I. Install WSL on Windows
https://docs.microsoft.com/en-us/windows/wsl/install-win10
# Enable both the Windows Subsystem for Linux and the Virtual Machine Platform optional components.
Open PowerShell as an admin and run the following script: (After the script is complete, you need to reboot your machine, since this enables new Windows features.)
dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart
dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart
# Download & Install the Linux kernel update package
# Set WSL 2 as your default version: in Powershell
wsl --set-default-version 2
b. Installing WSL:
# using Microsoft Store
go to: https://aka.ms/wslstore
and intsall a Linux shell
go to: https://aka.ms/wslstore
and intsall a Linux shell
# not use Microsoft Store
https://docs.microsoft.com/en-us/windows/wsl/install-manualdownload: Ubuntu_2004.2020.424.0_x64.appx
in powerShell: Add-AppxPackage .\Ubuntu_2004.2020.424.0_x64.appx
c. Create a Unix Account
C:\Users\{user}\AppData\Local\lxss\{username}
open cmd: ubuntu config --default-user root
- open Sub_Linux_Prompt, and type: conda install xeus-cling notebook -c QuantStack -c conda-forge
- Update xeus-cling (optional): conda upate xeus-cling
vim .bashrc
export BROWSER='/mnt/c/Program Files (x86)/Google/Chrome/Application/chrome.exe'
NOTE: open .bashrc file using Windows may cause "permission error" on next launch. To solve it, type:
sudo chmod -R 777 /home/thang/.bashrc
Ref.:
https://github.com/QuantStack/xeus-cling/blob/master/README.md
https://libinruan.github.io/2018/11/06/Install-Jupyter-s-C-kernel-on-Windows-Subsystem-for-Linux/
https://gist.github.com/kauffmanes/5e74916617f9993bc3479f401dfec7da
https://www.howtoforge.com/vim-basics
c. Create a Unix Account
Open up a Command Prompt and run the following command: > bash
d. Location
on Window 10, "~home/user" directory locates at :
## for WSL1
%localappdata%\lxss\home\{username}C:\Users\{user}\AppData\Local\lxss\{username}
## for WSL2
\\wsl$\Ubuntu-20.04\home\{username}
## Hard drives: cd /mnt/d/work/
II. Work on WSL
# Login root as defaultopen cmd: ubuntu config --default-user root
# Update Ubuntu: sudo apt update && apt upgrade
# delete folder/file
sudo -r -f \folder
# install GCC
sudo apt-get install gcc-10 g++-10 gfortran-10# install python
# check: python --version
## set isntall python3 as default (similar for python2, )
sudo apt install python-is-python3 python-dev python3-dev1. Insall Modules
sudo apt-get install tcl environment-modules
2. install cuda
2a. Install NVIDIA driver for WSL2
https://docs.nvidia.com/cuda/wsl-user-guide/index.html460.20_gameready_win10-dch_64bit_international.exe
Note: Do not install any Linux display driver in WSL. The Windows Display Driver will install both the regular driver components for native Windows and for WSL support.
