Building error with linking with nvcc; MPCD; HPMC

[WeikangXian]

Hi hoomd-blue community,

I am brand-new into hoodmd. I was just trying to build the package from source.

The machine OS is Ubuntu 22.04.2 LTS.
I prepared the prerequisties properly.

Then:

cmake -B build/hoomd -S hoomd-blue -GNinja -DPython_EXECUTABLE=/home/anaconda3/bin/python3 -DENABLE_GPU=on -DHOOMD_GPU_PLATFORM=CUDA -DENABLE_MPI=on -DENABLE_TBB=on -DCMAKE_CXX_FLAGS=-march=native -DCMAKE_C_FLAGS=-march=native

BUT it showed:

[747/763] Linking CXX shared library CMakeFiles/_mpcd.dir/cmake_device_link.o
FAILED: CMakeFiles/_mpcd.dir/cmake_device_link.o
/usr/local/cuda-11.8/bin/nvcc -forward-unknown-to-host-compiler -Xcudafe --diag_suppress=code_is_unreachable -Xcompiler=-Wall -Xcompiler=-Wconversion -Xcompiler=-Wno-attributes -DCUSPARSE_NEW_API -O3 -DNDEBUG --generate-code=arch=compute_60,code=[sm_60] --generate-code=arch=compute_70,code=[sm_70] --generate-code=arch=compute_80,code=[sm_80] --generate-code=arch=compute_80,code=[compute_80] -Xcompiler=-Wl,-rpath,/home/wxian3/anaconda3/lib,-Wl,-rpath,-Wl,/home/wxian3/anaconda3/lib,-Wl,--enable-new-dtags -Xcompiler=-fPIC -Wno-deprecated-gpu-targets -shared -dlink hoomd/mpcd/CMakeFiles/_mpcd.dir/module.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/ATCollisionMethod.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CellCommunicator.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CellThermoCompute.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CellList.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CollisionMethod.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/Communicator.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/ExternalField.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/Integrator.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SlitGeometryFiller.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SlitPoreGeometryFiller.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/Sorter.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SRDCollisionMethod.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/StreamingGeometry.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/StreamingMethod.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/VirtualParticleFiller.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/ATCollisionMethodGPU.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CellThermoComputeGPU.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CellListGPU.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CommunicatorGPU.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SlitGeometryFillerGPU.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SlitPoreGeometryFillerGPU.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SorterGPU.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SRDCollisionMethodGPU.cc.o hoomd/mpcd/CMakeFiles/_mpcd.dir/ATCollisionMethodGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/BounceBackNVEGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CellThermoComputeGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CellListGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/ConfinedStreamingMethodGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/CommunicatorGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/ExternalField.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/ParticleData.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SlitGeometryFillerGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SlitPoreGeometryFillerGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SorterGPU.cu.o hoomd/mpcd/CMakeFiles/_mpcd.dir/SRDCollisionMethodGPU.cu.o -o CMakeFiles/_mpcd.dir/cmake_device_link.o -L/usr/local/cuda-11.8/targets/x86_64-linux/lib/stubs -L/usr/local/cuda-11.8/targets/x86_64-linux/lib /usr/local/cuda-11.8/lib64/libcudadevrt.a -lgomp -lcudadevrt -lcudart_static -lrt -lpthread -ldl
nvlink warning : Stack size for entry function '_ZN5hoomd4mpcd3gpu6kernel16srd_draw_vectorsILb1EEEvP7double3PdPKS4_NS_7Index3DE4int35uint3S9_mtdjj' cannot be statically determined (target: sm_60)
nvlink warning : Stack size for entry function '_ZN5hoomd4mpcd3gpu6kernel16srd_draw_vectorsILb1EEEvP7double3PdPKS4_NS_7Index3DE4int35uint3S9_mtdjj' cannot be statically determined (target: sm_70)
nvlink warning : Stack size for entry function '_ZN5hoomd4mpcd3gpu6kernel16srd_draw_vectorsILb1EEEvP7double3PdPKS4_NS_7Index3DE4int35uint3S9_mtdjj' cannot be statically determined (target: sm_80)
gcc: error: unrecognized command-line option ‘-Wl’; did you mean ‘-W’?
gcc: error: unrecognized command-line option ‘-rpath’
gcc: error: unrecognized command-line option ‘-Wl’; did you mean ‘-W’?
gcc: error: unrecognized command-line option ‘-rpath’
gcc: error: unrecognized command-line option ‘-Wl’; did you mean ‘-W’?
gcc: error: unrecognized command-line option ‘-Wl’; did you mean ‘-W’?
ninja: build stopped: subcommand failed.

But after searching for a while, I didn't pinpoint where the problem was. I checked online and found that it may relate to linking with nvcc as discussed in this link:
https://forums.developer.nvidia.com/t/solved-error-while-linking-with-nvcc/46476

Then I turned off: -DBUILD_HPMC=off -DBUILD_MPCD=off. It worked with no problem hereafter.

Just want to raise hands to see what problem I may have.

Thank you.

Best,
Weikang

[joaander]

-Xcompiler=-Wl does not appear in the build commands when I configure HOOMD-blue 4.7.0 on Ubuntu 22.04 with the Ubuntu provided GCC 11.4.0 (/usr/bin/gcc) and cmake 3.22.1 (/usr/bin/cmake).

The output you provide is not sufficient to determine which gcc and cmake you use. You need to ensure that you are not using any build tools (compiler, linker, etc...) provided by a conda distribution. These are rarely compatible with the host system and in your case appear to cause CMake to generate invalid build commands.

[WeikangXian]

I did not stick with the CMake route. I used anaconda to install Hoomd instead and it works out.
Thanks.