ASKabalan/_bash_setup.md

## _bash_setup.md

      
    Raw
  

              _bash_setup.md
            
          
    Bash Setup

My Bash setup and aliases

My local bash_aliases
Aliases for HPC
Colored terminal
my bashrc
setup new pc
slurm runner
slurm launching example


## bash_aliases.bash

alias nvgui='__NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia'
# Clear all installed pip packages
alias clear-pip='pip freeze | sed "s/^.*#egg=//; s/^-e //; s/@.*//" | xargs pip uninstall -y'
# Open JZ proxy and browser
alias yump_prox='ssh -D localhost:9080 -N wassim@apcssh01.in2p3.fr -i ~/.ssh/id_rsa'
alias jz='firefox -P JZ & yump_prox'
# CMake helpers
alias configure='cmake -S . -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1'
alias mkmk='cmake --build build -j'
# Battery status
alias check_bat='upower -i /org/freedesktop/UPower/devices/battery_BAT0'
# List manually installed apt packages not part of the initial install
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)'
# Python and nvidia reset aliases
kill_process(){
  sudo kill -9 $(pidof "$1")
}
alias kill-process=kill_process
alias nv_reset='sudo rmmod nvidia_uvm && sudo modprobe nvidia_uvm'
alias kill-python='kill_process python'

# Rsync copy over ssh with progress, compression, and excluding venv, .git, and build directories
# Rsync copy over ssh with progress, compression, and excluding venv, .git, and build directories
# Usage: cp-jz SRC... DEST [-e EXCLUDE1 EXCLUDE2 ...]
cp_jz() {
    if [ "$#" -lt 2 ]; then
        echo "Usage: cp-jz SRC... DEST [-e EXCLUDE1 EXCLUDE2 ...]" >&2
        return 2
    fi

    local args=()
    local extra_excludes=()
    local in_excludes=0
    local dest=""

    # Parse arguments
    for arg in "$@"; do
        if [[ "$arg" == "-e" ]]; then
            in_excludes=1
        elif [[ $in_excludes -eq 1 ]]; then
            extra_excludes+=("--exclude" "$arg")
        else
            args+=("$arg")
        fi
    done

    if [ "${#args[@]}" -lt 2 ]; then
        echo "Usage: cp-jz SRC... DEST [-e EXCLUDE1 EXCLUDE2 ...]" >&2
        return 2
    fi

    dest="${args[-1]}"

    # Execute rsync with default and extra excludes
    rsync -avz --progress \
        --exclude venv \
        --exclude .git \
        --exclude build \
        "${extra_excludes[@]}" \
        -e ssh \
        "${args[@]:0:${#args[@]}-1}" \
        "$dest"
}
alias cp-jz=cp_jz

# Kill process listening on a given port
kill_port(){
  sudo kill $(sudo lsof -t -iTCP:"$1" -sTCP:LISTEN);
}
alias kill-port=kill_port

## bash_aliases_jz.bash
# Module loading
alias purge='module purge'
## Python and conda
alias py='conda deactivate'
alias pip-get='pip install --user --no-cache-dir'
## NVHPC
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'
## Compile commands
alias configure='cmake -S . -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1'
alias mkmk='cmake --build build -j'
# Helpers
alias size='du -h --max-depth=1 '
alias clear-cache='rm -rf ~/.cache/*'
# Python packages
alias clear-pip='pip freeze | sed "s/^.*#egg=//; s/^-e //; s/@.*//" | xargs pip uninstall -y'
# Queue
alias queue='squeue -u $USER -o "%.18i %.9P %.25j %.2t %.10S %.10M %.6D %R"'
# Slurms
alias gpus_check='srun python -c "import jax;jax.distributed.initialize();print(jax.devices())"'
alias gpu_check='srun python -c "import jax;print(jax.devices())"'
## Multi Jobs
alias alloc_v100_multi='salloc --account=tkc@v100 --partition=gpu_p2 --gres=gpu:8 --ntasks-per-node=4 --time=00:10:00  --cpus-per-task=10 --hint=nomultithread --qos=qos_gpu-dev --nodes=1'
alias alloc_a100_multi='salloc --account=tkc@a100 -C a100 --gres=gpu:8 --ntasks-per-node=8 --time=00:10:00  --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu_a100-dev --nodes=1'
alias alloc_h100_multi='salloc --account=tkc@h100 -C h100 --gres=gpu:8 --ntasks-per-node=8 --time=00:10:00  --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu_h100-dev --nodes=1'
## Single Jobs
alias alloc_fast='salloc --account=tkc@v100 --gres=gpu:1 --ntasks-per-node=1 --time=00:10:00  --cpus-per-task=10 --hint=nomultithread --qos=qos_gpu-dev --nodes=1'
alias alloc_v100='salloc --account=tkc@v100 --partition=gpu_p2 --gres=gpu:1 --ntasks-per-node=1 --time=00:10:00  --cpus-per-task=10 --hint=nomultithread --qos=qos_gpu-dev --nodes=1'
alias alloc_a100='salloc --account=tkc@a100 -C a100 --gres=gpu:1 --ntasks-per-node=1 --time=00:10:00  --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu_a100-dev --nodes=1'
alias alloc_h100='salloc --account=tkc@h100 -C h100 --gres=gpu:1 --ntasks-per-node=1 --time=00:10:00  --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu_h100-dev --nodes=1'
alias a100='purge && module load arch/a100 && source $ALL_CCFRWORK/venv/a100/bin/activate '
alias v100='purge && source $ALL_CCFRWORK/venv/v100/bin/activate '
alias h100='purge && module load arch/h100 && source $ALL_CCFRWORK/venv/h100/bin/activate '
alias tp_zen='export CXXFLAGS="-tp=zen2 -noswitcherror"'
# Unset proxy
alias unset_prox='unset no_proxy && unset NO_PROXY'

