Scipion をテンプレートにして作成
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開始行:
本家様 [[http://scipion.i2pc.es/>+http://scipion.i2pc.es/]]
scipionがver3になりました
ここでは RockyLinux9 にscipion3を入れてます
***下準備 [#ea586f16]
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.2 (Blue Onyx)
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 535.54.03...
GCC version: gcc version 11.3.1 20221121 (Red Hat 11.3.1...
[root@rockylinux9 ~]# ls -ld /usr/local/cuda*
lrwxrwxrwx. 1 root root 22 Sep 30 16:06 /usr/local/cud...
lrwxrwxrwx. 1 root root 25 Sep 30 16:06 /usr/local/cud...
drwxr-xr-x. 15 root root 4096 Sep 30 16:06 /usr/local/cud...
[root@rockylinux9 ~]# alternatives --list | grep cuda
cufile.json auto /usr/local/cuda-12.2/gds/...
cuda auto /usr/local/cuda-12.2
cuda-12 auto /usr/local/cuda-12.2
[root@rockylinux9 ~]# dnf install libzstd-devel hdf5-dev...
wget fftw-devel libti...
[root@rockylinux9 ~]#
(RHEL8系)
dnf install libzstd-devel hdf5-devel python3-devel pytho...
wget fftw-devel libtiff-devel java-1.8.0-openjdk-devel li...
}}
#code(nonumber){{
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f6...
[root@rockylinux9 ~]#
}}
***インストール [#l9bfe37e]
まずはconda環境を準備します. ここでは pyenv-anaconda3 環...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2023.07-2
pyenv global anaconda3-2023.07-2
export PATH=$PYENV_ROOT/versions/anaconda3-2023.07-2/bin:...
conda install conda-build=3.26.1
conda update conda -y
(既にpyenv-anaconda3環境があれば)
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
export PATH=$PYENV_ROOT/versions/anaconda3-2023.07-2/bin:...
}}
確認. 現在conda経由で提供しているpython実行環境は下記にな...
#code(nonumber){{
[root@rockylinux9 ~]# conda env list
# conda environments:
#
base /apps/pyenv/versions/anaconda3-2...
[root@rockylinux9 ~]#
}}
この環境リストにscipion実行環境を増やす形なのだが、まず「...
#code(nonumber){{
[root@rockylinux9 ~]# which pip
/apps/pyenv/versions/anaconda3-2023.07-2/bin/pip
[root@rockylinux9 ~]# pip install scipion-installer
}}
そしてコンパイル環境を整備してscipionを入れます
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/anacond...
[root@rockylinux9 ~]# which mpirun
/apps/pyenv/versions/anaconda3-2023.07-2/bin/mpirun
[root@rockylinux9 ~]# module load mpi/openmpi-x86_64
[root@rockylinux9 ~]# which mpirun
/usr/lib64/openmpi/bin/mpirun
[root@rockylinux9 ~]# python -m scipioninstaller -conda -...
:
:
------------------------------------
Scipion core successfully installed.
------------------------------------
________________________________________________________...
| ...
| Installation successfully finished!! Happy EM processin...
________________________________________________________...
You can launch Scipion using the launcher at: /apps/sci...
________________________________________________________...
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# conda env list
# conda environments:
#
base /apps/pyenv/versions/anaconda3-2...
scipion3 /apps/pyenv/versions/anaconda3-2...
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# /apps/scipion3/scipion3 config --ov...
:
:
Press <enter> to continue: <--- リター...
/apps/scipion3/config/hosts.conf hosts
* Creating configuration file: /apps/scipion3/config/host...
Please edit it to reflect the configuration of your system.
Checking paths in /apps/scipion3/config/scipion.conf ...
All seems fine with /apps/scipion3/config/scipion.conf
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# vi /apps/scipion3/config/scipion.conf
}}
「/apps/scipion3/config/scipion.conf」の末尾に下記を追加
#code(nonumber){{
CUDA = True
CUDA_BIN = /usr/local/cuda-12.2/bin
CUDA_LIB = /usr/local/cuda-12.2/lib64
MPI_BINDIR = /usr/lib64/openmpi/bin
MPI_LIBDIR = /usr/lib64/openmpi/lib
MPI_INCLUDE = /usr/include/openmpi-x86_64
OPENCV = False
}}
っで続き
#code(nonumber){{
[root@rockylinux9 ~]# conda activate scipion3
(scipion3) [root@rockylinux9 ~]# pip install scons
(scipion3) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# /apps/scipion3/scipion3 installp -p...
