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#author("2023-09-19T13:44:48+00:00","default:sysosa","sysosa") #author("2023-09-19T14:22:48+00:00","default:sysosa","sysosa") &size(10){過去記事[[xray/Phenix200716]]}; 本家様 [[https://www.phenix-online.org/>+https://www.phenix-online.org/]] リリース状況 [[https://phenix-online.org/download/nightly_builds.cgi>+https://phenix-online.org/download/nightly_builds.cgi]] 最近だとcryoem系も対応されているみたい. ここではphenixをCentOS8にインストールしてみた. [[Phenix/cryoFIT]] ***入手 [#z47fcd22] アプリケーションを入手するためにはユーザ登録が必要で、[[http://www.phenix-online.org/phenix_request/index.cgi>+http://www.phenix-online.org/phenix_request/index.cgi]]からその登録を行う 登録が完了すると登録したメールアドレスにログインユーザ名とパスワードが送られる。 それを使って、ダウンロードページ[[https://www.phenix-online.org/download/>+https://www.phenix-online.org/download/]]の &color(orangered){Download};リンクボタンを押下して認証を進めます。 ダウンロード可能なファイルはLinux, macOS, windows毎に用意されている。 ここでは「&color(magenta){phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6.tar.gz};」を取得した ***展開 [#ked4eef3] 取得したファイルをまずは展開します #code(nonumber){{ [root@centos8 ~]# cd /apps/src/ [root@centos8 src]# tar xzf phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6.tar.gz [root@centos8 src]# cd phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6/ [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# }} っで、普通ならinstallコマンドを実行すればそれで終わりなのだが、、、 #code(nonumber){{ [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# ./install --prefix=/apps ./install: line 15: /usr/bin/python: No such file or directory [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# }} と無碍なく終わる. インストールスクリプトの中身を確認すると #code(nonumber){{ [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# cat install #!/bin/bash if [ -z "$PYTHON_EXE" ]; then PYTHON_EXE='/usr/bin/python' if [ -f "/usr/bin/python2.7" ]; then PYTHON_EXE='/usr/bin/python2.7' elif [ -f "/usr/bin/python2.6" ]; then PYTHON_EXE='/usr/bin/python2.6' elif [ -f "/usr/bin/python2" ]; then PYTHON_EXE='/usr/bin/python2' elif [ -f "./conda_base/bin/python" ]; then PYTHON_EXE='./conda_base/bin/python' fi fi unset CONDA_PREFIX $PYTHON_EXE ./bin/install.py $@ [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# }} とある. 現状まだpython3には対応されていないご様子. CentOS8のpython2.7環境は標準では用意されていないので、まずはそこから準備します #code(nonumber){{ [root@centos8 ~]# dnf install python2 }} その上でインストールを試みると #code(nonumber){{ [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# ./install --prefix=/apps ========================================================================== Phenix Installation version: 1.18.2-3874 machine type: intel-linux-2.6-x86_64 OS version: 4.18.0-193.6.3.el8_2.x86_64 destination: /apps/phenix-1.18.2-3874 # of processors: 4 ========================================================================= /usr/bin/env: ‘python’: No such file or directory Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/apps/src/phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 200, in install self.install_from_binary() File "/apps/src/phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 335, in install_from_binary subprocess.check_call([unpack_cmd]) File "/usr/lib64/python2.7/subprocess.py", line 190, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['./bin/conda-unpack']' returned non-zero exit status 127 [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# }} と言われてしまう... 「&color(red){/usr/bin/env: ‘python’: No such file or directory};」 なので、python は python2 を示すように調整する。使うのは「alternatives」コマンド #code(nonumber){{ [root@centos8 ~]# alternatives --config python There are 3 programs which provide 'python'. Selection Command ----------------------------------------------- *+ 1 /usr/libexec/no-python 2 /usr/bin/python3 3 /usr/bin/python2 Enter to keep the current selection[+], or type selection number: 3 <--[3]と入力 [root@centos8 ~]# [root@centos8 ~]# python -V Python 2.7.17 [root@centos8 ~]# }} このように「python」と打てば python2 が対応するようになる. 