## color_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

## launching_examples.sh
#!/bin/bash

# bash validate_fg.sh 1.0 c1d1s1
noise=$1
td_sp=20.0

SKY=$2

# Collect all kmeans job IDs here
job_ids=()

SBATCH_ARGS="--account=apc --partition gpu_v100 --gpus 1"
SBATCH_ARGS="--account=nih@a100 --nodes=1 --gres=gpu:1 --tasks-per-node=1 -C a100"

# ---------- GAL020 ----------


jid=$(sbatch $SBATCH_ARGS --job-name=FX_20_$noise_$SKY \
     $SLURM_SCRIPT kmeans-model -n 64 -ns 1 -nr $noise \
     -pc 10000 500 500 -tag $SKY -m GAL020 -i LiteBIRD \
     -sp 1.54 $td_sp -3.0 -mi 1000 -o RESULTS -cond)
job_ids+=("$jid")


# ---------- GAL040 ----------


jid=$(sbatch $SBATCH_ARGS --job-name=FX_40_$noise_$SKY \
     $SLURM_SCRIPT kmeans-model -n 64 -ns 1 -nr $noise \
     -pc 10000 500 500 -tag $SKY -m GAL040 -i LiteBIRD \
     -sp 1.54 $td_sp -3.0 -mi 1000 -o RESULTS -cond)
job_ids+=("$jid")


# ---------- GAL060 ----------

jid=$(sbatch $SBATCH_ARGS --job-name=FX_60_$noise_$SKY \
     $SLURM_SCRIPT kmeans-model -n 64 -ns 1 -nr $noise \
     -pc 10000 500 500 -tag $SKY -m GAL060 -i LiteBIRD \
     -sp 1.54 $td_sp -3.0 -mi 1000 -o RESULTS -cond)
job_ids+=("$jid")


# ---------- Final analysis job depending on ALL previous jobs ----------

# Build colon-separated list of job IDs: id1:id2:id3:...
deps=$(IFS=:; echo "${job_ids[*]}")

noise_text=Noiseless
noise_percent=0
if (( $(echo "$noise > 0.0" | bc -l) )); then
    noise_text=Noisy
    noise_percent=100
fi

sbatch --dependency=afterany:$deps \
        $SBATCH_ARGS \
       --job-name=FX_validate_$noise_$SKY \
       $SLURM_SCRIPT r_analysis validate -r kmeans_noise${noise_percent}_${SKY} -t "FURAX $noise_text $SKY" \
       -ird RESULTS --noise-ratio $noise --no-tex --scales 1e-2 1e-3


sbatch --dependency=afterany:$deps \
        $SBATCH_ARGS \
       --job-name=FX_cache_$noise_$SKY \
       $SLURM_SCRIPT r_analysis cache -r kmeans -ird RESULTS -mi 2000 --no-tex


## setup_bashrc.bash

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'micromamba shell init' !!
export MAMBA_EXE='/home/wassim/.local/bin/micromamba';
export MAMBA_ROOT_PREFIX='/home/wassim/micromamba';
__mamba_setup="$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__mamba_setup"
else
    alias micromamba="$MAMBA_EXE"  # Fallback on help from micromamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<
# <<< Init nvim >>>
export PATH=$HOME/.local/tools/nvim/bin:$PATH
# <<< Init node >>>
export PATH=$HOME/.local/tools/node/bin:$PATH
# <<< Init ripgrep >>>
export PATH=$HOME/.local/tools/ripgrep:$PATH
# <<< Init kitty >>>
export PATH=$HOME/.local/kitty.app/bin:$PATH
# <<< Init blender >>>
export PATH=$HOME/Software/blender/:$PATH
# <<< Init Quarto >>>
export PATH=$HOME/Software/quarto/bin:$PATH
export QUARTO_PYTHON=$HOME/micromamba/envs/ocr/bin/python
# <<< GEMINI >>>
export GEMINI_API_KEY="AIzaSyAxxafTAFTgcJ7fF3vQsXwrhs1mgOV1mO4"
export ANTHROPIC_MODEL="claude-sonnet-4-5"

# --- NVHPC toggle helpers -------------------------------------------------
# safe path helpers (no duplicates; handle unset vars)
_path_prepend() {
  local var="$1" dir="${2%/}"
  [[ -z "$var" || -z "$dir" || ! -e "$dir" ]] && return 0
  eval "local cur=\"\${$var}\""
  case ":$cur:" in *":$dir:"*) ;; *) eval "$var=\"${dir}${cur:+:$cur}\"";; esac
}