}}
***メモ [#efcf8d8f]
scipionのパッケージ置き場所 [[http://scipion.cnb.csic.es/...
***EnvironmentModules [#acac77da]
EnvironmentModules 向けに「/etc/modulefiles/scipion3」を...
#code(nonumber){{
#%Module1.0
set-alias scipion3 /apps/scipion3/scipion3
}}
***plug-in [#sff9a971]
scipionを起動して、「create project」でプロジェクトを作り...
&ref(2023y09m30d_175609262.png,nolink);
使用できるツールはインストール直後は「Xmipp3」由来のみです.
この他にもツールが搭載できる.
いったいどんなツールがこのscipionに追加できるかは scipion...
あるいはコマンドラインで「scipion3 installp --help」でも...
#code(nonumber){{
[root@rockylinux9 ~]# module load scipion3
[root@rockylinux9 ~]# scipion3 installp --checkUpdates
Scipion v3.1.0 - Eugenius
Available plugins: ([ ] not installed, [X] seems already ...
scipion-em-appion [ ]
scipion-em-aretomo [ ]
scipion-em-atomstructutils [ ]
scipion-em-atsas [ ]
scipion-em-bamfordlab [ ]
scipion-em-bsoft [ ]
scipion-em-ccp4 [ ]
scipion-em-chimera [ ]
scipion-em-cistem [ ]
scipion-em-continuousflex [ ]
scipion-em-cryoassess [ ]
scipion-em-cryodrgn [ ]
scipion-em-cryoef [ ]
scipion-em-cryosparc2 [ ]
scipion-em-dynamo [ ]
scipion-em-eman2 [ ]
scipion-em-emantomo [ ]
scipion-em-embuild [ ]
scipion-em-empiar [ ]
scipion-em-emready [ ]
scipion-em-emxlib [ ]
scipion-em-facilities [ ]
scipion-em-fsc3d [ ]
scipion-em-gautomatch [ ]
scipion-em-gctf [ ]
scipion-em-imagic [ ]
scipion-em-imod [ ]
scipion-em-isonet [ ]
scipion-em-localrec [ ]
scipion-em-locscale [ ]
scipion-em-modelangelo [ ]
scipion-em-motioncorr [ ]
scipion-em-novactf [ ]
scipion-em-phenix [ ]
scipion-em-prody [ ]
scipion-em-relion [ ]
scipion-em-reliontomo [ ]
scipion-em-repic [ ]
scipion-em-resmap [ ]
scipion-em-sidesplitter [ ]
scipion-em-sphire [ ]
scipion-em-spider [ ]
scipion-em-spoc [ ]
scipion-em-susantomo [ ]
scipion-em-tomo [ ]
scipion-em-tomo3d [ ]
scipion-em-tomotwin [ ]
scipion-em-tomoviz [ ]
scipion-em-topaz [ ]
scipion-em-warp [ ]
scipion-em-xmipp 23.7.0.0 [X]
scipion-em-xmipp2 [ ]
scipion-em-xmipptomo [ ]
[root@rockylinux9 ~]#
}}
&color(red){*};&size(10){これ以外にもbeta版とかがあり、そ...
例えば、scipionからrelionを実行したいなら、relionのplug-i...
しかし既にインストール済みのrelionがあって、そのバイナリ...
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-relion --noBin
(確認)
[root@s ~]# scipion3 installp --checkUpdates | grep relion
scipion-em-relion 3.1.2 [X]
(加えたこのpluginを削除したければ)
[root@s ~]# scipion3 uninstallp -p scipion-em-relion
}}
これでrelionへのpluginインターフェースは用意できました. ...
定義すべき環境変数は「scipion3 config -p <プログラム名>」...
#code(nonumber){{
[root@s ~]# scipion3 config -p relion
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'relion':
RELION_HOME = /apps/scipion/software/em/relion-3.1.2
RELION_CUDA_LIB = /usr/local/cuda/lib64
These variables can be added/edited in '/apps/scipion/con...
[root@s ~]#
}}
この場合、「&color(orangered){RELION_HOME};」と「&color(o...
それは「/apps/scipion/config/scipion.conf」で明記される必...
これで既にインストールされているrelionプログラムを使い回...
&size(10){その前に「scipion3 installb」でrelionのどのバー...
