Ubuntuでpipを使ってgmshをインストールする方法を紹介する
| OS | Windows 10 Home 64bit |
| Ubuntu | 20.04 LTS |
| OpenFOAM | v2006 |
はじめに
↓Ubuntuのインストールはについてはこちら
UbuntuにデフォルトでインストールされているPythonはOSのシステムを機能させるためのものなので，そのまま使うことはできない
↓自分で使うためのPythonのインストールはこれ
それではいってみよう
gmshのインストール
今回はデスクトップに作ったgmshというフォルダーにgmshを使うための仮想環境を構築する
次のコマンドを実行して，Pythonの仮想環境（.gmshvenv）を作成しする
cd /mnt/c/Users/mtkbirdman/Desktop/gmsh
python3 -m venv .gmshvenv
. .gmshvenv/bin/activate:/mnt/c/Users/mtkbirdman/Desktop/gmsh$ python3 -m venv .gmshvenv
:/mnt/c/Users/mtkbirdman/Desktop/gmsh$ . .gmshvenv/bin/activategmshはUbuntu上でpipを使ってインストールすることができる
gmsh
Gmsh is a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities.
pypi.org
次のコマンドを実行して，pipを使ってgmshをインストールする
pip install --upgrade pip
pip install --upgrade gmsh(.gmshvenv) :/mnt/c/Users/mtkbirdman/Desktop/gmsh$ pip install --upgrade pip
Requirement already satisfied: pip in ./.gmshvenv/lib/python3.10/site-packages (22.2.2)
Collecting pip
Using cached pip-22.3-py3-none-any.whl (2.1 MB)
Installing collected packages: pip
Attempting uninstall: pip
Found existing installation: pip 22.2.2
Uninstalling pip-22.2.2:
Successfully uninstalled pip-22.2.2
Successfully installed pip-22.3
(.gmshvenv) :/mnt/c/Users/mtkbirdman/Desktop/gmsh$ pip list
Package Version
---------- -------
pip 22.2.2
setuptools 63.2.0(.gmshvenv) :/mnt/c/Users/mtkbirdman/Desktop/gmsh$ pip install --upgrade gmsh
Collecting gmsh
Downloading gmsh-4.10.5-py2.py3-none-manylinux1_x86_64.whl (38.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.3/38.3 MB 10.4 MB/s eta 0:00:00
Installing collected packages: gmsh
Successfully installed gmsh-4.10.5
(.gmshvenv) :/mnt/c/Users/mtkbirdman/Desktop/gmsh$ pip list
Package Version
---------- -------
gmsh 4.10.5
pip 22.3
setuptools 63.2.0そのほか必要なライブラリをインストールする
sudo apt -y install libglu1 libxcursor-dev libxft2 libxinerama1 libfltk1.3-dev libfreetype6-dev libgl1-mesa-dev libocct-foundation-dev libocct-data-exchange-dev (.gmshvenv) :/mnt/c/Users/mtkbirdman/Desktop/gmsh$ sudo apt-get -y install libglu1 libxcursor-dev libxft2 libxinerama1 libfltk1.3-dev libfreetype6-dev libgl1-mesa-dev libocct-foundation-dev libocct-data-exchange-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'libglu1-mesa' instead of 'libglu1'
libxft2 is already the newest version (2.3.3-0ubuntu1).
libxinerama1 is already the newest version (2:1.1.4-2).
libfreetype6-dev is already the newest version (2.10.1-2ubuntu0.2).
libfreetype6-dev set to manually installed.
libgl1-mesa-dev is already the newest version (21.2.6-0ubuntu0.1~20.04.2).
