error in installing rosetta for use in phenix

[Anonymous]

Hi everybody!

I’m trying to install Rosetta (version 3.10) for use in Phenix on Ubuntu 20. No problem with Phenix installation, but when I run “rosetta.build_phenix_interface nproc=2” I got the following:

Substituting phenix.python into build shell scripts

  update_options.sh

  update_ResidueType_enum_files.sh

  Phenix modules found : /home/stefano/programmi/phenix-1.19.1-4122/modules/phenix

False

/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source

  ~> phenix.python scons.py bin mode=release extras=python  -j 1

scons: Reading SConscript files …

Traceback (most recent call last):

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/SConstruct”, line 150, in main

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

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py”, line 614, in __call__

    return method(*args, **kw)

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py”, line 551, in SConscript

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

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py”, line 260, in _SConscript

    exec _file_ in call_stack[-1].globals

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/tools/build/setup.py”, line 451, in <module>

    build = setup()

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/tools/build/setup.py”, line 441, in setup

    build.options_requested, build.options = setup_build_options()

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/tools/build/setup.py”, line 109, in setup_build_options

    naive_settings = setup_build_settings(requested)

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/tools/build/setup.py”, line 166, in setup_build_settings

    supported = Settings.load(“basic.settings”, “settings”)

  File “/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/tools/build/settings.py”, line 130, in load

    execfile(file, settings)

  File “basic.settings”, line 61, in <module>

IndexError: list index out of range

scons: done reading SConscript files.

scons: Building targets …

scons: *** Do not know how to make File target `bin’ (/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source/bin).  Stop.

scons: building terminated because of errors.

 

 

I copied the suggested site.setting ìs file in ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings for the ABI change before running the command.

I also tried installing “python-is-python2” package, but I got the error…

Any suggestions?

Thanks

Stefano

[Anonymous]

The issue is that the build-with-Python needs to use the same Python that you’ll be using with Phenix. In your case, it looks to be Python3, and even installing python-is-python2 won’t help here, as you’re explicitly calling the python associated with the Phenix build, rather than the default `python`.

The easiest way to fix this is to use a more recent Rosetta version, rather than Rosetta 3.10 (2018.33 weekly). Anything more recent than the 2019.12 weekly should have the appropriate fixes, including Rosetta 3.11 and 3.12.

If, for some reason, you need to use 3.10 exactly, and a more recent release won’t work, then the fix would be to copy over the fixes to the build system from the more recent releases to the 3.10 release. Unfortunately, I believe there’s a number of them, so you may have to play whack-a-mole, finding and copying over the individual fixes as the errors arise.

 

 

[Anonymous]

Thanks for the reply. 

I tried downloading rosetta3.12 (the most recent I found)and repeated the process, but I got exactly the same issue (past below).

Apparently now I’m using pytho3 by default…

stefano

 

stefano@stefano-VirtualBox:/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle % rosetta.build_phenix_interface nproc=1

Substituting phenix.python into build shell scripts

  update_options.sh

  update_ResidueType_enum_files.sh

  Phenix modules found : /home/stefano/programmi/phenix-1.19.1-4122/modules/phenix

False

/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source

  ~> phenix.python scons.py bin mode=release extras=python  -j 1

scons: Reading SConscript files …

Traceback (most recent call last):

  File “/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/SConstruct”, line 149, in main

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

  File “/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/external/scons-local/scons-local-3.0.4/SCons/Script/SConscript.py”, line 667, in __call__

    return method(*args, **kw)

  File “/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/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/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/external/scons-local/scons-local-3.0.4/SCons/Script/SConscript.py”, line 285, in _SConscript

    call_stack[-1].globals)

  File “/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/tools/build/setup.py”, line 451, in <module>

    build = setup()

  File “/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/tools/build/setup.py”, line 441, in setup

    build.options_requested, build.options = setup_build_options()

  File “/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/tools/build/setup.py”, line 109, in setup_build_options

    naive_settings = setup_build_settings(requested)

  File “/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/tools/build/setup.py”, line 166, in setup_build_settings

    supported = Settings.load(“basic.settings”, “settings”)

  File “/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/tools/build/settings.py”, line 131, in load

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

  File “basic.settings”, line 62, in <module>

  File “/home/stefano/programmi/phenix-1.19.1-4122/conda_base/lib/python2.7/subprocess.py”, line 223, in check_output

    raise CalledProcessError(retcode, cmd, output=output)

subprocess.CalledProcessError: Command ” returned non-zero exit status 1

scons: done reading SConscript files.

scons: Building targets …

scons: *** Do not know how to make File target `bin’ (/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle/main/source/bin).  Stop.

scons: building terminated because of errors.

stefano@stefano-VirtualBox:/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle % python -V

Python 3.8.5

stefano@stefano-VirtualBox:/home/stefano/programmi/rosetta/rosetta_src_2020.08.61146_bundle % 

 

 

[Anonymous]

Well, you’re further along in the process.

Do you have a compiler installed? It’s looking like things are complaining that the compiler ‘gcc’ can’t be found.  You’ll need to have a compiler availible, and for Ubuntu that defaults to gcc. (For Ubuntu you can install a compiler and other needed tools with something like `sudo apt install build-essential`). You’ll also need the zlib library (`sudo apt install zlib1g-dev`).

If you do have a compiler and everything else needed to build C++ programs already installed, then you can try just deleting the `shell_gcc = subprocess.check_output([“which”, “gcc”]).split()[0]` line in main/source/tools/build/basic.settings  — from a quick glance, it looks to actually be unused.

[Anonymous]

Now it’s working! It seems for any reason I have lost the compiler after Ubuntu20 upgrade..

thanks a lot

stefano

[Author]

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