EMReady をテンプレートにして作成
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開始行:
本家様 [[http://huanglab.phys.hust.edu.cn/EMReady/>+http:...
#code(nonumber){{
EMReady is a three-dimensional nested U-net-based framewo...
(DeepL様翻訳)
EMReadyは、類似性と相関に導かれたディープラーニングを用い...
}}
単体アプリとして作れるし、[[Scipion]]のplug-inとしても利...
ここでは単体アプリとして作ってみる
***構築 [#c3d35078]
condaアプリなので pyenv/anaconda を敷いてその上に EMRead...
#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 miniforge3-25.3.1-0
source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profi...
conda update -n base -c conda-forge conda -y
(既にpyenv/anacondaが用意されているなら下記の実行)
source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profi...
}}
その上で
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.6 (Blue Onyx)
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# cd /apps/src
[root@rockylinux9 src]# wget http://huanglab.phys.hust.ed...
[root@rockylinux9 src]# cd ..
[root@rockylinux9 apps]# tar xf src/EMReady_v1.3.tgz
[root@rockylinux9 apps]# cd EMReady_v1.3/
[root@rockylinux9 EMReady_v1.3]# ls -lF
total 72
-rwxr-x---. 1 573 514 4526 Aug 14 11:13 EMReady.sh*
-rwxr-x---. 1 573 514 357 Jun 17 11:34 environment.yml*
-rwxrwx---. 1 573 514 3719 Jun 17 11:28 frn.py*
-rwxrwx---. 1 573 514 6004 Aug 14 10:58 interp3d.py*
-rwxrwx---. 1 573 514 1278 Aug 14 10:59 interp.py*
-rwxr-x---. 1 573 514 288 Aug 14 11:20 LICENSE*
drwxr-x---. 2 573 514 68 Jun 17 11:28 model_state_dicts/
-rwxrwx---. 1 573 514 12289 Aug 14 11:23 pred.py*
-rwxrwx---. 1 573 514 11223 Jun 17 11:28 scunet.py*
-rwxrwx---. 1 573 514 9883 Aug 14 11:12 utils.py*
[root@rockylinux9 EMReady_v1.3]#
[root@rockylinux9 EMReady_v1.3]# conda env create -f envi...
[root@rockylinux9 EMReady_v1.3]# conda activate emready_env
(emready_env) [root@rockylinux9 EMReady_v1.3]#
(emready_env) [root@rockylinux9 EMReady_v1.3]# chmod 755 ...
(emready_env) [root@rockylinux9 EMReady_v1.3]# chmod 755 ...
(emready_env) [root@rockylinux9 EMReady_v1.3]# chmod 644 ...
(emready_env) [root@rockylinux9 EMReady_v1.3]# chmod 644 ...
(emready_env) [root@rockylinux9 EMReady_v1.3]# chown -R r...
(emready_env) [root@rockylinux9 EMReady_v1.3]# vi EMReady...
:
EMReady_home="/apps/EMReady_v1.3"
activate="/apps/pyenv/versions/miniforge3-25.3.1-0/bi...
EMReady_env="emready_env"
:
(emready_env) [root@rockylinux9 EMReady_v1.3]# conda deac...
[root@rockylinux9 EMReady_v1.3]#
}}
***EnvironmentModules [#pfb31c1e]
「/apps/modulefiles/EMReady/1.3」
#code(nonumber){{
#%Module
set em /apps/EMReady_v1.3
prepend-path PATH $em
}}
***テスト [#zd4f0b81]
本家様にテストデータがあります. まずはそれを入手して
#code(nonumber){{
[saber@rockylinux9 ~]$ wget http://huanglab.phys.hust.edu...
[saber@rockylinux9 ~]$ ls -lh emd_22216.map.gz
-rw-r--r--. 1 saber saber 15M Aug 31 2020 emd_22216.map.gz
[saber@rockylinux9 ~]$ gzip -d emd_22216.map.gz
[saber@rockylinux9 ~]$ ls -lh
total 16M
-rw-r--r--. 1 saber saber 16M Aug 31 2020 emd_22216.map
[saber@rockylinux9 ~]$
}}
計算してみます.
