search

dptech-corp / Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program
188 stars 40 forks source link

cmake -B build -D FETCH_BOOST=ON does not fetch boost #93

Closed james-vincent closed 6 months ago

james-vincent commented 6 months ago

Describe the bug

Using cmake build process, boost fails to download/build:

This command: cd Uni-Dock-1.1.0/unidock cmake -B build -D FETCH_BOOST=ON

produces:

CMake Error at /build/x86_64-linux/cmake/3.22.2/cmake_extlib/cmake-3.22.2-tvg7/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find Boost (missing: Boost_INCLUDE_DIR system thread serialization filesystem program_options timer) (Required is at least version "1.72") Call Stack (most recent call first): /build/x86_64-linux/cmake/3.22.2/cmake_extlib/cmake-3.22.2-tvg7/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE) /build/x86_64-linux/cmake/3.22.2/cmake_extlib/cmake-3.22.2-tvg7/share/cmake-3.22/Modules/FindBoost.cmake:2375 (find_package_handle_standard_args) CMakeLists.txt:42 (find_package)

Expected behavior

No response

To Reproduce

No response

Environment

No response

Additional Context

No response

ysyecust commented 6 months ago

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' -- [download 0% complete] -- [download 1% complete] -- [download 2% complete] -- [download 3% complete] -- [download 4% complete] -- [download 5% complete] -- [download 6% complete] -- [download 7% complete] -- [download 8% complete] -- [download 9% complete] -- [download 10% complete] -- [download 11% complete] -- [download 12% complete] -- [download 13% complete] -- [download 14% complete] -- [download 15% complete] -- [download 16% complete] -- [download 17% complete] -- [download 18% complete] -- [download 19% complete] -- [download 20% complete] -- [download 21% complete] -- [download 22% complete] -- [download 23% complete] -- [download 24% complete] -- [download 25% complete] -- [download 26% complete] -- [download 27% complete] -- [download 28% complete] -- [download 29% complete] -- [download 30% complete] -- [download 31% complete] -- [download 32% complete] -- [download 33% complete] -- [download 34% complete] -- [download 35% complete] -- [download 36% complete] -- [download 37% complete] -- [download 38% complete] -- [download 39% complete] -- [download 40% complete] -- [download 41% complete] -- [download 42% complete] -- [download 43% complete] -- [download 44% complete] -- [download 45% complete] -- [download 46% complete] -- [download 47% complete] -- [download 48% complete] -- [download 49% complete] -- [download 50% complete] -- [download 51% complete] -- [download 52% complete] -- [download 53% complete] -- [download 54% complete] -- [download 55% complete] -- [download 56% complete] -- [download 57% complete] -- [download 58% complete] -- [download 59% complete] -- [download 60% complete] -- [download 61% complete] -- [download 62% complete] -- [download 63% complete] -- [download 64% complete] -- [download 65% complete] -- [download 66% complete] -- [download 67% complete] -- [download 68% complete] -- [download 69% complete] -- [download 70% complete] -- [download 71% complete] -- [download 72% complete] -- [download 73% complete] -- [download 74% complete] -- [download 75% complete] -- [download 76% complete] -- [download 77% complete] -- [download 78% complete] -- [download 79% complete] -- [download 80% complete] -- [download 81% complete] -- [download 82% complete] -- [download 83% complete] -- [download 84% complete] -- [download 85% complete] -- [download 86% complete] -- [download 87% complete] -- [download 88% complete] -- [download 89% complete] -- [download 90% complete] -- [download 91% complete] -- [download 92% complete] -- [download 93% complete] -- [download 94% complete] -- [download 95% complete] -- [download 96% complete] -- [download 97% complete] -- [download 98% complete] -- [download 99% complete] -- [download 100% complete] -- 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_FLAGffile_prefix_maphome_ysy_Uni_Dock_unidock_builddeps_catch2_src -- Performing Test HAVE_FLAGffile_prefix_maphome_ysy_Uni_Dock_unidock_builddeps_catch2_src - Success -- Configuring done -- Generating done -- Build files have been written to: /home/ysy/Uni-Dock/unidock/build“

james-vincent commented 6 months ago

Here is the full log of just the command and output to screen. I can send cmake error log alos if needed, but it looks like pthreads is the issue:

