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Virtual Cell Framework
http://vcell.org/
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mvn clean install dependency:copy-dependencies fails on "Running org.vcell.vcellij.api.SimulationServiceImplTest" in Ubuntu 17.10 #4

Closed cirosantilli closed 3 years ago

cirosantilli commented 6 years ago

7e2ffe2059cb9057e7d5c42eaa995e50bd1fb76f

I'll try Docker later. It would be awesome if there was an example that shows how to run something interesting and get interesting results out, with zero effort.

Running org.vcell.vcellij.api.SimulationServiceImplTest
 WARN (Model.java:4805) - registerIds: the object org.sbml.jsbml.ext.spatial.CompartmentMapping is neither a UniqueNamedSBase, a LocalParameter or a UnitDefinition so its id will not be registered in the Model.
 WARN (Model.java:4805) - registerIds: the object org.sbml.jsbml.ext.spatial.CompartmentMapping is neither a UniqueNamedSBase, a LocalParameter or a UnitDefinition so its id will not be registered in the Model.
 WARN (Model.java:4805) - registerIds: the object org.sbml.jsbml.ext.spatial.CompartmentMapping is neither a UniqueNamedSBase, a LocalParameter or a UnitDefinition so its id will not be registered in the Model.
ERROR (SpatialModelPlugin.java:266) - The spatial id "EC" is already present in the spatial model assigned to the model optoPlexin_PRG_rule_based_1_Dimensional. The new element will not be added to the model.
ERROR (IdentifierException.java:75) - An element with the metaid "EC" is already present in the SBML document. The element analyticVolume will not be annotated with it.
 WARN (AnalyticVolume.java:394) - Could not recognized the value EC for the attribute id on the 'analyticVolume' element.
ERROR (SpatialModelPlugin.java:266) - The spatial id "Cyt" is already present in the spatial model assigned to the model optoPlexin_PRG_rule_based_1_Dimensional. The new element will not be added to the model.
ERROR (IdentifierException.java:75) - An element with the metaid "Cyt" is already present in the SBML document. The element analyticVolume will not be annotated with it.
 WARN (AnalyticVolume.java:394) - Could not recognized the value Cyt for the attribute id on the 'analyticVolume' element.
 WARN (SBMLCoreParser.java:386) - No UnitDefinition matches the unitsID 'um3' of compartment 'Cyt'.
 WARN (SBMLCoreParser.java:386) - No UnitDefinition matches the unitsID 'um3' of compartment 'EC'.
SBML 'item' unit found, interpreted as 'molecule'
SBML 'item' unit found, interpreted as 'molecule'
SBML 'item' unit found, interpreted as 'molecule'
MembraneMapping.getTotalVolumeCorrection(): volume correction for a resolved membrane is meaningless, but maybe a 1.0 would be harmless
MathMapping.refresh Start
PotentialMapping.getTotalMembraneCurrent(): ASSUMING NO MEMBRANE CURRENTS IF 'CALCULATE_VOLTAGE' == false
MathMapping.refresh End
<SpatialObjects><SpatialObject Name="vobj_EC0" Type="Volume" subVolume="EC" regionId="0"><QuantityCategoryList><QuantityCategory Name="VolumeCentroid" Enabled="false" /><QuantityCategory Name="InteriorVelocity" Enabled="false" /><QuantityCategory Name="VolumeRegionSize" Enabled="true" /></QuantityCategoryList></SpatialObject><SpatialObject Name="vobj_Cyt1" Type="Volume" subVolume="Cyt" regionId="1"><QuantityCategoryList><QuantityCategory Name="VolumeCentroid" Enabled="false" /><QuantityCategory Name="InteriorVelocity" Enabled="false" /><QuantityCategory Name="VolumeRegionSize" Enabled="true" /></QuantityCategoryList></SpatialObject><SpatialObject Name="sobj_Cyt1_EC0" Type="Surface" subVolumeInside="Cyt" regionIdInside="1" subVolumeOutside="EC" regionIdOutside="0"><QuantityCategoryList><QuantityCategory Name="SurfaceNormal" Enabled="false" /><QuantityCategory Name="SurfaceVelocity" Enabled="false" /><QuantityCategory Name="DistanceToSurface" Enabled="false" /><QuantityCategory Name="DirectionToSurface" Enabled="false" /><QuantityCategory Name="SurfaceSize" Enabled="true" /></QuantityCategoryList></SpatialObject></SpatialObjects>
-----Setting executable LD_LIBRARY_PATH to /usr/lib:/usr/local/lib:/usr/local/lib64:/home/ciro/git/vcell/vcell-core/../localsolvers/linux64
/home/ciro/git/vcell/vcell-core/../localsolvers/linux64/FiniteVolume_x64: error while loading shared libraries: libssl.so.10: cannot open shared object file: No such file or directory

