Error with compilation of Rosetta_3.12 in a large computational cluster

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    • May 27, 2020 at 2:31 am #3440
      Anonymous

        Dear all,

        I am trying to compilation of Rosetta_scr_3.12 (using gcc-7 as the compiler) in  large computational cluster with the following command:

            ./scons.py bin mode=release extras=mpi -j 24

         

        I get the following error message:

           /WORK/app/osenv/ln1/usr/local/mpi3-dynamic/lib/libmpi.so: undefined reference to `__intel_sse2_strdup’

        build/src/release/linux/2.6/64/x86/gcc/7.5/mpi/libprotocols.7.so: undefined reference to `ompi_mpi_comm_world’

        build/external/release/linux/2.6/64/x86/gcc/7.5/mpi/libsqlite3.so: undefined reference to `_intel_fast_memcmp’

        build/src/release/linux/2.6/64/x86/gcc/7.5/mpi/libprotocols.3.so: undefined reference to `ompi_mpi_op_sum’

        build/src/release/linux/2.6/64/x86/gcc/7.5/mpi/libprotocols.3.so: undefined reference to `ompi_mpi_comm_null’

        collect2: error: ld returned 1 exit status

        scons: *** [build/src/release/linux/2.6/64/x86/gcc/7.5/mpi/ddg_monomer.mpi.linuxgccrelease] Error 1

        scons: building terminated because of errors.

         

        I am a common customer of the computational cluster system and do not have a root access. Do you know how to solve the problem?

        Thank you in advance.

      • May 27, 2020 at 5:26 am #15314
        Anonymous

          Looks like you’re trying to build the MPI version and it’s not finding the MPI libraries.  Check with your sysadmins about whether there’s an MPI module you need to load or something else that you need to do.

          Note that you may need to help scons to see the system environment.  If you edit Rosetta/main/source/tools/build/user.settings, you can uncomment the “import os”, “program_path”, and “ENV” lines.

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