dmlc / dmlc/dgl

DGL build from source is failing

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#7,277 5 comments 0 reactions 1 assignee Claimed by @pyynb View on GitHub
stale-issue
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Description

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
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[ 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

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