On 02/15/2013 12:40 PM, Keith Robison wrote:
> I've run into problems compiling libz into Ray on the Amazon EC2 AMI
> ami-4583572c, which I believe is the correct AMI to run the HPC cluster
> instances.
>
> I changed HAVE_LIBZ to y (and the other files are compling with it), but the
> final link step is failing; any suggestions? FastqGzLoader complilation is
> apparently
>not being attempted. I tried compiling the FastqGzLoader by hand, but that
>didn't help; still fails at linking.
>
> Any suggestions?
>
Hello,
This issue has been fixed in the git repository a while ago (but after v2.1.0).
Here is a patch that changes 2 lines in the Makefile to fix this:
https://raw.github.com/sebhtml/patches/master/ray/ray-v2.1.0-aws-ec2.patch
To use the patch on one AWS cc2.8xlarge instance running ami-4583572c:
wget http://downloads.sourceforge.net/project/denovoassembler/Ray-v2.1.0.tar.bz2
tar -xjf Ray-v2.1.0.tar.bz2
cd Ray-v2.1.0/
wget https://raw.github.com/sebhtml/patches/master/ray/ray-v2.1.0-aws-ec2.patch
patch -p1 < ray-v2.1.0-aws-ec2.patch
make HAVE_LIBZ=y -j 30
./Ray -version|grep HAVE_LIBZ
>
> make[1]: Leaving directory
> `/data2/2013-02-public-soil/packages/Ray-v2.1.0/code'
> mpicxx -lz code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
> code/TheRayGenomeAssembler.a(Loader.o): In function
> `Loader::load(std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, bool)':
> Loader.cpp:(.text+0xb89): undefined reference to
> `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, int)'
> Loader.cpp:(.text+0xbac): undefined reference to `FastqGzLoader::getSize()'
> Loader.cpp:(.text+0xc42): undefined reference to
> `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, int)'
> code/TheRayGenomeAssembler.a(Loader.o): In function `Loader::loadSequences()':
> Loader.cpp:(.text+0x1322): undefined reference to `FastqGzLoader::load(int,
> ArrayOfReads*, MyAllocator*, int)'
> collect2: ld returned 1 exit status
> make: *** [Ray] Error 1
>
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