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
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)