Aborted: SOLVER_ABORTED:Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida) []{} ERROR (SundialsSolver:295) - /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida (No such file or directory) []{} java.io.FileNotFoundException: /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida (No such file or directory) at java.base/java.io.FileInputStream.open0(Native Method) ~[?:?] at java.base/java.io.FileInputStream.open(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:289) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:186) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:428) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (SolverHandler:494) - Solver status: 3 []{} ERROR (SolverHandler:495) - Solver message: Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida) []{} ERROR (SolverHandler:501) - Failed execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:507) - Running simulation for 82 ms []{} ERROR (SolverHandler:525) - Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1926310382_0_.ida) []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:597) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:273) - Generating outputs... []{} INFO (SedmlJob:327) - Generating CSV file... []{} INFO (RunUtils:202) - Generating report `report`. []{} ERROR (SedmlJob:435) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null []{} java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.NullPointerException: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.sbml.vcell.SBMLNonspatialSimResults.getDataForSBMLVar(SBMLNonspatialSimResults.java:30) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:294) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 18 more WARN (SedmlJob:225) - Outputs could not be processed. []{} org.vcell.cli.exceptions.ExecutionException: error while processing outputs: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:292) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 16 more Caused by: java.lang.NullPointerException: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.sbml.vcell.SBMLNonspatialSimResults.getDataForSBMLVar(SBMLNonspatialSimResults.java:30) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:294) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 16 more ERROR (SedmlJob:435) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:306) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is nullFailure executing the sed document. []{} ERROR (ExecutionJob:144) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@492be039 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{} INFO (ExecutionJob:172) - Omex archive.omex processing completed (3s) []{} ```
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (9.6 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` Simulator did not generate the following expected reports - `subdir/BIOMD0000000912_sim.sedml/report` - `subdir__copy/BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:93) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:115) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:509) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:477) - TempPath Created: /tmp/vcell_temp_f16fa909-0568-4d04-b518-81e6a25f04eb617216222138561406 []{} INFO (SedmlJob:107) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:183) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 ERROR (Executable:165) - Command "/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64" ecountered a problem: : /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) []{} java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (Executable:439) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more ERROR (AbstractSolver:175) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more INFO (SolverHandler:425) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@261f359f []{} INFO (SolverHandler:426) - Status: Aborted: SOLVER_ABORTED:Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida) []{} ERROR (SundialsSolver:295) - /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida (No such file or directory) []{} java.io.FileNotFoundException: /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida (No such file or directory) at java.base/java.io.FileInputStream.open0(Native Method) ~[?:?] at java.base/java.io.FileInputStream.open(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:289) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:186) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:428) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (SolverHandler:494) - Solver status: 3 []{} ERROR (SolverHandler:495) - Solver message: Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida) []{} ERROR (SolverHandler:501) - Failed execution: Model 'archive_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:507) - Running simulation for 79 ms []{} ERROR (SolverHandler:525) - Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.cvodeInput /tmp/out/subdir/BIOMD0000000912_sim.sedml/SimID_1629712732_0_.ida) []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:597) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:273) - Generating outputs... []{} INFO (SedmlJob:327) - Generating CSV file... []{} INFO (RunUtils:202) - Generating report `report`. []{} ERROR (SedmlJob:435) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null []{} java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.NullPointerException: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.sbml.vcell.SBMLNonspatialSimResults.getDataForSBMLVar(SBMLNonspatialSimResults.java:30) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:294) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 18 more WARN (SedmlJob:225) - Outputs could not be processed. []{} org.vcell.cli.exceptions.ExecutionException: error while processing outputs: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:292) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 16 more Caused by: java.lang.NullPointerException: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.sbml.vcell.SBMLNonspatialSimResults.getDataForSBMLVar(SBMLNonspatialSimResults.java:30) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:294) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 16 more ERROR (SedmlJob:435) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:306) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is nullFailure executing the sed document. []{} ERROR (ExecutionJob:144) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@b1b471 []{} INFO (SedmlJob:107) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:183) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 ERROR (Executable:165) - Command "/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64" ecountered a problem: : /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) []{} java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run ...
