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Published 20 hours ago • verified publisher icon rusty1s

Problem with METIS for generating own wheel for torch-sparse

Open osllogon opened this issue 3 years ago • 10 comments
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I try to follow the instructions for installing METIS, as I think the link is not working now, I suppose the correct repo is this one: https://github.com/KarypisLab/METIS.

I run the following commands to install it:

make config shared=1 cc=gcc prefix=~/local i64=1 
make install

and everything seems to work fine. However, when I run the following command to create the wheel:

python setup.py bdist_wheel

I receive the following error:

running bdist_wheel
running build
running build_py
running egg_info
writing torch_sparse.egg-info/PKG-INFO
writing dependency_links to torch_sparse.egg-info/dependency_links.txt
writing requirements to torch_sparse.egg-info/requires.txt
writing top-level names to torch_sparse.egg-info/top_level.txt
reading manifest file 'torch_sparse.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'torch_sparse.egg-info/SOURCES.txt'
running build_ext
building 'torch_sparse._convert_cpu' extension
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DWITH_PYTHON -DWITH_METIS -Icsrc -I/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/include -I/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/include/TH -I/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/include/THC -I/mnt/c/Users/elloosc/envs/venus/include -I/usr/include/python3.8 -c csrc/convert.cpp -o build/temp.linux-x86_64-3.8/csrc/convert.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=_convert_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DWITH_PYTHON -DWITH_METIS -Icsrc -I/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/include -I/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/include/TH -I/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/include/THC -I/mnt/c/Users/elloosc/envs/venus/include -I/usr/include/python3.8 -c csrc/cpu/convert_cpu.cpp -o build/temp.linux-x86_64-3.8/csrc/cpu/convert_cpu.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE="_gcc" -DPYBIND11_STDLIB="_libstdcpp" -DPYBIND11_BUILD_ABI="_cxxabi1011" -DTORCH_EXTENSION_NAME=_convert_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/csrc/convert.o build/temp.linux-x86_64-3.8/csrc/cpu/convert_cpu.o -L/mnt/c/Users/elloosc/envs/venus/lib/python3.8/site-packages/torch/lib -lmetis -lc10 -ltorch 
-ltorch_cpu -ltorch_python -o build/lib.linux-x86_64-3.8/torch_sparse/_convert_cpu.so -s
/usr/bin/ld: cannot find -lmetis
collect2: error: ld returned 1 exit status
error: command 'x86_64-linux-gnu-g++' failed with exit status 1

Thanks in advance

osllogon avatar Jul 09 '22 15:07 osllogon

Where did you install METIS to? Can you ensure that the installation part is included in LD_LIBRARY_PATH?

rusty1s avatar Jul 10 '22 14:07 rusty1s

I install it in ~local/. You were right I forgot to add it to LD_LIBRARY_PATH. To clarify all the things that I have done:

https://github.com/KarypisLab/GKlib.git
cd GKlib

sudo apt-get install build-essential
sudo apt-get install cmake

make config
make
make install

cd ..
git clone https://github.com/KarypisLab/METIS.git
cd METIS

make config shared=1 cc=gcc prefix=~/local i64=1 
make install

cd..
git clone https://github.com/rusty1s/pytorch_sparse.git
cd pytorch_sparse

export WITH_METIS=1
export CPLUS_INCLUDE_PATH=~/local/include
export LIBRARY_PATH=~/local/lib
export LD_LIBRARY_PATH=~/local/lib

pip wheel .
pip install torch_sparse-0.6.14-cp38-cp38-linux_x86_64.whl
python
>>>import torch_sparse

and by importing torch_sparse I receive the following error

>>> import torch_sparse
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/mnt/c/Users/elloosc/envs/urano/lib/python3.8/site-packages/torch_sparse/__init__.py", line 19, in <module>
    torch.ops.load_library(spec.origin)
  File "/mnt/c/Users/elloosc/envs/urano/lib/python3.8/site-packages/torch/_ops.py", line 220, in load_library
    ctypes.CDLL(path)
  File "/usr/lib/python3.8/ctypes/__init__.py", line 373, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: /home/elloosc/local/lib/libmetis.so: undefined symbol: gk_jbufs

osllogon avatar Jul 10 '22 19:07 osllogon

Mh, this one is new to me. It looks like libmetis wasn't installed correctly. Does its installation log reveal any potential error?

