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PONVCC linking error in C and CUDA-C code
 

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  1. PONVCC linking error in C and CUDA-C code
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    <p>I'm working on an DNA Fragment Assembly program. The CPU-only version is built in C language using GCC and I'm trying to build a GPU version using NVCC.</p> <p>Here is the makefile</p> <pre><code>all : clean FragmentAssembly.exe FragmentAssembly.exe : Common.o Fragment.o ILS.o Consensus.o main.o nvcc -pg -o FragmentAssembly.exe Common.o Fragment.o ILS.o Consensus.o main.o Common.o : Common.cu nvcc -pg -o Common.o -c Common.cu Fragment.o : Fragment.cu nvcc -pg -o Fragment.o -c Fragment.cu ILS.o : ILS.cu nvcc -pg -o ILS.o -c ILS.cu Consensus.o : Consensus.cu nvcc -pg -o Consensus.o -c Consensus.cu main.o : main.cu nvcc -pg -o main.o -c main.cu clean : rm -f *.exe *.o </code></pre> <p>As seen, the original <code>.c</code> files became .cu files for <code>nvcc</code> to compile them correctly. All of the cu files contain includes of their corresponding files (Common.h for Common.cu, etc..) except for <code>main.cu</code>.</p> <p>ILS.h contians definition of global variables <code>p_instanceFragments</code> and <code>p_instanceLength</code></p> <p>The problem is when compiling NVCC, for an unknown reason, I get the following errors :</p> <pre><code>Consensus.o:(.bss+0x0): multiple definition of `p_instanceFragments' ILS.o:(.bss+0x0): first defined here Consensus.o:(.bss+0x8): multiple definition of `p_instanceLength' ILS.o:(.bss+0x8): first defined here </code></pre> <p>There is no real multiple definitions since the same code is built correctly using GCC. It looks as if <code>ILS.h</code> is getting included twice in nvcc, by <code>ILS.cu</code> and <code>Consensus.cu</code>. This is also not possible since I've wrapped all my header files with an <code>#ifndef .. #define .. #endif</code> statements to avoid multiple includes and infinite include loops.</p> <p>Maybe something with the makefile commands ? or should I use gcc for linking ? Can you tell me how to deal with it ?</p> <p>Regards,</p>
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    1. USARMBouhali
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    1. COWithout any of the code (especially the definitions of p_instanceFragments in the header file), it is more or less impossible to tell what's wrong... Just a hint: Is it possible that in `ILS.h` you used something like `int p_instanceFragments;` ? (Of course instead of `int` you probably have a more complex type). That's actually a linker problem. I guess you need to use `extern int p_instanceFragments;` in `ILS.h` and then in either `Consensus.cu` **or** (not BOTH!) `ILS.cu` you need to declare `int p_InstanceFragments;`. Of course all of this is complete guess work without code...
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      1. PONVCC linking error in C and CUDA-C code
      1. USIngo Blackman
    2. COThat solved the problem, thanks :)
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      1. PONVCC linking error in C and CUDA-C code
      1. USARMBouhali
 

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