biosimulators-daemon commented 9 months ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.7 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' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' 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: None
cli.CliDisplaysHelpInline (3.7 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interfaces should display basic help when no arguments are provided. The command-line interface displayed the following when no argument was provided: docker: Command recieved::<> <> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} ERROR (BiosimulationsCommand:107) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{} java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null at org.vcell.cli.CLIRecorder.(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.CLIRecorder.(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:49) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ``` ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: docker: Command recieved::<-h> <-h> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: docker: Command recieved::<--help> <--help> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} Usage: CLIStandalone biosimulations [-dhqv] [-i=] [-o=] BioSimulators-compliant command-line interface to the vcell simulation program . -d, --debug full application debug mode -h, --help show this help message and exit -i, --archive= Path to a COMBINE/OMEX archive file which contains one or more SED-ML-encoded simulation experiments -o, --out-dir= Directory to save outputs -q, --quiet suppress all console output -v, --version show program's version number and exit ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.3 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: - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
docker_image.HasBioContainersLabels (0.2 s)
Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (8.4 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Warnings: ``` Plots were not produced: BIOMD0000000912_sim.sedml/Figure_1_bottom_left ``` Log: ``` docker: Command recieved::<-i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:93) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:115) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:509) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:477) - TempPath Created: /tmp/vcell_temp_06244b3b-0df4-46cf-b457-45c6bb64c46c18232569245478485744 []{} INFO (SedmlJob:107) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:183) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 ERROR (Executable:165) - Command "/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64" ecountered a problem: : /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) []{} java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (Executable:439) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more ERROR (AbstractSolver:175) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more INFO (SolverHandler:425) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@5a4dda2 []{} INFO (SolverHandler:426) - Status: Aborted: SOLVER_ABORTED:Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida) []{} ERROR (SundialsSolver:295) - /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida (No such file or directory) []{} java.io.FileNotFoundException: /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida (No such file or directory) at java.base/java.io.FileInputStream.open0(Native Method) ~[?:?] at java.base/java.io.FileInputStream.open(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:289) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:186) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:428) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (SolverHandler:494) - Solver status: 3 []{} ERROR (SolverHandler:495) - Solver message: Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida) []{} ERROR (SolverHandler:501) - Failed execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations_BIOMD0000000912_sim.sedml_BIOMD0000000912' Task 'Caravagna2010'. []{} INFO (SolverHandler:507) - Running simulation for 84 ms []{} ERROR (SolverHandler:525) - Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_2007119815_0_.ida) []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:597) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:273) - Generating outputs... []{} INFO (SedmlJob:327) - Generating CSV file... []{} INFO (RunUtils:196) - Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. []{} INFO (RunUtils:202) - Generating report `report`. []{} ERROR (SedmlJob:435) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null []{} java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.NullPointerException: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.sbml.vcell.SBMLNonspatialSimResults.getDataForSBMLVar(SBMLNonspatialSimResults.java:30) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:294) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 18 more WARN (SedmlJob:225) - Outputs could not be processed. []{} org.vcell.cli.exceptions.ExecutionException: error while processing outputs: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:292) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 16 more Caused by: java.lang.NullPointerException: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.sbml.vcell.SBMLNonspatialSimResults.getDataForSBMLVar(SBMLNonspatialSimResults.java:30) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:294) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 16 more ERROR (SedmlJob:435) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:306) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is nullFailure executing the sed document. []{} ERROR (ExecutionJob:144) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@357f6391 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{} INFO (ExecutionJob:172) - Omex Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex processing completed (3s) []{} ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (10.2 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Warnings: ``` Plots were not produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:93) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:115) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:509) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:477) - TempPath Created: /tmp/vcell_temp_82cf452e-8ee8-4a4e-941d-07bb3250195b6570706370555481506 []{} INFO (SedmlJob:107) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:120) - Processing SED-ML: simulation_1.sedml []{} INFO (SedmlJob:156) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:161) - Successful translation of SED-ML file : simulation_1.