Cannot run binaries after successful compilation

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    • August 14, 2017 at 9:56 am #2719
      Anonymous

        Dear all,

        I have been trying to compile rosetta 3.8 for a while now without success (meathod worked will with 3.7). I have a 17.04 Ubuntu Gnome Operating System.

        Compile Commands:

        sudo apt install zlib1g-dev scons build-essential -y

        tar -xvzf rosetta_src_3.8_bundle.tgz

        cd {ROSETTA}/main/source

        ./scons.py mode=release bin

         

        Result:

        Successfully compiles everything, no errors printed.

         

        Command to test a binary:

        /home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/bin/AbinitioRelax.default.linuxgccrelease

         

        Result:

        /home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/bin/AbinitioRelax.default.linuxgccrelease: error while loading shared libraries: libsqlite3.so: cannot open shared object file: No such file or directory

         

        I am not sure how to diagnose this issue because I DO have binaries in the {ROSETTA}/main/source/bin directory (the execute command is not miss spelled because it is typed with TAB auto complete).

         

        Please help?

      • August 14, 2017 at 4:15 pm #13660
        Anonymous

          The issue is that it can’t find the libsqlite3.so library file (not the executable file). During the normal compiliation, things should be setup such that the executable has an internal path to that file. However, that can be broken in a few ways.

          Did you move the directory after compilation?  Or is it in on a mounted drive which has different full directory name from how it was mounted when it was compiled? Either of these can mess up the auto-pathing which happens.

          If neither of these is the case, there may be issues with the rpath mechanism on your system (though I don’t know why that would be the case). A workaround is to add the appropriate path to your $LD_LIBRARY_PATH variable. This path will be something like /home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/build/external/release/linux/2.6/64/x86/gcc/5.2/default/ — but it may be different depending on your compiler and version. Do a `find /home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/build/external/  -name libsqlite3.so` to find the appropriate directory.

          Failing that, you can always try compiling with `extras=static` to get the static version of the executables, which shouldn’t have the libary pathing issue.

        • August 15, 2017 at 9:42 am #13667
          Anonymous

            Ok.

             

            I ran the search command and this is the path I got:

            /home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/build/external/release/linux/4.10/64/x86/gcc/6.3/default/libsqlite3.so

             

            How do I add this path to my $LD_LIBRARY_PATH variable?

            is it this way?

            LD_LIBRARY_PATH =/home/acresearch/rosetta_s………

             

            UPDATE

            When I run:

            $LD_LIBRARY_PATH=/home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/build/external/release/linux/4.10/64/x86/gcc/6.3/default/libsqlite3.so

            I get this:

            bash: /home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/build/external/release/linux/4.10/64/x86/gcc/6.3/default/libsqlite3.so=/home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/build/external/release/linux/4.10/64/x86/gcc/6.3/default/libsqlite3.so: No such file or directory

             

            • August 15, 2017 at 2:34 pm #13668
              Anonymous

                Here’s how to add that variable in bash (I would put this in your .bashrc) (Remember, if you put it in your .bashrc file, you’ll want to source it first [source ~/.bashrc] or open up a new terminal).

                 

                export LD_LIBRARY_PATH=/home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/build/external/release/linux/4.10/64/x86/gcc/6.3/default/libsqlite3.so:$LD_LIBRARY_PATH

                (The above should be all one line [sorry, having trouble with formatting])

                This sets the variable “LD_LIBRARY_PATH” to include that path WITHOUT overwriting what else is in your LD_LIBRARY_PATH (i.e. it appends your new path to existing paths).

              • August 16, 2017 at 9:28 am #13671
                Anonymous

                  I tried this method but unfortunatly that did not work either.

                   

                  I think I will compile it as rmoretti advised (using extras=static):

                  ./scons.py mode=release bin extras=static

                   

                  Is this correct?

                   

                • August 16, 2017 at 12:34 pm #13672
                  Anonymous

                    Sorry, I realized the variable I posted is wrong.  You need to put the path where the library is located, whereas I accidently copied the full path for the file.  You should use this instead:

                    export LD_LIBRARY_PATH=/home/acresearch/rosetta_src_2017.08.59291_bundle/main/source/build/external/release/linux/4.10/64/x86/gcc/6.3/default/:$LD_LIBRARY_PATH

                    The difference is dropping the “libsqlite3.so”

                • August 18, 2017 at 7:57 am #13682
                  Anonymous

                    It works now

                     

                    Thank you

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