Issue compiling pyrosetta

[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

[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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