rosetta compile

Member Site › Forums › Rosetta 3 › Rosetta 3 – General › rosetta compile

Viewing 3 reply threads
  • Author
    Posts
    • April 26, 2017 at 7:46 am #2645
      Anonymous

        Hi, I am beginner using rosetta, I used Scons to compile rosetta code and it is successful. I used Anjuta(IDE) to compile AbinitioRelax.cc and generated an AbinitioRelax.o file,when i used g++ to Compile it into executable file, it return the wrong information, as follows:

        root@ma:/home/ma/rosetta/main/source/src/apps/public# g++ AbinitioRelax.o

        AbinitioRelax.o: In function `main’:

        AbinitioRelax.cc:(.text+0x2b): undefined reference to `protocols::abinitio::AbrelaxApplication::register_options()’

        AbinitioRelax.cc:(.text+0x42): undefined reference to `devel::init(int, char**)’

        AbinitioRelax.cc:(.text+0x47): undefined reference to `basic::options::OptionKeys::run::checkpoint’

        AbinitioRelax.cc:(.text+0x4c): undefined reference to `basic::options::option’

        AbinitioRelax.cc:(.text+0x65): undefined reference to `basic::options::OptionKeys::run::checkpoint_interval’

        AbinitioRelax.cc:(.text+0x6a): undefined reference to `basic::options::option’

        AbinitioRelax.cc:(.text+0x9a): undefined reference to `basic::options::OptionKeys::run::checkpoint_interval’

        AbinitioRelax.cc:(.text+0x9f): undefined reference to `basic::options::option’

        AbinitioRelax.cc:(.text+0xb5): undefined reference to `protocols::checkpoint::checkpoint_with_interval(int)’

        AbinitioRelax.cc:(.text+0xc4): undefined reference to `protocols::abinitio::AbrelaxApplication::AbrelaxApplication()’

        AbinitioRelax.cc:(.text+0xd3): undefined reference to `protocols::abinitio::AbrelaxApplication::run()’

        I don’t know how to solve this error and hope you help me. Thank you  very much.

      • April 27, 2017 at 2:00 pm #12312
        Anonymous

          Rosetta is a *large* program. Not all of the code that AbinitioRelax requires is in the AbinitioRelax.cc file — in fact, very little of the AbinitoRelax code is in AbinitioRelax.cc. Most of it is in the other files in the Rosetta source directory. That’s why we have the scons build system. Scons takes care of compiling all the files and linking them together in the correct order. 

          When you did the compilation in your IDE, it sounds like you set things up such that it only compiles the one file as a program – that isn’t going to work. Theoretically, you might be able to take all the build instructions that scons does and set things up for your IDE, but that’s going to be a lot of work. I wouldn’t recommend it. Instead, I’d suggest sticking to the scons build system to rebuild Rosetta.

          That’s not to say you can enable compilation through the IDE to facilitate on-the-fly checking of various features, but I’d set that up for compiling as an intermediate object file, not as a full program, and only as much as you need to get the on-the-fly checking working. For actually building of the program, I’d drop to the commandline and invoke scons. (Actually, your IDE might even have a feature to run the external scons command when you click the “build” button, instead of the internal one. You might want to look into that.)

        • April 27, 2017 at 2:00 pm #12833
          Anonymous

            Rosetta is a *large* program. Not all of the code that AbinitioRelax requires is in the AbinitioRelax.cc file — in fact, very little of the AbinitoRelax code is in AbinitioRelax.cc. Most of it is in the other files in the Rosetta source directory. That’s why we have the scons build system. Scons takes care of compiling all the files and linking them together in the correct order. 

            When you did the compilation in your IDE, it sounds like you set things up such that it only compiles the one file as a program – that isn’t going to work. Theoretically, you might be able to take all the build instructions that scons does and set things up for your IDE, but that’s going to be a lot of work. I wouldn’t recommend it. Instead, I’d suggest sticking to the scons build system to rebuild Rosetta.

            That’s not to say you can enable compilation through the IDE to facilitate on-the-fly checking of various features, but I’d set that up for compiling as an intermediate object file, not as a full program, and only as much as you need to get the on-the-fly checking working. For actually building of the program, I’d drop to the commandline and invoke scons. (Actually, your IDE might even have a feature to run the external scons command when you click the “build” button, instead of the internal one. You might want to look into that.)

          • April 27, 2017 at 2:00 pm #13354
            Anonymous

              Rosetta is a *large* program. Not all of the code that AbinitioRelax requires is in the AbinitioRelax.cc file — in fact, very little of the AbinitoRelax code is in AbinitioRelax.cc. Most of it is in the other files in the Rosetta source directory. That’s why we have the scons build system. Scons takes care of compiling all the files and linking them together in the correct order. 

              When you did the compilation in your IDE, it sounds like you set things up such that it only compiles the one file as a program – that isn’t going to work. Theoretically, you might be able to take all the build instructions that scons does and set things up for your IDE, but that’s going to be a lot of work. I wouldn’t recommend it. Instead, I’d suggest sticking to the scons build system to rebuild Rosetta.

              That’s not to say you can enable compilation through the IDE to facilitate on-the-fly checking of various features, but I’d set that up for compiling as an intermediate object file, not as a full program, and only as much as you need to get the on-the-fly checking working. For actually building of the program, I’d drop to the commandline and invoke scons. (Actually, your IDE might even have a feature to run the external scons command when you click the “build” button, instead of the internal one. You might want to look into that.)

            • April 28, 2017 at 1:53 am #12316
              Anonymous

                Thank you for your help, yor advice give me great help.

              • April 28, 2017 at 1:53 am #12837
                Anonymous

                  Thank you for your help, yor advice give me great help.

                • April 28, 2017 at 1:53 am #13358
                  Anonymous

                    Thank you for your help, yor advice give me great help.

                • Author
                  Posts
                Viewing 3 reply threads
                • You must be logged in to reply to this topic.