Comments (6)
Hi @james-vincent, It seems that the boost library was not downloaded correctly, can you show me the full cmake error log,
The correct cmake output is like this ”cmake -B build -D FETCH_BOOST=ON
-- The CXX compiler identification is GNU 11.4.0
-- The CUDA compiler identification is NVIDIA 12.2.140
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting CUDA compiler ABI info
-- Detecting CUDA compiler ABI info - done
-- Check for working CUDA compiler: /usr/local/cuda/bin/nvcc - skipped
-- Detecting CUDA compile features
-- Detecting CUDA compile features - done
CMAKE_CUDA_FLAGS_RELEASE updated for fast_math: -O3 -DNDEBUG --use_fast_math
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Populating boost
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ysy/Uni-Dock/unidock/build/_deps/boost-subbuild
[ 11%] Creating directories for 'boost-populate'
[ 22%] Performing download step (download, verify and extract) for 'boost-populate'
-- Downloading...
dst='/home/ysy/Uni-Dock/unidock/build/deps/boost-subbuild/boost-populate-prefix/src/boost-1.84.0.tar.gz'
timeout='none'
inactivity timeout='none'
-- Using src='https://github.com/boostorg/boost/releases/download/boost-1.84.0/boost-1.84.0.tar.gz'
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-- Downloading... done
-- extracting...
src='/home/ysy/Uni-Dock/unidock/build/deps/boost-subbuild/boost-populate-prefix/src/boost-1.84.0.tar.gz'
dst='/home/ysy/Uni-Dock/unidock/build/deps/boost-src'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 33%] No update step for 'boost-populate'
[ 44%] No patch step for 'boost-populate'
[ 55%] No configure step for 'boost-populate'
[ 66%] No build step for 'boost-populate'
[ 77%] No install step for 'boost-populate'
[ 88%] No test step for 'boost-populate'
[100%] Completed 'boost-populate'
[100%] Built target boost-populate
-- Boost: Release build, static libraries, MPI OFF, Python OFF, testing OFF
-- Boost: libraries included: system;thread;serialization;filesystem;program_options;timer
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Performing Test BOOST_ATOMIC_TARGET_X86
-- Performing Test BOOST_ATOMIC_TARGET_X86 - Success
-- Performing Test BOOST_ATOMIC_COMPILER_HAS_SSE2
-- Performing Test BOOST_ATOMIC_COMPILER_HAS_SSE2 - Success
-- Performing Test BOOST_ATOMIC_COMPILER_HAS_SSE41
-- Performing Test BOOST_ATOMIC_COMPILER_HAS_SSE41 - Success
-- The C compiler identification is GNU 11.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Performing Test BOOST_FILESYSTEM_HAS_INIT_PRIORITY
-- Performing Test BOOST_FILESYSTEM_HAS_INIT_PRIORITY - Success
-- Performing Test BOOST_FILESYSTEM_HAS_CXX20_ATOMIC_REF
-- Performing Test BOOST_FILESYSTEM_HAS_CXX20_ATOMIC_REF - Failed
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_BLKSIZE
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_BLKSIZE - Success
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_MTIM
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_MTIM - Success
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_MTIMENSEC
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_MTIMENSEC - Failed
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_MTIMESPEC
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_MTIMESPEC - Failed
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_BIRTHTIMENSEC
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_BIRTHTIMENSEC - Failed
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_BIRTHTIMESPEC
-- Performing Test BOOST_FILESYSTEM_HAS_STAT_ST_BIRTHTIMESPEC - Failed
-- Performing Test BOOST_FILESYSTEM_HAS_STATX
-- Performing Test BOOST_FILESYSTEM_HAS_STATX - Success
-- Performing Test BOOST_FILESYSTEM_HAS_FDOPENDIR_NOFOLLOW
-- Performing Test BOOST_FILESYSTEM_HAS_FDOPENDIR_NOFOLLOW - Success
-- Performing Test BOOST_FILESYSTEM_HAS_DIRENT_D_TYPE
-- Performing Test BOOST_FILESYSTEM_HAS_DIRENT_D_TYPE - Success
-- Performing Test BOOST_FILESYSTEM_HAS_POSIX_AT_APIS
-- Performing Test BOOST_FILESYSTEM_HAS_POSIX_AT_APIS - Success
-- Found the following ICU libraries:
-- data (required)
-- i18n (required)
-- uc (required)
-- Found ICU: /usr/include (found version "70.1")
-- Boost.Thread: threading API is pthread
-- Populating catch2
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ysy/Uni-Dock/unidock/build/deps/catch2-subbuild
[ 11%] Creating directories for 'catch2-populate'
[ 22%] Performing download step (git clone) for 'catch2-populate'
Cloning into 'catch2-src'...
HEAD is now at 6e79e682 v3.4.0
[ 33%] Performing update step for 'catch2-populate'
[ 44%] No patch step for 'catch2-populate'
[ 55%] No configure step for 'catch2-populate'
[ 66%] No build step for 'catch2-populate'
[ 77%] No install step for 'catch2-populate'
[ 88%] No test step for 'catch2-populate'
[100%] Completed 'catch2-populate'
[100%] Built target catch2-populate
-- Performing Test HAVE_FLAG__ffile_prefix_map__home_ysy_Uni_Dock_unidock_build__deps_catch2_src
-- Performing Test HAVE_FLAG__ffile_prefix_map__home_ysy_Uni_Dock_unidock_build__deps_catch2_src - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ysy/Uni-Dock/unidock/build“
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@james-vincent You can add find_package(Threads)
in CMakeLists.txt at line 61
Uni-Dock/unidock/CMakeLists.txt
Line 61 in 883671c
from uni-dock.
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@james-vincent I understand your problem. We will release a new version soon. Thank you for your feedback on the problem.
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Related Issues (20)
- 1.1.1 source release contains version string 1.1.0 HOT 1
- Error in vina score HOT 2
- typo in examples HOT 1
- missing installation instruction in unidock_tools
- How to dock
- WARNING: Could not find any conformations
- run unidock, report segmentation fault while using file index
- OOM using ad4 scoring function
- CUDA Runtime Error when using ad4 maps HOT 4
- Fail on screening test case mmp13 on version v1.1.x HOT 2
- Unidock pipeline fails to read ligand index HOT 1
- target_compile_features no known features for CXX compiler HOT 6
- Unknown order of ligands in the output HOT 2
- in ligand index, unable to find mol file, only first without others. HOT 1
- Seed doesn't seem to be working properly. HOT 3
- Cuda runtime error =
- Segmentation Fault (Core Dumped)
- v1.1.2 randomly changes its output without any valid cause HOT 1
- Compiling error on CUDA 11
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