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DGL build from source is failing

Open Aratiganesh123 opened this issue 1 year ago • 5 comments

Hi,

I am trying do build DGL from source for cpu and I am running into this below bug.

-- The C compiler identification is GNU 10.3.0 -- The CXX compiler identification is GNU 10.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Start configuring project dgl -- Build for dev -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5")
-- Build with OpenMP. -- Build with LIBXSMM optimization. -- Looking for sys/epoll.h -- Looking for sys/epoll.h - found -- Conda environment detected: /home/hice1/aganesh83/scratch/dgl-dev-cpu -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for fopen64 -- Looking for fopen64 - not found -- Looking for C++ include cxxabi.h -- Looking for C++ include cxxabi.h - found -- Looking for nanosleep -- Looking for nanosleep - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include
-- /home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/cmake/build_config.h.in -> include/dmlc/build_config.h -- Performing Test SUPPORT_MSSE2 -- Performing Test SUPPORT_MSSE2 - Success -- Looking for execinfo.h -- Looking for execinfo.h - found -- Looking for getline -- Looking for getline - found -- Build with unittest -- Found Python3: /home/hice1/aganesh83/scratch/dgl-dev-cpu/bin/python3.8 (found version "3.8.19") found components: Interpreter -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE
-- Configuring DGL sparse library -- DGL include directories: /home/hice1/aganesh83/scratch/GNNsys/dgl/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dlpack/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/phmap;/home/hice1/aganesh83/scratch/GNNsys/dgl/tensoradapter/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/pcg/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/nanoflann/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/libxsmm/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/GKlib;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/googletest/googletest/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/googletest/googletest;/home/hice1/aganesh83/scratch/GNNsys/dgl/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dlpack/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/phmap;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/libxsmm/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/pcg/include -- DGL link directories: /home/hice1/aganesh83/scratch/GNNsys/dgl/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dlpack/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/phmap;/home/hice1/aganesh83/scratch/GNNsys/dgl/tensoradapter/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/pcg/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/nanoflann/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/libxsmm/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/GKlib;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/googletest/googletest/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/googletest/googletest;/home/hice1/aganesh83/scratch/GNNsys/dgl/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dlpack/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/phmap;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/libxsmm/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/pcg/include -- Configuring graphbolt library -- Configuring done -- Generating done -- Build files have been written to: /home/hice1/aganesh83/scratch/GNNsys/dgl/build [ 1%] Building CXX object third_party/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o [ 1%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/recordio.cc.o [ 1%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/blas.c.o [ 2%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/b64.c.o [ 2%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/data.cc.o [ 3%] Creating directories for 'liburing' [ 3%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/config.cc.o [ 4%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/io.cc.o [ 5%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/evaluate.c.o [ 6%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/csr.c.o [ 6%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/error.c.o [ 7%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/getopt.c.o [ 7%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/fkvkselect.c.o [ 7%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/io/recordio_split.cc.o [ 7%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/io/input_split_base.cc.o [ 7%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/io/line_split.cc.o [ 8%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/fs.c.o [ 9%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/gkregex.c.o [ 10%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/io.c.o [ 10%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/io/local_filesys.cc.o [ 10%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/io/filesys.cc.o [ 11%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/gk_util.c.o [ 11%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/io/indexed_recordio_split.cc.o [ 11%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/mcore.c.o [ 11%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/graph.c.o [ 12%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/seq.c.o [ 13%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/string.c.o [ 12%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/htable.c.o [ 13%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/rw.c.o [ 13%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/sort.c.o [ 15%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/memory.c.o [ 16%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/random.c.o [ 16%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/pqueue.c.o [ 16%] No download step for 'liburing' [ 17%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/timers.c.o [ 18%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/itemsets.c.o [ 19%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/auxapi.c.o [ 19%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/tokenizer.c.o [ 19%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/fm.c.o [ 20%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/bucketsort.c.o [ 20%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/checkgraph.c.o [ 20%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/frename.c.o [ 20%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/balance.c.o [ 20%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/graph.c.o [ 21%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/initpart.c.o [ 21%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/kmetis.c.o [ 21%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/compress.c.o [ 22%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/mmd.c.o [ 22%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/ometis.c.o [ 22%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/kwayfm.c.o [ 23%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/options.c.o [ 24%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/kwayrefine.c.o [ 24%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/debug.c.o [ 25%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/gklib.c.o [ 26%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/fortran.c.o [ 26%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/meshpart.c.o [ 26%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/pmetis.c.o [ 26%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/mcutil.c.o [ 27%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/mincover.c.o [ 27%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/contig.c.o [ 28%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/mesh.c.o [ 29%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/coarsen.c.o [ 30%] No update step for 'liburing' [ 31%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/parmetis.c.o [ 31%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/separator.c.o [ 31%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/srefine.c.o [ 31%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/wspace.c.o [ 31%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/stat.c.o [ 31%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/timing.c.o [ 34%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/minconn.c.o [ 34%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/util.c.o [ 34%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/refine.c.o [ 35%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/sfm.c.o [ 35%] No patch step for 'liburing' [ 35%] Performing configure step for 'liburing' prefix / includedir //include libdir //lib libdevdir //lib relativelibdir
mandir //man datadir //share libgcc_link_flag /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/libgcc.a stringop_overflow yes array_bounds yes __kernel_rwf_t no __kernel_timespec no open_how no statx no glibc_statx no C++ yes has_ucontext yes NVMe uring command support no futex waitv support no has_idtype_t yes nolibc yes has_fanotify yes CC /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/bin/gcc CXX /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/bin/g++ [ 36%] Performing build step for 'liburing' -- Using Python interpreter: python3 [ 36%] Linking C static library libmetis.a [ 36%] Built target metis -- find_cmake.py output: /home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/share/cmake;1.13.0 -- Configuring for PyTorch 1.13.0 -- Setting directory to /home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/share/cmake/Torch -- tensoradapter found PyTorch includes: /home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/include;/home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -- tensoradapter found PyTorch lib: torch -- Configured target tensoradapter_pytorch_1.13.0 -- Configuring done -- Generating done -- Build files have been written to: /home/hice1/aganesh83/scratch/GNNsys/dgl/tensoradapter/pytorch/build/1.13.0 Consolidate compiler generated dependencies of target tensoradapter_pytorch_1.13.0 [100%] Built target tensoradapter_pytorch_1.13.0 ‘libtensoradapter_pytorch_1.13.0.so’ -> ‘/home/hice1/aganesh83/scratch/GNNsys/dgl/build/tensoradapter/pytorch/libtensoradapter_pytorch_1.13.0.so’ [ 36%] Built target tensoradapter_pytorch [ 36%] Linking CXX static library ../../../lib/libgtest.a [ 36%] Built target gtest [ 36%] Building CXX object third_party/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o [ 37%] Building CXX object third_party/googletest/googlemock/CMakeFiles/gmock.dir/src/gmock-all.cc.o [ 38%] Linking CXX static library ../../../lib/libgtest_main.a [ 38%] Built target gtest_main [ 38%] Linking CXX static library ../../../lib/libgmock.a [ 38%] Built target gmock [ 38%] Linking CXX static library libdmlc.a [ 38%] Built target dmlc ar: creating liburing.a ar: creating liburing-ffi.a CMake Warning at /home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:22 (message): static library kineto_LIBRARY-NOTFOUND not found. Call Stack (most recent call first): /home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:127 (append_torchlib_if_found) CMakeLists.txt:26 (find_package) In file included from send-zerocopy.c:15: /usr/include/linux/ipv6.h:19:8: error: redefinition of 'struct in6_pktinfo' 19 | struct in6_pktinfo { | ^~~~~~~~~~~ In file included from /usr/include/arpa/inet.h:22, from send-zerocopy.c:13: /usr/include/netinet/in.h:538:8: note: originally defined here 538 | struct in6_pktinfo | ^~~~~~~~~~~ In file included from send-zerocopy.c:15: /usr/include/linux/ipv6.h:24:8: error: redefinition of 'struct ip6_mtuinfo' 24 | struct ip6_mtuinfo { | ^~~~~~~~~~~ In file included from /usr/include/arpa/inet.h:22, from send-zerocopy.c:13: /usr/include/netinet/in.h:545:8: note: originally defined here 545 | struct ip6_mtuinfo | ^~~~~~~~~~~ make[4]: *** [send-zerocopy.t] Error 1 make[4]: *** Waiting for unfinished jobs.... make[3]: *** [all] Error 2 make[2]: *** [liburing-prefix/src/liburing-stamp/liburing-build] Error 2 make[1]: *** [CMakeFiles/liburing.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... make: *** [all] Error 2