The following additional packages will be installed:
fltk1.3-doc fluid libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfreeimage-dev libfreeimage3 libglu1-mesa-dev libilmbase24 libjxr0 libocct-data-exchange-7.3 libocct-foundation-7.3
libocct-modeling-algorithms-7.3 libocct-modeling-algorithms-dev libocct-modeling-data-7.3 libocct-modeling-data-dev libocct-ocaf-7.3 libocct-ocaf-dev libocct-visualization-7.3 libocct-visualization-dev libopenexr24 libraw19 libtbb2
libxfixes-dev libxmu-dev libxmu-headers
Suggested packages:
libcairo2-dev libjpeg-dev libxinerama-dev
The following NEW packages will be installed:
fltk1.3-doc fluid libfltk-cairo1.3 libfltk-forms1.3 libfltk-gl1.3 libfltk-images1.3 libfltk1.3 libfltk1.3-dev libfreeimage-dev libfreeimage3 libglu1-mesa libglu1-mesa-dev libilmbase24 libjxr0 libocct-data-exchange-7.3
libocct-data-exchange-dev libocct-foundation-7.3 libocct-foundation-dev libocct-modeling-algorithms-7.3 libocct-modeling-algorithms-dev libocct-modeling-data-7.3 libocct-modeling-data-dev libocct-ocaf-7.3 libocct-ocaf-dev
libocct-visualization-7.3 libocct-visualization-dev libopenexr24 libraw19 libtbb2 libxcursor-dev libxfixes-dev libxmu-dev libxmu-headers
0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded.
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OSError: libGLU.so.1:
Hi, I have followed the instructions for fenics on Docker. But when I was trying to run my host python code, it came up with the following error: OSError ...
fenicsproject.discourse.group
インストールできたか確かめる
gmsh -version(.gmshvenv) :/mnt/c/Users/mtkbirdman/Desktop/gmsh$ gmsh -version
4.10.5これでgmshのインストールは完了である
まとめ
Ubuntuでpipを使ってgmshをインストールすることができた
Ubuntuでpipを使ってgmshをインストールする方法を紹介する
gmshのインストール
gmshは，Ubuntu上でpipを使ってインストールすることができる
≫gmsh · PyPI
Ubuntuにはデフォルトでpythonがインストールされているが，このpythonを使ってインストールしてもうまくいかなかった
具体的にいうと，pythonのプログラム内でimport gmshを実行するとModuleNotFoundというエラーが出た
≫pipでモジュールを確かにインストールしたはずがModuleNotFoundErrorと出た時の解決法初心者的理解 - Qiita
原因を調べてみると，sys.pathに含まれているディレクトリにgmsh-4.6.0.dist-infoしかインストールされておらず，肝心のgmshがインストールできていなかった．(原因は不明)
途方に暮れてLinuxに造詣の深い友人に相談したところ，pythonはバージョンの違いにうるさく，ちょっとしたバージョンの違いでこういうエラーが起こると教えてもらった
というわけで，pythonの仮想環境を構築することにした
Pythonの仮想環境を構築する
仮想環境ってなんぞやとなったので調べてみると，次のような記事を見つけた
まとめると，
・pythonはバージョンが違うと動かないことがよくある
・PCに1つのバージョンのpythonしか入っていないと，いろいろなバージョンのpythonで書かれたプログラムに対応できない
・Pythonのライブラリを大量にインストールすると，それらが干渉しあって悪さすることがある
→作業をするディレクトリごとに適したバージョンのPythonを設定し，必要な分だけのライブラリをインポートした環境(=仮想環境)を作ろう！
ということらしい．
面倒くさい．FortranならgfortranをインストールしてPATHを設定するだけなのに
仮想環境を設定するために，次のサイトを参考にpyenvをインストールした
仮想環境でgmshをインストールする
実際に仮想環境を構築してgmshをインストールしてみる
≫pyenvのインストール、使い方、pythonのバージョン切り替えできない時の対処法 - Qiita
まず，pyenvでインストールできるPythonのバージョンを確認する
/test$ pyenv install --list
Available versions:
2.1.3
2.2.3
(中略)
3.7.8
3.8.0
3.8-dev
3.8.1
3.8.2
3.8.3
(後略)むちゃくちゃ長いリストが表示されるが，ここでは3.8.3をインストールする
ところが次のようなエラーが出てきた
/test$ pyenv install 3.8.3
Downloading Python-3.8.3.tar.xz...
