Error MPI build rosetta2014.35 on Ubuntu14.04 LTS

This topic has 1 reply, 2 voices, and was last updated 10 years ago by Anonymous.

Viewing 1 reply thread

Author

Posts
- December 16, 2014 at 10:35 am #2104
  Anonymous
  Hello!
  
  Recently, I posted some post about install Rosetta3.5 on cygwin.
  
  Finally, I changed the OS and succeeded to install them on the Ubuntu on Virtual box(Win7)
  Normal install was good. and docking protocol was worked(I only checked that exe).
  ./scons.py -j4 mode=release bin
  
  But,I couldn’t MPI install by follow command in another new Virtual machine. The first one hour from the beginning was good but I got some error.
  I did all command as superuser
  
  sudo apt-get install openmpi-bin
  sudo su
  ./scons.py -j4 mode=release bin extras=mpi
  
  mpiCC -o build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/libutility.so -Wl,-rpath=/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/build/external/release/linux/3.13/64/x86/gcc/4.8/mpi -Wl,-rpath=$ORIGIN -Wl,-rpath=$ORIGIN/../lib -shared build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/libsvm/Svm_rosetta.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/libsvm/Svm.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/tag/Tag.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/lua/LuaIterator.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/lua/LuaObject.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/pointer/ReferenceCount.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/pointer/ReferenceCountMI_.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/options/keys/OptionKeys.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/excn/Exceptions.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/thread/ReadWriteMutex.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/json_spirit/json_spirit_reader.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/json_spirit/json_spirit_value.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/json_spirit/json_spirit_writer.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/json_spirit/json_spirit_tools.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/basic_sys_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/Binary_Util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/exit.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/heap.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/inline_file_provider.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/integer_mapping.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/LexicographicalIterator.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/mpi_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/SimulateMPI.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/PyExitCallback.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/recent_history_queue.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/static_database.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/string_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/curl.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/options/mpi_stderr.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/options/OptionCollection.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/options/ResidueChainVectorOption.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/sql_database/DatabaseSessionManager.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/sql_database/types.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/boinc/boinc_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/icstream.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/izstream.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/ocstream.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/ozstream.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/io/FileContentsMap.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/file/file_sys_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/file/FileName.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/file/gzip_util.os build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/utility/file/PathName.os -Lexternal/lib -Lbuild/src/release/linux/3.13/64/x86/gcc/4.8/mpi -Lsrc -Lbuild/external/release/linux/3.13/64/x86/gcc/4.8/mpi -Lexternal -L/usr/lib -L/usr/local/lib -lObjexxFCL -lz -lcppdb -lsqlite3
  /usr/bin/ld: cannot find -lz
  collect2: error: ld returned 1 exit status
  scons: *** [build/src/release/linux/3.13/64/x86/gcc/4.8/mpi/libutility.so] Error 1
  scons: building terminated because of errors.
  
  Also,I retried to install after copy command at /main/source/tools/build
  cp site.settings.topsail site.settings
  cd brabra/main/source/
  ./scons.py -j4 mode=release bin extras=mpi
  
  Immediately,I got follow errors
  
  root@tan-VirtualBox:/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source# ./scons.py -j4 mode=release bin extras=mpi
  scons: Reading SConscript files …
  Traceback (most recent call last):
  File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/SConstruct”, line 150, in main
  build = SConscript(“tools/build/setup.py”)
  File “/home/tan/rosetta/rosetta_2014.35.57232_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/tan/rosetta/rosetta_2014.35.57232_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/tan/rosetta/rosetta_2014.35.57232_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/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/tools/build/setup.py”, line 421, in
  build = setup()
  File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/tools/build/setup.py”, line 413, in setup
  build.settings = setup_build_settings(build.options)
  File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/tools/build/setup.py”, line 210, in setup_build_settings
  site = Settings.load(“site.settings”, “settings”)
  File “/home/tan/rosetta/rosetta_2014.35.57232_bundle/main/source/tools/build/settings.py”, line 86, in load
  execfile(file, settings)
  File “site.settings”, line 27, in
  File “/usr/lib/python2.7/UserDict.py”, line 23, 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.
  
  What should I do to solve this problem?
  
  Best regards
- December 16, 2014 at 11:22 am #10703
  Anonymous
  Several things going on here.
  
  The first is you need to have the zlib libraries installed. On Ubuntu this should be the zlib1g-dev package.
  
  The second issue you’re running into is that you don’t have the environment variables set up appropriately for your MPI compile. There’s a number of environment variables you need to specify.
  
  First off, you need to have the path to the MPI compiler in your PATH environment variable. This probably will happen by default, if you install it to the standard location.
  
  Next, you need to have the path to the MPI libraries in your INCLUDE environment variable. This is what you’re missing with the second error. You’ll need to install the libopenmpi-dev package on Ubuntu to get these headers. That won’t fix the environment variable issue, though. You’ll have to set it to something like “/usr/lib/openmpi/include/” yourself.
  
  The final environment variable to worry about is LD_LIBRARY_PATH. This may or may not be set appropriately yet. You want to make sure that the path /usr/lib/ (Where the MPI shared libraries should be) is in it.
Author

Posts

Viewing 1 reply thread

You must be logged in to reply to this topic.