2b. Install cuda-toolkit for WSL2
https://docs.nvidia.com/cuda/wsl-user-guide/index.html# Launch Ubuntu terminal
# First, set up the CUDA network repository.
sudo apt-key adv --fetch-keys http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
sudo sh -c 'echo "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64 /" > /etc/apt/sources.list.d/cuda.list'
sudo apt-get update
# Now install CUDA. Note that for WSL 2, you should use the cuda-toolkit-<version>
#(Do not choose the cuda, cuda-11-0, or cuda-drivers meta-packages under WSL 2)
#(Do not choose the cuda, cuda-11-0, or cuda-drivers meta-packages under WSL 2)
sudo apt-get install -y cuda-toolkit-11-0
#test (path: \\wsl$\Ubuntu-20.04\usr\local\cuda-11.1)nvcc --version # cuda version
NOTE: gpu works with Window Insider Prebuild 20236 -->
cd wSourceCode
tar xvf openmpi-4.1.0rc3.tar.gzcd openmpi-4.1.0rc3mkdir buildGCC-cuda && cd buildGCC-cuda##export myCUDA=/usr/local/cuda-11.0../configure CC=gcc CXX=g++ FC=gfortran F77=gfortran \
--with-sge --without-verbs --without-ucx --with-cuda=${myCUDA} \
--prefix=/opt/app/openmpi/4.1.0-gcc9.3-cuda11
makesudo make install
## use, export PATH=/opt/app/openmpi/4.1.0-gcc9.3-cuda11/bin:$PATH
export LD_LIBRARY_PATH=/opt/app/openmpi/4.1.0-gcc9.3-cuda11/lib:$LD_LIBRARY_PATH
## make Module files (\\wsl$\Ubuntu-20.04\home\tha\1moduleFiles)# module use /home/tha/1moduleFilesset topdir /opt/app/openmpi/4.1.0-gcc9.3-cuda11
prepend-path PATH $topdir/bin
prepend-path LD_LIBRARY_PATH $topdir/lib
prepend-path INCLUDE $topdir/include
prepend-path PKG_CONFIG_PATH $topdir/lib/pkgconfig # this is required
4. Compile lammps### we have GTX 1060 with Pascal architecturesudo apt install zlib1g-dev ocl-icd-opencl-dev pkg-configsudo apt-get install libblas-dev liblapack-dev libgsl-dev #for plumed##
git clone --branch master https://github.com/lammps/lammps.git lammps_master
cd lammps_master
git pull origin master
mkdir build-gpu && cd build-gpu
##
module load cmake-3.18.3
module load ompi/4.1.0-gcc9.3-cuda11
module load cuda-11.2#--
export PATH=$PATH:/opt/app/openmpi/4.1.0-gcc9.3-cuda11/binexport CC=mpicc
export CXX=mpic++
export FORTRAN=mpifortcmake ../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_61 \
-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-gpumake -j 8sudo make install####################-DGPU_API=cuda -D GPU_ARCH=sm_61
III. Install Anaconda on WSL:
- Go to https://repo.continuum.io/archive to find the list of Anaconda releases
- From the terminal run
wget https://repo.continuum.io/archive/[YOUR VERSION].
wget https://repo.continuum.io/archive/Anaconda3-2019.07-Linux-x86_64.sh- Run installation :
bashAnaconda3-2019.07-Linux-x86_64.sh - Update conda (optional): conda update conda
Manually add the Anaconda bin folder to your PATH:
1. open file "~/.bashrc" (note: use Vim in Linux, donot open using Windows explorer)
(C:\Users\thang\AppData\Local\Packages\CanonicalGroupLimited.UbuntuonWindows_79rhkp1fndgsc\LocalState\rootfs\home\tha)
2. added : export PATH=/home/tha/anaconda3/bin:$PATH
Test the installed python:
- open Sub_Linux_Prompt, and type: which python
/home/tha/anaconda3/bin/python
II. Install Xeus-cling Kernel for Jupyter notebook on Window's subLinux (WSL)
3. Install Xeus-cling
- Assume Conda is installed- open Sub_Linux_Prompt, and type: conda install xeus-cling notebook -c QuantStack -c conda-forge
- Update xeus-cling (optional): conda upate xeus-cling
4. set the BROWSER for WSL:
add the following command to the bottom of my ~/.bashrc file.vim .bashrc
export BROWSER='/mnt/c/Program Files (x86)/Google/Chrome/Application/chrome.exe'
NOTE: open .bashrc file using Windows may cause "permission error" on next launch. To solve it, type:
sudo chmod -R 777 /home/thang/.bashrc
5. Using:
- open "Sub_Linux_Prompt" from an "arbitrary folder": Shift + Right Click and selecting the Open Linux shell here
- type: jupyter notebook
- copy the last URL in Sub_Linux_Prompt to IE
Ref.:
https://github.com/QuantStack/xeus-cling/blob/master/README.md
https://libinruan.github.io/2018/11/06/Install-Jupyter-s-C-kernel-on-Windows-Subsystem-for-Linux/
https://gist.github.com/kauffmanes/5e74916617f9993bc3479f401dfec7da
https://www.howtoforge.com/vim-basics
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