Unit test fails (SpanFileIOTests)

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    • #1908


        I try to install the latest release of Rosetta (Saturday, May 17, 2014). I have compiled the debug mode of Rosetta with succes, but I when I try to run the Unit test I have this error on the consol :

        Unit test summary

        Total number of tests: 1527
        number tests passed: 1520
        number tests failed: 7
        failed tests:
        core.test: SpanFileIOTests:test_emptyInput
        core.test: SpanFileIOTests:test_helixOutofBounds
        core.test: SpanFileIOTests:test_singleHelix
        core.test: SpanFileIOTests:test_negativeTotalRes
        core.test: SpanFileIOTests:test_multipleHelix
        core.test: SpanFileIOTests:test_fullHelix
        core.test: SpanFileIOTests:test_edgeHelix
        Success rate: 99%

        End of Unit test summary

        I have tried to recompile another time this release of Rosetta and the previous one but I still have this seven tests which fails.

        Francois Inizan

      • #10087

          It’s a little hard to debug with just the summary. I’d recommend re-running just the SpanFileIOTests suite, with output on (remove “–mute all” from your test/run.py script if you used it, and add “-1 SpanFileIOTests”). Seeing the output of that command would greatly help with debugging.

          The other option is just to ignore it, especially if you’re not working with membrane proteins. The SpanFileIO tests are somewhat recent additions, and the code it tests is only used for working with membrane proteins. The test passed on our test server for that revision (http://benchmark.graylab.jhu.edu/revision/master/56838, assuming you’re using weekly version 2014.20.56838), and it doesn’t look like other tests are having problems. It could be some numeric precision/compiler issues on your machine that makes a (spurious) change in the test result. What compiler and platform are you using?

        • #10088

            Hello, thank you for your reply,

            I re-run the SpanFileIOTest, this is the result :

            Identifying platform…

            Platform found: debug/linux/3.13/64/x86/gcc/4.8/default
            Command line:: cd build/test/debug/linux/3.13/64/x86/gcc/4.8/default && ./core.test SpanFileIOTests –database /home/frini/Programms/ROSETTA/rosetta_2014.20.56838_bundle/main/database
            Running one suite: SpanFileIOTests
            Test suite: SpanFileIOTests (test/core/membrane/io/SpanFileIO.cxxtest.hh)
            core.init: Rosetta version from
            core.init: command: ./core.test –database /home/frini/Programms/ROSETTA/rosetta_2014.20.56838_bundle/main/database
            core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-122285480 seed_offset=0 real_seed=-122285480
            core.init.random: RandomGenerator:init: Normal mode, seed=-122285480 RG_type=mt19937
            core.init.random: RandomGenerator:init: _RND_TestRun_ mode, seed=1000 RG_type=mt19937
            Trace: Testing response to empty or null input…
            core.test: src/ObjexxFCL/DynamicIndexRange.hh:103: ObjexxFCL::DynamicIndexRange::DynamicIndexRange(int): Assertion `legal_static()’ failed.
            core.membrane.io.SpanFileIO: Building topology object from spanfile

            I’m using gcc-4.8 and g++-4.8 on the weekly version 2014.20.56838. with Xubuntu 14.04.
            In my case, I want to run for an Ab Initio prediction, is it possible ?

            Thanks again for your help !
            François Inizan

          • #10090

              So the test that is failing is one to test parsing of malformed span files. Reading the code, it looks like we’re currently lacking enough good checks for error conditions, so depending on how things run, it’s very possible that this test might fail on a your system.

              If you’re not using membrane proteins, I wouldn’t worry about it. Even if you are using membrane proteins, as long as you have a well-formatted spanfile you should be okay.

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