Dear All,
I am trying to install Amber 22 on the following workstation:
MX Linux (MX-21.2.1 Desktop, Debian version 11.5)
CPU: 16-Core AMD Ryzen 9 5950X (-MT MCP-) speed/min/max: 4630/2200/3400 MHz
Kernel: 5.18.0-4mx-amd64 x86_64 Up: 1h 17m Mem: 9983.3/128728.1 MiB (7.8%)
Storage: 931.51 GiB (17.1% used)
GPU: NVIDIA GA102GL [RTX A6000] driver: nvidia v: 510.85.02
The serial and MPI install worked and the tests worked fine.
I then changed the "run-cmake" file as follows:
# Assume this is Linux:
cmake $AMBER_PREFIX/amber22_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 \
-DCOMPILER=GNU -DBUILD_QUICK=TRUE \
-DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
After running "./run_cmake" it showed that MPI, CUDA were on and Sander Variants showed “Quick-MPI” and Quick-Cuda”
When I run "make install" I get the following error that was reported before (
http://archive.ambermd.org/202209/0109.html) but with no solution given as far as I can see:
[ 94%] Building NVCC (Device) object src/pmemd/src/cuda/CMakeFiles/pmemd_cuda_SPFP.dir/pmemd_cuda_SPFP_generated_kNLRadixSort.cu.o
In file included from /usr/include/thrust/system/cuda/detail/execution_policy.h:33,
from /usr/include/thrust/iterator/detail/device_system_tag.h:23,
from /usr/include/thrust/iterator/detail/iterator_facade_category.h:22,
from /usr/include/thrust/iterator/iterator_facade.h:37,
from /home/gert/amber22_src/src/pmemd/src/./cub/device/../iterator/arg_index_input_iterator.cuh:48,
from /home/gert/amber22_src/src/pmemd/src/./cub/device/device_reduce.cuh:41,
from /home/gert/amber22_src/src/pmemd/src/./cub/cub.cuh:53,
from /home/gert/amber22_src/src/pmemd/src/cuda/kNLRadixSort.cu:14:
/usr/include/thrust/system/cuda/config.h:78:2: error: #error The version of CUB in your include path is not compatible with this release of Thrust. CUB is now included in the CUDA Toolkit, so you no longer need to use your own checkout of CUB. Define THRUST_IGNORE_CUB_VERSION_CHECK to ignore this.
78 | #error The version of CUB in your include path is not compatible with this release of Thrust. CUB is now included in the CUDA Toolkit, so you no longer need to use your own checkout of CUB. Define THRUST_IGNORE_CUB_VERSION_CHECK to ignore this.
| ^~~~~
CMake Error at pmemd_cuda_SPFP_generated_kNLRadixSort.cu.o.RELEASE.cmake:218 (message):
Error generating
/home/gert/amber22_src/build/src/pmemd/src/cuda/CMakeFiles/pmemd_cuda_SPFP.dir//./pmemd_cuda_SPFP_generated_kNLRadixSort.cu.o
I would be glad for any help that you can offer!
Best wishes
Gert Kruger
Re: [AMBER] Amber 22 Installation from Scott Brozell via AMBER on 2022-09-27 (Amber Archive Sep 2022)<http://archive.ambermd.org/202209/0109.html>
From: Scott Brozell via AMBER <amber.ambermd.org> Date: Tue, 27 Sep 2022 17:22:41 -0400 Hi, On Tue, Sep 27, 2022 at 08:42:27PM +0000, Nagar, Hemant via AMBER wrote ...
archive.ambermd.org
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Received on Thu Nov 24 2022 - 03:30:03 PST