rusty1s avatar Jul 11 '22 05:07 rusty1s

I do not think so but I leave here the logs for METIS installation just in case:

elloosc@ES-00004010:/mnt/c/Users/elloosc/Projects/METIS$ make config shared=1 cc=gcc prefix=~/local i64=1
rm -rf build
mkdir -p build
mkdir -p build/xinclude
echo "#define IDXTYPEWIDTH 64" > build/xinclude/metis.h
echo "#define REALTYPEWIDTH 32" >> build/xinclude/metis.h
cat include/metis.h >> build/xinclude/metis.h
cp include/CMakeLists.txt build/xinclude
cd build && cmake /mnt/c/Users/elloosc/Projects/METIS -DCMAKE_VERBOSE_MAKEFILE=1 -DGKLIB_PATH=/mnt/c/Users/elloosc/Projects/METIS/~/local -DCMAKE_INSTALL_PREFIX=/home/elloosc/local -DSHARED=1 -DCMAKE_C_COMPILER=gcc
-- The C compiler identification is GNU 9.4.0
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for execinfo.h
-- Looking for execinfo.h - found
-- Looking for getline
-- Looking for getline - found
-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/c/Users/elloosc/Projects/METIS/build
elloosc@ES-00004010:/mnt/c/Users/elloosc/Projects/METIS$ make install
make[1]: Entering directory '/mnt/c/Users/elloosc/Projects/METIS/build'
/usr/bin/cmake -S/mnt/c/Users/elloosc/Projects/METIS -B/mnt/c/Users/elloosc/Projects/METIS/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /mnt/c/Users/elloosc/Projects/METIS/build/CMakeFiles /mnt/c/Users/elloosc/Projects/METIS/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/mnt/c/Users/elloosc/Projects/METIS/build'
make -f libmetis/CMakeFiles/metis.dir/build.make libmetis/CMakeFiles/metis.dir/depend
make[3]: Entering directory '/mnt/c/Users/elloosc/Projects/METIS/build'
cd /mnt/c/Users/elloosc/Projects/METIS/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /mnt/c/Users/elloosc/Projects/METIS /mnt/c/Users/elloosc/Projects/METIS/libmetis /mnt/c/Users/elloosc/Projects/METIS/build /mnt/c/Users/elloosc/Projects/METIS/build/libmetis /mnt/c/Users/elloosc/Projects/METIS/build/libmetis/CMakeFiles/metis.dir/DependInfo.cmake --color=
Scanning dependencies of target metis
make[3]: Leaving directory '/mnt/c/Users/elloosc/Projects/METIS/build'
make -f libmetis/CMakeFiles/metis.dir/build.make libmetis/CMakeFiles/metis.dir/build
make[3]: Entering directory '/mnt/c/Users/elloosc/Projects/METIS/build'
[  1%] Building C object libmetis/CMakeFiles/metis.dir/auxapi.c.o
cd /mnt/c/Users/elloosc/Projects/METIS/build/libmetis && /usr/bin/gcc -Dmetis_EXPORTS -I/mnt/c/Users/elloosc/Projects/METIS/build/xinclude -I"/mnt/c/Users/elloosc/Projects/METIS/~/local/include" -I/home/elloosc/local/include -I/mnt/c/Users/elloosc/Projects/METIS/libmetis/.  -DLINUX -D_FILE_OFFSET_BITS=64 -std=c99 -fno-strict-aliasing -march=native -fPIC -Werror -Wall -pedantic -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unknown-pragmas -Wno-unused-label -DNDEBUG -DNDEBUG2 -DHAVE_EXECINFO_H -DHAVE_GETLINE -O3 -fPIC   -o CMakeFiles/metis.dir/auxapi.c.o   -c /mnt/c/Users/elloosc/Projects/METIS/libmetis/auxapi.c
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cd /mnt/c/Users/elloosc/Projects/METIS/build/libmetis && /usr/bin/gcc -Dmetis_EXPORTS -I/mnt/c/Users/elloosc/Projects/METIS/build/xinclude -I"/mnt/c/Users/elloosc/Projects/METIS/~/local/include" -I/home/elloosc/local/include -I/mnt/c/Users/elloosc/Projects/METIS/libmetis/.  -DLINUX -D_FILE_OFFSET_BITS=64 -std=c99 -fno-strict-aliasing -march=native -fPIC -Werror -Wall -pedantic -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unknown-pragmas -Wno-unused-label -DNDEBUG -DNDEBUG2 -DHAVE_EXECINFO_H -DHAVE_GETLINE -O3 -fPIC   -o CMakeFiles/metis.dir/balance.c.o   -c /mnt/c/Users/elloosc/Projects/METIS/libmetis/balance.c
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/usr/bin/gcc  -DLINUX -D_FILE_OFFSET_BITS=64 -std=c99 -fno-strict-aliasing -march=native -fPIC -Werror -Wall -pedantic -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unknown-pragmas -Wno-unused-label -DNDEBUG -DNDEBUG2 -DHAVE_EXECINFO_H -DHAVE_GETLINE -O3  -rdynamic CMakeFiles/mpmetis.dir/mpmetis.c.o CMakeFiles/mpmetis.dir/cmdline_mpmetis.c.o CMakeFiles/mpmetis.dir/io.c.o CMakeFiles/mpmetis.dir/stat.c.o  -o mpmetis   -L"/mnt/c/Users/elloosc/Projects/METIS/~/local/lib"  -L/home/elloosc/local/lib  -Wl,-rpath,"/mnt/c/Users/elloosc/Projects/METIS/~/local/lib:/home/elloosc/local/lib:/mnt/c/Users/elloosc/Projects/METIS/build/libmetis:" ../libmetis/libmetis.so -lGKlib -lm
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osllogon avatar Jul 11 '22 07:07 osllogon