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SBMLImporter:2877) - failed to transform lumped reaction R1 to distributed: linear factor was null, lumped reaction R1 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R2 to distributed: linear factor was null, lumped reaction R2 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R3 to distributed: linear factor was null, lumped reaction R3 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R4 to distributed: linear factor was null, lumped reaction R4 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R5 to distributed: linear factor was null, lumped reaction R5 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R6 to distributed: linear factor was null, lumped reaction R6 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R7 to distributed: linear factor was null, lumped reaction R7 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R8 to distributed: linear factor was null, lumped reaction R8 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R9 to distributed: linear factor was null, lumped reaction R9 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R10 to distributed: linear factor was null, lumped reaction R10 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R11 to distributed: linear factor was null, lumped reaction R11 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R12 to distributed: linear factor was null, lumped reaction R12 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R13 to distributed: linear factor was null, lumped reaction R13 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R14 to distributed: linear factor was null, lumped reaction R14 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R15 to distributed: linear factor was null, lumped reaction R15 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R16 to distributed: linear factor was null, lumped reaction R16 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R18 to distributed: linear factor was null, lumped reaction R18 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R19 to distributed: linear factor was null, lumped reaction R19 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R20 to distributed: linear factor was null, lumped reaction R20 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R21 to distributed: linear factor was null, lumped reaction R21 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R22 to distributed: linear factor was null, lumped reaction R22 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R23 to distributed: linear factor was null, lumped reaction R23 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R24 to distributed: linear factor was null, lumped reaction R24 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R25 to distributed: linear factor was null, lumped reaction R25 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R26 to distributed: linear factor was null, lumped reaction R26 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R27 to distributed: linear factor was null, lumped reaction R27 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R28 to distributed: linear factor was null, lumped reaction R28 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R29 to distributed: linear factor was null, lumped reaction R29 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R30 to distributed: linear factor was null, lumped reaction R30 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R31 to distributed: linear factor was null, lumped reaction R31 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R32 to distributed: linear factor was null, lumped reaction R32 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R33 to distributed: linear factor was null, lumped reaction R33 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R34 to distributed: linear factor was null, lumped reaction R34 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R35 to distributed: linear factor was null, lumped reaction R35 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R36 to distributed: linear factor was null, lumped reaction R36 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R37 to distributed: linear factor was null, lumped reaction R37 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R38 to distributed: linear factor was null, lumped reaction R38 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R39 to distributed: linear factor was null, lumped reaction R39 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R40 to distributed: linear factor was null, lumped reaction R40 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R41 to distributed: linear factor was null, lumped reaction R41 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R42 to distributed: linear factor was null, lumped reaction R42 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R43 to distributed: linear factor was null, lumped reaction R43 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R44 to distributed: linear factor was null, lumped reaction R44 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R45 to distributed: linear factor was null, lumped reaction R45 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R46 to distributed: linear factor was null, lumped reaction R46 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R47 to distributed: linear factor was null, lumped reaction R47 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R48 to distributed: linear factor was null, lumped reaction R48 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R49 to distributed: linear factor was null, lumped reaction R49 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R50 to distributed: linear factor was null, lumped reaction R50 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R51 to distributed: linear factor was null, lumped reaction R51 could not be transformed to distributed []{} WARN (SBMLImporter:2877) - failed to transform lumped reaction R52 to distributed: linear factor was null, lumped reaction R52 could not be transformed to distributed []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:183) - Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 ERROR (Executable:165) - Command "/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64" ecountered a problem: : /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) []{} java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (Executable:439) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/simulation_1.sedml/SimID_1587378141_0_.cvodeInput /tmp/out/simulation_1.sedml/SimID_1587378141_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/simulation_1.sedml/SimID_1587378141_0_.cvodeInput /tmp/out/simulation_1.sedml/SimID_1587378141_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more ERROR (AbstractSolver:175) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/simulation_1.sedml/SimID_1587378141_0_.cvodeInput /tmp/out/simulation_1.sedml/SimID_1587378141_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/simulation_1.sedml/SimID_1587378141_0_.cvodeInput /tmp/out/simulation_1.sedml/SimID_1587378141_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsol ...