$ tar zxf 1.1.0.tar.gz @. [] /build/source/uni-dock/1.1.0/linux  $ cd Uni-Dock-1.1.0/unidock @. [] /build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock  $ pwd /build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock @.*** [] /build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock  $ cmake -B build -D FETCH_BOOST=ON -- The CXX compiler identification is GNU 9.3.0 -- The CUDA compiler identification is NVIDIA 11.8.89 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /programs/x86_64-linux/gcc/9.3.0/bin/g++ - 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: /programs/x86_64-linux/cuda/11.8/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") -- 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 - Failed -- 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 CMake Error at /build/x86_64-linux/cmake/3.22.2/cmake_extlib/cmake-3.22.2-tvg7/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message):   Could NOT find Boost (missing: Boost_INCLUDE_DIR system thread   serialization filesystem program_options timer) (Required is at least   version "1.72") Call Stack (most recent call first):   /build/x86_64-linux/cmake/3.22.2/cmake_extlib/cmake-3.22.2-tvg7/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)   /build/x86_64-linux/cmake/3.22.2/cmake_extlib/cmake-3.22.2-tvg7/share/cmake-3.22/Modules/FindBoost.cmake:2375 (find_package_handle_standard_args)   CMakeLists.txt:42 (find_package)

-- Configuring incomplete, errors occurred! See also "/build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock/build/CMakeFiles/CMakeOutput.log". See also "/build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock/build/CMakeFiles/CMakeError.log".

James Vincent, PhD Bioinformatics Software Curator Dept. of BCMP, Harvard Medical School — BioGrids.org --

On Mar 6, 2024 at 9:53 AM -0500, YANG SHAOYI @.***>, wrote:

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' -- [download 0% complete] -- [download 1% complete] -- [download 2% complete] -- [download 3% complete] -- [download 4% complete] -- [download 5% complete] -- [download 6% complete] -- [download 7% complete] -- [download 8% complete] -- [download 9% complete] -- [download 10% complete] -- [download 11% complete] -- [download 12% complete] -- [download 13% complete] -- [download 14% complete] -- [download 15% complete] -- [download 16% complete] -- [download 17% complete] -- [download 18% complete] -- [download 19% complete] -- [download 20% complete] -- [download 21% complete] -- [download 22% complete] -- [download 23% complete] -- [download 24% complete] -- [download 25% complete] -- [download 26% complete] -- [download 27% complete] -- [download 28% complete] -- [download 29% complete] -- [download 30% complete] -- [download 31% complete] -- [download 32% complete] -- [download 33% complete] -- [download 34% complete] -- [download 35% complete] -- [download 36% complete] -- [download 37% complete] -- [download 38% complete] -- [download 39% complete] -- [download 40% complete] -- [download 41% complete] -- [download 42% complete] -- [download 43% complete] -- [download 44% complete] -- [download 45% complete] -- [download 46% complete] -- [download 47% complete] -- [download 48% complete] -- [download 49% complete] -- [download 50% complete] -- [download 51% complete] -- [download 52% complete] -- [download 53% complete] -- [download 54% complete] -- [download 55% complete] -- [download 56% complete] -- [download 57% complete] -- [download 58% complete] -- [download 59% complete] -- [download 60% complete] -- [download 61% complete] -- [download 62% complete] -- [download 63% complete] -- [download 64% complete] -- [download 65% complete] -- [download 66% complete] -- [download 67% complete] -- [download 68% complete] -- [download 69% complete] -- [download 70% complete] -- [download 71% complete] -- [download 72% complete] -- [download 73% complete] -- [download 74% complete] -- [download 75% complete] -- [download 76% complete] -- [download 77% complete] -- [download 78% complete] -- [download 79% complete] -- [download 80% complete] -- [download 81% complete] -- [download 82% complete] -- [download 83% complete] -- [download 84% complete] -- [download 85% complete] -- [download 86% complete] -- [download 87% complete] -- [download 88% complete] -- [download 89% complete] -- [download 90% complete] -- [download 91% complete] -- [download 92% complete] -- [download 93% complete] -- [download 94% complete] -- [download 95% complete] -- [download 96% complete] -- [download 97% complete] -- [download 98% complete] -- [download 99% complete] -- [download 100% complete] -- 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_FLAGffile_prefix_maphome_ysy_Uni_Dock_unidock_builddeps_catch2_src -- Performing Test HAVE_FLAGffile_prefix_maphome_ysy_Uni_Dock_unidock_builddeps_catch2_src - Success -- Configuring done -- Generating done -- Build files have been written to: /home/ysy/Uni-Dock/unidock/build“ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

