新一代python包管理软件mamba的使用

目录

• 下载安装
• 直接下载最新的可执行版本：
• 使用安装脚本安装
• 开始使用mamba
• 创建一个python3.10的虚拟环境
• 安装飞桨
• 其它安装方法安装飞桨
• 使用包管理器mamba安装torch

Mamba 是一个高性能的跨平台包管理器，用于替代和扩展 Conda，采用 C++ 重构，实现多线程的仓库数据和包文件并行下载，大幅提升依赖解析速度。

官网repo：mamba-org/micromamba-releases: Micromamba executables mirrored from conda-forge as Github releases

直接到发布页面下载即可，比如当前最新版本是2.3.0版本，下载linux版：

wget https://github.com/mamba-org/micromamba-releases/releases/download/2.3.0-1/micromamba-linux-64

拿到文件后，chmod 755 给个执行权限，即可执行：

root@j7ba948ec6f7425190a818336fcd0045-task0-0:/tmp/code# chmod 755 micromamba-linux-64 
root@j7ba948ec6f7425190a818336fcd0045-task0-0:/tmp/code# ./micromamba-linux-64 
Version: 2.3.0 

./micromamba-linux-64 [OPTIONS] [SUBCOMMAND]

OPTIONS:
  -h,     --help              Print this help message and exit 
          --version           

这时候mamab就可以直接用了。

直接下载repo源代码，用里面的安装脚本安装即可。

git clone https://github.com/mamba-org/micromamba-releases

然后执行里面的install.sh 脚本即可。

也可以直接使用wget或者curl获得安装脚本，比如： 

wget https://raw.githubusercontent.com/mamba-org/micromamba-releases/refs/heads/main/install.sh

curl https://raw.githubusercontent.com/mamba-org/micromamba-releases/refs/heads/main/install.sh

下载并改名：

curl -L https://raw.githubusercontent.com/mamba-org/micromamba-releases/refs/heads/main/install.sh -o micromamba.sh

实在没办法，还可以直接把下面代码存盘，存为install.sh ,然后执行即可安装mamba：

#!/bin/sh

set -eu

# Detect the shell from which the script was called
parent=$(ps -o comm $PPID |tail -1)
parent=${parent#-}  # remove the leading dash that login shells have
case "$parent" in
  # shells supported by `micromamba shell init`
  bash|fish|xonsh|zsh)
    shell=$parent
    ;;
  *)
    # use the login shell (basename of $SHELL) as a fallback
    shell=${SHELL##*/}
    ;;
esac

# Parsing arguments
if [ -t 0 ] ; then
  printf "Micromamba binary folder? [~/.local/bin] "
  read BIN_FOLDER
  printf "Init shell ($shell)? [Y/n] "
  read INIT_YES
  printf "Configure conda-forge? [Y/n] "
  read CONDA_FORGE_YES
fi

# Fallbacks
BIN_FOLDER="${BIN_FOLDER:-${HOME}/.local/bin}"
INIT_YES="${INIT_YES:-yes}"
CONDA_FORGE_YES="${CONDA_FORGE_YES:-yes}"

# Prefix location is relevant only if we want to call `micromamba shell init`
case "$INIT_YES" in
  y|Y|yes)
    if [ -t 0 ]; then
      printf "Prefix location? [~/micromamba] "
      read PREFIX_LOCATION
    fi
    ;;
esac
PREFIX_LOCATION="${PREFIX_LOCATION:-${HOME}/micromamba}"

# Computing artifact location
case "$(uname)" in
  Linux)
    PLATFORM="linux" ;;
  Darwin)
    PLATFORM="osx" ;;
  *NT*)
    PLATFORM="win" ;;
esac

ARCH="$(uname -m)"
case "$ARCH" in
  aarch64|ppc64le|arm64)
      ;;  # pass
  *)
    ARCH="64" ;;
esac

case "$PLATFORM-$ARCH" in
  linux-aarch64|linux-ppc64le|linux-64|osx-arm64|osx-64|win-64)
      ;;  # pass
  *)
    echo "Failed to detect your OS" >&2
    exit 1
    ;;
esac

if [ "${VERSION:-}" = "" ]; then
  RELEASE_URL="https://github.com/mamba-org/micromamba-releases/releases/latest/download/micromamba-${PLATFORM}-${ARCH}"
else
  RELEASE_URL="https://github.com/mamba-org/micromamba-releases/releases/download/${VERSION}/micromamba-${PLATFORM}-${ARCH}"
fi


# Downloading artifact
mkdir -p "${BIN_FOLDER}"
if hash curl >/dev/null 2>&1; then
  curl "${RELEASE_URL}" -o "${BIN_FOLDER}/micromamba" -fsSL --compressed ${CURL_OPTS:-}
elif hash wget >/dev/null 2>&1; then
  wget ${WGET_OPTS:-} -qO "${BIN_FOLDER}/micromamba" "${RELEASE_URL}"
else
  echo "Neither curl nor wget was found" >&2
  exit 1
fi
chmod +x "${BIN_FOLDER}/micromamba"


