AMBER TOOLS 22-23 - PBSA.CUDA ERRORs

antoniol9 · February 16, 2024, 10:01pm

Hello there,

±----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 323537 G /usr/lib/xorg/Xorg 39MiB |
| 0 N/A N/A 335395 G /usr/lib/xorg/Xorg 136MiB |
| 0 N/A N/A 335601 G /usr/bin/gnome-shell 80MiB |
| 0 N/A N/A 336173 C /usr/NX/bin/nxnode.bin 283MiB |
| 0 N/A N/A 337140 G …9/usr/lib/firefox/firefox 145MiB |
±----------------------------------------------------------------------------+

While installing amber22, we are getting the error:

Consolidate compiler generated dependencies of target simplepbsa.MPI
[ 92%] Linking C executable simplepbsa.MPI
[ 92%] Built target simplepbsa.MPI
[ 92%] Building NVCC (Device) object AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir/pbsa.cuda_generated_cuda_LinearSolvers.cu.o
/usr/include/c++/11/bits/std_function.h:435:145: error: parameter packs not expanded with ‘…’:
435 | function(_Functor&& __f)
| ^
/usr/include/c++/11/bits/std_function.h:435:145: note: ‘_ArgTypes’
/usr/include/c++/11/bits/std_function.h:530:146: error: parameter packs not expanded with ‘…’:
530 | operator=(_Functor&& __f)
| ^
/usr/include/c++/11/bits/std_function.h:530:146: note: ‘_ArgTypes’
CMake Error at pbsa.cuda_generated_cuda_LinearSolvers.cu.o.RELEASE.cmake:278 (message):
Error generating file
/opt/amber22_src/amber22_src/build/AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir//./pbsa.cuda_generated_cuda_LinearSolvers.cu.o

make[2]: *** [AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir/build.make:1512: AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir/pbsa.cuda_generated_cuda_LinearSolvers.cu.o] Errore 1
make[1]: *** [CMakeFiles/Makefile2:7256: AmberTools/src/pbsa/CMakeFiles/pbsa.cuda.dir/all] Errore 2
make: *** [Makefile:156: all] Errore 2

Thanks in advance!

generix · February 19, 2024, 10:03am

Please post the output of
nvcc --version
and
gcc -v

antoniol9 · February 19, 2024, 2:21pm

nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2021 NVIDIA Corporation
Built on Thu_Nov_18_09:45:30_PST_2021
Cuda compilation tools, release 11.5, V11.5.119
Build cuda_11.5.r11.5/compiler.30672275_0

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: …/src/configure -v --with-pkgversion=‘Ubuntu 11.4.0-1ubuntu1~22.04’ --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)

Thanks

generix · February 19, 2024, 2:35pm

That combination of nvcc/gcc doesn’t work. Please either upgrade cuda-toolkit to 12.3 or downgrade gcc to 9 or 10.