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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
272 stars 49 forks source link

CUDA #150

Open Sumsarium opened 4 years ago

Sumsarium commented 4 years ago

I am trying to make racon work with CUDA (NVIDA Tesla V100, CUDA version 10.1, Ubuntu 18.04 LTS). However, I seem to get the below error. How can I overcome this problem?

`Scanning dependencies of target logger
[ 62%] Building CXX object vendor/logger/CMakeFiles/logger.dir/src/logger.cpp.o
[ 64%] Linking CXX static library lib/liblogger.a
[ 64%] Built target logger
[ 66%] Building NVCC (Device) object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_nw_banded.cu.o
[ 68%] Building NVCC (Device) object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_kernels.cu.o
/home/anon/racon/vendor/ClaraGenomicsAnalysis/3rdparty/spdlog/include/spdlog/details/pattern_formatter.h:665:66: error: expected primary-expression before \u2018const\u2019
     log_clock::time_point last_update_{std::chrono::seconds(0)};
                                                                  ^    
/home/anon/racon/vendor/ClaraGenomicsAnalysis/3rdparty/spdlog/include/spdlog/details/pattern_formatter.h:665:66: error: expected \u2018}\u2019 before \u2018const\u2019
/home/anon/racon/vendor/ClaraGenomicsAnalysis/3rdparty/spdlog/include/spdlog/details/pattern_formatter.h:665:66: error: could not convert \u2018{<expression error>}\u2019 from \u2018<brace-enclosed initializer list>\u2019 to \u2018std::chrono::_V2::system_clock::time_point {aka std::chrono::time_point<std::chrono::_V2::system_clock, std::chrono::duration<long int, std::ratio<1l, 1000000000l> > >}\u2019
/home/anon/racon/vendor/ClaraGenomicsAnalysis/3rdparty/spdlog/include/spdlog/details/pattern_formatter.h:665:66: error: expected \u2018;\u2019 before \u2018const\u2019
CMake Error at cudapoa_generated_cudapoa_kernels.cu.o.Release.cmake:279 (message):
  Error generating file
  /home/anon/racon/build/ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/./cudapoa_generated_cudapoa_kernels.cu.o

ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/build.make:63: recipe for target 'ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_kernels.cu.o' failed
make[2]: *** [ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_kernels.cu.o] Error 1
CMakeFiles/Makefile2:880: recipe for target 'ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/all' failed
make[1]: *** [ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2`
rvaser commented 4 years ago

Hello, I am adding the authors of that part of code to take a look at this.

@tijyojwad, @vellamike, could you please have a look?

Best regards, Robert

vellamike commented 4 years ago

This seems to have been also reported by @SamStudio8 here.

vellamike commented 4 years ago

@Sumsarium can you try and using Racon from this repository. We are no longer maintaining this repository and the lcb-sci repo is the official one. Please let me know if this fixes the problem.

Kirk3gaard commented 3 years ago

Hi Will you consider adding that to the mainpage of this repository?

Sumsarium commented 3 years ago

Please excuse my overdue reply. Seems I forgot to comment. I got it working from the new repo :-) Thanks a lot!

rvaser commented 3 years ago

@Kirk3gaard, if you mean a note about the new repository, it can be found in the about section. If something else, please elaborate.