Error in building fragment_picker with boost_thread

This topic has 5 replies, 2 voices, and was last updated 4 years, 6 months ago by Anonymous.

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- June 4, 2020 at 4:33 pm #3453
  Anonymous
  Hi all,
  
  I am new to the whole Rosetta community and am asking for some help in compiling Rosetta3. I have downloaded build Rosetta3.12 build 2020.08.61146 and tried to compile the thread boost version of fragment pick by using
  
  ./scons.py mode=release extras=boost_thread bin/fragment_picker.boost_thread.linuxgccrelease -j 20
  
  The error message that I get is:
  
  **************************************************
  
  g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/boost_thread/libzmq.so -Wl,–disable-new-dtags -shared -Wl,-rpath=/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/boost_thread -Wl,-rpath=$ORIGIN -Wl,-rpath=$ORIGIN/../lib build/external/release/linux/3.10/64/x86/gcc/4.8/boost_thread/dummy.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/boost_thread -Lexternal -L/usr/lib/oracle/12.2/client64/lib -L/usr/lib -L/usr/local/lib -L/usr/local/lib -L/opt/boost/lib -lpthread -lpthread -lboost_thread
  
  /usr/bin/ld: cannot find -lboost_thread
  
  collect2: error: ld returned 1 exit status
  
  scons: *** [build/external/release/linux/3.10/64/x86/gcc/4.8/boost_thread/libzmq.so] Error 1
  
  *************************************************
  
  Here is some information about the machine that I am trying to compile Rosetta on;
  
  gcc version 4.8.5 20150623
  
  CentOS7
  
  kernel version: Linux 3.10.0-862.el7.x86_64 x86_64
  
  Can someone with more experience point me to what the problem is?
  
  Best,
  
  Ken
- June 4, 2020 at 5:04 pm #15327
  Anonymous
  Hi, Ken. The Boost::thread build is one that we unfortunately no longer test or actively support. It looks like it has succumbed to bit-rot. We plan to switch the fragment picker to use C++11 threads in the near future (to be in line with the rest of Rosetta). Until then, the single-threaded build is unfortunately the best option.
- June 4, 2020 at 5:12 pm #15328
  Anonymous
  Correction: it looks like there’s already C++11 thread support there. So you can compile with `extras=cxx11thread` instead of `extras=boost_thread`.
- June 4, 2020 at 6:22 pm #15329
  Anonymous
  Thanks vmullgan. If I downloaded the binary executable bundle instead of the source and only want to compile fragment picker, can you tell me what the name would be? I am asking because I am getting this error when I use
  
  ./scons.py mode=release extras=cx11thread bin/fragment_picker.boost_thread.linuxgccrelease -j 20
  
  error:
  
  ******************************
  
  scons: Reading SConscript files …
  
  Traceback (most recent call last):
  
  File “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_2020.08.61146_bundle/main/source/SConstruct”, line 149, in main
  
  build = SConscript(“tools/build/setup.py”)
  
  File “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_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 “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_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 “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_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 “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_2020.08.61146_bundle/main/source/tools/build/setup.py”, line 451, in <module>
  
  build = setup()
  
  File “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_2020.08.61146_bundle/main/source/tools/build/setup.py”, line 441, in setup
  
  build.options_requested, build.options = setup_build_options()
  
  File “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_2020.08.61146_bundle/main/source/tools/build/setup.py”, line 72, in setup_build_options
  
  env = Environment(options = options)
  
  File “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_2020.08.61146_bundle/main/source/external/scons-local/scons-local-3.0.4/SCons/Environment.py”, line 965, in __init__
  
  variables.Update(self)
  
  File “/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_2020.08.61146_bundle/main/source/external/scons-local/scons-local-3.0.4/SCons/Variables/__init__.py”, line 221, in Update
  
  raise SCons.Errors.UserError(‘Error converting option: %sn%s’%(option.key, x))
  
  SCons.Errors.UserError: Error converting option: extras
  
  Invalid value(s) for option: cx11thread
  
  scons: done reading SConscript files.
  
  scons: Building targets …
  
  scons: *** Do not know how to make File target `bin/fragment_picker.boost_thread.linuxgccrelease’ (/nfs/peptide/home/lok2/tmp/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/fragment_picker.boost_thread.linuxgccrelease). Stop.
  
  scons: building terminated because of errors.
  
  *****************************************
  
  Best,
  
  Ken
  - June 7, 2020 at 11:11 pm #15331
    Anonymous
    Hi, Ken:
    
    It’s extras=cxx11thread, not extras=cx11thread. And the executable is bin/fragment_picker.cxx11thread.linuxgccrelease, though you needn’t provide the whole executable name. Scons is smart enough to figure it out if you just say fragment_picker. So:
    
    ./scons.py -j 20 mode=release extras=cxx11thread fragment_picker
- June 10, 2020 at 4:45 pm #15333
  Anonymous
  Thanks vmulligan! Worked like a charm.
  
  Best,
  
  Ken
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