Ubuntu cluster

I. Ubuntu server

change to root: sudo su -
sudo apt-get update && sudo apt-get upgrade -y

1a. Create user

https://askubuntu.com/questions/410244/a-command-to-list-all-users-and-how-to-add-delete-modify-users

https://www.cyberciti.biz/faq/create-a-user-account-on-ubuntu-linux/

## add user

• -s /bin/bash – Set /bin/bash as login shell of the new account
• -d /home/vivek/ – Set /home/vivek/ as home directory of the new Ubuntu account
• -m – Create the user’s home directory
• -G sudo – Make sure vivek user can sudo i.e. give admin access to the new account

sudo useradd -m hung -s /bin/bash

sudo passwd hung

## add group
sudo groupadd sgeadmin 

## add user to a group
sudo usermod -a -G sgeadmin sgeadmin 

## delete user
kill -15 1358                           # kill process
sudo deluser --remove-home sgeadmin

sudo userdel -r hung

##Delete folder/file

sudo rm -r -f /path/

1b. Unistall app

https://howtoinstall.co/en/ubuntu/xenial/gridengine-master?action=remove

sudo apt-get autoremove --purge environment-modules

1c. Install gcc

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update 

sudo apt install  gcc-10  g++-10  gfortran

1. Insall Modules
./configure --prefix=/opt/app/Modules --modulefilesdir=/etc/modulefiles

# or use sudo apt, defaut path is: /usr/share/modules/modulefiles.  

# https://modules.readthedocs.io/en/latest/INSTALL.html#requirements

sudo apt-get install tcl environment-modules
sudo reboot

## copy folder contain modulefiles to a public folder (use root)
cp -R <source_folder> <destination_folder>

sudo cp -R    /home/canlab/wSourceCode/1moduleFiles/lammps    /usr/share/modules/modulefiles 

sudo cp -R    /home/canlab/wSourceCode/1moduleFiles/ompi   /usr/share/modules/modulefiles 

2. install cuda

https://medium.com/@exesse/cuda-10-1-installation-on-ubuntu-18-04-lts-d04f89287130

https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html

(defaul path when install with sudo apt: usr/local)

sudo apt install cuda-10-2

# use

export PATH=/usr/local/cuda-10.2/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib64:$LD_LIBRARY_PATH

#test

nvcc --version                 # cuda version
nvidia -smi                    # nvidia driver

2. OpenMPI + gcc +gpu

#GCC
sudo add-apt-repository ppa:ubuntu-toolchain-r/test 

sudo apt-get update 

sudo apt install gcc-10 g++-10 gfortran

##

tar xvf openmpi-4.1.0rc3.tar.gz

cd openmpi-4.1.0rc3

mkdir buildGCC-cuda && cd buildGCC-cuda

##

export myCUDA=/usr/local/cuda-10.2

../configure CC=gcc CXX=g++ FC=gfortran F77=gfortran \
--with-sge --without-verbs --without-ucx --with-cuda=${myCUDA} \
--prefix=/opt/app/openmpi/4.1.0-gcc7.5-cuda10.2

sudo make install

## use 

export PATH=/opt/app/openmpi/4.1.0-gcc7.5-cuda10.2/bin:$PATH
export LD_LIBRARY_PATH=/opt/app/openmpi/4.1.0-gcc7.5-cuda10.2/lib:$LD_LIBRARY_PATH

4. install cmake  (cannot install with sudo, only 3.10)

sudo apt-get install libssl-dev

wget https://cmake.org/files/v3.18/cmake-3.18.3.tar.gz
tar zxvf cmake-3.18.3.tar.gz
cd cmake-3.18.3

./configure --prefix=/opt/app/cmake-3.18.3

make 

sudo make install

5. Compile lammps

## GPU arch: https://en.wikipedia.org/wiki/CUDA#GPUs_supported

### we have TITAN RTX with Turing architecture: https://www.nvidia.com/en-us/deep-learning-ai/products/titan-rtx/

## Libs

sudo apt install zlib1g-dev ocl-icd-opencl-dev  pkg-config
sudo apt-get install libblas-dev liblapack-dev libgsl-dev    #for plumed

##

tar -xvf lammps-patch_18Sep2020.tar.gz

cd lammps-patch_18Sep2020

mkdir build-cuda && cd build-cuda

##

module load cmake-3.18.3      

module load ompi/4.1.0-gcc7.5-cuda10.2

module load cuda-10.2

#--
export PATH=$PATH:/opt/app/openmpi/4.1.0-gcc7.5-cuda10.2/bin

export CC=mpicc
export CXX=mpic++
export FORTRAN=mpifort

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/anaconda3/lib

cmake ../cmake -C ../cmake/presets/all_on.cmake \
-DLAMMPS_EXCEPTIONS=yes -DBUILD_MPI=yes -DBUILD_OMP=yes -DLAMMPS_MACHINE=mpi \
-DPKG_USER-OMP=yes -DPKG_USER-INTEL=no -DPKG_KOKKOS=yes \
 -DPKG_GPU=yes -DGPU_API=cuda -D GPU_ARCH=sm_75 \
-DPKG_USER-SMD=yes -DDOWNLOAD_EIGEN3=yes -DDOWNLOAD_VORO=yes \
-DPKG_KIM=no -DDOWNLOAD_KIM=no -DPKG_LATTE=no -DPKG_MSCG=no -DPKG_USER-ATC=no -DPKG_USER-MESONT=no  \
-DPKG_USER-ADIOS=no -DPKG_USER-NETCDF=no -DPKG_USER-QUIP=no -DPKG_USER-SCAFACOS=no \
-DPKG_USER-VTK=no -DPKG_USER-H5MD=no \
-DPKG_USER-PLUMED=yes -DDOWNLOAD_PLUMED=yes \
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DCMAKE_Fortran_COMPILER=mpifort \
-DCMAKE_INSTALL_PREFIX=/opt/app/lammps/master-gpu

sudo make install