なので、
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
RELION_CUDA_LIB = /usr/local/cuda-11.2/lib64
RELION_CUDA_BIN = /usr/local/cuda-11.2/bin
RELION_HOME = /apps/relion-3.1.2
[root@s ~]#
}}
&size(10){実際には「RELION_CUDA_BIN」の塚も要求された};
その後scipionを再起動するとrelionの機能が追加されます
&ref(2021y07m08d_225847094.png,nolink);
***plug-in Gautomatch [#kb124d20]
次がGautomatchを入れてみる. これも既に手元にあって使える...
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-gautomatch --...
(確認)
[root@s ~]# scipion3 installp --checkUpdates | grep gauto...
scipion-em-gautomatch 3.0.14 [X]
(必要となる環境変数の確認)
[root@s ~]# scipion3 config -p gautomatch
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'gautomatch':
GAUTOMATCH_HOME = /apps/scipion/software/em/gautomatch-0.56
GAUTOMATCH = Gautomatch_v0.56_sm30-75_cu10.1
GAUTOMATCH_CUDA_LIB = /usr/local/cuda/lib64
These variables can be added/edited in '/apps/scipion/con...
(なので)
[root@s ~]# vi /apps/scipion/config/scipion.conf
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
（略
GAUTOMATCH_HOME = /apps/GCTF_Gautomatch_Cu10.1/
GAUTOMATCH = Gautomatch_v0.56_sm30-75_cu10.1
GAUTOMATCH_CUDA_LIB = /usr/local/cuda-10.2/lib64
[root@s ~]#
}}
これでscipionを起動します
&ref(2021y07m08d_230737299.png,nolink);
***plug-in Sphire [#e3ff7c9f]
このSphire Plug-inの中に[[crYOLO]]が入ってます.
っで
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-sphire --noBin
(必要となる環境変数の確認)
[root@s ~]# scipion3 config -p sphire
[root@s ~]# scipion3 config -p sphire
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'sphire':
CRYOLO_ENV_ACTIVATION_CPU = conda activate cryoloCPU-1.7.6
CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6
CRYOLO_GENERIC_MODEL = /apps/scipion/software/em/cryolo_m...
CRYOLO_GENERIC_DENOISED_MODEL = /apps/scipion/software/em...
JANNI_GENERIC_MODEL = /apps/scipion/software/em/janni_mod...
CRYOLO_NS_GENERIC_MODEL = /apps/scipion/software/em/cryol...
CRYOLO_CUDA_LIB = /usr/local/cuda/lib64
These variables can be added/edited in '/apps/scipion/con...
[root@s ~]#
}}
どうやらモデルがいるの指定もここでするみたい.
加えて「conda activate」でpython実行環境に移行するような...
#code(nonumber){{
[root@s ~]# conda env list |grep -i cryolo
crYOLO /apps/pyenv/versions/anaconda3-5...
[root@s ~]#
}}
なので「/apps/scipion/config/scipion.conf」は下記のように...
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
（略
CRYOLO_ENV_ACTIVATION = conda activate crYOLO
CRYOLO_GENERIC_MODEL = /apps/crYOLO/gmodel_phosnet_202005...
CRYOLO_GENERIC_DENOISED_MODEL = /apps/crYOLO/gmodel_phosn...
JANNI_GENERIC_MODEL = /apps/janni/gmodel_janni_20190703.h5
CRYOLO_NS_GENERIC_MODEL = /apps/crYOLO/gmodel_phosnet_neg...
CRYOLO_CUDA_LIB = /usr/local/cuda/lib64
}}
&color(red){*};&size(10){「CRYOLO_ENV_ACTIVATION_CPU 」は...
***plug-in Topaz [#r0ff80c8]
次にpickツールのTopazを入れてみる. 同じくバイナリーは既に...
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-topaz --noBin
[root@s ~]# scipion3 config -p topaz
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'topaz':
TOPAZ_ENV_ACTIVATION = conda activate topaz-0.2.4
These variables can be added/edited in '/apps/scipion/con...
[root@s ~]#
}}
condaで「topaz-0.2.4」なるpython実行環境をロードしている...
それを借用してみる
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
（略
TOPAZ_ENV_ACTIVATION = conda activate topaz
[root@s ~]#
}}
&color(red){*};&size(10){「module load topaz」とかでもい...
&ref(2021y07m09d_005654817.png,nolink);
***deepfinder [#oa7ddd96]
[[https://github.com/scipion-em/scipion-em-deepfinder>+ht...
「scipion3 installp --checkUpdates」には表示されていない...
バイナリーも一緒に入れるので、「--noBin」は付けない.
#code(nonumber){{
[root@s ~]# scipion3 installp -p https://github.com/scipi...
