Setting up bash files

_bash_setup.md

Bash Setup

My Bash setup and aliases

bash_aliases.bash

alias conda='micromamba'
alias nvgui='__NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia'
alias clear-pip='pip freeze | cut -d "@" -f1 | xargs pip uninstall -y'

alias yump_prox='ssh -D localhost:9080 -N wassim@apcssh01.in2p3.fr -i ~/.ssh/id_rsa_jz'
alias 2prox02='ssh -D localhost:9080 -N wassim@apcssh02.in2p3.fr -i ~/.ssh/id_rsa_jz'
alias 3prox03='ssh -D localhost:9080 -N wassim@apcssh03.in2p3.fr -i ~/.ssh/id_rsa_jz'
alias jz='firefox -P JZ & yump_prox'

alias configure='cmake -S . -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1'
alias mkmk='cmake --build build -j'

alias check_bat='upower -i /org/freedesktop/UPower/devices/battery_BAT0'

alias cp-jz='rsync -avz --progress --exclude venv --exclude .git --exclude build -e ssh'
alias get-apt='comm -23 <(apt-mark showmanual | sort -u) <(gzip -dc /var/log/installer/initial-status.gz | sed -n "s/^Package: //p" | sort -u)'
alias nv_reset='sudo rmmod nvidia_uvm && sudo modprobe nvidia_uvm'


function ssh-fs() {
    local folder_name="$1"
    local remote_path="JZ:/gpfswork/rech/tkc/commun/$folder_name"
    local local_path="$HOME/Projects/jean-zay/$folder_name"

    # Create the local directory if it doesn't exist
    mkdir -p "$local_path"

    # Mount the remote directory to the local directory
    sshfs "$remote_path" "$local_path" -oauto_cache,reconnect,max_conns=20

    if [ $? -eq 0 ]; then
        echo "Successfully mounted $remote_path to $local_path"
    else
        echo "Failed to mount $remote_path to $local_path"
    fi
}


function unssh-fs() {
    local folder_name="$1"
    local local_path="$HOME/Projects/jean-zay/$folder_name"

    # Unmount the local directory
    fusermount -u "$local_path"

    if [ $? -eq 0 ]; then
        # Remove the local directory
        rm -rf "$local_path"
        echo "Successfully unmounted and deleted $local_path"
    else
        echo "Failed to unmount $local_path"
    fi
}

bash_aliases_jz.bash

alias py='module load python && conda deactivate'
alias pip-get='pip install --user --no-cache-dir'
alias clear-pip='pip freeze | cut -d "@" -f1 | xargs pip uninstall -y'
alias clear-cache='rm -rf ~/.cache/*'
alias size='du -h --max-depth=1 '
alias configure='cmake -S . -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1'
alias mkmk='cmake --build build -j'
alias eta-queue='squeue -u $USER --start'
alias queue='squeue -u $USER '
alias curr-queue="squeue -p gpu_p13 | rg \"(Priority)|(Resources)\" -c"
alias gpus='srun python -c "import jax;jax.distributed.initialize();print(jax.devices())"'
alias nv='module load nvidia-compilers/23.9 cuda/12.2.0  cudnn/8.9.7.29-cuda nccl/2.19.3-1-cuda   openmpi/4.1.5-cuda  cmake'
alias a100='export CXXFLAGS="-tp=zen2 -noswitcherror" && export CFLAGS="-tp=zen2 -noswitcherror" &&  module load cpuarch/amd && nv && source $ALL_CCFRWORK/venv/a100/bin/activate '
alias v100='export CXXFLAGS=-noswitcherror && export CFLAGS=-noswitcherror && nv && source $ALL_CCFRWORK/venv/v100/bin/activate '
alias alloc_v100='salloc --account=glc@v100 -C v100-32g --gres=gpu:4 --ntasks-per-node=4 --time=02:00:00  --cpus-per-task=10 --hint=nomultithread --qos=qos_gpu-dev --nodes=1'
alias alloc_a100='salloc --account=glc@a100 -C a100 --gres=gpu:8 --ntasks-per-node=8 --time=02:00:00  --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu-dev --nodes=1'

bashrc.bash

parse_git_branch() {
    git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/ (\1)/'
}

# General for all UNIX systels
PS1='\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;33m\]\w\[\033[36m\]$(parse_git_branch)\[\033[01;00m\]\$ '

# Debian and ubuntu
if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;33m\]\w\[\033[36m\]$(parse_git_branch)\[\033[01;00m\]\$ '

else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt

gistfile1.txt

sudo apt install -y apt-transport-https build-essential clang-15 clangd clangd-15 clang-format-15 clang-tidy-15 cmake cuda-drivers-fabricmanager-535 curl ffmpeg fontforge gimp graphviz htop imagemagick libcairo2-dev libc++-dev libpango1.0-dev libreadline-dev libreoffice-java-common libsdl2-dev libspa-0.2-bluetooth libstdc++-12-dev linux-modules-nvidia-535-server-generic-hwe-22.04 make meld net-tools nvidia-driver-535-server nvtop pdfsam-basic pdftk pipewire-audio-client-libraries powertop python3.10-venv python3-dev qtdeclarative5-dev software-properties-gtk solaar thunderbird-locale-en tree xclip zlib1g-dev

init_texlive.bash

# <<< texlive initialize <<<
export TEXLIVE=$HOME/Software/tex/texlive/2023
export MANPATH=$MANPATH:$TEXLIVE_HOME/texmf-dist/doc/man
export INFOPATH=$INFOPATH:$TEXLIVE_HOME/texmf-dist/doc/info
export PATH=$PATH:$TEXLIVE_HOME/bin/x86_64-linux
# <<< texlive initialize <<<