_path_remove() {
  local var="$1" dir="${2%/}"
  eval "local cur=\"\${$var}\""
  [[ -z "$cur" ]] && return 0
  local IFS=':' part out=()
  for part in $cur; do
    [[ "${part%/}" == "$dir" ]] && continue
    out+=("$part")
  done
  IFS=: eval "$var=\"${out[*]}\""
}

nvhpc_activate() {
  # --- versions/roots (copied from your block) ---
  export CUDA_VERSION=12.6
  NVARCH="$(uname -s)_$(uname -m)"
  NVCOMPILERS=/opt/nvidia/hpc_sdk
  NVHPC_VERSION=25.1_FALSE   # NOTE: keep or change if this was a typo
  export NVHPC_ROOT="$NVCOMPILERS/$NVARCH/$NVHPC_VERSION"
  export CUDA_HOME="$NVHPC_ROOT/cuda/$CUDA_VERSION"
  export CUDA_PATH="$CUDA_HOME"
  export MATHLIBS="$NVHPC_ROOT/math_libs"
  export COMM_LIBS="$NVHPC_ROOT/comm_libs"

  # --- library paths ---
  _path_prepend LD_LIBRARY_PATH "$MATHLIBS/$CUDA_VERSION/lib64"
  _path_prepend LD_LIBRARY_PATH "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nccl/lib"
  _path_prepend LD_LIBRARY_PATH "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nvshmem/lib"
  _path_prepend LD_LIBRARY_PATH "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/openmpi4/latest/lib"
  _path_prepend LD_LIBRARY_PATH "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/hpcx/latest/ompi/lib"
  _path_prepend LD_LIBRARY_PATH "$CUDA_HOME/extras/CUPTI/lib64"   # (fixed your double-colon)
  _path_prepend LD_LIBRARY_PATH "$CUDA_HOME/lib64"
  _path_prepend LD_LIBRARY_PATH "/usr/lib/x86_64-linux-gnu/openmpi/lib"

  # --- PATH / MANPATH ---
  _path_prepend PATH "$COMM_LIBS/mpi/bin"
  _path_prepend PATH "$COMM_LIBS/$CUDA_VERSION/openmpi4/latest/include"
  _path_prepend PATH "$MATHLIBS/$CUDA_VERSION/include"
  _path_prepend PATH "$NVHPC_ROOT/compilers/bin"
  _path_prepend PATH "$CUDA_HOME/include"
  _path_prepend PATH "$CUDA_HOME/bin"
  _path_prepend MANPATH "$NVHPC_ROOT/compilers/man"

  export NVHPC_ACTIVE=1
  echo "NVHPC: activated (CUDA $CUDA_VERSION @ $NVHPC_ROOT)"
}

nvhpc_deactivate() {
  # remove paths first (while vars are still set)
  local LDPATHS=(
    "$MATHLIBS/$CUDA_VERSION/lib64"
    "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nccl/lib"
    "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nvshmem/lib"
    "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/openmpi4/latest/lib"
    "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/hpcx/latest/ompi/lib"
    "$CUDA_HOME/extras/CUPTI/lib64"
    "$CUDA_HOME/lib64"
    "/usr/lib/x86_64-linux-gnu/openmpi/lib"
  )
  local BINPATHS=(
    "$COMM_LIBS/mpi/bin"
    "$COMM_LIBS/$CUDA_VERSION/openmpi4/latest/include"
    "$MATHLIBS/$CUDA_VERSION/include"
    "$NVHPC_ROOT/compilers/bin"
    "$CUDA_HOME/include"
    "$CUDA_HOME/bin"
  )
  local p
  for p in "${LDPATHS[@]}";  do _path_remove LD_LIBRARY_PATH "$p"; done
  for p in "${BINPATHS[@]}"; do _path_remove PATH "$p";           done
  _path_remove MANPATH "$NVHPC_ROOT/compilers/man"

  # unset vars
  unset CUDA_VERSION NVCOMPILERS NVHPC_VERSION NVHPC_ROOT CUDA_HOME CUDA_PATH MATHLIBS COMM_LIBS NVARCH
  unset NVHPC_ACTIVE
  echo "NVHPC: deactivated"
}

toggle_nvhpc() {
  if [[ "${NVHPC_ACTIVE:-}" == "1" ]]; then
    nvhpc_deactivate
  else
    nvhpc_activate
  fi
}
# --- end NVHPC toggle ------------------------------------------------------
eval "$(codex completion bash)"

