Issue compiling pyrosetta

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    • September 28, 2018 at 12:54 am #3008
      Anonymous

        Hi,

        I’m having an issue compiling pyrosetta.  I’m using ubuntu16.04 and python3.7.  I’m using rosetta_src_2018.33.60351_bundle

        I tried compiling with the following command:

        >python build.py –create-package /opt/software/pyrosetta/pyrosetta37

        and after a while, I get this error:

        Generating bindings…

        cd /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/ && /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/prefix/llvm-4.0.0/llvm-4.0.0.linux.calculon.release/bin/binder –config ./rosetta.config –root-module rosetta –prefix /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/ /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/all_rosetta_includes.hh — -std=c++11  -isystem external -isystem external/include -isystem external/boost_1_55_0 -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -Isrc -Isrc/platform/linux  -DPYROSETTA -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG

        Generate bindings, pass 1…

        Generate bindings, pass 2…

        Generate bindings, pass 3…

        Generate bindings, pass 4…

        Generate bindings, pass 5…

        Generate bindings, pass 6…

        Generate bindings, pass 7…

        Generate bindings, pass 8…

        Sorting Binders…

        Sorting Binders… Done.

        Writing code…

        Writing code… Done.

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols.8.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols.7.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_e.6.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_d.6.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_c.6.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_b.6.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_a.6.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_h.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_g.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_f.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_e.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_d.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_c.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_b.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_a.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols.4.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols.3.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_b.2.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols_a.2.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/protocols.1.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/core.5.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/core.4.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/core.3.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/core.2.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/core.1.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/basic.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/numeric.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/utility.cmake

        Writing /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/build/PyRosetta/linux/clang/python-3.7/release/source/ObjexxFCL.cmake

        Traceback (most recent call last):

          File “build.py”, line 826, in <module>

            main(sys.argv)

          File “build.py”, line 808, in main

            generate_bindings(rosetta_source_path)

          File “build.py”, line 607, in generate_bindings

            modified = generate_cmake_file(rosetta_source_path, sources)

          File “build.py”, line 458, in generate_cmake_file

            l2, m2 = generate_rosetta_external_cmake_files(rosetta_source_path, prefix)

          File “build.py”, line 378, in generate_rosetta_external_cmake_files

            for h in os.listdir(rosetta_source_path+’/external/’ + dir_):

        FileNotFoundError: [Errno 2] No such file or directory: ‘/opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/external/libzmq/src’

         

        There’ a directory at /opt/software/rosetta/rosetta_src_2018.33.60351_bundle/main/source/external/libzmq  but it’s empty.

         

        Any ideas?

         

        Thanks

      • September 28, 2018 at 1:49 am #14453
        Anonymous

          It’s a submodule missing in the distribution.  I think we normally expect people to use precompiled pyrosetta instead of compiling it themselves.  We haven’t updated the “make the tarball” script to deal with (all of) the submodules.  

          If you put 8fb5b10d8a60e06b9adebd22ecc118f13580375c of https://github.com/zeromq/libzmq there, it is likely to work in the meantime.  (so CD into libzqm, git clone https://github.com/zeromq/libzmq.git, git checkout 8fb5b10d8a60e06b9adebd22ecc118f13580375c)

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