localcolabfold をテンプレートにして作成
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開始行:
本家様 [[https://github.com/YoshitakaMo/localcolabfold>+h...
pixiを使ってインストールになったみたい
***下準備 [#k0c0081f]
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.8 (Blue Onyx)
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA RTX PRO 2000 Blackwell (UUID: GPU-40660e37-...
[root@rockylinux9 ~]#
}}
「/usr/local/cuda-12.4」とかのcudaライブラリは入れてませ...
***インストール [#h91238f0]
#code(nonumber){{
[root@rockylinux9 ~]# curl -fsSL https://pixi.sh/install....
[root@rockylinux9 ~]# cd /apps
[root@rockylinux9 apps]# git clone https://github.com/Yos...
[root@rockylinux9 apps]# cd localcolabfold/
[root@rockylinux9 localcolabfold]# git log -1
commit 9101b9940a2c15e7bd428c56c94bea0d9deb763c (HEAD -> ...
Author: Yoshitaka Moriwaki <virgospica93@gmail.com>
Date: Wed Apr 22 00:54:39 2026 +0900
Remove Agg backend
[root@rockylinux9 localcolabfold]# pixi install
[root@rockylinux9 localcolabfold]# pixi run setup
}}
alphafold2のモデルファイルを取得して展開
#code(nonumber){{
[root@rockylinux9 ~]# wget https://storage.googleapis.com...
[root@rockylinux9 ~]# tar tvf alphafold_params_2022-12-06...
-rw-rw-r-- htomlinson/primarygroup 373069562 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 373069562 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 373103340 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 373103340 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 18657 2020-03-24 0...
[root@rockylinux9 ~]# mkdir -p /apps/alphafold_params_202...
[root@rockylinux9 ~]# tar xf ./alphafold_params_2022-12-0...
[root@rockylinux9 ~]# touch /apps/alphafold_params_2022-1...
[root@rockylinux9 ~]# ls -l /apps/alphafold_params_2022-1...
total 5457016
-rw-r--r-- 1 root root 0 Jun 26 03:03 download...
-rw-rw-r-- 1 995210 89939 18657 Mar 24 2020 LICENSE
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 373069562 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373103340 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 373069562 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373103340 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_m...
[root@rockylinux9 ~]# rm -f alphafold_params_2022-12-06.tar
}}
***EnvironmentModules [#l57a3ebb]
#code(nonumber){{
[root@rockylinux9 ~]# vi /apps/modulefiles/localcolabfold
#%Module1.0
set root /apps/localcolabfold/.pixi/e...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
[root@rockylinux9 ~]#
}}
***テスト [#o63cfa75]
予測対象の配列は別途ファイルで用意するみたい
#code(nonumber){{
[saber@rockylinux test]$ module use /apps/modulefiles
[saber@rockylinux test]$ module load localcolabfold
[saber@rockylinux test]$ colabfold_batch -h
WARNING: All log messages before absl::InitializeLog() is...
E0000 00:00:1782410861.258811 9752 cuda_dnn.cc:8579] U...
E0000 00:00:1782410861.261547 9752 cuda_blas.cc:1407] ...
W0000 00:00:1782410861.268067 9752 computation_placer....
W0000 00:00:1782410861.268078 9752 computation_placer....
W0000 00:00:1782410861.268080 9752 computation_placer....
W0000 00:00:1782410861.268081 9752 computation_placer....
usage: colabfold_batch [-h] [--msa-only] [--msa-mode {mms...
[--pair-strategy {complete,greedy}...
[--max-template-date MAX_TEMPLATE_...
[--recycle-early-stop-tolerance RE...
[--model-type {auto,alphafold2,alp...
[--initial-guess [INITIAL_GUESS]] ...
[--no-use-probs-extra] [--data DAT...
[--relax-stiffness RELAX_STIFFNESS...
[--jobname-prefix JOBNAME_PREFIX] ...
[--zip] [--sort-queries-by {none,l...
[--debug-logging] [--af3-json]
input results
:
:
[illya@rockylinux test]$ cat<<_EOF_>query.fasta
>sample
PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK
_EOF_
[saber@rockylinux test]$ colabfold_batch --amber --templa...
WARNING: All log messages before absl::InitializeLog() is...
E0000 00:00:1782411337.430049 10576 cuda_dnn.cc:8579] U...
E0000 00:00:1782411337.432625 10576 cuda_blas.cc:1407] ...
W0000 00:00:1782411337.439027 10576 computation_placer....
W0000 00:00:1782411337.439038 10576 computation_placer....
W0000 00:00:1782411337.439040 10576 computation_placer....
W0000 00:00:1782411337.439041 10576 computation_placer....
