[BioPython] Another problem with Biopython compilation on AMD64

[d.lapointe at comcast.net]

Sebastian,

I encountered the exact same  problem using SUSE 9.1  with X86_64.  There are  a few customizations that need to be made to makefiles for some packages when moving to x86_64, The NCBI toolbox is one.   I will just mention that there are some math libraries  optimized for AMD64 that can be used to advantage. AMD supplies one,  and there are several BLAS based ones also for AMD64.

<OT> I compiled R with the GOTO BLAS library for X86_64.  A 3000x3000 matrix multiply ( m %*% m) went from 320 sec w/o to 9 sec with the library. solve(m) went from about 300 sec to 28 seconds.  Of course only operations using BLAS benefit from this. </OT>

David


> Hello,
> 
> When I tried to compile Biopython with python setup.py build I got this:
> 
> (cuted some output...)
> building 'Bio.KDTree._CKDTree' extension
> creating build/temp.linux-x86_64-2.3/Bio/KDTree
> g++ -pthread -I/usr/include/python2.3 -c Bio/KDTree/KDTree.cpp -o
> build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o
> g++ -pthread -I/usr/include/python2.3 -c Bio/KDTree/KDTree.swig.cpp -o
> build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.swig.o
> g++ -pthread -shared build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o
> build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.swig.o -lstdc++ -o
> build/lib.linux-x86_64-2.3/Bio/KDTree/_CKDTree.so
> /usr/bin/ld: build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: relocation
> R_X86_64_32 can not be used when making a shared object; recompile with
> -fPIC
> build/temp.linux-x86_64-2.3/Bio/KDTree/KDTree.o: could not read symbols:
> Bad value
> collect2: ld returned 1 exit status
> error: command 'g++' failed with exit status 1
> 
> I googled and I found this post that seems related:
> http://www.mail-archive.com/debian-ocaml-maint@lists.debian.org/msg05778.html
> But I am not sure about wwhat to do :(
> 
> 
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