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#author("2025-10-29T06:23:52+00:00","default:sysosa","sysosa") #author("2025-10-29T06:35:03+00:00","default:sysosa","sysosa") 本家様 [[http://pymol.org/>+http://pymol.org/]] シュレーディンガー社様から販売されております. 一方でそのオープンソース版が存在していてここではそのオープンソース版を作ってみました. [[https://github.com/schrodinger/pymol-open-source>+https://github.com/schrodinger/pymol-open-source]] &size(10){有償版PyMOLはopen source版よりも機能が強化されてます}; &size(10){windowsOS向けopen source版は試してないです..}; ver3.1.0になったので改めて作ってみた. RHEL系はOSに直に作るのは難しいみたい. 直前の3.1.0a0ならいけたけど、今後はcondaの上で作る事にします. ubuntu22はPyMOLのWorkflowに載っているのですんなり行ける. けどubuntu24.04はテストrunが出来なかった. ***Rockylinux10 [#y99f7069] condaでコンパイル環境を作って実行したが「__cxa_call_terminate」のundefined symbolで起動しない. 恐らくcondaのコンパイル環境の問題っぽいのでOS上に作ってみた #code(nonumber){{ dnf install epel-release -y dnf config-manager --enable crb dnf install xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil -y dnf install https://dl.rockylinux.org/pub/rocky/9/devel/x86_64/os/Packages/g/glm-devel-0.9.9.8-3.el9.noarch.rpm -y dnf --enablerepo=devel install cmake netcdf-devel glew-devel libpng-devel libxml2-devel freetype-devel catch2-devel msgpack-devel python3-qt5-devel python3-devel python3-numpy -y wget -nv https://anaconda.org/schrodinger/collada2gltf/2.1.4/download/linux-64/collada2gltf-2.1.4-h6bb024c_0.tar.bz2 bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf - -C /usr/local rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2 git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git cp -R mmtf-cpp/include/mmtf* /usr/local/include rm -rf mmtf-cpp cd /apps/src/ git clone https://github.com/schrodinger/pymol-open-source cd pymol-open-source/ python3 setup.py install --prefix=/apps/pymol }} 修正「/apps/pymol/bin/pymol」 #code(nonumber){{ exec "/usr/bin/python3" "/usr/local/lib/python3.12/site-packages/pymol/__init__.py" "$@" exec "/usr/bin/python3" "/apps/pymol/lib64/python3.12/site-packages/pymol/__init__.py" "$@" }} /apps/modulefiles/pymol #code(nonumber){{ #%Module1.0 set root /apps/pymol prepend-path PATH $root/bin prepend-path PYTHONPATH $root/lib64/python3.12/site-packages }} ***Rockylinux9 [#h332c459] 既定のpythonは3.9 で gcc は gcc-11.5 #code(nonumber){{ (OSパッケージの追加インストールと関連アプリのインストール) dnf groupinstall "Development Tools" -y dnf install epel-release -y dnf install xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil -y dnf --enablerepo=devel install cmake netcdf-devel glew-devel glm-devel libpng-devel libxml2-devel freetype-devel catch2-devel msgpack-devel -y wget -nv https://anaconda.org/schrodinger/collada2gltf/2.1.4/download/linux-64/collada2gltf-2.1.4-h6bb024c_0.tar.bz2 bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf - -C /usr/local rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2 git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git cp -R mmtf-cpp/include/mmtf* /usr/local/include rm -rf mmtf-cpp/ (pyenv-anacondaの敷設) git clone https://github.com/yyuu/pyenv.git /apps/pyenv export PYENV_ROOT=/apps/pyenv export PATH=$PYENV_ROOT/bin:$PATH pyenv install miniforge3-25.3.1-0 }} #code(nonumber){{ [root@rockylinux9 ~]# source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profile.d/conda.sh [root@rockylinux9 ~]# conda create -n pymol-open-source python=3.10 openldap pyqt qt biopython msgpack-python vtk-m=2.3=cuda* -y [root@rockylinux9 ~]# conda activate pymol-open-source (pymol-open-source) [root@rockylinux9 ~]# cd /apps/src/ (pymol-open-source) [root@rockylinux9 src]# git clone https://github.com/schrodinger/pymol-open-source (pymol-open-source) [root@rockylinux9 src]# cd pymol-open-source/ (pymol-open-source) [root@rockylinux9 pymol-open-source]# }} ここで vtk-m を有効にするためにちょいとソースコードを修正します #code(diff,nonumber){{ diff --git a/layer0/ContourSurf.cpp b/layer0/ContourSurf.cpp index 143ce83a..380fcf04 100644 --- a/layer0/ContourSurf.cpp +++ b/layer0/ContourSurf.cpp @@ -82,7 +82,7 @@ using ::copysign; #include <vtkm/Version.h> #include <vtkm/cont/DataSetBuilderUniform.h> -#include <vtkm/filter/Contour/Contour.h> +#include <vtkm/filter/contour/Contour.h> #include <cassert> #include <set> }} その上で #code(nonumber){{ (pymol-open-source) [root@rockylinux9 pymol-open-source]# (pymol-open-source) [root@rockylinux9 pymol-open-source]# INCFLAGS="-I/apps/pyenv/versions/miniforge3-25.3.1-0/envs/pymol-open-source/include/vtkm-2.3" \ pip install --prefix=/apps/pymol --config-settings use-vtkm=2.3 --config-settings use-openmp=true . (pymol-open-source) [root@rockylinux9 pymol-open-source]# }} EnvironmentModules は下記になる. 「/apps/modulefiles/pymol」 #code(nonumber){{ #%Module1.0 set root /apps/pymol prepend-path PATH $root/bin prepend-path PYTHONPATH $root/lib/python3.10/site-packages }} &ref(2025y09m16d_040350139.png,nolink); ***Rockylinux8 [#o04b017b] condaで仮想環境を作りpymolをコンパイルします。 #code(nonumber){{ (OSパッケージの追加インストールと関連アプリのインストール) dnf groupinstall "Development Tools" -y dnf install epel-release -y dnf install xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil gcc-toolset-11 -y dnf install --enablerepo=epel,devel cmake netcdf-devel glew-devel libpng-devel libxml2-devel freetype-devel catch-devel mmtf-cpp-devel -y dnf remove glm-devel -y dnf install https://dl.rockylinux.org/pub/rocky/9/devel/x86_64/os/Packages/g/glm-devel-0.9.9.8-3.el9.noarch.rpm -y wget -nv https://anaconda.org/schrodinger/collada2gltf/2.1.4/download/linux-64/collada2gltf-2.1.4-h6bb024c_0.tar.bz2 bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf - -C /usr/local rm -rf collada2gltf-2.1.4-h6bb024c_0.tar.bz2 git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git cp -R mmtf-cpp/include/mmtf* /usr/local/include rm -rf mmtf-cpp/ (pyenv-anacondaの敷設) git clone https://github.com/yyuu/pyenv.git /apps/pyenv export PYENV_ROOT=/apps/pyenv export PATH=$PYENV_ROOT/bin:$PATH pyenv install miniforge3-25.3.1-0 }} #code(nonumber){{ [root@rockylinux8 ~]# source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profile.d/conda.sh [root@rockylinux9 ~]# conda create -n pymol-open-source python=3.10 openldap pyqt qt biopython msgpack-python vtk-m=2.3=cuda* -y [root@rockylinux8 ~]# conda activate pymol-open-source (pymol-open-source) [root@rockylinux8 ~]# cd /apps/src/ (pymol-open-source) [root@rockylinux8 src]# git clone https://github.com/schrodinger/pymol-open-source (pymol-open-source) [root@rockylinux8 src]# cd pymol-open-source/ (pymol-open-source) [root@rockylinux8 pymol-open-source]# }} vtk-m を有効にしたいのですが、ソースコード側でタイポがあるのでちょいと修正 #code(nonumber){{ (pymol-open-source) [root@rockylinux8 pymol-open-source]# vi layer0/ContourSurf.cpp #include <vtkm/filter/Contour/Contour.h> ↓ #include <vtkm/filter/contour/Contour.h> }} その上で #code(nonumber){{ (pymol-open-source) [root@rockylinux8 pymol-open-source]# source scl_source enable gcc-toolset-11 (pymol-open-source) [root@rockylinux8 pymol-open-source]# INCFLAGS="-I/apps/pyenv/versions/miniforge3-25.3.1-0/envs/pymol-open-source/include/vtkm-2.3" \ pip install --prefix=/apps/pymol --config-settings use-vtkm=2.3 --config-settings use-openmp=true . (pymol-open-source) [root@rockylinux8 pymol-open-source]# conda