fragment_picker.mpi.linuxgccrelease can’t find : libsqlite3.so

This topic has 11 replies, 3 voices, and was last updated 8 years, 6 months ago by Anonymous.

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- June 21, 2016 at 2:22 am #2448
  Anonymous
  I’m sorry… I’m sure this is just something basic I overlooked but I’m not sure how this is happening since it seems that a basic component is missing….
  
  I have Rosetta compiled with “extras = mpi” and I have OpenMPI installed.
  
  I ran:
  
  (mpirun –mca btl_tcp_if_exclude lo,virbr0 –hostfile hostfile -np 1 /home/starone/Public/Rosetta/main/source/bin/fragment_picker.mpi.linuxgccrelease @flags > frag.out) >& frag.err
  
  And found this in frag.err:
  
  /Rosetta/main/source/bin/fragment_picker.mpi.linuxgccrelease: error while loading shared libraries: libsqlite3.so: cannot open shared object file: No such file or directory
- June 21, 2016 at 2:31 am #11676
  Anonymous
  Often when one of the “external” libraries (libsqlite, libcppdb, libcifparse) can’t be found that indicates an issue with compilation, or that you moved the executables.
  
  In the Rosetta build process, the “external” libraries are built in a separate directory from the “internal” libraries. During compilation the Rosetta programs should be annotated with the location of the external libraries. However, sometimes this doesn’t work. Also, if you move the Rosetta installation after it’s built (or even just run if from a different absolute path – for example if your mount point changes, or you have it on a network drive) then the annotations no longer work.
  
  My recommendation is to try to re-run the compilation step, making sure to compile it from the same directory name as you are going to run it from in the production case.
- June 21, 2016 at 2:08 pm #11678
  Anonymous
  If you did that recompile AFTER changing your MPI version, then the recompile after changing the version should have worked. That said, the standard thing to try first here is “recompile” – it’s the equivalent of “turn if off and then on again”, and worth doing before we try diagnosing any further.
- June 22, 2016 at 1:37 am #11680
  Anonymous
  Doesn’t look like the output of a recompilation… ? Is there a specific option I can set to specify “recompile”?
  
  scons: Reading SConscript files …
  
  Running versioning script … fatal: Not a git repository (or any of the parent directories): .git
  
  Done. (0.1 seconds)
  
  file ./options.dox being updated
  
  file ./full-options-list.md being updated
  
  Number of option files updated: 2
  
  Total 3670 options.
  
  Finished updating ResidueProperty code — no changes needed
  
  Finished updating VariantType code — no changes needed
  
  scons: done reading SConscript files.
  
  scons: Building targets …
  
  scons: `bin’ is up to date.
  
  scons: done building targets.
- June 23, 2016 at 2:00 am #11682
  Anonymous
  Will do… But I was just wondering, could it be that I usually download Rosetta with binaries and only ever build the MPI binaries, so I never needed sqlite before? Because it’s not installed on my machine… then again I don’t remember seeing it mentioned in the Rosetta build documentation.
  
  If I do need it, how do I install it using that “sudo apt-get…” thing
  
  Thanks again for all your help!
  
  -Scott
- June 24, 2016 at 1:47 am #11685
  Anonymous
  This is what I get when I use that command:
  
  ./ide/VisualStudio/sqlite3
  
  ./ide/VisualStudio/sqlite3/sqlite3.vcxproj
  
  ./ide/VisualStudio/sqlite3/sqlite3.vcproj
  
  ./external/SConscript.external.sqlite3
  
  ./external/dbio/cppdb/sqlite3_backend.cpp
  
  ./external/dbio/sqlite3
  
  ./external/dbio/sqlite3/sqlite3.h
  
  ./external/dbio/sqlite3/sqlite3.c
  
  ./build/external/release/linux/4.2/64/x86/gcc/4.8/mpi/dbio/cppdb/sqlite3_backend.os
  
  ./build/external/release/linux/4.2/64/x86/gcc/4.8/mpi/dbio/sqlite3
  
  ./build/external/release/linux/4.2/64/x86/gcc/4.8/mpi/dbio/sqlite3/sqlite3.os
  
  ./build/external/release/linux/4.2/64/x86/gcc/4.8/mpi/libsqlite3.so
- June 24, 2016 at 2:52 am #11686
  Anonymous
  I didn’t know where apps.src.settings was and a friend suggested I run this command: sudo apt-get install libsqlite3-dev
  
  This solved the problem, though I’m thinking it’s not the kind of solution that works well given what you said about only requiring a dependency on the compiler and MPI. I’ll mark this one solved unless you want me to do something further to help find a more satisfactory solution.
- June 21, 2016 at 2:43 am #11677
  Anonymous
  Thank you very much for you quick reply! Just to be sure I’m giving you all the information before following your suggestion…
  
  I didn’t move the executables, but I did want to do a clean rebuild after I changed from the MPI package that comes with Ubuntu to OpenMPI. I couldn’t find a “clean build” option for Rosetta so I followed the instructions I found from a search:
  
  I ran:
  
  You *should* clean your compiled copy and rebuild. The simplest way to do this is:
  
  cd build
  
  rm -rf external src (and whatever else is there)
  
  cd ../bin
  
  rm -rf *release *debug (and anything else)
  
  cd ..
  
  rm .sconsign.dblite
  
  Would any of this cause the problem? Would the re-compile still solve it?
  
  Thank you!
  
  Take care,
  
  Scott
- June 22, 2016 at 2:44 pm #11681
  Anonymous
  That’s a recompile where it didn’t do anything (specifically, it didn’t re-link, which is the problem you appear to have). Your cleaning procedure (delete the contents of build and .sconsign.dblite) was correct – try that again and then compile.
- June 23, 2016 at 2:11 pm #11683
  Anonymous
  0:18:28 KLAW-GOR ~/ROSETTA/Rosetta/main/source> find . -name “*sqli*”
  
  ./build/external/release/macos/15.5/64/x86/clang/7.3/default/dbio/cppdb/sqlite3_backend.os
  
  ./build/external/release/macos/15.5/64/x86/clang/7.3/default/dbio/sqlite3
  
  ./build/external/release/macos/15.5/64/x86/clang/7.3/default/dbio/sqlite3/sqlite3.os
  
  ./build/external/release/macos/15.5/64/x86/clang/7.3/default/libsqlite3.dylib
  
  ./external/dbio/cppdb/sqlite3_backend.cpp
  
  ./external/dbio/sqlite3
  
  ./external/dbio/sqlite3/sqlite3.c
  
  ./external/dbio/sqlite3/sqlite3.h
  
  ./external/SConscript.external.sqlite3
  
  It should already be in your Rosetta download, so you don’t need the system dependency. We try to make it so that the only external dependency is the compiler and MPI.
  
  If recompiling doesn’t work, try adding sqlite3 to the list at the bottom of apps.src.settings.
- June 24, 2016 at 2:36 pm #11688
  Anonymous
  src/protocols/apps.src.settings.
  
  If it’s working for you, I’m happy! If you aren’t using the sqlite3 hookups, and you probably aren’t, then it will be fine.
- June 25, 2016 at 1:29 am #11693
  Anonymous
  Ok.. thanks for helping me. Let me know if there’s anything I can do.
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