james-vincent commented 6 months ago

Here is the cmake error log:

 $ more CMakeError.log Performing C++ SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output: Change Dir: /build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_60ed2/fast && /usr/bin/gmake  -f CMakeFiles/cmTC_60ed2.dir/build.make CMakeFiles/cmTC_60ed2.dir/build gmake[1]: Entering directory /nfs/build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_60ed2.dir/src.cxx.o /programs/x86_64-linux/gcc/4.9.4/bin/c++ -DCMAKE_HAVE_LIBC_PTHREAD  -std=gnu++14 -o CMakeFiles/cmTC_60ed2.dir/src.cxx.o -c /build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock/build/CMakeFiles/CMakeTmp/src.cxx Linking CXX executable cmTC_60ed2 /nfs/build/x86_64-linux/cmake/3.22.2/cmake_extlib/cmake-3.22.2-tvg7/bin/cmake -E cmake_link_script CMakeFiles/cmTC_60ed2.dir/link.txt --verbose=1 /programs/x86_64-linux/gcc/4.9.4/bin/c++ CMakeFiles/cmTC_60ed2.dir/src.cxx.o -o cmTC_60ed2 CMakeFiles/cmTC_60ed2.dir/src.cxx.o: In functionmain': src.cxx:(.text+0x2d): undefined reference to pthread_create' src.cxx:(.text+0x39): undefined reference topthread_detach' src.cxx:(.text+0x45): undefined reference to pthread_cancel' src.cxx:(.text+0x56): undefined reference topthread_join' src.cxx:(.text+0x6a): undefined reference to pthread_atfork' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTC_60ed2] Error 1 gmake[1]: Leaving directory/nfs/build/source/uni-dock/1.1.0/linux/Uni-Dock-1.1.0/unidock/build/CMakeFiles/CMakeTmp' gmake: *** [cmTC_60ed2/fast] Error 2

James Vincent, PhD Bioinformatics Software Curator Dept. of BCMP, Harvard Medical School — BioGrids.org --

On Mar 6, 2024 at 9:53 AM -0500, YANG SHAOYI @.***>, wrote:

