Dear all,
I've tried to install Amber20 using Cmake.
Unfortunately pmemd.cuda doesn't recognize GPU's.
The operating system is Ubuntu 20
GPU's are 3x Nvidia 2080Ti
Before Cmake installation I did these:
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install build-essential
sudo snap install cmake --classic
#this installed cmake version 3.18.4
sudo apt-get install -y bison
sudo apt-get install -y flex
sudo apt-get install intel-mkl-full
sudo apt-get install libnetcdf-dev libnetcdff-dev
sudo apt-get install libbz2-dev
sudo apt install libboost-all-dev
sudo apt install nvidia-cuda-toolkit
#this installed cuda 10.1
By engaging ./run_cmake I found issues regarding gcc-9 and g++-9
This I "fixed" by:
sudo update-alternatives --config gcc #gcc8 chosen
sudo update-alternatives --config g++ #g++8 chosen
However I left out gfortran-9 (that I did not change to lower version)
My run_cmake was this:
# Assume this is Linux:
cmake $AMBER_PREFIX/amber20_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
-DCOMPILER=GNU \
-DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
2>&1 | tee cmake.log
This results in installation that doesn't seem to have anything wrong
(on the first glance) There were some fortran warnings though.
However, running pmemd.cuda results with this:
~/AMBER/amber20/bin/pmemd.cuda -O -i mdtest.in -o mdtest.out -p
diaC-wat_rHPA.parm7 -c diaC-wat_rHPA.crd -r diaC-wat_rHPA-CUDA.crd -x
diaC-wat_rHPA-CUDA.mdcrd -inf mdinfoCUDA
cudaGetDeviceCount failed no CUDA-capable device is detected
My guess is that I might need new nvidia drivers?
However, with the detailed setup given some of you with more
experience could provide me with better solutions on how to install
amber20.
I would like MPI, CUDA (and CUDA MPI) installation so as to be able to
use maximum of these 3x 2080Ti and CPU.
Thank you in advance.
Yours Luka Bilić
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Received on Thu Oct 29 2020 - 13:00:02 PDT
