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Installation issue with CUDA #12

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pr0xxy opened this issue Nov 14, 2019 · 0 comments
Open

Installation issue with CUDA #12

pr0xxy opened this issue Nov 14, 2019 · 0 comments

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@pr0xxy
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pr0xxy commented Nov 14, 2019

I am trying to install racon-gpu with CUDA and I keep getting stopped with missing files:

-- The C compiler identification is GNU 9.2.0
-- The CXX compiler identification is GNU 9.2.0
-- Check for working C compiler: /XXXX/XXXXXX/gcc/9.2.0/bin/gcc
-- Check for working C compiler: /XXXX/XXXXXX/gcc/9.2.0/bin/gcc -- 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: /XXXX/XXXXXX/gcc/9.2.0/bin/g++
-- Check for working CXX compiler: /XXXX/XXXXXX/gcc/9.2.0/bin/g++ -- 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
-- /XXXX/XXXXXX/racon-gpu/1.4.3/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
-- Building ClaraGenomicsAnalysis libraries as static objects
-- Found CUDA: /usr/local/cuda (found suitable version "10.1", minimum required is "9.0")
-- Using CUDA 10.1 from /usr/local/cuda
-- Build type: Release
-- Package generator - RPM
-- Using CUDA 10.1 from /usr/local/cuda
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen dot
-- clang-format not found. Auto-formatting disabled.
-- Configuring done
-- Generating done
-- Build files have been written to: /XXXX/XXXXXX/racon-gpu/1.4.3/build
[root@LocalSerer build]# make
Scanning dependencies of target logging
[ 2%] Building CXX object ClaraGenomicsAnalysis/common/logging/CMakeFiles/logging.dir/src/logging.cpp.o
In file included from /XXXX/XXXXXX/racon-gpu/1.4.3/vendor/ClaraGenomicsAnalysis/3rdparty/spdlog/include/spdlog/spdlog.h:12,
from /XXXX/XXXXXX/racon-gpu/1.4.3/vendor/ClaraGenomicsAnalysis/common/logging/include/claragenomics/logging/logging.hpp:93,
from /XXXX/XXXXXX/racon-gpu/1.4.3/vendor/ClaraGenomicsAnalysis/common/logging/src/logging.cpp:11:
/XXXX/XXXXXX/racon-gpu/1.4.3/vendor/ClaraGenomicsAnalysis/3rdparty/spdlog/include/spdlog/common.h:10:10: fatal error: atomic: No such file or directory
10 | #include
| ^~~~~~~~
compilation terminated.
make[2]: *** [ClaraGenomicsAnalysis/common/logging/CMakeFiles/logging.dir/src/logging.cpp.o] Error 1
make[1]: *** [ClaraGenomicsAnalysis/common/logging/CMakeFiles/logging.dir/all] Error 2
make: *** [all] Error 2

Any clues as to what I need to do to get passed this?

gcc (GCC) 9.2.0
cmake version 3.14.4
CUDA 10.1
Description: CentOS Linux release 7.7.1908 (Core)
Release: 7.7.1908

Thanks in advanced.

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