}}
これでdeepfinderのplug-inとバイナリー(プログラム)がインス...
次に、環境設定. 必要な環境変数を調べる
#code(nonumber){{
[root@s ~]# scipion3 config -p deepfinder
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'deepfinder':
DF_HOME = /apps/scipion/software/em/deepfinder-0.1
DF_ENV_ACTIVATION = conda activate deepfinder-0.1
These variables can be added/edited in '/apps/scipion/con...
[root@s ~]#
}}
環境変数として「DF_HOME」と「DF_ENV_ACTIVATION」が必要な...
plug-inの追加の際に、「--noBin」を付けないと、ここで提示...
確認のために、condaの環境リストを調べると
#code(nonumber){{
[root@s ~]# conda env list | grep deepfinder
deepfinder-0.1 /apps/pyenv/versions/anaconda3-5...
[root@s ~]#
}}
そして、バイナリーの存在を確認すると下記のようになっている.
#code(nonumber){{
[root@s ~]# ls -l /apps/scipion/software/em/deepfinder-0....
total 24
-rwxrwxr-x 1 root root 1021 May 20 19:03 annotate
-rwxrwxr-x 1 root root 1614 May 20 19:03 cluster
-rwxrwxr-x 1 root root 842 May 20 19:03 display
-rwxrwxr-x 1 root root 1554 May 20 19:03 generate_target
-rwxrwxr-x 1 root root 2330 May 20 19:03 segment
-rwxrwxr-x 1 root root 1925 May 20 19:03 train
[root@s ~]#
}}
なので、「/apps/scipion/config/scipion.conf」への記載は「...
#code(nonumber){{
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
（略
DF_HOME = /apps/scipion/software/em/deepfinder-0.1
DF_ENV_ACTIVATION = conda activate deepfinder-0.1
}}
***plug-in Gctf [#nbae3731]
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-gctf --noBin
[root@s ~]# scipion3 config -p gctf
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'gctf':
GCTF_HOME = /apps/scipion3/software/em/gctf-1.18
GCTF = Gctf_v1.18_sm30-75_cu10.1
GCTF_CUDA_LIB = /usr/local/cuda/lib64
These variables can be added/edited in '/apps/scipion3/co...
[root@s ~]#
}}
なので
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
:
GCTF_HOME = /apps/GCTF_Gautomatch_Cu10.1/
GCTF = GCTF_v1.18_sm30-75_cu10.1
GCTF_CUDA_LIB = /usr/local/cuda-10.1/targets/x86_64-linux...
[root@s ~]#
}}
***plug-in chimeraX [#u6603198]
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-chimera --noBin
[root@s ~]# scipion3 config -p chimera
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'chimera':
CHIMERA_HOME = /apps/scipion3/software/em/chimerax-1.1
These variables can be added/edited in '/apps/scipion3/co...
[root@s ~]#
}}
なので
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
:
CHIMERA_HOME = /usr/libexec/UCSF-ChimeraX
[root@s ~]#
}}
***plug-in cisTEM [#uebaaa76]
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-cistem --noBin
[root@s ~]# scipion3 config -p cistem
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'cistem':
CISTEM_HOME = /apps/scipion3/software/em/cistem-1.0.0-beta
CTFFIND4_HOME = /apps/scipion3/software/em/ctffind4-4.1.14
These variables can be added/edited in '/apps/scipion3/co...
[root@s ~]#
}}
なので
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
:
CISTEM_HOME = /apps/cistem-1.0.0-beta
CTFFIND4_HOME = /apps/ctffind-4.1.14
[root@s ~]#
}}
***メモ [#waf08d5a]
cuda-11.3とかを絡めたい場合、centos7ではエラーになる. gcc...
[[CentOS/devtoolset]]でGCC-9とかにして行うと回避される
#code(nonumber){{
source scl_source enable devtoolset-9
module load mpi
CXX_CUDA=g++ CUDA_BIN=/usr/local/cuda-11.3/bin CUDA_LIB=/...
}}
***メモ２ [#l04c29b2]
scipion3を起動すると下記メッセージが表示される
#code(nonumber){{
Scipion v3.0.12 - Eugenius
/apps/pyenv/versions/anaconda3-2022.10/envs/scipion3/lib/...
warnings.warn("Setuptools is replacing distutils.")
}}
これは
「conda install 'setuptools<60'」でsetuptoolsを古いものに...
終了行:
本家様 [[http://scipion.i2pc.es/>+http://scipion.i2pc.es/]]
scipionがver3になりました
ここでは RockyLinux9 にscipion3を入れてます
***下準備 [#ea586f16]
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.2 (Blue Onyx)
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 535.54.03...