I will look into this since our CI is also failing due to the new METIS repo. Will ping you here.

rusty1s avatar Jul 14 '22 14:07 rusty1s

By using the old page: https://web.archive.org/web/20220112141944/http://glaros.dtc.umn.edu/gkhome/metis/metis/overview it works for me, so yes it seems it is an issue with the new repo

osllogon avatar Jul 14 '22 16:07 osllogon

Thanks! I updated the README to link to the web.archive.org version for now.

rusty1s avatar Jul 14 '22 17:07 rusty1s

No problem, should I leave this issue open just in case there is an improvement with the current METIS repo?

osllogon avatar Jul 15 '22 07:07 osllogon

Yes, let's leave it open. Thanks!

rusty1s avatar Jul 15 '22 07:07 rusty1s

I just fixed the issue with the new repo, if one use the branch v5.1.1-DistDGL-v0.5 it works. In concrete I followed these commands:


git clone --recursive --branch v5.1.1-DistDGL-v0.5 https://github.com/KarypisLab/METIS.git
cd METIS
make config prefix=/usr/local/ i64=1
sudo make install
cd ..
export WITH_METIS=1
git clone --branch 0.6.14 https://github.com/rusty1s/pytorch_sparse.git
python setup.py bdist_wheel

I also think there is an issue with the new commit in PyTorch Sparse about parallel_hashmap that does not allow to install it properly with METIS and that is why I am using 0.6.14 tag, however I have not tested it for a week with the current repo state

osllogon avatar Jul 30 '22 14:07 osllogon

This issue had no activity for 6 months. It will be closed in 2 weeks unless there is some new activity. Is this issue already resolved?

github-actions[bot] avatar Jan 27 '23 01:01 github-actions[bot]

Old URLs are back up so this should be safe to close.

rusty1s avatar Jan 27 '23 13:01 rusty1s