(/home/ciro/git/vcell/vcell-core/../localsolvers/linux64/FiniteVolume_x64 /home/ciro/.vcell/simdata/temp/SimID_561491369_0_.fvinput)
org.vcell.util.DataAccessException: simulation data for [VCSimulationIdentifier[561491369,0,temp(123)]] newStyle=SimID_561491369_0_.log oldStyle=SimID_561491369.log not exist in primary /home/ciro/.vcell/simdata/temp dir or secondary null dir or Archive server.
        at cbit.vcell.simdata.DataSetControllerImpl.getDataSetTimes(DataSetControllerImpl.java:2879)
        at org.vcell.vcellij.SimulationServiceImpl.getDataSetController(SimulationServiceImpl.java:383)
        at org.vcell.vcellij.SimulationServiceImpl.getVariableList(SimulationServiceImpl.java:446)
        at org.vcell.vcellij.api.SimulationServiceImplTest.test(SimulationServiceImplTest.java:61)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
        at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
        at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
        at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
        at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
        at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
        at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
        at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
        at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
        at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
        at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
        at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
        at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
        at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:367)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:274)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
        at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:161)
        at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:290)
        at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:242)
        at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:121)
java.lang.RuntimeException: failed to read dataset: simulation data for [VCSimulationIdentifier[561491369,0,temp(123)]] newStyle=SimID_561491369_0_.log oldStyle=SimID_561491369.log not exist in primary /home/ciro/.vcell/simdata/temp dir or secondary null dir or Archive server.
        at org.vcell.vcellij.SimulationServiceImpl.getDataSetController(SimulationServiceImpl.java:388)
        at org.vcell.vcellij.SimulationServiceImpl.getVariableList(SimulationServiceImpl.java:446)
        at org.vcell.vcellij.api.SimulationServiceImplTest.test(SimulationServiceImplTest.java:61)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
        at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
        at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
        at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
        at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
        at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
        at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
        at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
        at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
        at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
        at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
        at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
        at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
        at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:367)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:274)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
        at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:161)
        at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:290)
        at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:242)
        at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:121)
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 1.6 sec <<< FAILURE! - in org.vcell.vcellij.api.SimulationServiceImplTest
test(org.vcell.vcellij.api.SimulationServiceImplTest)  Time elapsed: 1.6 sec  <<< ERROR!
java.lang.Exception: failed to retrieve variable list: failed to read dataset: simulation data for [VCSimulationIdentifier[561491369,0,temp(123)]] newStyle=SimID_561491369_0_.log oldStyle=SimID_561491369.log not exist in primary /home/ciro/.vcell/simdata/temp dir or secondary null dir or Archive server.
        at org.vcell.vcellij.api.SimulationServiceImplTest.test(SimulationServiceImplTest.java:61)

Results :

Tests in error:
  SimulationServiceImplTest.test:61 »  failed to retrieve variable list: failed ...

Tests run: 45, Failures: 0, Errors: 1, Skipped: 14

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Virtual Cell Project ............................... SUCCESS [ 19.480 s]
[INFO] ojdbc6 ............................................. SUCCESS [  0.489 s]
[INFO] ucp ................................................ SUCCESS [  0.015 s]
[INFO] vcell-util ......................................... SUCCESS [ 15.501 s]
[INFO] vcell-math ......................................... SUCCESS [  7.538 s]
[INFO] vcell-apiclient .................................... SUCCESS [ 15.302 s]
[INFO] vcell-core ......................................... FAILURE [02:29 min]
[INFO] vcell-client ....................................... SKIPPED
[INFO] vcell-server ....................................... SKIPPED
[INFO] vcell-vmicro ....................................... SKIPPED
[INFO] vcell-oracle ....................................... SKIPPED
[INFO] vcell-admin ........................................ SKIPPED
[INFO] vcell-api .......................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:38 min
[INFO] Finished at: 2018-04-01T17:27:33+01:00
[INFO] Final Memory: 105M/2547M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.19.1:test (default-test) on project vcell-core: There are test failures.
[ERROR]
[ERROR] Please refer to /home/ciro/git/vcell/vcell-core/target/surefire-reports for the individual test results.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :vcell-core
~/git/vcell

Then if I try to run:

./vcell.sh

it fails with:

java -Dvcell.installDir=/home/ciro/git/vcell -Dvcell.softwareVersion=standalone_VCell_7.0 -Dvcell.bioformatsJarFileName=vcell-bioformats-0.0.1-SNAPSHOT-jar-with-dependencies.jar -Dvcell.bioformatsJarDownloadURL=http://vcell.org/webstart/vcell-bioformats-0.0.1-SNAPSHOT-jar-with-dependencies.jar -cp ./vcell-client/target/maven-jars/*:./vcell-client/target/* cbit.vcell.client.test.VCellClientTest vcellapi.cam.uchc.edu:443
Error: Could not find or load main class cbit.vcell.client.test.VCellClientTest
cirosantilli commented 4 years ago

Was it fixed?

gmarupilla commented 3 years ago

Please follow the instructions from here for installing the requirements.

cirosantilli commented 3 years ago

Thanks for the info GMarupilla, feel free to close if you feel this is solved, I don't have time to reproduce currently, cheers.