Re: [Denovoassembler-users] Compiling with libz

Sébastien Boisvert Fri, 18 May 2012 13:41:55 -0700

Hi,

This is due to library dependencies.


Most of the time, the linker will re-order the libraries to avoid any error.


Out of curiosity, which instance are you using on Amazon EC2 ?

Yesterday, I did a network test on 1 micro instance.

http://dskernel.blogspot.ca/2012/05/computing-assembly-in-cloud.html


And also
a successful assembly using 4 small instances using message passing.

http://dskernel.blogspot.ca/2012/05/passing-message-in-cloud.html

Running Ray on Amazon EC2 Cluster Compute Eight Extra Large Instanceswould be very fast, I think.




1 Small Instance:

1.7 GB memory
1 EC2 Compute Unit (1 virtual core with 1 EC2 Compute Unit)
160 GB instance storage
32-bit or 64-bit platform
I/O Performance: Moderate
API name: m1.small


1 Cluster Compute Eight Extra Large Instance

60.5 GB of memory

88 EC2 Compute Units (2 x Intel Xeon E5-2670, eight-core "Sandy Bridge"architecture)

3370 GB of instance storage
64-bit platform
I/O Performance: Very High (10 Gigabit Ethernet)
API name: cc2.8xlarge


Le 2012-05-18 14:39, Keith Robison a écrit :

I found this tip with a Google search & it seems to have fixed thisfor me on an Amazon EC2 instance -- it's a bit unbelievable, but theplacement of the -lz flag can matter.

mpicxx -lz code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a-o Ray # fails

mpicxx code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -oRay -lz # succeeds

On Fri, May 18, 2012 at 2:15 PM, Sébastien Boisvert<sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>> wrote:


    Someone else is having problem linking the code os Mac OS

    Le 2012-05-18 12:57, Egon Ozer a écrit :

    I'm running into a little problem compiling 2.0.0-rc7 on OSX 10.6.8.  When 
I make with HAVE_LIBZ=y, I get the following error:

    mpicxx -lz  code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
    Undefined symbols:
       "FastqGzLoader::getSize()", referenced from:
           Loader::load(std::basic_string<char, std::char_traits<char>, 
std::allocator<char>  >, bool)in TheRayGenomeAssembler.a(Loader.o)
       "FastqGzLoader::open(std::basic_string<char, std::char_traits<char>, 
std::allocator<char>  >, int)", referenced from:
           Loader::load(std::basic_string<char, std::char_traits<char>, 
std::allocator<char>  >, bool)in TheRayGenomeAssembler.a(Loader.o)
           Loader::load(std::basic_string<char, std::char_traits<char>, 
std::allocator<char>  >, bool)in TheRayGenomeAssembler.a(Loader.o)
       "FastqGzLoader::load(int, ArrayOfReads*, MyAllocator*, int)", referenced 
from:
           Loader::loadSequences()      in TheRayGenomeAssembler.a(Loader.o)
    ld: symbol(s) not found
    collect2: ld returned 1 exit status
    make: *** [Ray] Error 1

    When I run make with HAVE_LIBZ=n, compilation runs without a hitch.  I had 
no problems compiling 2.0.0-rc5 with libz.



    This is strange because the build system of Ray has not changed
    since 2.0.0-rc5.


    Did you change something since 2.0.0-rc5 ?

       Just to make sure, I updated zlib with MacPorts to 1.2.7 (universal), 
but still no dice.   Any suggestions?


    If you have cmake installed, you can build Ray with it instead.
    CMake is cross-platform.



    To build Ray with CMake:


    tar xjf Ray-v2.0.0-rc7.tar.bz2

    cd Ray-v2.0.0-rc7

    remove the line " RayPlatform/scheduling/SwitchMan_adapters.cpp"
    from CMakeLists.txt

    cd ..

    mkdir Build-with-CMAKE

    cd Build-with-CMAKE

    cmake ../Ray-v2.0.0-rc7

    make

    ls Ray



    Let me know if that works for you.

    Thanks,
    - Egon
    
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Re: [Denovoassembler-users] Compiling with libz

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