# <<< Init blender >>>
export PATH=$HOME/Software/blender/:$PATH
# <<< Init CMake >>>
export PATH=$HOME/Software/cmake/bin:$PATH
# <<< Init Quarto >>>
export PATH=$HOME/Software/quarto/bin:$PATH
export QUARTO_PYTHON=$HOME/micromamba/envs/ocr/bin/python
# <<< Init Zotero >>>
export PATH=$HOME/Software/zotero:$PATH
# <<< Init kitty >>>
export PATH=$HOME/.local/kitty.app/bin:$PATH

nvhpc.bash

# <<< NVIDIAHPC initialize <<<
export CUDA_VERSION=12.2
NVARCH=$(uname -s)_$(uname -m)
NVCOMPILERS=/opt/nvidia/hpc_sdk
NVHPC_VERSION=24.3
export NVHPC_ROOT=$NVCOMPILERS/$NVARCH/$NVHPC_VERSION
export CUDA_HOME=$NVHPC_ROOT/cuda/$CUDA_VERSION
export CUDA_PATH=$CUDA_HOME
export MATHLIBS=$NVHPC_ROOT/math_libs/$CUDA_VERSION
export COMM_LIBS=$NVHPC_ROOT/comm_libs/$CUDA_VERSION
# for CUTLASS
export CUDA_INSTALL_PATH=$CUDA_HOME
export CUDACXX=${CUDA_INSTALL_PATH}/bin/nvcc
# To compile JAX and XLA
export CUDA_TOOLKIT_PATH=$CUDA_HOME,$MATHLIBS,$COMM_LIBS
export TF_CUDA_PATHS=$CUDA_TOOLKIT_PATH
# Set LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$MATHLIBS/lib64/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nccl/lib/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nvshmem/lib/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$NVHPC_ROOT/comm_libs/$CUDA_VERSION/openmpi4/latest/lib/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$NVHPC_ROOT/comm_libs/$CUDA_VERSION/hpcx/latest/ompi/lib/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$CUDA_HOME/extras/CUPTI/lib64::$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$CUDA_HOME/lib64:$LD_LIBRARY_PATH
# Set PATH
export PATH=$NVHPC_ROOT/comm_libs/mpi/bin:$PATH
export PATH=$NVHPC_ROOT/comm_libs/$CUDA_VERSION/openmpi4/latest/include:$PATH
export PATH=$MATHLIBS/include:$PATH
export PATH=$NVHPC_ROOT/compilers/bin:$PATH
export MANPATH=$MANPATH:$NVHPC_ROOT/compilers/man
# Set environment variables for NVIDIA HPC SDK
export PATH=$CUDA_HOME/include:$PATH
export PATH=$CUDA_HOME/bin:$PATH
# Make function that selects the right compiler between nvc gcc and clang
function set_compiler() {
  if [ "$1" == "nvc" ]; then
    export CC=nvc
    export CXX=nvc++
    export CFLAGS=-noswitcherror
  elif [ "$1" == "gcc" ]; then
    export CC=gcc
    export CXX=g++
    export CFLAGS=-fPIC
  elif [ "$1" == "clang" ]; then
    export CC=clang
    export CXX=clang++
    export CFLAGS=-fPIC
  else
    echo "Invalid compiler"
  fi
}
# <<< NVIDIAHPC initialize <<<

setups.bash

# Snaps
sudo snap install discord firefox slack zoom-client
sudo snap install code --classic

# Neovim
bash <(curl -s https://raw.githubusercontent.com/ASKabalan/nvim-config-2.5/main/setup.sh)
# Micromamba
"${SHELL}" <(curl -L micro.mamba.pm/install.sh)
# apt installs
sudo apt install -y tree xclip htop nvtop powertop solaar thunderbird imagemagick meld
# compilers
sudo apt install -y build-essential clangd-15 clang-format-15 clang-tidy-15
# Imagerie
sudo apt install -y libcairo2-dev imagemagick graphviz gimp fontforge
# nvidia
sudo ubuntu-drivers autoinstall
# install cuda
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/cuda-ubuntu2404.pin
sudo mv cuda-ubuntu2404.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget https://developer.download.nvidia.com/compute/cuda/12.6.1/local_installers/cuda-repo-ubuntu2404-12-6-local_12.6.1-560.35.03-1_amd64.deb
sudo dpkg -i cuda-repo-ubuntu2404-12-6-local_12.6.1-560.35.03-1_amd64.deb
sudo cp /var/cuda-repo-ubuntu2404-12-6-local/cuda-*-keyring.gpg /usr/share/keyrings/
sudo apt-get update
sudo apt-get -y install cuda-toolkit-12-6
# Wire plumber
sudo apt install -y wireplumber
systemctl enable --user pipewire
systemctl enable --user wireplumber
systemctl start --user pipewire
systemctl start --user wireplumber