-> https://www.python.org/ftp/python/3.8.3/Python-3.8.3.tar.xz
error: failed to download Python-3.8.3.tar.xz
BUILD FAILED (Ubuntu 20.04 using python-build 1.2.19-5-g0164e2bd)
/test$わけがわからない
Linuxに造詣の深い友人のアドバイスをもとに，-vオプションをつけてやってみる
≫install コマンド – ファイルの権限などを設定してコピー _ Linuxコマンド.NET
/test$ pyenv install 3.8.3 -v
/tmp/python-build.20200711221713.915 /mnt/c/Users/mtk_m/OneDrive/Documents/OpenFOAM/test
Downloading Python-3.8.3.tar.xz...
-> https://www.python.org/ftp/python/3.8.3/Python-3.8.3.tar.xz
aria2c: /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /lib/x86_64-linux-gnu/libaria2.so.0)
error: failed to download Python-3.8.3.tar.xz
BUILD FAILED (Ubuntu 20.04 using python-build 1.2.19-5-g0164e2bd)
/test$aria2c: /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /lib/x86_64-linux-gnu/libaria2.so.0) というエラー文が出てきた
なにやらC++に関するGLIBCXX_3.4.26というファイルがないらしい
≫libstdc++.so.6_ version `GLIBCXX_3.4.22' not found - Qiita
このサイトを参考に，確認してみる
/test$ strings /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libs
tdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_DEBUG_MESSAGE_LENGTHたしかにGLIBCXX_3.4.22までしかない
さらに調べてみると，同じようなエラーで苦しんで，解決した人を発見した
≫[OpenFOAM.com] openfoam v2006 wsl2 ubuntu 20.04 GLIBCXX_3.4.26 not found -- CFD Online Discussion Forums
解決策は次の通り
≫GLIBCXX_3.4.26 not found in RCall - Usage - JuliaLang
GLIBCXX_3.4.26がないなら別の場所からコピーして持ってくればいいじゃない，という解決策．それでいいのかLinux
/usr/lib/x86_64-linux-gnu/の方を調べてみると普通にGLIBCXX_3.4.28まであったので，これをいただいてくることにした
/test$ strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28次のコマンドを実行する
cp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/確認してみる
/test$ strings /opt/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6 | grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_3.4.26
GLIBCXX_3.4.27
GLIBCXX_3.4.28
GLIBCXX_DEBUG_MESSAGE_LENGTH成功した
これでようやくpython3.8.3をインストールできる
/test$ pyenv install 3.8.3
(略)
/test$ pyenv local 3.8.3
/test$ python --version
Python 3.8.3というわけで，仮想環境が構築できた
最後に，gmshをpipでインストールする
≫gmsh · PyPI
/test$ pip install --upgrade gmsh
Collecting gmsh
Using cached https://files.pythonhosted.org/packages/1d/ed/372df81ed068fbee7dfbdcca391168dcc30e34b1bd016066625330d9362a/gmsh-4.6.0.tar.gz
Installing collected packages: gmsh
Running setup.py install for gmsh ... done
Successfully installed gmsh-4.6.0
WARNING: You are using pip version 19.2.3, however version 20.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
/test$本当にできているか確認してみる
/test$ gmsh -version
4.6.0
/test$きちんと最新バージョンがインストールできている
Pythonのインタラクティブシェルでgmshをimportしてみる
/test$ python
Python 3.8.3 (default, Jul 11 2020, 22:44:23)
[GCC 6.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import gmsh
>>> exit()
/test$問題なくimportできた
これでgmshのインストールは完了である
まとめ
Ubuntuでpipを使ってgmshをインストールすることができた
まあこの記事で大事なことは「持つべきものはLinuxに造詣の深い友人」ってこと
ありがとう
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