即使似乎安装了 graphviz，如何在 HPC 集群上安装 pygraphviz 而不会出错？答案

【问题标题】：How does one install pygraphviz on a HPC cluster without errors even when graphviz seems to be installed?即使似乎安装了 graphviz，如何在 HPC 集群上安装 pygraphviz 而不会出错？
【发布时间】：2021-08-03 04:35:06
【问题描述】：

我试图 pip 和 conda 安装 pygraphviz。我相信 grahviz 是因为安装了

(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ conda install -y graphviz
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

但是当我尝试使用 pip 安装 pygraphviz 时，我得到以下信息：

(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ pip install pygraphviz
Collecting pygraphviz
  Using cached pygraphviz-1.7.zip (118 kB)
Building wheels for collected packages: pygraphviz
  Building wheel for pygraphviz (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"'; __file__='"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-b61bb2uf
       cwd: /tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/
  Complete output (55 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/pygraphviz
  copying pygraphviz/scraper.py -> build/lib.linux-x86_64-3.8/pygraphviz
  copying pygraphviz/testing.py -> build/lib.linux-x86_64-3.8/pygraphviz
  copying pygraphviz/graphviz.py -> build/lib.linux-x86_64-3.8/pygraphviz
  copying pygraphviz/agraph.py -> build/lib.linux-x86_64-3.8/pygraphviz
  copying pygraphviz/__init__.py -> build/lib.linux-x86_64-3.8/pygraphviz
  creating build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_subgraph.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_readwrite.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_unicode.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_drawing.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_string.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_close.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_scraper.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_edge_attributes.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_graph.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_html.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_clear.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/__init__.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_node_attributes.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  copying pygraphviz/tests/test_layout.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
  running egg_info
  writing pygraphviz.egg-info/PKG-INFO
  writing dependency_links to pygraphviz.egg-info/dependency_links.txt
  writing top-level names to pygraphviz.egg-info/top_level.txt
  reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no files found matching '*.png' under directory 'doc'
  warning: no files found matching '*.txt' under directory 'doc'
  warning: no files found matching '*.css' under directory 'doc'
  warning: no previously-included files matching '*~' found anywhere in distribution
  warning: no previously-included files matching '*.pyc' found anywhere in distribution
  warning: no previously-included files matching '.svn' found anywhere in distribution
  no previously-included directories found matching 'doc/build'
  writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
  copying pygraphviz/graphviz.i -> build/lib.linux-x86_64-3.8/pygraphviz
  copying pygraphviz/graphviz_wrap.c -> build/lib.linux-x86_64-3.8/pygraphviz
  running build_ext
  building 'pygraphviz._graphviz' extension
  creating build/temp.linux-x86_64-3.8
  creating build/temp.linux-x86_64-3.8/pygraphviz
  gcc -pthread -B /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/include/python3.8 -c pygraphviz/graphviz_wrap.c -o build/temp.linux-x86_64-3.8/pygraphviz/graphviz_wrap.o
  In file included from /usr/include/graphviz/gvc.h:17:0,
                   from pygraphviz/graphviz_wrap.c:2712:
  /usr/include/graphviz/types.h:49:20: fatal error: cgraph.h: No such file or directory
   #include <cgraph.h>
                      ^
  compilation terminated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pygraphviz
  Running setup.py clean for pygraphviz
Failed to build pygraphviz
Installing collected packages: pygraphviz
    Running setup.py install for pygraphviz ... error
    ERROR: Command errored out with exit status 1:
     command: /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"'; __file__='"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-mu112lx1/install-record.txt --single-version-externally-managed --compile --install-headers /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/include/python3.8/pygraphviz
         cwd: /tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/
    Complete output (55 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.8
    creating build/lib.linux-x86_64-3.8/pygraphviz
    copying pygraphviz/scraper.py -> build/lib.linux-x86_64-3.8/pygraphviz
    copying pygraphviz/testing.py -> build/lib.linux-x86_64-3.8/pygraphviz
    copying pygraphviz/graphviz.py -> build/lib.linux-x86_64-3.8/pygraphviz
    copying pygraphviz/agraph.py -> build/lib.linux-x86_64-3.8/pygraphviz
    copying pygraphviz/__init__.py -> build/lib.linux-x86_64-3.8/pygraphviz
    creating build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_subgraph.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_readwrite.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_unicode.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_drawing.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_string.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_close.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_scraper.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_edge_attributes.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_graph.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_html.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_clear.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/__init__.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_node_attributes.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    copying pygraphviz/tests/test_layout.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
    running egg_info
    writing pygraphviz.egg-info/PKG-INFO
    writing dependency_links to pygraphviz.egg-info/dependency_links.txt
    writing top-level names to pygraphviz.egg-info/top_level.txt
    reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no files found matching '*.png' under directory 'doc'
    warning: no files found matching '*.txt' under directory 'doc'
    warning: no files found matching '*.css' under directory 'doc'
    warning: no previously-included files matching '*~' found anywhere in distribution
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '.svn' found anywhere in distribution
    no previously-included directories found matching 'doc/build'
    writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
    copying pygraphviz/graphviz.i -> build/lib.linux-x86_64-3.8/pygraphviz
    copying pygraphviz/graphviz_wrap.c -> build/lib.linux-x86_64-3.8/pygraphviz
    running build_ext
    building 'pygraphviz._graphviz' extension
    creating build/temp.linux-x86_64-3.8
    creating build/temp.linux-x86_64-3.8/pygraphviz
    gcc -pthread -B /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/include/python3.8 -c pygraphviz/graphviz_wrap.c -o build/temp.linux-x86_64-3.8/pygraphviz/graphviz_wrap.o
    In file included from /usr/include/graphviz/gvc.h:17:0,
                     from pygraphviz/graphviz_wrap.c:2712:
    /usr/include/graphviz/types.h:49:20: fatal error: cgraph.h: No such file or directory
     #include <cgraph.h>
                        ^
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"'; __file__='"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-mu112lx1/install-record.txt --single-version-externally-managed --compile --install-headers /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/include/python3.8/pygraphviz Check the logs for full command output.