GCC version: gcc version 11.3.1 20221121 (Red Hat 11.3.1...
[root@rockylinux9 ~]# ls -ld /usr/local/cuda*
lrwxrwxrwx. 1 root root 22 Sep 30 16:06 /usr/local/cud...
lrwxrwxrwx. 1 root root 25 Sep 30 16:06 /usr/local/cud...
drwxr-xr-x. 15 root root 4096 Sep 30 16:06 /usr/local/cud...
[root@rockylinux9 ~]# alternatives --list | grep cuda
cufile.json auto /usr/local/cuda-12.2/gds/...
cuda auto /usr/local/cuda-12.2
cuda-12 auto /usr/local/cuda-12.2
[root@rockylinux9 ~]# dnf install libzstd-devel hdf5-dev...
wget fftw-devel libti...
[root@rockylinux9 ~]#
(RHEL8系)
dnf install libzstd-devel hdf5-devel python3-devel pytho...
wget fftw-devel libtiff-devel java-1.8.0-openjdk-devel li...
}}
#code(nonumber){{
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f6...
[root@rockylinux9 ~]#
}}
***インストール [#l9bfe37e]
まずはconda環境を準備します. ここでは pyenv-anaconda3 環...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2023.07-2
pyenv global anaconda3-2023.07-2
export PATH=$PYENV_ROOT/versions/anaconda3-2023.07-2/bin:...
conda install conda-build=3.26.1
conda update conda -y
(既にpyenv-anaconda3環境があれば)
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
export PATH=$PYENV_ROOT/versions/anaconda3-2023.07-2/bin:...
}}
確認. 現在conda経由で提供しているpython実行環境は下記にな...
#code(nonumber){{
[root@rockylinux9 ~]# conda env list
# conda environments:
#
base /apps/pyenv/versions/anaconda3-2...
[root@rockylinux9 ~]#
}}
この環境リストにscipion実行環境を増やす形なのだが、まず「...
#code(nonumber){{
[root@rockylinux9 ~]# which pip
/apps/pyenv/versions/anaconda3-2023.07-2/bin/pip
[root@rockylinux9 ~]# pip install scipion-installer
}}
そしてコンパイル環境を整備してscipionを入れます
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/anacond...
[root@rockylinux9 ~]# which mpirun
/apps/pyenv/versions/anaconda3-2023.07-2/bin/mpirun
[root@rockylinux9 ~]# module load mpi/openmpi-x86_64
[root@rockylinux9 ~]# which mpirun
/usr/lib64/openmpi/bin/mpirun
[root@rockylinux9 ~]# python -m scipioninstaller -conda -...
:
:
------------------------------------
Scipion core successfully installed.
------------------------------------
________________________________________________________...
| ...
| Installation successfully finished!! Happy EM processin...
________________________________________________________...
You can launch Scipion using the launcher at: /apps/sci...
________________________________________________________...
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# conda env list
# conda environments:
#
base /apps/pyenv/versions/anaconda3-2...
scipion3 /apps/pyenv/versions/anaconda3-2...
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# /apps/scipion3/scipion3 config --ov...
:
:
Press <enter> to continue: <--- リター...
/apps/scipion3/config/hosts.conf hosts
* Creating configuration file: /apps/scipion3/config/host...
Please edit it to reflect the configuration of your system.
Checking paths in /apps/scipion3/config/scipion.conf ...
All seems fine with /apps/scipion3/config/scipion.conf
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# vi /apps/scipion3/config/scipion.conf
}}
「/apps/scipion3/config/scipion.conf」の末尾に下記を追加
#code(nonumber){{
CUDA = True
CUDA_BIN = /usr/local/cuda-12.2/bin
CUDA_LIB = /usr/local/cuda-12.2/lib64
MPI_BINDIR = /usr/lib64/openmpi/bin
MPI_LIBDIR = /usr/lib64/openmpi/lib
MPI_INCLUDE = /usr/include/openmpi-x86_64
OPENCV = False
}}
っで続き
#code(nonumber){{
[root@rockylinux9 ~]# conda activate scipion3
(scipion3) [root@rockylinux9 ~]# pip install scons
(scipion3) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# /apps/scipion3/scipion3 installp -p...
}}
***メモ [#efcf8d8f]
scipionのパッケージ置き場所 [[http://scipion.cnb.csic.es/...
***EnvironmentModules [#acac77da]
EnvironmentModules 向けに「/etc/modulefiles/scipion3」を...