2026-06-26 03:15:38,577 Running colabfold 1.6.1 (0ff47949...
2026-06-26 03:15:38,817 Running on GPU
W0000 00:00:1782411338.842585 10576 gpu_device.cc:2430]...
2026-06-26 03:15:38,963 Found 9 citations for tools or da...
2026-06-26 03:15:38,963 Query 1/1: sample (length 59)
COMPLETE: 100%|------------------------------------------...
2026-06-26 03:15:43,190 Sequence 0 found templates: ['3mb...
2026-06-26 03:15:43,475 Setting max_seq=512, max_extra_se...
WARNING: All log messages before absl::InitializeLog() is...
I0000 00:00:1782411347.135745 10576 mlir_graph_optimiza...
2026-06-26 03:17:05,222 alphafold2_ptm_model_1_seed_000 r...
2026-06-26 03:17:06,024 alphafold2_ptm_model_1_seed_000 r...
2026-06-26 03:17:06,780 alphafold2_ptm_model_1_seed_000 r...
2026-06-26 03:17:07,537 alphafold2_ptm_model_1_seed_000 r...
2026-06-26 03:17:07,537 alphafold2_ptm_model_1_seed_000 t...
2026-06-26 03:17:08,297 alphafold2_ptm_model_2_seed_000 r...
2026-06-26 03:17:09,056 alphafold2_ptm_model_2_seed_000 r...
2026-06-26 03:17:09,816 alphafold2_ptm_model_2_seed_000 r...
2026-06-26 03:17:10,576 alphafold2_ptm_model_2_seed_000 r...
2026-06-26 03:17:10,576 alphafold2_ptm_model_2_seed_000 t...
2026-06-26 03:17:34,557 alphafold2_ptm_model_3_seed_000 r...
2026-06-26 03:17:35,323 alphafold2_ptm_model_3_seed_000 r...
2026-06-26 03:17:36,090 alphafold2_ptm_model_3_seed_000 r...
2026-06-26 03:17:36,857 alphafold2_ptm_model_3_seed_000 r...
2026-06-26 03:17:36,858 alphafold2_ptm_model_3_seed_000 t...
2026-06-26 03:17:37,628 alphafold2_ptm_model_4_seed_000 r...
2026-06-26 03:17:38,397 alphafold2_ptm_model_4_seed_000 r...
2026-06-26 03:17:39,166 alphafold2_ptm_model_4_seed_000 r...
2026-06-26 03:17:39,936 alphafold2_ptm_model_4_seed_000 r...
2026-06-26 03:17:39,936 alphafold2_ptm_model_4_seed_000 t...
2026-06-26 03:17:40,708 alphafold2_ptm_model_5_seed_000 r...
2026-06-26 03:17:41,478 alphafold2_ptm_model_5_seed_000 r...
2026-06-26 03:17:42,249 alphafold2_ptm_model_5_seed_000 r...
2026-06-26 03:17:43,019 alphafold2_ptm_model_5_seed_000 r...
2026-06-26 03:17:43,019 alphafold2_ptm_model_5_seed_000 t...
2026-06-26 03:17:43,021 reranking models by 'plddt' metric
2026-06-26 03:17:44,817 Relaxation took 1.8s
2026-06-26 03:17:44,817 rank_001_alphafold2_ptm_model_2_s...
2026-06-26 03:17:45,677 Relaxation took 0.9s
2026-06-26 03:17:45,677 rank_002_alphafold2_ptm_model_1_s...
2026-06-26 03:17:46,360 Relaxation took 0.7s
2026-06-26 03:17:46,361 rank_003_alphafold2_ptm_model_3_s...
2026-06-26 03:17:47,207 Relaxation took 0.8s
2026-06-26 03:17:47,207 rank_004_alphafold2_ptm_model_4_s...
2026-06-26 03:17:47,901 Relaxation took 0.7s
2026-06-26 03:17:47,901 rank_005_alphafold2_ptm_model_5_s...
2026-06-26 03:17:48,230 Done
[saber@rockylinux test]$
}}
***特定のGPUで計算させたい [#i320936e]
slurmとかopenPBSでGPUのリソース管理をきちんとできていれば...
&size(10){全てのGPUを使っているように見えるが実際には１つ...
２枚刺しGPUマシンで、cryoSPARCを流して、localcolabfoldを...
その場合は環境変数 CUDA_VISIBLE_DEVICES を使って使用するG...
#code(nonumber){{
CUDA_VISIBLE_DEVICES=1 colabfold_batch --amber --template...
}}
CUDA_VISIBLE_DEVICESは0から始まるようで、２枚目は「１」と...