Could you please help me with the root cause of the issue. My gcc version is 10.3. I cannot upgrade this system because i do not have sudo priveleges.

Appreciate any pointers Thank you

Aratiganesh123 avatar Apr 07 '24 21:04 Aratiganesh123

https://github.com/srsran/srsRAN_4G/issues/424 seems to be related.

https://github.com/srsran/srsRAN_4G/issues/424#issuecomment-565027420 seems to be the solution

mfbalin avatar Apr 07 '24 23:04 mfbalin

Unfortunately, the issue still seems to persist. Is there any other workaround?

(/storage/ice1/1/4/aganesh83/dgl-dev-cpu) [aganesh83@login-ice-2 build]$ cmake .. -DUSE_GLIBC_IPV6=False

-- The C compiler identification is GNU 10.3.0 -- The CXX compiler identification is GNU 10.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Start configuring project dgl -- Build for dev -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Build with OpenMP. -- Build with LIBXSMM optimization. -- Looking for sys/epoll.h -- Looking for sys/epoll.h - found -- Conda environment detected: /storage/ice1/1/4/aganesh83/dgl-dev-cpu CMake Deprecation Warning at third_party/dmlc-core/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for fopen64 -- Looking for fopen64 - not found -- Looking for C++ include cxxabi.h -- Looking for C++ include cxxabi.h - found -- Looking for nanosleep -- Looking for nanosleep - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- /home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/cmake/build_config.h.in -> include/dmlc/build_config.h -- Performing Test SUPPORT_MSSE2 -- Performing Test SUPPORT_MSSE2 - Success -- Looking for execinfo.h -- Looking for execinfo.h - found -- Looking for getline -- Looking for getline - found -- Build with unittest -- Found Python3: /home/hice1/aganesh83/scratch/dgl-dev-cpu/bin/python3.8 (found version "3.8.19") found components: Interpreter -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Configuring DGL sparse library -- DGL include directories: /home/hice1/aganesh83/scratch/GNNsys/dgl/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dlpack/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/phmap;/home/hice1/aganesh83/scratch/GNNsys/dgl/tensoradapter/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/pcg/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/nanoflann/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/libxsmm/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/GKlib;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/googletest/googletest/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/googletest/googletest;/home/hice1/aganesh83/scratch/GNNsys/dgl/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dlpack/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/phmap;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/libxsmm/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/pcg/include -- DGL link directories: /home/hice1/aganesh83/scratch/GNNsys/dgl/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dlpack/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/phmap;/home/hice1/aganesh83/scratch/GNNsys/dgl/tensoradapter/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/pcg/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/nanoflann/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/libxsmm/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/GKlib;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/METIS/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/googletest/googletest/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/googletest/googletest;/home/hice1/aganesh83/scratch/GNNsys/dgl/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dlpack/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/dmlc-core/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/phmap;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/libxsmm/include;/home/hice1/aganesh83/scratch/GNNsys/dgl/third_party/pcg/include -- Configuring graphbolt library -- Configuring done (13.4s) -- Generating done (0.4s) CMake Warning: Manually-specified variables were not used by the project:

USE_GLIBC_IPV6

-- Build files have been written to: /home/hice1/aganesh83/scratch/GNNsys/dgl/build (/storage/ice1/1/4/aganesh83/dgl-dev-cpu) [aganesh83@login-ice-2 build]$ (/storage/ice1/1/4/aganesh83/dgl-dev-cpu) [aganesh83@login-ice-2 build]$ makr -j4 bash: makr: command not found... (/storage/ice1/1/4/aganesh83/dgl-dev-cpu) [aganesh83@login-ice-2 build]$ make -j4 [ 2%] Creating directories for 'liburing' [ 2%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/config.cc.o [ 2%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/b64.c.o [ 3%] No download step for 'liburing' [ 4%] No update step for 'liburing' [ 4%] No patch step for 'liburing' [ 4%] Performing configure step for 'liburing' prefix / includedir //include libdir //lib libdevdir //lib relativelibdir
mandir //man datadir //share libgcc_link_flag /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/libgcc.a [ 4%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/blas.c.o stringop_overflow yes array_bounds yes kernel_rwf_t no kernel_timespec no open_how no statx no glibc_statx no C++ yes has_ucontext yes NVMe uring command support no futex waitv support no [ 5%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/csr.c.o has_idtype_t yes nolibc yes has_fanotify yes CC /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/bin/gcc CXX /usr/local/pace-apps/spack/packages/linux-rhel7-x86_64/gcc-4.8.5/gcc-10.3.0-o57x6h2gubo7bzh7evmy4mvibdqrlghr/bin/g++ [ 5%] Building CXX object third_party/dmlc-core/CMakeFiles/dmlc.dir/src/data.cc.o [ 6%] Performing build step for 'liburing' make[3]: warning: -jN forced in submake: disabling jobserver mode. ar: creating liburing.a ar: creating liburing-ffi.a [ 6%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/error.c.o [ 7%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/evaluate.c.o [ 7%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/fkvkselect.c.o [ 8%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/fs.c.o [ 8%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/getopt.c.o [ 9%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/gk_util.c.o [ 9%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/gkregex.c.o [ 9%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/graph.c.o [ 10%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/htable.c.o -- Using Python interpreter: python3 [ 10%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/io.c.o [ 11%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/itemsets.c.o [ 11%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/mcore.c.o [ 12%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/memory.c.o [ 12%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/pqueue.c.o [ 13%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/random.c.o [ 13%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/rw.c.o -- find_cmake.py output: /storage/ice1/1/4/aganesh83/dgl-dev-cpu/lib/python3.8/site-packages/torch/share/cmake;1.13.0 -- Configuring for PyTorch 1.13.0 -- Setting directory to /storage/ice1/1/4/aganesh83/dgl-dev-cpu/lib/python3.8/site-packages/torch/share/cmake/Torch [ 13%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/seq.c.o CMake Warning at /home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:22 (message): static library kineto_LIBRARY-NOTFOUND not found. Call Stack (most recent call first): /home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/share/cmake/Torch/TorchConfig.cmake:127 (append_torchlib_if_found) CMakeLists.txt:26 (find_package)

