Compiling Rosetta with MPI, site.settings, Ubuntu

[Anonymous]

Hello everybody,

I want to setup Rosetta with MPI support.

“./scons.py bin mode=release extras=mpi -j2”

outputs

scons: Reading SConscript files …

Traceback (most recent call last):

  File “/home/schmue/rosetta/rosetta_bin/main/source/SConstruct”, line 149, in main

    build = SConscript(“tools/build/setup.py”)

  File “/home/schmue/rosetta/rosetta_bin/main/source/external/scons-local/scons-local-3.0.4/SCons/Script/SConscript.py”, line 667, in __call__

    return method(*args, **kw)

  File “/home/schmue/rosetta/rosetta_bin/main/source/external/scons-local/scons-local-3.0.4/SCons/Script/SConscript.py”, line 604, in SConscript

    return _SConscript(self.fs, *files, **subst_kw)

  File “/home/schmue/rosetta/rosetta_bin/main/source/external/scons-local/scons-local-3.0.4/SCons/Script/SConscript.py”, line 285, in _SConscript

    call_stack[-1].globals)

  File “/home/schmue/rosetta/rosetta_bin/main/source/tools/build/setup.py”, line 451, in <module>

    build = setup()

  File “/home/schmue/rosetta/rosetta_bin/main/source/tools/build/setup.py”, line 441, in setup

    build.options_requested, build.options = setup_build_options()

  File “/home/schmue/rosetta/rosetta_bin/main/source/tools/build/setup.py”, line 109, in setup_build_options

    naive_settings = setup_build_settings(requested)

  File “/home/schmue/rosetta/rosetta_bin/main/source/tools/build/setup.py”, line 232, in setup_build_settings

    site = Settings.load(“site.settings”, “settings”)

  File “/home/schmue/rosetta/rosetta_bin/main/source/tools/build/settings.py”, line 131, in load

    exec(compile(open(file).read(), file, ‘exec’), settings)

  File “site.settings”, line 27, in <module>

  File “/usr/lib/python2.7/UserDict.py”, line 40, in __getitem__

    raise KeyError(key)

KeyError: ‘INCLUDE’

scons: done reading SConscript files.

scons: Building targets …

scons: `bin’ is up to date.

scons: done building targets.

 

I think that site.settings file is not suitable for my local system. I just copied the site.settings.topsail like it’s said in the tutorial.

I don’t know what the correct syntax and directories for libraries and headers are. Can someone help?

I am using default Ubuntu 18.04 and installed MPI by just “sudo apt-get install libopenmpi-dev”.

My goal is to test MPI-Rosetta on a 4core-pc to run it on a bigger cluster in the future.

[Anonymous]

The site.settings.topsail file assumes that the path to the MPI library headers are in the INCLUDE environment variable.

You might want to try the site.settings.release file instead of the site.settings.topsail file. It’s slightly more general, and will be more robust to not having the INCLUDE environment variable.  (That said, if you don’t have the path to the MPI library headers in the standard seach paths, this approach will fail, and you’ll need to add them to the INCLUDE variable.)

 

[Author]

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