Error compiling pyrosetta – Rosetta Commons

This topic has 6 replies, 2 voices, and was last updated 7 years, 1 month ago by Anonymous.

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- October 27, 2017 at 5:18 pm #2764
  Anonymous
  Hi,
  
  I’m running into an issue when trying to compile pyrosetta from source. I’m following these directions:
  
  http://www.pyrosetta.org/documentation#TOC-Building-PyRosetta-from-source
  
  Those directions worked for me when I was using rosetta3.8.
  
  I recently downloaded rosetta_src_2017.39.59729_bundle and get this issue:
  
  >pwd
  
  /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/src/python/PyRosetta
  
  >python build.py -j4 –create-package /opt/software/pyrosetta/pyrosetta_curr
  
  Creating PyRosetta in “Release” mode in: /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release
  
  Updating Binder and other Git submodules…
  
  cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/.. && git submodule update –init –recursive — source/src/python/PyRosetta/binder
  
  fatal: Not a git repository (or any of the parent directories): .git
  
  Encounter error while executing: cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/.. && git submodule update –init –recursive — source/src/python/PyRosetta/binder
  
  Encounter error while executing: cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/.. && git submodule update –init –recursive — source/src/python/PyRosetta/binder
  
  fatal: Not a git repository (or any of the parent directories): .git
  
  Any ideas how to fix this?
- October 27, 2017 at 6:55 pm #13832
  Anonymous
  This looks like an error that i fixed a few release cycles ago. How recent is your Rosetta source? Could you please post its version here (and what package you use and where it was obtained) and then try the same command line with most recent release?
  - October 27, 2017 at 7:33 pm #13833
    Anonymous
    Hi Sergey,
    
    This is the most recent version that’s available for download (2017 wk 39)
    
    Branched off:af0fe23c4f7abb07b1e74df46596171cd53e814b
    
    The only version info I can find is in “.release.json”:
    
    {
    
    “date”: “2017-09-28 07:58:22.502995”,
    
    “release”: 154,
    
    “source”: {
    
    “binder”: “0dbb5c08c1ff9208cc94f5875f129e1e147272ee”,
    
    “demos”: “f8e337cddb4089603de5ac2e5d88b00033cdb2f1”,
    
    “documentation”: “0882942db2f9c0d02fc7f61bde35ecc74297b547”,
    
    “main”: “af0fe23c4f7abb07b1e74df46596171cd53e814b”,
    
    “tools”: “2a9d2b68a8d46b58e5f6a9be399c8f82deb2019a”
    
    },
    
    “version”: “rosetta.source.release-154”,
    
    “week”: 39,
    
    “year”: 2017
    
    }
- October 28, 2017 at 4:50 pm #13835
  Anonymous
  I will look this up. As an immediate workaround you can do the following: in build.py edit code around lines ~664 and change it from
  
  if not Options.binder:
  
  execute(‘Updating…
  
  output = execute(‘Checking if Binder submodule present…’,
  
  if ‘source/src/python/PyRosetta/binder’ not in output:
  
  Options.binder = install_llvm_tool(‘binder’, rosetta_source_path+’/src/python/PyRosetta/binder/source’, rosetta_source_path + ‘/build/prefix’, Options.binder_debug)
  
  to
  
  if not Options.binder:
  
  Options.binder = install_llvm_tool(‘binder’, rosetta_source_path+’/src/python/PyRosetta/binder/source’, rosetta_source_path + ‘/build/prefix’, Options.binder_debug)
  
  and then try to re-run the build
  - October 28, 2017 at 5:20 pm #13836
    Anonymous
    Hi Sergey,
    
    I tried that and get a new error:
    
    >python build.py -j4 –create-package /opt/software/pyrosetta/pyrosetta_curr
    
    Creating PyRosetta in “Release” mode in: /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/build/PyRosetta/linux/clang/python-2.7/release
    
    fatal: Not a git repository (or any of the parent directories): .git
    
    Encounter error while executing: cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/src/python/PyRosetta/binder/source && git rev-parse HEAD
    
    Encounter error while executing: cd /opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main/source/src/python/PyRosetta/binder/source && git rev-parse HEAD
    
    fatal: Not a git repository (or any of the parent directories): .git
- November 1, 2017 at 3:00 pm #13849
  Anonymous
  I’ve gotten PyRosetta to compile (starting from rosetta_src_2017.39 in Ubuntu 16.04). In addition to commenting out the lines described above, I made the following changes (starting at ~line 133).
  
  Commenting out the line that starts:
  
  binder_head = execute(‘Getting binder HEAD ….
  
  Comment out the next line:
  
  signature = dict(config = “LLVM …”)
  
  replace that signature line with this:
  
  signature = dict(config = ‘LLVM install by install_llvm_tool version: 1.0’, binder = ‘ unknown’)
  
  Compiles fine now. Probably not an ideal way to solve the problem, but just documentating this in case anyone else needs a workaround.
- November 2, 2017 at 12:14 am #13856
  Anonymous
  Thank you for posting workaround! I am working on fixign this issue so hopefully this will be ready before next weekly release.
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