#code(nonumber){{
#%Module1.0
set-alias scipion3 /apps/scipion3/scipion3
}}
***plug-in [#sff9a971]
scipionを起動して、「create project」でプロジェクトを作り...
&ref(2023y09m30d_175609262.png,nolink);
使用できるツールはインストール直後は「Xmipp3」由来のみです.
この他にもツールが搭載できる.
いったいどんなツールがこのscipionに追加できるかは scipion...
あるいはコマンドラインで「scipion3 installp --help」でも...
#code(nonumber){{
[root@rockylinux9 ~]# module load scipion3
[root@rockylinux9 ~]# scipion3 installp --checkUpdates
Scipion v3.1.0 - Eugenius
Available plugins: ([ ] not installed, [X] seems already ...
scipion-em-appion [ ]
scipion-em-aretomo [ ]
scipion-em-atomstructutils [ ]
scipion-em-atsas [ ]
scipion-em-bamfordlab [ ]
scipion-em-bsoft [ ]
scipion-em-ccp4 [ ]
scipion-em-chimera [ ]
scipion-em-cistem [ ]
scipion-em-continuousflex [ ]
scipion-em-cryoassess [ ]
scipion-em-cryodrgn [ ]
scipion-em-cryoef [ ]
scipion-em-cryosparc2 [ ]
scipion-em-dynamo [ ]
scipion-em-eman2 [ ]
scipion-em-emantomo [ ]
scipion-em-embuild [ ]
scipion-em-empiar [ ]
scipion-em-emready [ ]
scipion-em-emxlib [ ]
scipion-em-facilities [ ]
scipion-em-fsc3d [ ]
scipion-em-gautomatch [ ]
scipion-em-gctf [ ]
scipion-em-imagic [ ]
scipion-em-imod [ ]
scipion-em-isonet [ ]
scipion-em-localrec [ ]
scipion-em-locscale [ ]
scipion-em-modelangelo [ ]
scipion-em-motioncorr [ ]
scipion-em-novactf [ ]
scipion-em-phenix [ ]
scipion-em-prody [ ]
scipion-em-relion [ ]
scipion-em-reliontomo [ ]
scipion-em-repic [ ]
scipion-em-resmap [ ]
scipion-em-sidesplitter [ ]
scipion-em-sphire [ ]
scipion-em-spider [ ]
scipion-em-spoc [ ]
scipion-em-susantomo [ ]
scipion-em-tomo [ ]
scipion-em-tomo3d [ ]
scipion-em-tomotwin [ ]
scipion-em-tomoviz [ ]
scipion-em-topaz [ ]
scipion-em-warp [ ]
scipion-em-xmipp 23.7.0.0 [X]
scipion-em-xmipp2 [ ]
scipion-em-xmipptomo [ ]
[root@rockylinux9 ~]#
}}
&color(red){*};&size(10){これ以外にもbeta版とかがあり、そ...
例えば、scipionからrelionを実行したいなら、relionのplug-i...
しかし既にインストール済みのrelionがあって、そのバイナリ...
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-relion --noBin
(確認)
[root@s ~]# scipion3 installp --checkUpdates | grep relion
scipion-em-relion 3.1.2 [X]
(加えたこのpluginを削除したければ)
[root@s ~]# scipion3 uninstallp -p scipion-em-relion
}}
これでrelionへのpluginインターフェースは用意できました. ...
定義すべき環境変数は「scipion3 config -p <プログラム名>」...
#code(nonumber){{
[root@s ~]# scipion3 config -p relion
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'relion':
RELION_HOME = /apps/scipion/software/em/relion-3.1.2
RELION_CUDA_LIB = /usr/local/cuda/lib64
These variables can be added/edited in '/apps/scipion/con...
[root@s ~]#
}}
この場合、「&color(orangered){RELION_HOME};」と「&color(o...
それは「/apps/scipion/config/scipion.conf」で明記される必...
これで既にインストールされているrelionプログラムを使い回...
&size(10){その前に「scipion3 installb」でrelionのどのバー...
なので、
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
RELION_CUDA_LIB = /usr/local/cuda-11.2/lib64
RELION_CUDA_BIN = /usr/local/cuda-11.2/bin
RELION_HOME = /apps/relion-3.1.2
[root@s ~]#
}}
&size(10){実際には「RELION_CUDA_BIN」の塚も要求された};
その後scipionを再起動するとrelionの機能が追加されます
&ref(2021y07m08d_225847094.png,nolink);
***plug-in Gautomatch [#kb124d20]
次がGautomatchを入れてみる. これも既に手元にあって使える...
