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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
268 stars 48 forks source link

error will installation with cuda enabled #131

Closed michieitel closed 5 years ago

michieitel commented 5 years ago

Hi!

I am trying to install Racon v 1.4.2 with CUDA (10.1) enabled but it throws an error during make (below). Can you please help to identify the issue.

Thanks Michael

cmake (v. 3.10.2) ran without error cmake -DCMAKE_BUILD_TYPE=Release -Dracon_enable_cuda=ON -Dracon_build_tests=ON ..

-- The C compiler identification is GNU 7.4.0 -- The CXX compiler identification is GNU 7.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- Using CUDA 10.1 from /usr/local/cuda -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for unistd.h -- Looking for unistd.h - found -- Renaming -- /home/ubuntu/racon/vendor/bioparser/vendor/zlib/zconf.h -- to 'zconf.h.included' because this file is included with zlib -- but CMake generates it automatically in the build directory. -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes Setting warning flags -- Build type: Release -- Using CUDA 10.1 from /usr/local/cuda -- Using CUDA 10.1 from /usr/local/cuda -- Found Doxygen: /usr/bin/doxygen (found version "1.8.13") found components: doxygen dot -- Found PythonInterp: /usr/bin/python (found version "2.7.15") -- Configuring done -- Generating done -- Build files have been written to: /home/ubuntu/racon/build

running make resulted in an error:

