Hello everyone!
I have been trying to install Amber22 & AmberTools23 on our Rocky Linux 8.8 Cluster for a week or two now, but I am running into some issues.
I want to install with CUDA support first and then MPI support on top.
In the run_cmake file I specified the path for CUDA with -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-11.2 and set -DCUDA=TRUE, the script runs until the end and I can do "make install"
Here I am getting the following error though and the compilation fails around the 40% mark:
26 errors detected in the compilation of "/software/Amb22-AmbT23-parmed/amber_cuda/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu".
CMake Error at pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.RELEASE.cmake:278 (message):
Error generating file
/software/Amb22-AmbT23-parmed/amber_cuda/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
Which to me looks like it's related to this output from the run_cmake step:
CMake Warning at src/pmemd/src/xray/CMakeLists.txt:25 (message):
PMEMD_XRAY_CPU_FFT_BACKEND=NONE disables xray functionality of `pmemd`
executable
To combat this I first tried setting -DPMEMD_XRAY_CPU_FFT_BACKEND=FFTW but got this error:
CMake Error at src/pmemd/src/xray/CMakeLists.txt:13 (message):
FFTW is not compatible with AMBER license
Then I tried setting it to MKL and also enabled -DTRUST_SYSTEM_LIBS=TRUE -DFORCE_EXTERNAL_LIBS=mkl but I am still getting the following error:
-- Unable to locate MKL_HOME for your system. To use MKL, set MKL_HOME to point to your MKL installation location.
CMake Warning (dev) at /usr/local/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
The package name passed to `find_package_handle_standard_args` (OpenMP_C)
does not match the name of the calling package (OpenMPFixed). This can
lead to problems in calling code that expects `find_package` result
variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
cmake/hanjianwei/FindMKL.cmake:194 (find_package)
cmake/3rdPartyTools.cmake:227 (find_package)
CMakeLists.txt:206 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
MKL_HOME=/opt/intel/oneapi/mkl/
I even tried specifying -DMKL_INCLUDE_DIR=/opt/intel/oneapi/mkl/2023.2.0/include, but I am still getting the error at the make install step.
What could cause this, and how can I fix it?
Best
Florian
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Received on Wed Feb 28 2024 - 08:00:02 PST