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-gautomatch --...
(確認)
[root@s ~]# scipion3 installp --checkUpdates | grep gauto...
scipion-em-gautomatch 3.0.14 [X]
(必要となる環境変数の確認)
[root@s ~]# scipion3 config -p gautomatch
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'gautomatch':
GAUTOMATCH_HOME = /apps/scipion/software/em/gautomatch-0.56
GAUTOMATCH = Gautomatch_v0.56_sm30-75_cu10.1
GAUTOMATCH_CUDA_LIB = /usr/local/cuda/lib64
These variables can be added/edited in '/apps/scipion/con...
(なので)
[root@s ~]# vi /apps/scipion/config/scipion.conf
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
（略
GAUTOMATCH_HOME = /apps/GCTF_Gautomatch_Cu10.1/
GAUTOMATCH = Gautomatch_v0.56_sm30-75_cu10.1
GAUTOMATCH_CUDA_LIB = /usr/local/cuda-10.2/lib64
[root@s ~]#
}}
これでscipionを起動します
&ref(2021y07m08d_230737299.png,nolink);
***plug-in Sphire [#e3ff7c9f]
このSphire Plug-inの中に[[crYOLO]]が入ってます.
っで
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-sphire --noBin
(必要となる環境変数の確認)
[root@s ~]# scipion3 config -p sphire
[root@s ~]# scipion3 config -p sphire
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'sphire':
CRYOLO_ENV_ACTIVATION_CPU = conda activate cryoloCPU-1.7.6
CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6
CRYOLO_GENERIC_MODEL = /apps/scipion/software/em/cryolo_m...
CRYOLO_GENERIC_DENOISED_MODEL = /apps/scipion/software/em...
JANNI_GENERIC_MODEL = /apps/scipion/software/em/janni_mod...
CRYOLO_NS_GENERIC_MODEL = /apps/scipion/software/em/cryol...
CRYOLO_CUDA_LIB = /usr/local/cuda/lib64
These variables can be added/edited in '/apps/scipion/con...
[root@s ~]#
}}
どうやらモデルがいるの指定もここでするみたい.
加えて「conda activate」でpython実行環境に移行するような...
#code(nonumber){{
[root@s ~]# conda env list |grep -i cryolo
crYOLO /apps/pyenv/versions/anaconda3-5...
[root@s ~]#
}}
なので「/apps/scipion/config/scipion.conf」は下記のように...
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
（略
CRYOLO_ENV_ACTIVATION = conda activate crYOLO
CRYOLO_GENERIC_MODEL = /apps/crYOLO/gmodel_phosnet_202005...
CRYOLO_GENERIC_DENOISED_MODEL = /apps/crYOLO/gmodel_phosn...
JANNI_GENERIC_MODEL = /apps/janni/gmodel_janni_20190703.h5
CRYOLO_NS_GENERIC_MODEL = /apps/crYOLO/gmodel_phosnet_neg...
CRYOLO_CUDA_LIB = /usr/local/cuda/lib64
}}
&color(red){*};&size(10){「CRYOLO_ENV_ACTIVATION_CPU 」は...
***plug-in Topaz [#r0ff80c8]
次にpickツールのTopazを入れてみる. 同じくバイナリーは既に...
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-topaz --noBin
[root@s ~]# scipion3 config -p topaz
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'topaz':
TOPAZ_ENV_ACTIVATION = conda activate topaz-0.2.4
These variables can be added/edited in '/apps/scipion/con...
[root@s ~]#
}}
condaで「topaz-0.2.4」なるpython実行環境をロードしている...
それを借用してみる
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
（略
TOPAZ_ENV_ACTIVATION = conda activate topaz
[root@s ~]#
}}
&color(red){*};&size(10){「module load topaz」とかでもい...
&ref(2021y07m09d_005654817.png,nolink);
***deepfinder [#oa7ddd96]
[[https://github.com/scipion-em/scipion-em-deepfinder>+ht...
「scipion3 installp --checkUpdates」には表示されていない...
バイナリーも一緒に入れるので、「--noBin」は付けない.
#code(nonumber){{
[root@s ~]# scipion3 installp -p https://github.com/scipi...
}}
これでdeepfinderのplug-inとバイナリー(プログラム)がインス...