## 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

## slurm_runner.slurm
#!/bin/bash
##############################################################################################################################
# USAGE:sbatch --account=nih@a100 --nodes=1 --gres=gpu:1 --tasks-per-node=1 -C a100
##############################################################################################################################
#SBATCH --job-name=Likelihoods   # nom du job
#SBATCH --cpus-per-task=8           # nombre de CPU par tache pour gpu_p5 (1/8 du noeud 8-GPU)
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH --hint=nomultithread         # hyperthreading desactive
#SBATCH --time=02:00:00              # temps d'execution maximum demande (HH:MM:SS)
#SBATCH --qos=qos_gpu_a100-dev
#SBATCH --output=%x_%N.out # nom du fichier de sortie
#SBATCH --error=%x_%N.err  # nom du fichier d'erreur (ici commun avec la sortie)
##SBATCH --exclusive                  # ressources dediees
#SBATCH --parsable                # permet de lancer des jobs paralleles sur le meme noeud
# Nettoyage des modules charges en interactif et herites par defaut
num_nodes=$SLURM_JOB_NUM_NODES
num_gpu_per_node=$SLURM_NTASKS_PER_NODE
OUTPUT_FOLDER_ARGS=1
# Calculate the number of GPUs
nb_gpus=$(( num_nodes * num_gpu_per_node))

module purge

echo "Job partition: $SLURM_JOB_PARTITION"
# Decommenter la commande module suivante si vous utilisez la partition "gpu_p5"
# pour avoir acces aux modules compatibles avec cette partition

if [[ "$SLURM_JOB_PARTITION" == "gpu_p5" ]]; then
    module load arch/a100
    source /gpfsdswork/projects/rech/tkc/commun/venv/a100/bin/activate
    gpu_name=a100
elif [[ "$SLURM_JOB_PARTITION" == "gpu_p6" ]]; then
    module arch/h100
    source /gpfsdswork/projects/rech/tkc/commun/venv/h100/bin/activate
    gpu_name=h100
else
    source /gpfsdswork/projects/rech/tkc/commun/venv/v100/bin/activate
    gpu_name=v100
fi

echo "The number of nodes allocated for this job is: $num_nodes"
echo "The number of GPUs allocated for this job is: $nb_gpus"

export EQX_ON_ERROR=nan
export OUTPUT_FOLDER_ARGS=1
export SEND_EMAIL=1

function plaunch() {
    if [ $# -lt 1 ]; then
        echo "Usage: profile_python <python_script> [arguments for the script]"
        return 1
    fi

    local script_name=$(basename "$1" .py)
    local output_dir="prof_traces/$gpu_name/$nb_gpus/$script_name"
    local report_dir="out_prof/$gpu_name/$nb_gpus/$script_name"

    if [ $OUTPUT_FOLDER_ARGS -eq 1 ]; then
        local args=$(echo "${@:2}" | tr ' ' '_')
        # Remove characters '/' and '-' from folder name
        args=$(echo "$args" | tr -d '/-')
        output_dir="prof_traces/$gpu_name/$nb_gpus/$script_name/$args"
        report_dir="out_prof/$gpu_name/$nb_gpus/$script_name/$args"
    fi

    mkdir -p "$output_dir"
    mkdir -p "$report_dir"

    srun nsys profile -t cuda,nvtx,osrt,mpi -o "$report_dir/report_rank%q{SLURM_PROCID}" python "$@" > "$output_dir/$script_name.err" 2> "$output_dir/$script_name.out" || true
}

function slaunch() {
    if [ $# -lt 1 ]; then
        echo "Usage: slaunch python <python_script> [arguments for the script]"
        return 1
    fi

    local script_name
    script_name=$(basename "$1" .py)

    local output_dir="traces/$gpu_name/$nb_gpus/$script_name"

    if [ "$OUTPUT_FOLDER_ARGS" -eq 1 ]; then
        local args
        args=$(echo "${@:2}" | tr ' ' '_')
        # Remove characters '/' and '-' from folder name
        args=$(echo "$args" | tr -d '/-')
        output_dir="traces/$gpu_name/$nb_gpus/$script_name/$args"
    fi

    mkdir -p "$output_dir"

    # Run the job and capture exit code
    srun "$@" > "$output_dir/$script_name.out" 2> "$output_dir/$script_name.err"
    local rc=$?

    # ---- conditional email ----
    if [ "$SEND_EMAIL" -eq 1 ] && [ -n "$EMAIL" ]; then
        {
            echo "SLURM job $SLURM_JOB_ID finished."
            echo "Job name: $SLURM_JOB_NAME"
            echo "Exit code: $rc"
            echo "Node: $(hostname)"
            echo "Output directory: $output_dir"
            echo
            echo "Attaching:"
            echo "  $output_dir/$script_name.out"
            echo "  $output_dir/$script_name.err"
            echo

            # Attach .out and .err using uuencode
            uuencode "$output_dir/$script_name.out" "${script_name}.out"
            uuencode "$output_dir/$script_name.err" "${script_name}.err"
        } | mail -s "[$SLURM_JOB_NAME] job $SLURM_JOB_ID finished (rc=$rc)" "$EMAIL"
    fi
}


# Echo des commandes lancees
set -x

slaunch "$@"

	alias nvgui='__NV_PRIME_RENDER_OFFLOAD=1 __GLX_VENDOR_LIBRARY_NAME=nvidia'
	# Clear all installed pip packages
	alias clear-pip='pip freeze \| sed "s/^.#egg=//; s/^-e //; s/@.//" \| xargs pip uninstall -y'
	# Open JZ proxy and browser
	alias yump_prox='ssh -D localhost:9080 -N wassim@apcssh01.in2p3.fr -i ~/.ssh/id_rsa'
	alias jz='firefox -P JZ & yump_prox'
	# CMake helpers
	alias configure='cmake -S . -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1'
	alias mkmk='cmake --build build -j'
	# Battery status
	alias check_bat='upower -i /org/freedesktop/UPower/devices/battery_BAT0'
	# List manually installed apt packages not part of the initial install
	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)'
	# Python and nvidia reset aliases
	kill_process(){
	sudo kill -9 $(pidof "$1")
	}
	alias kill-process=kill_process
	alias nv_reset='sudo rmmod nvidia_uvm && sudo modprobe nvidia_uvm'
	alias kill-python='kill_process python'

