Running Casava Under Ubuntu 11.04

Question

[Stevelor]

Hey Guys,

trying to install CASAVA 1.8.1 on Ubuntu 11.04. Has anyone of you done it already...because it doesn't work! pthreads library is missing....but i can not find how to install it :(

plZ help!!

Cheers!

Answer 1

[Michael]

Install the compilers and build tools first, follow this guide: https://help.ubuntu.com/community/CompilingSoftware

POSIX threads library and headers should come with the gnu compiler.

[Pablo Marin-Garcia]

They come, but cmake in ubuntu 11.04 is not yet capable of multi-arch library locations, so it does not find libraries in non standard places libz.so and libpthreads are not in /usr/lib :-( ).

Answer 2

[Pablo Marin-Garcia]

I have tried but failed to install in ubuntu 11.04 several times before having it successfully installed. At the end after fixing some library paths, still was not working but because I used --static option. When I dropped this option then worked:

Success

[/usr/lib]$ sudo ln -s /usr/lib/x86_64-linux-gnu/libz.so /usr/lib
[/usr/lib]$ sudo ln -s /usr/lib/x86_64-linux-gnu/libpth* /usr/lib

[CASAVA-build]../CASAVA_v1.8.1/src/configure --prefix=/molgen

CASAVA comes with its own cmake (2.8.4) and Boost (1.44) that are newer that the latest updates for Ubuntu 11.04 cmake (2.8.3) and Boost (1.42)

Boost is not installing everything but I hope it would work well at least for CASAVA:

Component configuration:
- date_time                : building
- filesystem               : building
- graph                    : not building
- graph_parallel           : not building
- iostreams                : building
- math                     : not building
- mpi                      : not building
- program_options          : building
- python                   : not building
- random                   : not building
- regex                    : building
- serialization            : building
- signals                  : not building
- system                   : building
- test                     : not building
- thread                   : building
- wave                     : not building

Initial errors and explanations

    | CMake Error at cmake/cxxConfigure.cmake:74 (message):
    |   No support for gzip compression
    | Call Stack (most recent call first):
    |   c++/CMakeLists.txt:33 (include)
    |
    |
    | -- Configuring incomplete, errors occurred!
    | Couldn't configure the project:

Some libraries are in not standard place. For example libz.so is not in /usr/lib

 | [~/src/CASAVA_v1.8.1-build]$ locate libz.so
 | /lib/x86_64-linux-gnu/libz.so.1
 | /lib/x86_64-linux-gnu/libz.so.1.2.3.4
 | /usr/lib/x86_64-linux-gnu/libz.so
 | /usr/lib32/libz.so.1
 | /usr/lib32/libz.so.1.2.3.4

But you can symlink it.

[/usr/lib]$ ln -s /usr/lib/x86_64-linux-gnu/libz.so

Then from http://cmake.3232098.n2.nabble.com/FindZLIB-on-ubuntu-11-04-td6354236.html I have added the symlinks for libpthread

    [/usr/lib]$ ll  /usr/lib/x86_64-linux-gnu/libpth*
      /usr/lib/x86_64-linux-gnu/libpthread.a
      /usr/lib/x86_64-linux-gnu/libpthread_nonshared.a
      /usr/lib/x86_64-linux-gnu/libpthread.so
    [/usr/lib]$ sudo ln -s  /usr/lib/x86_64-linux-gnu/libpth* .

Other links talking about this

• http://seqanswers.com/forums/showthread.php?t=11106
• http://cmake.3232098.n2.nabble.com/FindZLIB-on-ubuntu-11-04-td6354236.html

Remember

The static compilation does not work! With the symlinks described before a normal compilation will work.

[Pablo Marin-Garcia]

Hummm I see now that CASAVA is using its own cmake: Decompressing ~/src/CASAVA_v1.8.1/src/../redist/cmake-2.8.4.tar.gz

[Delagoya]

Symbolic linking worked for me on 11.04: ln -s /usr/lib/x86_64-linux-gnu/libpthread /usr/lib/. ln -s /usr/lib/x86_64-linux-gnu/libpthread /usr/lib/.