#code(nonumber){{
[saber@rockylinux9 ~]$ module use /apps/modulefiles/
[saber@rockylinux9 ~]$ module load EMReady/1.3
[saber@rockylinux9 ~]$ EMReady.sh
EMReady by Huang Lab @ HUST (http://huanglab.phys.hust.ed...
USAGE: EMReady.sh in_map.mrc out_map.mrc [options]
Descriptions:
in_map.mrc : Input EM density map in MRC2014 format
out_map.mrc : Filename of the output processed dens...
-g : ID(s) of GPU devices to be used, e.g....
default: 0
-s : The stride of the sliding window to c...
default: 12
-b : Number of input boxes in one batch. U...
default: 10
-m : Input mask map in MRC2014 format
-c : The contour threshold to binarize the...
default: 0.0
-p : Input structure in PDB or mmCIF forma...
-r : Zone radius of the mask around the in...
default: 4.0
-mo : Filename of the output binary mask map
--use_cpu : Run EMReady on CPU instead of GPU
--inverse : Inverse the mask
[saber@rockylinux9 ~]$
[saber@rockylinux9 ~]$ EMReady.sh emd_22216.map emd_22216...
}}
GPUも使ってくれます.
***メモ [#p4e6e780]
EMReady_v1.2.1の時は f90 なプログラムがありましたが、以降...
***EMReady v2 [#w7d83171]
本家様 [[https://github.com/huang-laboratory/EMReady>+htt...
condaアプリなので pyenv/anaconda を敷いてその上に EMRead...
#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 miniforge3-26.3.2-3
source /apps/pyenv/versions/miniforge3-26.3.2-3/etc/profi...
conda update -n base -c conda-forge conda -y
(既にpyenv/anacondaが用意されているなら下記の実行)
source /apps/pyenv/versions/miniforge3-26.3.2-3/etc/profi...
}}
その上で
#code(nonumber){{
[root@rockylinux9 ~]# conda create -n emready python==3.1...
[root@rockylinux9 ~]# conda activate emready
(emready) [root@rockylinux9 ~]#
(emready) [root@rockylinux9 ~]# cd /apps/src/
(emready) [root@rockylinux9 src]# git clone https://githu...
(emready) [root@rockylinux9 src]# cd EMReady/
(emready) [root@rockylinux9 EMReady]#
(emready) [root@rockylinux9 EMReady]# pip install torch==...
*オリジナルの「pip install torch==2.4.1 torchvision==0.19...
(emready) [root@rockylinux9 EMReady]# pip install -r requ...
}}
「requirements_mamba.txt」を修正
&size(10){https://github.com/huang-laboratory/EMReady/iss...
#code(diff,nonumber){{
--- requirements_mamba.txt.orig 2026-07-16 08:54:15.38919...
+++ requirements_mamba.txt 2026-07-16 09:55:02.59834...
@@ -1,2 +1,2 @@
-causal-conv1d==1.4.0
-mamba-ssm==2.2.0
+causal-conv1d==1.6.1
+mamba-ssm==2.3.1
}}
その上で
#code(nonumber){{
(emready) [root@rockylinux9 EMReady]# module load cuda/12.8
(emready) [root@rockylinux9 EMReady]# nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2025 NVIDIA Corporation
Built on Fri_Feb_21_20:23:50_PST_2025
Cuda compilation tools, release 12.8, V12.8.93
Build cuda_12.8.r12.8/compiler.35583870_0
(emready) [root@rockylinux9 EMReady]#
(emready) [root@rockylinux9 EMReady]# pip install --no-bu...
(emready) [root@rockylinux9 EMReady]# pip install -e . --...
(emready) [root@rockylinux9 EMReady]# conda deactivate
[root@rockylinux9 EMReady]#
}}
environment-modulesは「/apps/modulefiles/EMReady」
#code(nonumber){{
#%Module1.0
set root /apps/pyenv/versions/miniforge3-26.3.2-...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
終了行:
本家様 [[http://huanglab.phys.hust.edu.cn/EMReady/>+http:...