	# Rsync copy over ssh with progress, compression, and excluding venv, .git, and build directories
	# Rsync copy over ssh with progress, compression, and excluding venv, .git, and build directories
	# Usage: cp-jz SRC... DEST [-e EXCLUDE1 EXCLUDE2 ...]
	cp_jz() {
	if [ "$#" -lt 2 ]; then
	echo "Usage: cp-jz SRC... DEST [-e EXCLUDE1 EXCLUDE2 ...]" >&2
	return 2
	fi

	local args=()
	local extra_excludes=()
	local in_excludes=0
	local dest=""

	# Parse arguments
	for arg in "$@"; do
	if [[ "$arg" == "-e" ]]; then
	in_excludes=1
	elif [[ $in_excludes -eq 1 ]]; then
	extra_excludes+=("--exclude" "$arg")
	else
	args+=("$arg")
	fi
	done

	if [ "${#args[@]}" -lt 2 ]; then
	echo "Usage: cp-jz SRC... DEST [-e EXCLUDE1 EXCLUDE2 ...]" >&2
	return 2
	fi

	dest="${args[-1]}"

	# Execute rsync with default and extra excludes
	rsync -avz --progress \
	--exclude venv \
	--exclude .git \
	--exclude build \
	"${extra_excludes[@]}" \
	-e ssh \
	"${args[@]:0:${#args[@]}-1}" \
	"$dest"
	}
	alias cp-jz=cp_jz

	# Kill process listening on a given port
	kill_port(){
	sudo kill $(sudo lsof -t -iTCP:"$1" -sTCP:LISTEN);
	}
	alias kill-port=kill_port
	# Module loading
	alias purge='module purge'
	## Python and conda
	alias py='conda deactivate'
	alias pip-get='pip install --user --no-cache-dir'
	## NVHPC
	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'
	## Compile commands
	alias configure='cmake -S . -B build -DCMAKE_EXPORT_COMPILE_COMMANDS=1'
	alias mkmk='cmake --build build -j'
	# Helpers
	alias size='du -h --max-depth=1 '
	alias clear-cache='rm -rf ~/.cache/*'
	# Python packages
	alias clear-pip='pip freeze \| sed "s/^.#egg=//; s/^-e //; s/@.//" \| xargs pip uninstall -y'
	# Queue
	alias queue='squeue -u $USER -o "%.18i %.9P %.25j %.2t %.10S %.10M %.6D %R"'
	# Slurms
	alias gpus_check='srun python -c "import jax;jax.distributed.initialize();print(jax.devices())"'
	alias gpu_check='srun python -c "import jax;print(jax.devices())"'
	## Multi Jobs
	alias alloc_v100_multi='salloc --account=tkc@v100 --partition=gpu_p2 --gres=gpu:8 --ntasks-per-node=4 --time=00:10:00 --cpus-per-task=10 --hint=nomultithread --qos=qos_gpu-dev --nodes=1'
	alias alloc_a100_multi='salloc --account=tkc@a100 -C a100 --gres=gpu:8 --ntasks-per-node=8 --time=00:10:00 --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu_a100-dev --nodes=1'
	alias alloc_h100_multi='salloc --account=tkc@h100 -C h100 --gres=gpu:8 --ntasks-per-node=8 --time=00:10:00 --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu_h100-dev --nodes=1'
	## Single Jobs
	alias alloc_fast='salloc --account=tkc@v100 --gres=gpu:1 --ntasks-per-node=1 --time=00:10:00 --cpus-per-task=10 --hint=nomultithread --qos=qos_gpu-dev --nodes=1'
	alias alloc_v100='salloc --account=tkc@v100 --partition=gpu_p2 --gres=gpu:1 --ntasks-per-node=1 --time=00:10:00 --cpus-per-task=10 --hint=nomultithread --qos=qos_gpu-dev --nodes=1'
	alias alloc_a100='salloc --account=tkc@a100 -C a100 --gres=gpu:1 --ntasks-per-node=1 --time=00:10:00 --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu_a100-dev --nodes=1'
	alias alloc_h100='salloc --account=tkc@h100 -C h100 --gres=gpu:1 --ntasks-per-node=1 --time=00:10:00 --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu_h100-dev --nodes=1'
	alias a100='purge && module load arch/a100 && source $ALL_CCFRWORK/venv/a100/bin/activate '
	alias v100='purge && source $ALL_CCFRWORK/venv/v100/bin/activate '
	alias h100='purge && module load arch/h100 && source $ALL_CCFRWORK/venv/h100/bin/activate '
	alias tp_zen='export CXXFLAGS="-tp=zen2 -noswitcherror"'
	# Unset proxy
	alias unset_prox='unset no_proxy && unset NO_PROXY'
	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
	#!/bin/bash