終了行:
本家様 [[https://github.com/YoshitakaMo/localcolabfold>+h...
pixiを使ってインストールになったみたい
***下準備 [#k0c0081f]
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.8 (Blue Onyx)
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA RTX PRO 2000 Blackwell (UUID: GPU-40660e37-...
[root@rockylinux9 ~]#
}}
「/usr/local/cuda-12.4」とかのcudaライブラリは入れてませ...
***インストール [#h91238f0]
#code(nonumber){{
[root@rockylinux9 ~]# curl -fsSL https://pixi.sh/install....
[root@rockylinux9 ~]# cd /apps
[root@rockylinux9 apps]# git clone https://github.com/Yos...
[root@rockylinux9 apps]# cd localcolabfold/
[root@rockylinux9 localcolabfold]# git log -1
commit 9101b9940a2c15e7bd428c56c94bea0d9deb763c (HEAD -> ...
Author: Yoshitaka Moriwaki <virgospica93@gmail.com>
Date: Wed Apr 22 00:54:39 2026 +0900
Remove Agg backend
[root@rockylinux9 localcolabfold]# pixi install
[root@rockylinux9 localcolabfold]# pixi run setup
}}
alphafold2のモデルファイルを取得して展開
#code(nonumber){{
[root@rockylinux9 ~]# wget https://storage.googleapis.com...
[root@rockylinux9 ~]# tar tvf alphafold_params_2022-12-06...
-rw-rw-r-- htomlinson/primarygroup 373069562 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 373069562 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 373103340 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 373103340 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 0...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 2...
-rw-rw-r-- htomlinson/primarygroup 18657 2020-03-24 0...
[root@rockylinux9 ~]# mkdir -p /apps/alphafold_params_202...
[root@rockylinux9 ~]# tar xf ./alphafold_params_2022-12-0...
[root@rockylinux9 ~]# touch /apps/alphafold_params_2022-1...
[root@rockylinux9 ~]# ls -l /apps/alphafold_params_2022-1...
total 5457016
-rw-r--r-- 1 root root 0 Jun 26 03:03 download...
-rw-rw-r-- 1 995210 89939 18657 Mar 24 2020 LICENSE
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 373069562 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373103340 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 373069562 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373103340 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_m...
-rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_m...
-rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_m...
[root@rockylinux9 ~]# rm -f alphafold_params_2022-12-06.tar
}}
***EnvironmentModules [#l57a3ebb]
#code(nonumber){{
[root@rockylinux9 ~]# vi /apps/modulefiles/localcolabfold
#%Module1.0
set root /apps/localcolabfold/.pixi/e...
prepend-path PATH $root/bin
prepend-path LD_LIBRARY_PATH $root/lib
[root@rockylinux9 ~]#
}}
***テスト [#o63cfa75]
予測対象の配列は別途ファイルで用意するみたい
#code(nonumber){{
[saber@rockylinux test]$ module use /apps/modulefiles
[saber@rockylinux test]$ module load localcolabfold
[saber@rockylinux test]$ colabfold_batch -h
WARNING: All log messages before absl::InitializeLog() is...
E0000 00:00:1782410861.258811 9752 cuda_dnn.cc:8579] U...
E0000 00:00:1782410861.261547 9752 cuda_blas.cc:1407] ...
W0000 00:00:1782410861.268067 9752 computation_placer....
W0000 00:00:1782410861.268078 9752 computation_placer....
W0000 00:00:1782410861.268080 9752 computation_placer....
W0000 00:00:1782410861.268081 9752 computation_placer....
usage: colabfold_batch [-h] [--msa-only] [--msa-mode {mms...
[--pair-strategy {complete,greedy}...
[--max-template-date MAX_TEMPLATE_...
[--recycle-early-stop-tolerance RE...
[--model-type {auto,alphafold2,alp...
[--initial-guess [INITIAL_GUESS]] ...
[--no-use-probs-extra] [--data DAT...
[--relax-stiffness RELAX_STIFFNESS...
[--jobname-prefix JOBNAME_PREFIX] ...
[--zip] [--sort-queries-by {none,l...
[--debug-logging] [--af3-json]
input results
:
:
[illya@rockylinux test]$ cat<<_EOF_>query.fasta
>sample
PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK
_EOF_
[saber@rockylinux test]$ colabfold_batch --amber --templa...
WARNING: All log messages before absl::InitializeLog() is...
E0000 00:00:1782411337.430049 10576 cuda_dnn.cc:8579] U...
E0000 00:00:1782411337.432625 10576 cuda_blas.cc:1407] ...
W0000 00:00:1782411337.439027 10576 computation_placer....
W0000 00:00:1782411337.439038 10576 computation_placer....
W0000 00:00:1782411337.439040 10576 computation_placer....