再びインストールを試みる #code(nonumber){{ [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# rm -rf /apps/phenix-1.18.2-3874/ <-- 一度削除する [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# ./install --prefix=/apps : : ========================================================================== PHENIX installation complete ---------------------------- You can begin using PHENIX now by setting your environment with the 'source' command: csh users: source /apps/phenix-1.18.2-3874/phenix_env.csh bash users: source /apps/phenix-1.18.2-3874/phenix_env.sh To use PHENIX, go to a work directory and type: phenix You may wish to put the source statement in your .cshrc or .bashrc file. ************************** * Installation complete! * ************************** [root@centos8 phenix-installer-1.18.2-3874-intel-linux-2.6-x86_64-centos6]# }} っでうまく行ったみたい. ***ubuntu20.04の上にphenix [#l39f486d] とある理由でsingularityの中で作ることになった っで製作 #code(nonumber){{ illya@ubuntu:~$ singularity build --sandbox ubuntu20.04 docker://ubuntu:20.04 illya@ubuntu:~$ illya@ubuntu:~$ singularity shell --writable --fakeroot --bind /Public/:/mnt/ ./ubuntu20.04/ Singularity> id uid=0(root) gid=0(root) groups=0(root) Singularity> Singularity> pwd /root Singularity> apt update Singularity> apt install xserver-xorg Singularity> apt install locales Singularity> apt install vim Singularity> mkdir /apps Singularity> cp /mnt/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6.tar.gz . Singularity> tar xf phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6.tar.gz Singularity> cd phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6 Singularity> ./install --prefix=/apps Singularity> vi /etc/locale.gen (en_GBの全てとen_US.UTF-8を有効にします) Singularity> locale-gen Generating locales (this might take a while)... en_GB.ISO-8859-1... done en_GB.ISO-8859-15... done en_GB.UTF-8... done en_US.UTF-8... done Generation complete. Singularity> Singularity> exit exit illya@ubuntu:~$ illya@ubuntu:~$ cat ubuntu20.04/apps/phenix-1.20.1-4487/phenix_env.sh >> ubuntu20.04/environment illya@ubuntu:~$ singularity build --fakeroot ubuntu20.04-phenix-1.20.1.sif ubuntu20.04/ }} 使う #code(nonumber){{ illya@ubuntu:~$ singularity exec ./ubuntu20.04-phenix-1.20.1.sif phenix }} ***rockylinux9.2のSingularityでphenix [#w8726ec0] #code(nonumber){{ [illya@slurm ~]$ singularity build --sandbox phenix docker://rockylinux:9.2 [illya@slurm ~]$ vi phenix.def BootStrap: docker From: rockylinux:9.2 [illya@slurm ~]$ singularity shell --writable --fakeroot -B /Public:/mnt phenix Singularity> id uid=0(root) gid=0(root) groups=0(root) Singularity> dnf install libXxf86vm langpacks-en Singularity> cd /usr/local Singularity> tar xf /mnt/em/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6.tar.gz Singularity> cd ./phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/ Singularity> ./install --prefix=../ Singularity> cd .. Singularity> rm -rf phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6 Singularity> exit %post dnf install libXxf86vm langpacks-en -y cd /usr/local curl -O http://c/em/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6.tar.gz <-- 内部に建てたemリポジトリ tar xf phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6.tar.gz cd ./phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/ ./install --prefix=../ cd .. rm -rf phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6 rm -rf phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6.tar.gz [illya@slurm ~]$ singularity shell phenix Singularity> export LC_ALL=C %environment export PHENIX=/usr/local/phenix-1.20.1-4487 export PHENIX_VERSION=1.20.1-4487 export PATH=/usr/local/phenix-1.20.1-4487/build/bin:$PATH [illya@slurm ~]$ [illya@slurm ~]$ singularity build --fakeroot phenix.sif phenix.def [illya@slurm ~]$ [illya@slurm ~]$ singularity exec ./phenix.sif phenix }}