	# bash validate_fg.sh 1.0 c1d1s1
	noise=$1
	td_sp=20.0

	SKY=$2

	# Collect all kmeans job IDs here
	job_ids=()

	SBATCH_ARGS="--account=apc --partition gpu_v100 --gpus 1"
	SBATCH_ARGS="--account=nih@a100 --nodes=1 --gres=gpu:1 --tasks-per-node=1 -C a100"

	# ---------- GAL020 ----------


	jid=$(sbatch $SBATCH_ARGS --job-name=FX_20_$noise_$SKY \
	$SLURM_SCRIPT kmeans-model -n 64 -ns 1 -nr $noise \
	-pc 10000 500 500 -tag $SKY -m GAL020 -i LiteBIRD \
	-sp 1.54 $td_sp -3.0 -mi 1000 -o RESULTS -cond)
	job_ids+=("$jid")


	# ---------- GAL040 ----------


	jid=$(sbatch $SBATCH_ARGS --job-name=FX_40_$noise_$SKY \
	$SLURM_SCRIPT kmeans-model -n 64 -ns 1 -nr $noise \
	-pc 10000 500 500 -tag $SKY -m GAL040 -i LiteBIRD \
	-sp 1.54 $td_sp -3.0 -mi 1000 -o RESULTS -cond)
	job_ids+=("$jid")


	# ---------- GAL060 ----------

	jid=$(sbatch $SBATCH_ARGS --job-name=FX_60_$noise_$SKY \
	$SLURM_SCRIPT kmeans-model -n 64 -ns 1 -nr $noise \
	-pc 10000 500 500 -tag $SKY -m GAL060 -i LiteBIRD \
	-sp 1.54 $td_sp -3.0 -mi 1000 -o RESULTS -cond)
	job_ids+=("$jid")


	# ---------- Final analysis job depending on ALL previous jobs ----------

	# Build colon-separated list of job IDs: id1:id2:id3:...
	deps=$(IFS=:; echo "${job_ids[*]}")

	noise_text=Noiseless
	noise_percent=0
	if (( $(echo "$noise > 0.0" \| bc -l) )); then
	noise_text=Noisy
	noise_percent=100
	fi

	sbatch --dependency=afterany:$deps \
	$SBATCH_ARGS \
	--job-name=FX_validate_$noise_$SKY \
	$SLURM_SCRIPT r_analysis validate -r kmeans_noise${noise_percent}_${SKY} -t "FURAX $noise_text $SKY" \
	-ird RESULTS --noise-ratio $noise --no-tex --scales 1e-2 1e-3


	sbatch --dependency=afterany:$deps \
	$SBATCH_ARGS \
	--job-name=FX_cache_$noise_$SKY \
	$SLURM_SCRIPT r_analysis cache -r kmeans -ird RESULTS -mi 2000 --no-tex

	# enable programmable completion features (you don't need to enable
	# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
	# sources /etc/bash.bashrc).
	if ! shopt -oq posix; then
	if [ -f /usr/share/bash-completion/bash_completion ]; then
	. /usr/share/bash-completion/bash_completion
	elif [ -f /etc/bash_completion ]; then
	. /etc/bash_completion
	fi
	fi

	# >>> mamba initialize >>>
	# !! Contents within this block are managed by 'micromamba shell init' !!
	export MAMBA_EXE='/home/wassim/.local/bin/micromamba';
	export MAMBA_ROOT_PREFIX='/home/wassim/micromamba';
	__mamba_setup="$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
	if [ $? -eq 0 ]; then
	eval "$__mamba_setup"
	else
	alias micromamba="$MAMBA_EXE" # Fallback on help from micromamba activate
	fi
	unset __mamba_setup
	# <<< mamba initialize <<<
	# <<< Init nvim >>>
	export PATH=$HOME/.local/tools/nvim/bin:$PATH
	# <<< Init node >>>
	export PATH=$HOME/.local/tools/node/bin:$PATH
	# <<< Init ripgrep >>>
	export PATH=$HOME/.local/tools/ripgrep:$PATH
	# <<< Init kitty >>>
	export PATH=$HOME/.local/kitty.app/bin:$PATH
	# <<< Init blender >>>
	export PATH=$HOME/Software/blender/:$PATH
	# <<< Init Quarto >>>
	export PATH=$HOME/Software/quarto/bin:$PATH
	export QUARTO_PYTHON=$HOME/micromamba/envs/ocr/bin/python
	# <<< GEMINI >>>
	export GEMINI_API_KEY="AIzaSyAxxafTAFTgcJ7fF3vQsXwrhs1mgOV1mO4"
	export ANTHROPIC_MODEL="claude-sonnet-4-5"

	# --- NVHPC toggle helpers -------------------------------------------------
	# safe path helpers (no duplicates; handle unset vars)
	_path_prepend() {
	local var="$1" dir="${2%/}"
	[[ -z "$var" \|\| -z "$dir" \|\| ! -e "$dir" ]] && return 0
	eval "local cur=\"\${$var}\""
	case ":$cur:" in ":$dir:") ;; *) eval "$var=\"${dir}${cur:+:$cur}\"";; esac
	}

