本家様 https://bio3d.colorado.edu/PEET/

imodのetomoからコールすることが可能なのでGUIで運転できます.
あとpeetはMatlabで書かれていて、そのバイナリーが提供されている. なのでMatlab runtimeを用意すれば動きます

入手

https://bio3d.colorado.edu/ftp/PEET/から
「linux/Particle_1.18.1_linux.sh」(24MB)

Matlab-runtimeの「linux/ParticleRuntimeR2023b_linux.tgz」(4.4GB)
を入手します

展開

[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.1 (Blue Onyx)
 
[root@rockylinux9 ~]# cd /apps/
 
[root@rockylinux9 apps]# bash src/Particle_1.18.1_linux.sh --help
 
This self-extracting installer will install PEET in a specified location
(default: /usr/local/) and configure startup files on Linux or Windows.
(The installed package  will be named Particle). Available options which
can enterred on the command line after the installer name are:
 
  --dir dir      Install or extract to dir (default = /usr/local). This
                 directory must exist and you must have write permission.
 
  -e, --extract  Extract the compressed package (only). Do not install.
 
  --script dir   Place the PEET startup scripts in directory dir
                 (default = /etc/profile.d).
 
  --skip         Skip copying or modifying system-wide startup scripts.
 
  --debian       Modify /etc/csh.cshrc and /etc/bash.bashrc instead of copying
                 startup scripts to /etc/profile.d. This option is set
                 automatically for Ubuntu versions prior to 10.
 
  -y, --yes      Do not prompt for confirmation.
 
  -?, -h, --help Print this help message
 
Long form (--) options my be abbreviated by their unique prefixes.
 
[root@rockylinux9 apps]#

インストールはimodと同じ感覚かな

[root@rockylinux9 apps]# bash src/Particle_1.15.1a_linux.sh --dir /apps --script /apps
 
This script will:
  remove any prior version and install PEET in /apps
  modify install dir in /apps/Particle/Particle.csh
  modify install dir in /apps/Particle/Particle.sh
  modify runtime dir in particle.cfg
  copy /apps/Particle/Particle.csh to /apps
  copy /apps/Particle/Particle.sh to /apps
 
Add the option --h to see a list of available alternatives.
 
Okay to proceed (y/n)? [n]: y
Extracting Particle_1.18.1_linux.tgz...
Installing...
Modifying install dir in /apps/Particle/Particle.csh
Modifying install dir in /apps/Particle/Particle.sh
Modifying runtime dir in particle.cfg
Copying /apps/Particle/Particle.csh to /apps
Copying /apps/Particle/Particle.sh to /apps
 
[root@rockylinux9 apps]# 
 
[root@rockylinux9 apps]# cat Particle.sh
#
# Set the location of the Particle directory
#
export PARTICLE_DIR=/apps/Particle
export PATH="$PARTICLE_DIR/bin:$PATH"
 
# Set MANPATH
if [ -z "${MANPATH}" ]
then
  export MANPATH="$PARTICLE_DIR/man:$(manpath)"
else
  export MANPATH="$PARTICLE_DIR/man:${MANPATH}"
fi
[root@rockylinux9 apps]#

「Particle.sh」は使わず、これと同等の Environment-modules を作って代替します。

次にMatlab-runtimeを展開します

まずは確認

[root@rockylinux9 apps]# tar tvf src/ParticleRuntimeR2023b_linux.tgz | head
drwxr-xr-x root/root         0 2024-08-04 09:48 ParticleRuntime/
drwxr-xr-x root/root         0 2024-08-04 09:48 ParticleRuntime/R2023b/
drwxr-xr-x root/root         0 2024-08-04 09:48 ParticleRuntime/R2023b/sys/
drwxr-xr-x root/root         0 2024-08-04 09:48 ParticleRuntime/R2023b/sys/opengl/
drwxr-xr-x root/root         0 2024-08-04 09:48 ParticleRuntime/R2023b/sys/opengl/lib/
drwxr-xr-x root/root         0 2024-08-04 09:48 ParticleRuntime/R2023b/sys/opengl/lib/glnxa64/
lrwxrwxrwx root/root         0 2023-08-02 03:55 ParticleRuntime/R2023b/sys/opengl/lib/glnxa64/libGLU.so.1 -> libGLU.so.1.3.1
-r--r--r-- root/root   3150040 2023-08-02 03:55 ParticleRuntime/R2023b/sys/opengl/lib/glnxa64/libGLU.so.1.3.1
-r--r--r-- root/root      1761 2023-08-02 03:55 ParticleRuntime/R2023b/sys/opengl/lib/glnxa64/libGLU.rights
lrwxrwxrwx root/root         0 2023-08-02 03:54 ParticleRuntime/R2023b/sys/opengl/lib/glnxa64/libGL.so.1 -> libGL.so.1.6.0
[root@rockylinux9 apps]#

ParticleRuntimeが親フォルダになるようなので、このまま /apps の直下に配置させます

[root@rockylinux9 apps]# tar xf src/ParticleRuntimeR2023b_linux.tgz

EnvironmentModules

そして EnvironmentModules は

[root@rockylinux9 ~]# vi /apps/modulefiles/PEET
#%Module1.0
 
puts stdout "bash /apps/local/bin/matlab-mkdir;"
 
set    PARTICLE  /apps/Particle
 
setenv PARTICLE_DIR  $PARTICLE
prepend-path PATH    $PARTICLE/bin
prepend-path MANPATH $PARTICLE/man
 
[root@rockylinux9 ~]#
rm -rf /apps/Particle/Particle.csh /apps/Particle/Particle.sh

メモ

imodのetomoと連携させるならimodのEnvironmentModules に加えた方がいいのかも

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