deactivate [root@rockylinux8 pymol-open-source]# }} EnvironmentModules は下記のようにします /apps/modulefiles/pymol #code(nonumber){{ #%Module1.0 prepend-path PATH /apps/pymol/bin prepend-path PYTHONPATH /apps/pymol/lib/python3.10/site-packages }} これで「module use /apps/modulefiles」「module load pymol」として「pymol」で起動します &ref(2025y10m29d_152254985.png,nolink); ***ubuntu24.04 [#z3365d01] Python 3.12.3 gcc 13.3.0 #code(nonumber){{ (準備) apt-get update apt-get install catch2 cmake libfreetype6-dev libglew-dev libglm-dev libmsgpack-dev libnetcdf-dev libpng-dev libxml2-dev python-is-python3 \ python3-biopython python3-dev python3-setuptools python3-numpy python3-pip git build-essential python3-qtpy -y wget -nv https://anaconda.org/schrodinger/collada2gltf/2.1.4/download/linux-64/collada2gltf-2.1.4-h6bb024c_0.tar.bz2 bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf - -C /usr/local git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git cp -R mmtf-cpp/include/mmtf* /usr/local/include }} っで構築 #code(nonumber){{ root@ubuntu22:~# mkdir -p /apps/src ; cd /apps/src root@ubuntu22:/apps/src# git clone https://github.com/schrodinger/pymol-open-source root@ubuntu22:/apps/src# cd pymol-open-source/ root@ubuntu22:/apps/src/pymol-open-source# pip install -v --prefix=/apps/PyMOL . }} テスト確認を行ってみたが、「catch2/catch.hpp」が存在しないと言われてエラーになる. testing=Trueで求められる項目がコンパイルできないみたい. #code(nonumber){{ rm -rf build/ pip install -v --config-settings testing=True --prefix=/apps/PyMOL '.[dev]' (途中でコンパイルエラー) export PATH=/apps/PyMOL/local/bin:$PATH export PYTHONPATH=/apps/PyMOL/local/lib/python3.12/dist-packages pymol -ckqy testing/testing.py --run all }} environment-modules 「/apps/modulefiles/PyMOL」 #code(nonumber){{ #%Module1.0 prepend-path PATH /apps/PyMOL/local/bin prepend-path PYTHONPATH /apps/PyMOL/local/lib/python3.12/dist-packages }} &ref(2025y02m01d_195740885.png,nolink); もし「&color(red){ERROR: Cannot uninstall numpy 1.26.4, RECORD file not found. Hint: The package was installed by debian};」と表示されたら、OS提供の python3-numpy が原因でこれを除くといいみたい &size(10){ただ、OS提供のパッケージなので影響があるかもしれない.. pyenv/anaconda で conda で用意した方がいいのかも}; ***ubuntu22.04 [#ae15f725] Python 3.10.12 gcc 11.4.0 #code(nonumber){{ apt-get update apt-get --no-install-recommends install catch2 cmake libfreetype6-dev libglew-dev libglm-dev libmsgpack-dev libnetcdf-dev libpng-dev libxml2-dev python-is-python3 \ python3-biopython python3-dev python3-setuptools python3-numpy python3-pip git build-essential python3-qtpy -y wget -nv https://anaconda.org/schrodinger/collada2gltf/2.1.4/download/linux-64/collada2gltf-2.1.4-h6bb024c_0.tar.bz2 bzip2 -cd collada2gltf-2.1.4-h6bb024c_0.tar.bz2 | tar xf - -C /usr/local git clone --depth 1 https://github.com/rcsb/mmtf-cpp.git cp -R mmtf-cpp/include/mmtf* /usr/local/include pip install --upgrade pip root@ubuntu22:~# mkdir -p /apps/src ; cd /apps/src root@ubuntu22:/apps/src# git clone https://github.com/schrodinger/pymol-open-source root@ubuntu22:/apps/src# cd pymol-open-source/ root@ubuntu22:/apps/src/pymol-open-source# pip install -v --prefix=/apps/PyMOL . (テスト確認) rm -rf build/ pip install -v --config-settings testing=True --prefix=/apps/PyMOL '.[dev]' export PATH=/apps/PyMOL/local/bin:$PATH export PYTHONPATH=/apps/PyMOL/local/lib/python3.10/dist-packages pymol -ckqy testing/testing.py --run all }} environment-modules 「/apps/modulefiles/PyMOL」 #code(nonumber){{ #%Module1.0 prepend-path PATH /apps/PyMOL/local/bin prepend-path PYTHONPATH /apps/PyMOL/local/lib/python3.10/dist-packages }} &ref(2025y02m01d_053045320.png,nolink);