#code(nonumber){{
EMReady is a three-dimensional nested U-net-based framewo...
(DeepL様翻訳)
EMReadyは、類似性と相関に導かれたディープラーニングを用い...
}}
単体アプリとして作れるし、[[Scipion]]のplug-inとしても利...
ここでは単体アプリとして作ってみる
***構築 [#c3d35078]
condaアプリなので pyenv/anaconda を敷いてその上に EMRead...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install miniforge3-25.3.1-0
source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profi...
conda update -n base -c conda-forge conda -y
(既にpyenv/anacondaが用意されているなら下記の実行)
source /apps/pyenv/versions/miniforge3-25.3.1-0/etc/profi...
}}
その上で
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.6 (Blue Onyx)
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# cd /apps/src
[root@rockylinux9 src]# wget http://huanglab.phys.hust.ed...
[root@rockylinux9 src]# cd ..
[root@rockylinux9 apps]# tar xf src/EMReady_v1.3.tgz
[root@rockylinux9 apps]# cd EMReady_v1.3/
[root@rockylinux9 EMReady_v1.3]# ls -lF
total 72
-rwxr-x---. 1 573 514 4526 Aug 14 11:13 EMReady.sh*
-rwxr-x---. 1 573 514 357 Jun 17 11:34 environment.yml*
-rwxrwx---. 1 573 514 3719 Jun 17 11:28 frn.py*
-rwxrwx---. 1 573 514 6004 Aug 14 10:58 interp3d.py*
-rwxrwx---. 1 573 514 1278 Aug 14 10:59 interp.py*
-rwxr-x---. 1 573 514 288 Aug 14 11:20 LICENSE*
drwxr-x---. 2 573 514 68 Jun 17 11:28 model_state_dicts/
-rwxrwx---. 1 573 514 12289 Aug 14 11:23 pred.py*
-rwxrwx---. 1 573 514 11223 Jun 17 11:28 scunet.py*
-rwxrwx---. 1 573 514 9883 Aug 14 11:12 utils.py*
[root@rockylinux9 EMReady_v1.3]#
[root@rockylinux9 EMReady_v1.3]# conda env create -f envi...
[root@rockylinux9 EMReady_v1.3]# conda activate emready_env
(emready_env) [root@rockylinux9 EMReady_v1.3]#
(emready_env) [root@rockylinux9 EMReady_v1.3]# chmod 755 ...
(emready_env) [root@rockylinux9 EMReady_v1.3]# chmod 755 ...
(emready_env) [root@rockylinux9 EMReady_v1.3]# chmod 644 ...
(emready_env) [root@rockylinux9 EMReady_v1.3]# chmod 644 ...
(emready_env) [root@rockylinux9 EMReady_v1.3]# chown -R r...
(emready_env) [root@rockylinux9 EMReady_v1.3]# vi EMReady...
:
EMReady_home="/apps/EMReady_v1.3"
activate="/apps/pyenv/versions/miniforge3-25.3.1-0/bi...
EMReady_env="emready_env"
:
(emready_env) [root@rockylinux9 EMReady_v1.3]# conda deac...
[root@rockylinux9 EMReady_v1.3]#
}}
***EnvironmentModules [#pfb31c1e]
「/apps/modulefiles/EMReady/1.3」
#code(nonumber){{
#%Module
set em /apps/EMReady_v1.3
prepend-path PATH $em
}}
***テスト [#zd4f0b81]
本家様にテストデータがあります. まずはそれを入手して
#code(nonumber){{
[saber@rockylinux9 ~]$ wget http://huanglab.phys.hust.edu...
[saber@rockylinux9 ~]$ ls -lh emd_22216.map.gz
-rw-r--r--. 1 saber saber 15M Aug 31 2020 emd_22216.map.gz
[saber@rockylinux9 ~]$ gzip -d emd_22216.map.gz
[saber@rockylinux9 ~]$ ls -lh
total 16M
-rw-r--r--. 1 saber saber 16M Aug 31 2020 emd_22216.map
[saber@rockylinux9 ~]$
}}
計算してみます.