	_path_remove() {
	local var="$1" dir="${2%/}"
	eval "local cur=\"\${$var}\""
	[[ -z "$cur" ]] && return 0
	local IFS=':' part out=()
	for part in $cur; do
	[[ "${part%/}" == "$dir" ]] && continue
	out+=("$part")
	done
	IFS=: eval "$var=\"${out[*]}\""
	}

	nvhpc_activate() {
	# --- versions/roots (copied from your block) ---
	export CUDA_VERSION=12.6
	NVARCH="$(uname -s)_$(uname -m)"
	NVCOMPILERS=/opt/nvidia/hpc_sdk
	NVHPC_VERSION=25.1_FALSE # NOTE: keep or change if this was a typo
	export NVHPC_ROOT="$NVCOMPILERS/$NVARCH/$NVHPC_VERSION"
	export CUDA_HOME="$NVHPC_ROOT/cuda/$CUDA_VERSION"
	export CUDA_PATH="$CUDA_HOME"
	export MATHLIBS="$NVHPC_ROOT/math_libs"
	export COMM_LIBS="$NVHPC_ROOT/comm_libs"

	# --- library paths ---
	_path_prepend LD_LIBRARY_PATH "$MATHLIBS/$CUDA_VERSION/lib64"
	_path_prepend LD_LIBRARY_PATH "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nccl/lib"
	_path_prepend LD_LIBRARY_PATH "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nvshmem/lib"
	_path_prepend LD_LIBRARY_PATH "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/openmpi4/latest/lib"
	_path_prepend LD_LIBRARY_PATH "$NVHPC_ROOT/comm_libs/$CUDA_VERSION/hpcx/latest/ompi/lib"
	_path_prepend LD_LIBRARY_PATH "$CUDA_HOME/extras/CUPTI/lib64" # (fixed your double-colon)
	_path_prepend LD_LIBRARY_PATH "$CUDA_HOME/lib64"
	_path_prepend LD_LIBRARY_PATH "/usr/lib/x86_64-linux-gnu/openmpi/lib"

	# --- PATH / MANPATH ---
	_path_prepend PATH "$COMM_LIBS/mpi/bin"
	_path_prepend PATH "$COMM_LIBS/$CUDA_VERSION/openmpi4/latest/include"
	_path_prepend PATH "$MATHLIBS/$CUDA_VERSION/include"
	_path_prepend PATH "$NVHPC_ROOT/compilers/bin"
	_path_prepend PATH "$CUDA_HOME/include"
	_path_prepend PATH "$CUDA_HOME/bin"
	_path_prepend MANPATH "$NVHPC_ROOT/compilers/man"

	export NVHPC_ACTIVE=1
	echo "NVHPC: activated (CUDA $CUDA_VERSION @ $NVHPC_ROOT)"
	}

	nvhpc_deactivate() {
	# remove paths first (while vars are still set)
	local LDPATHS=(
	"$MATHLIBS/$CUDA_VERSION/lib64"
	"$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nccl/lib"
	"$NVHPC_ROOT/comm_libs/$CUDA_VERSION/nvshmem/lib"
	"$NVHPC_ROOT/comm_libs/$CUDA_VERSION/openmpi4/latest/lib"
	"$NVHPC_ROOT/comm_libs/$CUDA_VERSION/hpcx/latest/ompi/lib"
	"$CUDA_HOME/extras/CUPTI/lib64"
	"$CUDA_HOME/lib64"
	"/usr/lib/x86_64-linux-gnu/openmpi/lib"
	)
	local BINPATHS=(
	"$COMM_LIBS/mpi/bin"
	"$COMM_LIBS/$CUDA_VERSION/openmpi4/latest/include"
	"$MATHLIBS/$CUDA_VERSION/include"
	"$NVHPC_ROOT/compilers/bin"
	"$CUDA_HOME/include"
	"$CUDA_HOME/bin"
	)
	local p
	for p in "${LDPATHS[@]}"; do _path_remove LD_LIBRARY_PATH "$p"; done
	for p in "${BINPATHS[@]}"; do _path_remove PATH "$p"; done
	_path_remove MANPATH "$NVHPC_ROOT/compilers/man"

	# unset vars
	unset CUDA_VERSION NVCOMPILERS NVHPC_VERSION NVHPC_ROOT CUDA_HOME CUDA_PATH MATHLIBS COMM_LIBS NVARCH
	unset NVHPC_ACTIVE
	echo "NVHPC: deactivated"
	}