W0000 00:00:1782411337.439041 10576 computation_placer....
2026-06-26 03:15:38,577 Running colabfold 1.6.1 (0ff47949...
2026-06-26 03:15:38,817 Running on GPU
W0000 00:00:1782411338.842585 10576 gpu_device.cc:2430]...
2026-06-26 03:15:38,963 Found 9 citations for tools or da...
2026-06-26 03:15:38,963 Query 1/1: sample (length 59)
COMPLETE: 100%|------------------------------------------...
2026-06-26 03:15:43,190 Sequence 0 found templates: ['3mb...
2026-06-26 03:15:43,475 Setting max_seq=512, max_extra_se...
WARNING: All log messages before absl::InitializeLog() is...
I0000 00:00:1782411347.135745 10576 mlir_graph_optimiza...
2026-06-26 03:17:05,222 alphafold2_ptm_model_1_seed_000 r...
2026-06-26 03:17:06,024 alphafold2_ptm_model_1_seed_000 r...
2026-06-26 03:17:06,780 alphafold2_ptm_model_1_seed_000 r...
2026-06-26 03:17:07,537 alphafold2_ptm_model_1_seed_000 r...
2026-06-26 03:17:07,537 alphafold2_ptm_model_1_seed_000 t...
2026-06-26 03:17:08,297 alphafold2_ptm_model_2_seed_000 r...
2026-06-26 03:17:09,056 alphafold2_ptm_model_2_seed_000 r...
2026-06-26 03:17:09,816 alphafold2_ptm_model_2_seed_000 r...
2026-06-26 03:17:10,576 alphafold2_ptm_model_2_seed_000 r...
2026-06-26 03:17:10,576 alphafold2_ptm_model_2_seed_000 t...
2026-06-26 03:17:34,557 alphafold2_ptm_model_3_seed_000 r...
2026-06-26 03:17:35,323 alphafold2_ptm_model_3_seed_000 r...
2026-06-26 03:17:36,090 alphafold2_ptm_model_3_seed_000 r...
2026-06-26 03:17:36,857 alphafold2_ptm_model_3_seed_000 r...
2026-06-26 03:17:36,858 alphafold2_ptm_model_3_seed_000 t...
2026-06-26 03:17:37,628 alphafold2_ptm_model_4_seed_000 r...
2026-06-26 03:17:38,397 alphafold2_ptm_model_4_seed_000 r...
2026-06-26 03:17:39,166 alphafold2_ptm_model_4_seed_000 r...
2026-06-26 03:17:39,936 alphafold2_ptm_model_4_seed_000 r...
2026-06-26 03:17:39,936 alphafold2_ptm_model_4_seed_000 t...
2026-06-26 03:17:40,708 alphafold2_ptm_model_5_seed_000 r...
2026-06-26 03:17:41,478 alphafold2_ptm_model_5_seed_000 r...
2026-06-26 03:17:42,249 alphafold2_ptm_model_5_seed_000 r...
2026-06-26 03:17:43,019 alphafold2_ptm_model_5_seed_000 r...
2026-06-26 03:17:43,019 alphafold2_ptm_model_5_seed_000 t...
2026-06-26 03:17:43,021 reranking models by 'plddt' metric
2026-06-26 03:17:44,817 Relaxation took 1.8s
2026-06-26 03:17:44,817 rank_001_alphafold2_ptm_model_2_s...
2026-06-26 03:17:45,677 Relaxation took 0.9s
2026-06-26 03:17:45,677 rank_002_alphafold2_ptm_model_1_s...
2026-06-26 03:17:46,360 Relaxation took 0.7s
2026-06-26 03:17:46,361 rank_003_alphafold2_ptm_model_3_s...
2026-06-26 03:17:47,207 Relaxation took 0.8s
2026-06-26 03:17:47,207 rank_004_alphafold2_ptm_model_4_s...
2026-06-26 03:17:47,901 Relaxation took 0.7s
2026-06-26 03:17:47,901 rank_005_alphafold2_ptm_model_5_s...
2026-06-26 03:17:48,230 Done
[saber@rockylinux test]$
}}
***特定のGPUで計算させたい [#i320936e]
slurmとかopenPBSでGPUのリソース管理をきちんとできていれば...
&size(10){全てのGPUを使っているように見えるが実際には１つ...
２枚刺しGPUマシンで、cryoSPARCを流して、localcolabfoldを...
その場合は環境変数 CUDA_VISIBLE_DEVICES を使って使用するG...
#code(nonumber){{
CUDA_VISIBLE_DEVICES=1 colabfold_batch --amber --template...
}}
CUDA_VISIBLE_DEVICESは0から始まるようで、２枚目は「１」と...
ページ名:
1
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