#code(nonumber){{
[saber@rockylinux9 ~]$ module use /apps/modulefiles/
[saber@rockylinux9 ~]$ module load EMReady/1.3
[saber@rockylinux9 ~]$ EMReady.sh
EMReady by Huang Lab @ HUST (http://huanglab.phys.hust.ed...
USAGE: EMReady.sh in_map.mrc out_map.mrc [options]
Descriptions:
in_map.mrc : Input EM density map in MRC2014 format
out_map.mrc : Filename of the output processed dens...
-g : ID(s) of GPU devices to be used, e.g....
default: 0
-s : The stride of the sliding window to c...
default: 12
-b : Number of input boxes in one batch. U...
default: 10
-m : Input mask map in MRC2014 format
-c : The contour threshold to binarize the...
default: 0.0
-p : Input structure in PDB or mmCIF forma...
-r : Zone radius of the mask around the in...
default: 4.0
-mo : Filename of the output binary mask map
--use_cpu : Run EMReady on CPU instead of GPU
--inverse : Inverse the mask
[saber@rockylinux9 ~]$
[saber@rockylinux9 ~]$ EMReady.sh emd_22216.map emd_22216...
}}
GPUも使ってくれます.
***メモ [#p4e6e780]
EMReady_v1.2.1の時は f90 なプログラムがありましたが、以降...
***EMReady v2 [#w7d83171]
本家様 [[https://github.com/huang-laboratory/EMReady>+htt...
condaアプリなので pyenv/anaconda を敷いてその上に EMRead...
#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 miniforge3-26.3.2-3
source /apps/pyenv/versions/miniforge3-26.3.2-3/etc/profi...
conda update -n base -c conda-forge conda -y
(既にpyenv/anacondaが用意されているなら下記の実行)
source /apps/pyenv/versions/miniforge3-26.3.2-3/etc/profi...
}}
その上で
#code(nonumber){{
[root@rockylinux9 ~]# conda create -n emready python==3.1...
[root@rockylinux9 ~]# conda activate emready
(emready) [root@rockylinux9 ~]#
(emready) [root@rockylinux9 ~]# cd /apps/src/
(emready) [root@rockylinux9 src]# git clone https://githu...
(emready) [root@rockylinux9 src]# cd EMReady/
(emready) [root@rockylinux9 EMReady]#
(emready) [root@rockylinux9 EMReady]# pip install torch==...
*オリジナルの「pip install torch==2.4.1 torchvision==0.19...
(emready) [root@rockylinux9 EMReady]# pip install -r requ...
}}
「requirements_mamba.txt」を修正
&size(10){https://github.com/huang-laboratory/EMReady/iss...
#code(diff,nonumber){{
--- requirements_mamba.txt.orig 2026-07-16 08:54:15.38919...
+++ requirements_mamba.txt 2026-07-16 09:55:02.59834...
@@ -1,2 +1,2 @@
-causal-conv1d==1.4.0
-mamba-ssm==2.2.0
+causal-conv1d==1.6.1
+mamba-ssm==2.3.1
}}
その上で
#code(nonumber){{
(emready) [root@rockylinux9 EMReady]# module load cuda/12.8
(emready) [root@rockylinux9 EMReady]# nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2025 NVIDIA Corporation
Built on Fri_Feb_21_20:23:50_PST_2025
Cuda compilation tools, release 12.8, V12.8.93
Build cuda_12.8.r12.8/compiler.35583870_0
(emready) [root@rockylinux9 EMReady]#
(emready) [root@rockylinux9 EMReady]# pip install --no-bu...
(emready) [root@rockylinux9 EMReady]# pip install -e . --...
(emready) [root@rockylinux9 EMReady]# conda deactivate
[root@rockylinux9 EMReady]#
}}
environment-modulesは「/apps/modulefiles/EMReady」
#code(nonumber){{
#%Module1.0
set root /apps/pyenv/versions/miniforge3-26.3.2-...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
}}
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