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' -- [download 0% complete] -- [download 1% complete] -- [download 2% complete] -- [download 3% complete] -- [download 4% complete] -- [download 5% complete] -- [download 6% complete] -- [download 7% complete] -- [download 8% complete] -- [download 9% complete] -- [download 10% complete] -- [download 11% complete] -- [download 12% complete] -- [download 13% complete] -- [download 14% complete] -- [download 15% complete] -- [download 16% complete] -- [download 17% complete] -- [download 18% complete] -- [download 19% complete] -- [download 20% complete] -- [download 21% complete] -- [download 22% complete] -- [download 23% complete] -- [download 24% complete] -- [download 25% complete] -- [download 26% complete] -- [download 27% complete] -- [download 28% complete] -- [download 29% complete] -- [download 30% complete] -- [download 31% complete] -- [download 32% complete] -- [download 33% complete] -- [download 34% complete] -- [download 35% complete] -- [download 36% complete] -- [download 37% complete] -- [download 38% complete] -- [download 39% complete] -- [download 40% complete] -- [download 41% complete] -- [download 42% complete] -- [download 43% complete] -- [download 44% complete] -- [download 45% complete] -- [download 46% complete] -- [download 47% complete] -- [download 48% complete] -- [download 49% complete] -- [download 50% complete] -- [download 51% complete] -- [download 52% complete] -- [download 53% complete] -- [download 54% complete] -- [download 55% complete] -- [download 56% complete] -- [download 57% complete] -- [download 58% complete] -- [download 59% complete] -- [download 60% complete] -- [download 61% complete] -- [download 62% complete] -- [download 63% complete] -- [download 64% complete] -- [download 65% complete] -- [download 66% complete] -- [download 67% complete] -- [download 68% complete] -- [download 69% complete] -- [download 70% complete] -- [download 71% complete] -- [download 72% complete] -- [download 73% complete] -- [download 74% complete] -- [download 75% complete] -- [download 76% complete] -- [download 77% complete] -- [download 78% complete] -- [download 79% complete] -- [download 80% complete] -- [download 81% complete] -- [download 82% complete] -- [download 83% complete] -- [download 84% complete] -- [download 85% complete] -- [download 86% complete] -- [download 87% complete] -- [download 88% complete] -- [download 89% complete] -- [download 90% complete] -- [download 91% complete] -- [download 92% complete] -- [download 93% complete] -- [download 94% complete] -- [download 95% complete] -- [download 96% complete] -- [download 97% complete] -- [download 98% complete] -- [download 99% complete] -- [download 100% complete] -- 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_FLAGffile_prefix_maphome_ysy_Uni_Dock_unidock_builddeps_catch2_src -- Performing Test HAVE_FLAGffile_prefix_maphome_ysy_Uni_Dock_unidock_builddeps_catch2_src - Success -- Configuring done -- Generating done -- Build files have been written to: /home/ysy/Uni-Dock/unidock/build“ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

ysyecust commented 6 months ago

@james-vincent You can add find_package(Threads) in CMakeLists.txt at line 61https://github.com/dptech-corp/Uni-Dock/blob/883671c330ceb9ee3cef4ca167bb12caa156ad43/unidock/CMakeLists.txt#L61, If that solves your problem I will update this part of the CMakeLists.txt

james-vincent commented 6 months ago

Thanks for the update. I was using the source tarball for version 1.1. It seems the CMakeLists file is different in that source tarball than what is now peresent in the repo itself. So, I cloned the repo instead. This worked finding boost with no further changes.

However, compilation fails finding some boost include files. Do I need to manually set BOOST_INCUDE_DIR or something similar?

-- Build files have been written to: /build/source/uni-dock/1.1.0/linux/Uni-Dock/unidock/build [  0%] Building CXX object _deps/boost-build/libs/atomic/CMakeFiles/boost_atomic.dir/src/lock_pool.cpp.o [  0%] Building CXX object CMakeFiles/lib.dir/src/lib/ad4cache.cpp.o [  2%] Building CUDA object CMakeFiles/cuda.dir/src/cuda/monte_carlo.cu.o [  2%] Building CXX object _deps/boost-build/libs/timer/CMakeFiles/boost_timer.dir/src/auto_timers_construction.cpp.o In file included from /build/source/uni-dock/1.1.0/linux/Uni-Dock/unidock/src/lib/ad4cache.cpp:23: /build/source/uni-dock/1.1.0/linux/Uni-Dock/unidock/src/lib/ad4cache.h:31:10: fatal error: boost/serialization/split_member.hpp: No such file or directory    31 | #include <boost/serialization/split_member.hpp>       |          ^~~~~~~~~~ compilation terminated.

James Vincent, PhD Bioinformatics Software Curator Dept. of BCMP, Harvard Medical School — BioGrids.org --

On Mar 6, 2024 at 11:39 AM -0500, YANG SHAOYI @.***>, wrote:

@james-vincent You can add find_package(Threads) in CMakeLists.txt at line 61https://github.com/dptech-corp/Uni-Dock/blob/883671c330ceb9ee3cef4ca167bb12caa156ad43/unidock/CMakeLists.txt#L61, If that solves your problem I will update this part of the CMakeLists.txt — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

ysyecust commented 6 months ago

@james-vincent I understand your problem. We will release a new version soon. Thank you for your feedback on the problem.