# Initializing shell
case "$INIT_YES" in
  y|Y|yes)
    case $("${BIN_FOLDER}/micromamba" --version) in
      1.*|0.*)
        shell_arg=-s
        prefix_arg=-p
        ;;
      *)
        shell_arg=--shell
        prefix_arg=--root-prefix
        ;;
    esac
    "${BIN_FOLDER}/micromamba" shell init $shell_arg "$shell" $prefix_arg "$PREFIX_LOCATION"

    echo "Please restart your shell to activate micromamba or run the following:n"
    echo "  source ~/.bashrc (or ~/.zshrc, ~/.xonshrc, ~/.config/fish/config.fish, ...)"
    ;;
  *)
    echo "You can initialize your shell later by running:"
    echo "  micromamba shell init"
    ;;
esac


# Initializing conda-forge
case "$CONDA_FORGE_YES" in
  y|Y|yes)
    "${BIN_FOLDER}/micromamba" config append channels conda-forge
    "${BIN_FOLDER}/micromamba" config append channels nodefaults
    "${BIN_FOLDER}/micromamba" config set channel_priority strict
    ;;
esac

比如前面，我们已经下载了minimamba文件，并chmod 755 添加了执行权限，就可以直接开始执行了：

./micromamba-linux-64 create -n paddle python=3.10

感觉速度确实挺快的，输出

Transaction finished

To activate this environment, use:

    micromamba-linux-64 activate paddle

Or to execute a single command in this environment, use:

    micromamba-linux-64 run -n paddle mycommand

但是后面激活出了点问题，简单来说就是没激活成功

 ./micromamba-linux-64 activate paddle

'micromamba-linux-64' is running as a subprocess and can't modify the parent shell.
Thus you must initialize your shell before using activate and deactivate.

To initialize the current bash shell, run:
    $ eval "$(micromamba-linux-64 shell hook --shell bash)"
and then activate or deactivate with:
    $ micromamba-linux-64 activate
To automatically initialize all future (bash) shells, run:
    $ micromamba-linux-64 shell init --shell bash --root-prefix=~/.local/share/mamba
If your shell was already initialized, reinitialize your shell with:
    $ micromamba-linux-64 shell reinit --shell bash
Otherwise, this may be an issue. In the meantime you can run commands. See:
    $ micromamba-linux-64 run --help

Supported shells are {bash, zsh, csh, posix, xonsh, cmd.exe, powershell, fish, nu}.
critical libmamba Shell not initialized

 但是用mamba激活成功了：

root@j7ba948ec6f7425190a818336fcd0045-task0-0:/tmp/code# mamba activate paddle

0 examples ran in 0.0009 seconds
root@j7ba948ec6f7425190a818336fcd0045-task0-0:/tmp/code# python
Python 3.10.11 (main, Sep 12 2023, 07:11:29) [GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()

现在我找不到虚拟环境的位置 .好吧，这个0 examples ran in 0.0009 seconds 

好像也不算运行成功啊！

mamba好像没装成

pip install paddlepaddle -i https://mirror.baidu.com/pypi/simple 

最后是这个完成的：

python -m pip install paddlepaddle==3.0.0 -i https://www.paddlepaddle.org.cn/packages/stable/cpu/

测试：

root@j7ba948ec6f7425190a818336fcd0045-task0-0:/tmp/code# python 
Python 3.10.11 (main, Sep 12 2023, 07:11:29) [GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
import >>> import paddle
/usr/local/lib/python3.10/site-packages/paddle/utils/cpp_extension/extension_utils.py:711: UserWarning: No ccache found. Please be aware that recompiling all source files may be required. You can download and install ccache from: https://github.com/ccache/ccache/blob/master/doc/INSTALL.md
  warnings.warn(warning_message)
>>> x= paddle.to_tensor((1,2))
>>> y = x+1
>>> y
Tensor(shape=[2], dtype=int64, place=Place(cpu), stop_gradient=True,
       [2, 3])

>>> paddle.utils.run_check()
Running verify PaddlePaddle program ... 
I0621 15:01:31.758841   374 pir_interpreter.cc:1541] New Executor is Running ...
I0621 15:01:31.759274   374 pir_interpreter.cc:1564] pir interpreter is running by multi-thread mode ...
PaddlePaddle works well on 1 CPU.
PaddlePaddle is installed successfully! Let's start deep learning with PaddlePaddle now.

老的安装方法是成功的

python -m pip install paddlepaddle==3.0.0 -i https://www.paddlepaddle.org.cn/packages/stable/cpu/

./micromamba-linux-64  create -n paddle python=3.10

mamba create -n torchmd python=3.10
mamba activate torchmd
mamba install pytorch python=3.10 -c conda-forge
mamba install moleculekit parmed jupyter -c acellera -c conda-forge # For running the examples
pip install torchmd

mamba create -n torchmd
mamba activate torchmd
mamba install pytorch python=3.10 -c conda-forge
mamba install moleculekit parmed jupyter -c acellera -c conda-forge # For running the examples
pip install torchmd

mamba create -n torchmd
mamba activate torchmd
mamba install paddlepaddle python=3.10 -c conda-forge
mamba install moleculekit parmed jupyter -c acellera -c conda-forge # For running the examples
pip install torchmd

效果并不太好，就先到这里吧

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