biosimulators-daemon commented 9 months ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (8.3 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:93) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:115) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:509) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:477) - TempPath Created: /tmp/vcell_temp_1b29f04a-814c-4489-a6ea-f93fa2074d3a2163247373001038628 []{} INFO (SedmlJob:107) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:156) - Found one SED-ML document with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:183) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 ERROR (Executable:165) - Command "/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64" ecountered a problem: : /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) []{} java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (Executable:439) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more ERROR (AbstractSolver:175) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more INFO (SolverHandler:425) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@6f85ee02 []{} INFO (SolverHandler:426) - Status: Aborted: SOLVER_ABORTED:Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida) []{} ERROR (SundialsSolver:295) - /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida (No such file or directory) []{} java.io.FileNotFoundException: /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida (No such file or directory) at java.base/java.io.FileInputStream.open0(Native Method) ~[?:?] at java.base/java.io.FileInputStream.open(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:289) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:186) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:428) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (SolverHandler:494) - Solver status: 3 []{} ERROR (SolverHandler:495) - Solver message: Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida) []{} ERROR (SolverHandler:501) - Failed execution: Model 'archive_BIOMD0000000912_sim.sedml___source__' Task 'Caravagna2010'. []{} INFO (SolverHandler:507) - Running simulation for 81 ms []{} ERROR (SolverHandler:525) - Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1141855803_0_.ida) []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:597) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:273) - Generating outputs... []{} INFO (SedmlJob:327) - Generating CSV file... []{} INFO (RunUtils:202) - Generating report `report`. []{} ERROR (SedmlJob:435) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null []{} java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.NullPointerException: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.sbml.vcell.SBMLNonspatialSimResults.getDataForSBMLVar(SBMLNonspatialSimResults.java:30) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:294) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 18 more WARN (SedmlJob:225) - Outputs could not be processed. []{} org.vcell.cli.exceptions.ExecutionException: error while processing outputs: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:292) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 16 more Caused by: java.lang.NullPointerException: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.sbml.vcell.SBMLNonspatialSimResults.getDataForSBMLVar(SBMLNonspatialSimResults.java:30) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:294) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] ... 16 more ERROR (SedmlJob:435) - Failure executing the sed document. []{} java.lang.RuntimeException: Failure executing the sed document. at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:298) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:227) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] WARN (SedmlJob:306) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is nullFailure executing the sed document. []{} ERROR (ExecutionJob:144) - Processing of SedML has failed. org.vcell.cli.run.SedmlStatistics@26457986 []{} INFO (NativeLib:33) - Loading jhdf5 []{} INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/tmp/out []{} INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{} INFO (ExecutionJob:172) - Omex archive.omex processing completed (3s) []{} ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (8.5 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out> <-i> Default case selected VCell shall execute WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release INFO (CLIStandalone:36) - Starting Vcell... []{} INFO (BiosimulationsCommand:93) - Beginning execution []{} INFO (CLIPythonManager:116) - Initializing Python... []{} INFO (CLIPythonManager:136) - Python initialization success! []{} INFO (ExecuteImpl:115) - Preparing output directory... []{} ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{} ERROR (RunUtils:509) - java.lang.Exception: File '/tmp/out' could not be deleted! []{} INFO (ExecutionJob:86) - Executing OMEX archive /tmp/in/archive.omex []{} ----------------------------------------------------------------------------------------------------- INFO (NativeLib:33) - Loading combinej []{} INFO (RunUtils:477) - TempPath Created: /tmp/vcell_temp_fe64ae96-2167-449d-b323-8de71232816e5348549571241209541 []{} INFO (SedmlJob:107) - Initializing SED-ML document... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:120) - Processing SED-ML: BIOMD0000000912_sim.sedml []{} INFO (SedmlJob:156) - Found one SED-ML document with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) []{} INFO (SedmlJob:161) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{} ----------------------------------------------------------------------------------------------------- INFO (SedmlJob:165) - Creating pseudo SED-ML for HDF5 conversion... []{} INFO (SedmlJob:177) - Creating Biomodel from pseudo SED-ML []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail INFO (SedmlJob:238) - Building solvers and starting simulation of all tasks... []{} SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} WARN (SolverUtilities:168) - KISAO - bad format, skipping []{} INFO (SEDMLImporter:183) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{} taskToSimulationMap: 1 taskToListOfSubTasksMap: 1 taskToVariableMap: 1 topTaskToBaseTask: 1 ERROR (Executable:165) - Command "/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64" ecountered a problem: : /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) []{} java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (Executable:439) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more ERROR (AbstractSolver:175) - /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida) []{} org.vcell.util.exe.ExecutableException: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida) at org.vcell.util.exe.Executable.executeProcess(Executable.java:168) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:437) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.util.exe.Executable.start(Executable.java:427) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solvers.AbstractCompiledSolver.runSolver(AbstractCompiledSolver.java:162) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:424) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] Caused by: java.lang.Exception: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) at org.vcell.util.exe.Executable.executeProcess(Executable.java:161) ~[vcell-core-0.0.1-SNAPSHOT.jar:?] ... 21 more INFO (SolverHandler:425) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@79ecc507 []{} INFO (SolverHandler:426) - Status: Aborted: SOLVER_ABORTED:Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida) []{} ERROR (SundialsSolver:295) - /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida (No such file or directory) []{} java.io.FileNotFoundException: /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida (No such file or directory) at java.base/java.io.FileInputStream.open0(Native Method) ~[?:?] at java.base/java.io.FileInputStream.open(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at java.base/java.io.FileInputStream.(Unknown Source) ~[?:?] at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:289) [vcell-core-0.0.1-SNAPSHOT.jar:?] at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:186) [vcell-core-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:428) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:240) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:220) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:123) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:96) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:18) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3] at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3] at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?] ERROR (SolverHandler:494) - Solver status: 3 []{} ERROR (SolverHandler:495) - Solver message: Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida) []{} ERROR (SolverHandler:501) - Failed execution: Model 'archive_BIOMD0000000912_sim.sedml___source__' Task 'Caravagna2010'. []{} INFO (SolverHandler:507) - Running simulation for 82 ms []{} ERROR (SolverHandler:525) - Could not execute code: /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64) (/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.cvodeInput /tmp/out/BIOMD0000000912_sim.sedml/SimID_1771888260_0_.ida) []{} ----------------------------------------------------------------------------------------------------- INFO (SolverHandler:597) - Ran 1 simulation jobs for 1 biomodels. []{} INFO (SedmlJob:273) - Generating outputs... []{} INFO (SedmlJob:327) - Generating CSV file... []{} INFO (RunUtils:202) - Generating report `report`. []{} ERROR (SedmlJob:435) - CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null []{} java.lang.RuntimeException: CSV generation failed: Cannot invoke "cbit.vcell.solver.ode.ODESolverResultSet.findColumn(String)" because "this.resultSet" is null at org.vcell.cli.run.RunUtils.generateReportsAsCSV(RunUtils.java:388) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.generateCSV(SedmlJob.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:276) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:223) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:140) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:199) [vcell-cli-0.0.1-SNAPSHOT.jar:?] at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java ...
biosimulators-daemon commented 9 months ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/7716370209). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/7716370209).