Scanning dependencies of target spoa Scanning dependencies of target logging Scanning dependencies of target gtest Scanning dependencies of target thread_pool Scanning dependencies of target zlibstatic Scanning dependencies of target edlib_static Scanning dependencies of target logger [ 3%] Building CXX object vendor/thread_pool/CMakeFiles/thread_pool.dir/src/thread_pool.cpp.o [ 6%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o [ 10%] Building CXX object ClaraGenomicsAnalysis/common/logging/CMakeFiles/logging.dir/src/logging.cpp.o [ 13%] Building CXX object vendor/edlib/CMakeFiles/edlib_static.dir/edlib/src/edlib.cpp.o [ 13%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/alignment_engine.cpp.o [ 16%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/graph.cpp.o [ 16%] Building CXX object vendor/spoa/CMakeFiles/spoa.dir/src/simd_alignment_engine.cpp.o [ 20%] Building CXX object vendor/logger/CMakeFiles/logger.dir/src/logger.cpp.o [ 23%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/crc32.o [ 23%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/deflate.o [ 23%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inflate.o [ 26%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzwrite.o [ 30%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/infback.o [ 30%] Building CXX object vendor/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o [ 30%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/compress.o [ 33%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/adler32.o [ 36%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzclose.o [ 36%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzread.o [ 36%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/gzlib.o [ 36%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inftrees.o [ 40%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/inffast.o [ 40%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/trees.o [ 43%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/uncompr.o [ 43%] Building C object vendor/bioparser/vendor/zlib/CMakeFiles/zlibstatic.dir/zutil.o [ 43%] Linking CXX static library lib/liblogger.a [ 43%] Built target logger /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:313:30: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(4) long long int []}’ [-Wignored-attributes] std::unique_ptr<mxxxi[]> sequence_profile_storage; ^ /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:318:30: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(4) long long int []}’ [-Wignored-attributes] std::unique_ptr<__mxxxi[]> M_storage; ^ /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:322:30: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(4) long long int []}’ [-Wignored-attributes] std::unique_ptr<__mxxxi[]> masks_storage; ^ /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:326:30: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(4) long long int []}’ [-Wignored-attributes] std::unique_ptr<mxxxi[]> penalties_storage; ^ /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp: In member function ‘void spoa::SimdAlignmentEngine::realloc(uint32_t, uint32_t, uint32_t)’: /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:386:69: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(4) long long int []}’ [-Wignored-attributes] pimpl_->sequence_profile_storage = std::unique_ptr<mxxxi[]>(storage); ^ /home/ubuntu/racon/vendor/spoa/src/simd_alignmentengine.cpp:397:54: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(4) long long int []}’ [-Wignored-attributes] pimpl->M_storage = std::unique_ptr<mxxxi[]>(storage); ^ /home/ubuntu/racon/vendor/spoa/src/simd_alignmentengine.cpp:405:58: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(4) long long int []}’ [-Wignored-attributes] pimpl->masks_storage = std::unique_ptr<mxxxi[]>(storage); ^ /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:413:62: warning: ignoring attributes on template argument ‘spoa::mxxxi [] {aka vector(4) long long int []}’ [-Wignored-attributes] pimpl_->penalties_storage = std::unique_ptr<mxxxi[]>(storage); ^ /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp: In instantiation of ‘T* spoa::allocateAlignedMemory(T**, uint32_t, uint32_t) [with T = vector(4) long long int; uint32_t = unsigned int]’: /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:384:61: required from here /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:36:16: warning: ‘new’ of type ‘vector(4) long long int’ with extended alignment 32 [-Waligned-new=] storage = new T[size + alignment - 1]; ^~~~~~~ /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:36:16: note: uses ‘void operator new ’, which does not have an alignment parameter /home/ubuntu/racon/vendor/spoa/src/simd_alignment_engine.cpp:36:16: note: use ‘-faligned-new’ to enable C++17 over-aligned new support [ 46%] Linking C static library ../../lib/libz.a [ 46%] Built target zlibstatic [ 46%] Linking CXX static library lib/libthread_pool.a [ 46%] Built target thread_pool [ 46%] Linking CXX static library ../../lib/libedlib_static.a [ 46%] Built target edlib_static [ 46%] Linking CXX static library lib/libspoa.a [ 46%] Built target spoa [ 50%] Linking CXX static library ../../../lib/libgtest.a [ 50%] Linking CXX static library ../../../lib/liblogging.a [ 50%] Built target gtest Scanning dependencies of target gtest_main [ 50%] Building CXX object vendor/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o [ 50%] Built target logging [ 50%] Building NVCC (Device) object ClaraGenomicsAnalysis/cudaaligner/CMakeFiles/cudaaligner.dir/src/cudaaligner_generated_ukkonen_gpu.cu.o [ 53%] Building NVCC (Device) object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_nw_banded.cu.o [ 53%] Building NVCC (Device) object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_kernels.cu.o [ 53%] Building NVCC (Device) object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_nw.cu.o [ 56%] Building NVCC (Device) object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_topsort.cu.o [ 56%] Building NVCC (Device) object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_generated_cudapoa_add_alignment.cu.o [ 56%] Linking CXX static library ../../../lib/libgtest_main.a [ 56%] Built target gtest_main Scanning dependencies of target cudaaligner [ 60%] Building CXX object ClaraGenomicsAnalysis/cudaaligner/CMakeFiles/cudaaligner.dir/src/cudaaligner.cpp.o [ 60%] Building CXX object ClaraGenomicsAnalysis/cudaaligner/CMakeFiles/cudaaligner.dir/src/aligner.cpp.o [ 63%] Building CXX object ClaraGenomicsAnalysis/cudaaligner/CMakeFiles/cudaaligner.dir/src/alignment_impl.cpp.o [ 63%] Building CXX object ClaraGenomicsAnalysis/cudaaligner/CMakeFiles/cudaaligner.dir/src/aligner_global.cpp.o Scanning dependencies of target cudapoa [ 63%] Building CXX object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa.cpp.o [ 66%] Building CXX object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/batch.cpp.o [ 66%] Building CXX object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/cudapoa_batch.cpp.o [ 70%] Building CXX object ClaraGenomicsAnalysis/cudapoa/CMakeFiles/cudapoa.dir/src/allocate_block.cpp.o [ 73%] Linking CXX static library ../../lib/libcudaaligner.a [ 73%] Built target cudaaligner [ 73%] Linking CXX static library ../../lib/libcudapoa.a [ 73%] Built target cudapoa Scanning dependencies of target racon_test Scanning dependencies of target racon [ 73%] Building CXX object CMakeFiles/racon.dir/src/cuda/cudabatch.cpp.o [ 76%] Building CXX object CMakeFiles/racon.dir/src/cuda/cudaaligner.cpp.o [ 76%] Building CXX object CMakeFiles/racon_test.dir/test/racon_test.cpp.o [ 80%] Building CXX object CMakeFiles/racon.dir/src/cuda/cudapolisher.cpp.o [ 80%] Building CXX object CMakeFiles/racon.dir/src/main.cpp.o [ 83%] Building CXX object CMakeFiles/racon_test.dir/src/polisher.cpp.o [ 83%] Building CXX object CMakeFiles/racon_test.dir/src/overlap.cpp.o [ 83%] Building CXX object CMakeFiles/racon.dir/src/overlap.cpp.o [ 86%] Building CXX object CMakeFiles/racon_test.dir/src/sequence.cpp.o [ 86%] Building CXX object CMakeFiles/racon_test.dir/src/window.cpp.o [ 86%] Building CXX object CMakeFiles/racon.dir/src/window.cpp.o [ 90%] Building CXX object CMakeFiles/racon.dir/src/sequence.cpp.o [ 93%] Building CXX object CMakeFiles/racon.dir/src/polisher.cpp.o [ 93%] Building CXX object CMakeFiles/racon_test.dir/src/cuda/cudabatch.cpp.o [ 96%] Building CXX object CMakeFiles/racon_test.dir/src/cuda/cudaaligner.cpp.o [100%] Building CXX object CMakeFiles/racon_test.dir/src/cuda/cudapolisher.cpp.o /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In member function ‘virtual void racon::CUDAPolisher::find_overlap_breaking_points(std::vector<std::uniqueptr >&)’: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:96:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log(); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In member function ‘virtual void racon::CUDAPolisher::find_overlap_breaking_points(std::vector<std::uniqueptr >&)’: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:96:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log(); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In lambda function: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:150:36: error: invalid use of incomplete type ‘class logger::Logger’ logger->bar("[racon::CUDAPolisher::initialize] aligning overlaps"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In lambda function: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:150:36: error: invalid use of incomplete type ‘class logger::Logger’ logger->bar("[racon::CUDAPolisher::initialize] aligning overlaps"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In member function ‘virtual void racon::CUDAPolisher::polish(std::vector<std::uniqueptr >&, bool)’: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:219:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log("[racon::CUDAPolisher::polish] allocated memory on GPUs"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:260:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log(); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In lambda function: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:297:36: error: invalid use of incomplete type ‘class logger::Logger’ logger->bar("[racon::CUDAPolisher::polish] generating consensus"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In member function ‘virtual void racon::CUDAPolisher::polish(std::vector<std::uniqueptr >&, bool)’: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:327:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log("[racon::CUDAPolisher::polish] polished windows on GPU"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:330:16: error: invalid use of incomplete type ‘class logger::Logger’ logger_->log(); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In member function ‘virtual void racon::CUDAPolisher::polish(std::vector<std::uniqueptr >&, bool)’: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:219:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log("[racon::CUDAPolisher::polish] allocated memory on GPUs"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:260:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log(); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:356:20: error: invalid use of incomplete type ‘class logger::Logger’ logger->log("[racon::CUDAPolisher::polish] polished remaining windows on CPU"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:357:20: error: invalid use of incomplete type ‘class logger::Logger’ logger->log(); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In lambda function: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:297:36: error: invalid use of incomplete type ‘class logger::Logger’ logger->bar("[racon::CUDAPolisher::polish] generating consensus"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp: In member function ‘virtual void racon::CUDAPolisher::polish(std::vector<std::uniqueptr >&, bool)’: /home/ubuntu/racon/src/cuda/cudapolisher.cpp:327:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log("[racon::CUDAPolisher::polish] polished windows on GPU"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:330:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log(); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:388:16: error: invalid use of incomplete type ‘class logger::Logger’ logger->log("[racon::CUDAPolisher::polish] generated consensus"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:356:20: error: invalid use of incomplete type ‘class logger::Logger’ logger->log("[racon::CUDAPolisher::polish] polished remaining windows on CPU"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:357:20: error: invalid use of incomplete type ‘class logger::Logger’ logger->log(); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ /home/ubuntu/racon/src/cuda/cudapolisher.cpp:388:16: error: invalid use of incomplete type ‘class logger::Logger’ logger_->log("[racon::CUDAPolisher::polish] generated consensus"); ^~ In file included from /home/ubuntu/racon/src/cuda/cudapolisher.hpp:11:0, from /home/ubuntu/racon/src/cuda/cudapolisher.cpp:13: /home/ubuntu/racon/src/polisher.hpp:29:11: note: forward declaration of ‘class logger::Logger’ class Logger; ^~ CMakeFiles/racon.dir/build.make:182: recipe for target 'CMakeFiles/racon.dir/src/cuda/cudapolisher.cpp.o' failed make[2]: [CMakeFiles/racon.dir/src/cuda/cudapolisher.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... CMakeFiles/racon_test.dir/build.make:182: recipe for target 'CMakeFiles/racon_test.dir/src/cuda/cudapolisher.cpp.o' failed make[2]: [CMakeFiles/racon_test.dir/src/cuda/cudapolisher.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... CMakeFiles/Makefile2:120: recipe for target 'CMakeFiles/racon_test.dir/all' failed make[1]: [CMakeFiles/racon_test.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... CMakeFiles/Makefile2:74: recipe for target 'CMakeFiles/racon.dir/all' failed make[1]: [CMakeFiles/racon.dir/all] Error 2 Makefile:129: recipe for target 'all' failed make: [all] Error 2

rvaser commented 5 years ago

Hi Michael, I was refactoring without a valid nvcc compiler, I hope I fixed it in the latest commit. Could you please verify that?

Best regards, Robert

michieitel commented 5 years ago

Fixed. Compilation work! Thanks a lot for that incredibly fast fix! Michael