-- tensoradapter found PyTorch includes: /home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/include;/home/hice1/aganesh83/scratch/dgl-dev-cpu/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -- tensoradapter found PyTorch lib: torch -- Configured target tensoradapter_pytorch_1.13.0 -- Configuring done (18.0s) -- Generating done (0.3s) -- Build files have been written to: /home/hice1/aganesh83/scratch/GNNsys/dgl/tensoradapter/pytorch/build/1.13.0 make[3]: warning: jobserver unavailable: using -j1. Add `+' to parent make rule. [ 14%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/sort.c.o [100%] Built target tensoradapter_pytorch_1.13.0 ‘libtensoradapter_pytorch_1.13.0.so’ -> ‘/home/hice1/aganesh83/scratch/GNNsys/dgl/build/tensoradapter/pytorch/libtensoradapter_pytorch_1.13.0.so’ [ 14%] Built target tensoradapter_pytorch [ 15%] Building CXX object third_party/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o [ 15%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/string.c.o [ 16%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/timers.c.o [ 16%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir//GKlib/tokenizer.c.o [ 17%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/auxapi.c.o In file included from send-zerocopy.c:15: /usr/include/linux/ipv6.h:19:8: error: redefinition of 'struct in6_pktinfo' 19 | struct in6_pktinfo { | ^~~~~~~~~~~ In file included from /usr/include/arpa/inet.h:22, from send-zerocopy.c:13: /usr/include/netinet/in.h:538:8: note: originally defined here 538 | struct in6_pktinfo | ^~~~~~~~~~~ In file included from send-zerocopy.c:15: /usr/include/linux/ipv6.h:24:8: error: redefinition of 'struct ip6_mtuinfo' 24 | struct ip6_mtuinfo { | ^~~~~~~~~~~ In file included from /usr/include/arpa/inet.h:22, from send-zerocopy.c:13: /usr/include/netinet/in.h:545:8: note: originally defined here 545 | struct ip6_mtuinfo | ^~~~~~~~~~~ make[4]: *** [send-zerocopy.t] Error 1 make[4]: *** Waiting for unfinished jobs.... [ 17%] Building C object third_party/METIS/libmetis/CMakeFiles/metis.dir/balance.c.o make[3]: *** [all] Error 2 make[2]: *** [liburing-prefix/src/liburing-stamp/liburing-build] Error 2 make[1]: *** [CMakeFiles/liburing.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs....

Aratiganesh123 avatar Apr 08 '24 01:04 Aratiganesh123

I recently encountered the same issue. I remember that these errors occurred in the files located in the example (and possibly the test?) folders of liburing. The simplest solution is to delete the files that are causing the errors.

e-yi avatar Apr 19 '24 03:04 e-yi

Due to various issue we recently met, we decided to disable liburing. A following PR will be ready.

Rhett-Ying avatar Apr 25 '24 02:04 Rhett-Ying

This issue has been automatically marked as stale due to lack of activity. It will be closed if no further activity occurs. Thank you

github-actions[bot] avatar May 26 '24 01:05 github-actions[bot]