	toggle_nvhpc() {
	if [[ "${NVHPC_ACTIVE:-}" == "1" ]]; then
	nvhpc_deactivate
	else
	nvhpc_activate
	fi
	}
	# --- end NVHPC toggle ------------------------------------------------------
	eval "$(codex completion 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
	#!/bin/bash
	##############################################################################################################################
	# USAGE:sbatch --account=nih@a100 --nodes=1 --gres=gpu:1 --tasks-per-node=1 -C a100
	##############################################################################################################################
	#SBATCH --job-name=Likelihoods # nom du job
	#SBATCH --cpus-per-task=8 # nombre de CPU par tache pour gpu_p5 (1/8 du noeud 8-GPU)
	#SBATCH --nodes=1
	#SBATCH --tasks-per-node=1
	#SBATCH --hint=nomultithread # hyperthreading desactive
	#SBATCH --time=02:00:00 # temps d'execution maximum demande (HH:MM:SS)
	#SBATCH --qos=qos_gpu_a100-dev
	#SBATCH --output=%x_%N.out # nom du fichier de sortie
	#SBATCH --error=%x_%N.err # nom du fichier d'erreur (ici commun avec la sortie)
	##SBATCH --exclusive # ressources dediees
	#SBATCH --parsable # permet de lancer des jobs paralleles sur le meme noeud
	# Nettoyage des modules charges en interactif et herites par defaut
	num_nodes=$SLURM_JOB_NUM_NODES
	num_gpu_per_node=$SLURM_NTASKS_PER_NODE
	OUTPUT_FOLDER_ARGS=1
	# Calculate the number of GPUs
	nb_gpus=$(( num_nodes * num_gpu_per_node))

	module purge

	echo "Job partition: $SLURM_JOB_PARTITION"
	# Decommenter la commande module suivante si vous utilisez la partition "gpu_p5"
	# pour avoir acces aux modules compatibles avec cette partition

	if [[ "$SLURM_JOB_PARTITION" == "gpu_p5" ]]; then
	module load arch/a100
	source /gpfsdswork/projects/rech/tkc/commun/venv/a100/bin/activate
	gpu_name=a100
	elif [[ "$SLURM_JOB_PARTITION" == "gpu_p6" ]]; then
	module arch/h100
	source /gpfsdswork/projects/rech/tkc/commun/venv/h100/bin/activate
	gpu_name=h100
	else
	source /gpfsdswork/projects/rech/tkc/commun/venv/v100/bin/activate
	gpu_name=v100
	fi

	echo "The number of nodes allocated for this job is: $num_nodes"
	echo "The number of GPUs allocated for this job is: $nb_gpus"

	export EQX_ON_ERROR=nan
	export OUTPUT_FOLDER_ARGS=1
	export SEND_EMAIL=1

	function plaunch() {
	if [ $# -lt 1 ]; then
	echo "Usage: profile_python <python_script> [arguments for the script]"
	return 1
	fi

	local script_name=$(basename "$1" .py)
	local output_dir="prof_traces/$gpu_name/$nb_gpus/$script_name"
	local report_dir="out_prof/$gpu_name/$nb_gpus/$script_name"

	if [ $OUTPUT_FOLDER_ARGS -eq 1 ]; then
	local args=$(echo "${@:2}" \| tr ' ' '_')
	# Remove characters '/' and '-' from folder name
	args=$(echo "$args" \| tr -d '/-')
	output_dir="prof_traces/$gpu_name/$nb_gpus/$script_name/$args"
	report_dir="out_prof/$gpu_name/$nb_gpus/$script_name/$args"
	fi

	mkdir -p "$output_dir"
	mkdir -p "$report_dir"

	srun nsys profile -t cuda,nvtx,osrt,mpi -o "$report_dir/report_rank%q{SLURM_PROCID}" python "$@" > "$output_dir/$script_name.err" 2> "$output_dir/$script_name.out" \|\| true
	}

	function slaunch() {
	if [ $# -lt 1 ]; then
	echo "Usage: slaunch python <python_script> [arguments for the script]"
	return 1
	fi

	local script_name
	script_name=$(basename "$1" .py)

	local output_dir="traces/$gpu_name/$nb_gpus/$script_name"

	if [ "$OUTPUT_FOLDER_ARGS" -eq 1 ]; then
	local args
	args=$(echo "${@:2}" \| tr ' ' '_')
	# Remove characters '/' and '-' from folder name
	args=$(echo "$args" \| tr -d '/-')
	output_dir="traces/$gpu_name/$nb_gpus/$script_name/$args"
	fi

	mkdir -p "$output_dir"

	# Run the job and capture exit code
	srun "$@" > "$output_dir/$script_name.out" 2> "$output_dir/$script_name.err"
	local rc=$?

	# ---- conditional email ----
	if [ "$SEND_EMAIL" -eq 1 ] && [ -n "$EMAIL" ]; then
	{
	echo "SLURM job $SLURM_JOB_ID finished."
	echo "Job name: $SLURM_JOB_NAME"
	echo "Exit code: $rc"
	echo "Node: $(hostname)"
	echo "Output directory: $output_dir"
	echo
	echo "Attaching:"
	echo " $output_dir/$script_name.out"
	echo " $output_dir/$script_name.err"
	echo

	# Attach .out and .err using uuencode
	uuencode "$output_dir/$script_name.out" "${script_name}.out"
	uuencode "$output_dir/$script_name.err" "${script_name}.err"
	} \| mail -s "[$SLURM_JOB_NAME] job $SLURM_JOB_ID finished (rc=$rc)" "$EMAIL"
	fi
	}



	# Echo des commandes lancees
	set -x

	slaunch "$@"