次に、環境設定. 必要な環境変数を調べる
#code(nonumber){{
[root@s ~]# scipion3 config -p deepfinder
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'deepfinder':
DF_HOME = /apps/scipion/software/em/deepfinder-0.1
DF_ENV_ACTIVATION = conda activate deepfinder-0.1
These variables can be added/edited in '/apps/scipion/con...
[root@s ~]#
}}
環境変数として「DF_HOME」と「DF_ENV_ACTIVATION」が必要な...
plug-inの追加の際に、「--noBin」を付けないと、ここで提示...
確認のために、condaの環境リストを調べると
#code(nonumber){{
[root@s ~]# conda env list | grep deepfinder
deepfinder-0.1 /apps/pyenv/versions/anaconda3-5...
[root@s ~]#
}}
そして、バイナリーの存在を確認すると下記のようになっている.
#code(nonumber){{
[root@s ~]# ls -l /apps/scipion/software/em/deepfinder-0....
total 24
-rwxrwxr-x 1 root root 1021 May 20 19:03 annotate
-rwxrwxr-x 1 root root 1614 May 20 19:03 cluster
-rwxrwxr-x 1 root root 842 May 20 19:03 display
-rwxrwxr-x 1 root root 1554 May 20 19:03 generate_target
-rwxrwxr-x 1 root root 2330 May 20 19:03 segment
-rwxrwxr-x 1 root root 1925 May 20 19:03 train
[root@s ~]#
}}
なので、「/apps/scipion/config/scipion.conf」への記載は「...
#code(nonumber){{
[PYWORKFLOW]
CONDA_ACTIVATION_CMD = eval "$(/apps/pyenv/versions/anaco...
[PLUGINS]
（略
DF_HOME = /apps/scipion/software/em/deepfinder-0.1
DF_ENV_ACTIVATION = conda activate deepfinder-0.1
}}
***plug-in Gctf [#nbae3731]
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-gctf --noBin
[root@s ~]# scipion3 config -p gctf
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'gctf':
GCTF_HOME = /apps/scipion3/software/em/gctf-1.18
GCTF = Gctf_v1.18_sm30-75_cu10.1
GCTF_CUDA_LIB = /usr/local/cuda/lib64
These variables can be added/edited in '/apps/scipion3/co...
[root@s ~]#
}}
なので
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
:
GCTF_HOME = /apps/GCTF_Gautomatch_Cu10.1/
GCTF = GCTF_v1.18_sm30-75_cu10.1
GCTF_CUDA_LIB = /usr/local/cuda-10.1/targets/x86_64-linux...
[root@s ~]#
}}
***plug-in chimeraX [#u6603198]
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-chimera --noBin
[root@s ~]# scipion3 config -p chimera
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'chimera':
CHIMERA_HOME = /apps/scipion3/software/em/chimerax-1.1
These variables can be added/edited in '/apps/scipion3/co...
[root@s ~]#
}}
なので
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
:
CHIMERA_HOME = /usr/libexec/UCSF-ChimeraX
[root@s ~]#
}}
***plug-in cisTEM [#uebaaa76]
#code(nonumber){{
[root@s ~]# scipion3 installp -p scipion-em-cistem --noBin
[root@s ~]# scipion3 config -p cistem
Scipion v3.0.8 - Eugenius
Variables defined by plugin 'cistem':
CISTEM_HOME = /apps/scipion3/software/em/cistem-1.0.0-beta
CTFFIND4_HOME = /apps/scipion3/software/em/ctffind4-4.1.14
These variables can be added/edited in '/apps/scipion3/co...
[root@s ~]#
}}
なので
#code(nonumber){{
[root@s ~]# vi /apps/scipion/config/scipion.conf
:
CISTEM_HOME = /apps/cistem-1.0.0-beta
CTFFIND4_HOME = /apps/ctffind-4.1.14
[root@s ~]#
}}
***メモ [#waf08d5a]
cuda-11.3とかを絡めたい場合、centos7ではエラーになる. gcc...
[[CentOS/devtoolset]]でGCC-9とかにして行うと回避される
#code(nonumber){{
source scl_source enable devtoolset-9
module load mpi
CXX_CUDA=g++ CUDA_BIN=/usr/local/cuda-11.3/bin CUDA_LIB=/...
}}
***メモ２ [#l04c29b2]
scipion3を起動すると下記メッセージが表示される
#code(nonumber){{
Scipion v3.0.12 - Eugenius
/apps/pyenv/versions/anaconda3-2022.10/envs/scipion3/lib/...
warnings.warn("Setuptools is replacing distutils.")
}}
これは
「conda install 'setuptools<60'」でsetuptoolsを古いものに...
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