与康达：

(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ conda install -y -c anaconda pygraphviz

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.                                                                                                                                                                                                                                                                                                                                                                           failed                                                                                                                                                                                                                                                                                                                                                                                                                            

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - pygraphviz -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']

Your python: python=3.8

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

我的错误的根源是什么？ [注意我在linux机器上，不是mac os，我的mac phygraphviz工作正常]

我看到了以下相关问题：

但他们没有帮助，因为我无法运行 apt-get

(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ apt-get install python-dev graphviz libgraphviz-dev pkg-config
-bash: apt-get: command not found

编辑：

请注意，我也尝试使用 pip 安装 grapviz，但这并没有解决我的问题：

(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ pip install graphviz
Collecting graphviz
  Downloading graphviz-0.16-py2.py3-none-any.whl (19 kB)
Installing collected packages: graphviz
Successfully installed graphviz-0.16

编辑 2：

我发现graphviz在那里，但为什么找不到呢？

(metalearningpy1.7.1c10.2) miranda9~ $ rpm -qa |grep graphviz
graphviz-gd-2.30.1-21.el7.x86_64
graphviz-2.30.1-21.el7.x86_64
graphviz-devel-2.30.1-21.el7.x86_64

编辑 3：

我也希望它与 pip install -e . 一起使用，例如查看终极工具的安装 (https://github.com/brando90/ultimate-utils)：

由于对 pygraphviz 的依赖，您可能需要先安装 graphviz。接下来，安装graphviz。在 mac 上，brew 安装 graphviz。在 Ubuntu 上，sudo apt install graphviz。安装graphviz后，以可食用模式安装uutils，并使用pip安装它的所有依赖项：

pip install -e ~/ultimate-utils/ultimate-utils-proj-src

作为一个 gitissue：https://github.com/brando90/ultimate-utils/issues/6

【问题讨论】：

似乎答案将是由系统管理员在 HPC 中的所有节点上下载原始 graphviz[graphviz.org/download/]（不是同名的 pytorch 包......令人困惑！）。
我也希望它与pip install -e .一起工作
有人知道为什么使用conda-forge 有效吗？

标签： python python-3.x linux graphviz pygraphviz

【解决方案1】：

我能够在安装了graphviz-devel 的 CentOS 上编译它。最初我得到了与上面相同的错误，缺少cgraph.h，但通过向编译器提供头文件查找路径，我可以构建它：

CPPFLAGS="-I/usr/include/graphviz" pip install pygraphviz

当我尝试使用该软件包时，虽然我遇到了符号查找错误。所以最后我放弃了，选择了 conda。

【讨论】：

【解决方案2】：

嗯，看来使用conda-forge 有效！

(metalearningpy1.7.1c10.2) miranda9~ $ conda install -y -c conda-forge pygraphviz

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2

  added / updated specs:
    - pygraphviz


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libgcc-ng-9.3.0            |      h2828fa1_19         7.8 MB  conda-forge
    libgomp-9.3.0              |      h2828fa1_19         376 KB  conda-forge
    pygraphviz-1.7             |   py38h0d738da_0         125 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         8.3 MB

The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_19
  pygraphviz         conda-forge/linux-64::pygraphviz-1.7-py38h0d738da_0

The following packages will be UPDATED:

  certifi            pkgs/main::certifi-2020.12.5-py38h06a~ --> conda-forge::certifi-2020.12.5-py38h578d9bd_1
  libgcc-ng           pkgs/main::libgcc-ng-9.1.0-hdf63c60_0 --> conda-forge::libgcc-ng-9.3.0-h2828fa1_19

The following packages will be SUPERSEDED by a higher-priority channel:

  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge
  ca-certificates    pkgs/main::ca-certificates-2021.4.13-~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0
  openssl              pkgs/main::openssl-1.1.1k-h27cfd23_0 --> conda-forge::openssl-1.1.1k-h7f98852_0



Downloading and Extracting Packages
libgcc-ng-9.3.0      | 7.8 MB    | ##################################################################################################################################################################################################################################################################################################################################################################################### | 100% 
pygraphviz-1.7       | 125 KB    | ##################################################################################################################################################################################################################################################################################################################################################################################### | 100% 
libgomp-9.3.0        | 376 KB    | ##################################################################################################################################################################################################################################################################################################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

注意：

但是，请注意 pygraphviz 出于某种原因不建议使用 conda 安装其 pkg

我们建议避免使用 Anaconda 和 conda-forge 来安装 Graphviz 和 PyGraphviz。

但是由于 pip 对我来说一直失败 - 尽管在集群中安装了 graphviz - 请参阅 rpm 的输出：

[rundblom@vision-12 ~]$ rpm -qa |grep graphviz
graphviz-devel-2.30.1-21.el7.x86_64
graphviz-2.30.1-21.el7.x86_64
graphviz-gd-2.30.1-21.el7.x86_64

所以我知道使用 pip 有什么问题。我本来希望以通常的 HPC 方式加载模块，但现在这不是我的选择......

【讨论】：

有人知道为什么使用conda-forge 有效吗？