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NVIDIA-Genomics-Research / GenomeWorks

SDK for GPU accelerated genome assembly and analysis
https://clara-parabricks.github.io/GenomeWorks/
Apache License 2.0
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Buils fails with gcc 9.3 #660

Closed dominik-handler closed 3 years ago

dominik-handler commented 3 years ago

Hi,

I tried to build racon and as part of it genomeworks is built. Per default I had gcc9.3 installed and the build of GenomeWorks failed. When I tried to build it separately from racon I had the same problem. I was able to install it nicely when switching back to gcc8.

I got this error message: 09:55:56 [ 36%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/cudaaligner.cpp.o 09:55:56 [ 36%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/aligner_global_ukkonen.cpp.o 09:55:56 [ 38%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/aligner.cpp.o 09:55:56 [ 38%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/aligner_global.cpp.o 09:55:56 [ 38%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/alignment.cpp.o 09:55:56 [ 39%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/alignment_impl.cpp.o 09:55:56 [ 39%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/aligner_global_myers.cpp.o 09:55:56 [ 40%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/ukkonen_cpu.cpp.o 09:55:56 [ 40%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/aligner_global_myers_banded.cpp.o 09:55:56 [ 40%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/aligner_global_hirschberg_myers.cpp.o 09:55:56 [ 42%] Building CXX object cudaaligner/CMakeFiles/cudaaligner.dir/src/needleman_wunsch_cpu.cpp.o 09:56:00 [ 43%] Linking CXX static library libcudaaligner.a 09:56:00 [ 43%] Built target cudaaligner 09:56:39 Scanning dependencies of target cudapoa 09:56:39 [ 45%] Building CXX object cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa.cpp.o 09:56:39 [ 45%] Building CXX object cudapoa/CMakeFiles/cudapoa.dir/version.cpp.o 09:56:39 [ 45%] Linking CXX static library libcudapoa.a 09:56:39 [ 45%] Built target cudapoa 09:56:39 Makefile:162: recipe for target 'all' failed 09:56:39 make: *** [all] Error 2

Unfortunately, I cannot easily extract the Makefile for these builds as I am building singularity images in a build pipeline.

Dominik

EpiSlim commented 3 years ago

Hi Dominik! The error message is not that explicit, but given your success with gcc8, my guess is that the issue is a cuda/gcc incompatibility problem. What distribution are you using for your builds and what version of CUDA do they include?

ahehn-nv commented 3 years ago

Hi Dominik. Did you build with make -j ...? If so, could you try to run make in the build directory again without any arguments? I guess the actual error happened further up.

dominik-handler commented 3 years ago

Hi,

I am sorry but I cannot reproduce the error anymore. I now tried various variants of CUDA and gcc together and all of them build at the moment.

Thank you in any case, Dominik

ahehn-nv commented 3 years ago

No worries. The best issues are the ones that solve themselves. :)