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#author("2026-06-26T19:33:13+00:00","default:sysosa","sysosa") #author("2026-07-03T06:21:22+00:00;2026-06-26T19:33:13+00:00","default:sysosa","sysosa") 本家様 [[https://github.com/YoshitakaMo/localcolabfold>+https://github.com/YoshitakaMo/localcolabfold]] 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_64 595.84 Release Build (dvs-builder@U22-I3-AM25-26-2) Wed Jun 10 21:06:37 UTC 2026 GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0-14) (GCC) [root@rockylinux9 ~]# nvidia-smi -L GPU 0: NVIDIA RTX PRO 2000 Blackwell (UUID: GPU-40660e37-0d35-d4f4-294a-eee3fe83049e) [root@rockylinux9 ~]# }} 「/usr/local/cuda-12.4」とかのcudaライブラリは入れてません. ***インストール [#h91238f0] #code(nonumber){{ [root@rockylinux9 ~]# curl -fsSL https://pixi.sh/install.sh | sh [root@rockylinux9 ~]# cd /apps [root@rockylinux9 apps]# git clone https://github.com/YoshitakaMo/localcolabfold [root@rockylinux9 apps]# cd localcolabfold/ [root@rockylinux9 localcolabfold]# git log -1 commit 9101b9940a2c15e7bd428c56c94bea0d9deb763c (HEAD -> main, origin/main, origin/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/alphafold/alphafold_params_2022-12-06.tar [root@rockylinux9 ~]# tar tvf alphafold_params_2022-12-06.tar -rw-rw-r-- htomlinson/primarygroup 373069562 2021-07-20 01:57 params_model_1.npz -rw-rw-r-- htomlinson/primarygroup 373069562 2021-07-20 01:57 params_model_2.npz -rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 01:57 params_model_3.npz -rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 01:57 params_model_4.npz -rw-rw-r-- htomlinson/primarygroup 371712506 2021-07-20 01:57 params_model_5.npz -rw-rw-r-- htomlinson/primarygroup 373103340 2021-07-20 01:57 params_model_1_ptm.npz -rw-rw-r-- htomlinson/primarygroup 373103340 2021-07-20 01:57 params_model_2_ptm.npz -rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 01:57 params_model_3_ptm.npz -rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 01:57 params_model_4_ptm.npz -rw-rw-r-- htomlinson/primarygroup 371746284 2021-07-20 01:57 params_model_5_ptm.npz -rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 23:31 params_model_1_multimer_v3.npz -rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 23:31 params_model_2_multimer_v3.npz -rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 23:31 params_model_3_multimer_v3.npz -rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 23:31 params_model_4_multimer_v3.npz -rw-rw-r-- htomlinson/primarygroup 373043148 2022-11-22 23:31 params_model_5_multimer_v3.npz -rw-rw-r-- htomlinson/primarygroup 18657 2020-03-24 08:05 LICENSE [root@rockylinux9 ~]# mkdir -p /apps/alphafold_params_2022-12-06/params [root@rockylinux9 ~]# tar xf ./alphafold_params_2022-12-06.tar -C /apps/alphafold_params_2022-12-06/params [root@rockylinux9 ~]# touch /apps/alphafold_params_2022-12-06/params/download_finished.txt <-- これ大事 [root@rockylinux9 ~]# ls -l /apps/alphafold_params_2022-12-06/params/ total 5457016 -rw-r--r-- 1 root root 0 Jun 26 03:03 download_finished.txt -rw-rw-r-- 1 995210 89939 18657 Mar 24 2020 LICENSE -rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_model_1_multimer_v3.npz -rw-rw-r-- 1 995210 89939 373069562 Jul 20 2021 params_model_1.npz -rw-rw-r-- 1 995210 89939 373103340 Jul 20 2021 params_model_1_ptm.npz -rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_model_2_multimer_v3.npz -rw-rw-r-- 1 995210 89939 373069562 Jul 20 2021 params_model_2.npz -rw-rw-r-- 1 995210 89939 373103340 Jul 20 2021 params_model_2_ptm.npz -rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_model_3_multimer_v3.npz -rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_model_3.npz -rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_model_3_ptm.npz -rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_model_4_multimer_v3.npz -rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_model_4.npz -rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_model_4_ptm.npz -rw-rw-r-- 1 995210 89939 373043148 Nov 22 2022 params_model_5_multimer_v3.npz -rw-rw-r-- 1 995210 89939 371712506 Jul 20 2021 params_model_5.npz -rw-rw-r-- 1 995210 89939 371746284 Jul 20 2021 params_model_5_ptm.npz [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/envs/default 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 called are written to STDERR E0000 00:00:1782410861.258811 9752 cuda_dnn.cc:8579] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered E0000 00:00:1782410861.261547 9752 cuda_blas.cc:1407] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered W0000 00:00:1782410861.268067 9752 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once. W0000 00:00:1782410861.268078 9752 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once. W0000 00:00:1782410861.268080 9752 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once. W0000 00:00:1782410861.268081 9752 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once. usage: colabfold_batch [-h] [--msa-only] [--msa-mode {mmseqs2_uniref_env,mmseqs2_uniref_env_envpair,mmseqs2_uniref,single_sequence}] [--pair-mode {unpaired,paired,unpaired_paired}] [--pair-strategy {complete,greedy}] [--templates] [--custom-template-path CUSTOM_TEMPLATE_PATH] [--custom-template-cache-path CUSTOM_TEMPLATE_CACHE_PATH] [--max-template-date MAX_TEMPLATE_DATE] [--max-template-hits MAX_TEMPLATE_HITS] [--pdb-hit-file PDB_HIT_FILE] [--local-pdb-path LOCAL_PDB_PATH] [--num-recycle NUM_RECYCLE] [--recycle-early-stop-tolerance RECYCLE_EARLY_STOP_TOLERANCE] [--num-ensemble NUM_ENSEMBLE] [--num-seeds NUM_SEEDS] [--random-seed RANDOM_SEED] [--num-models {1,2,3,4,5}] [--model-type {auto,alphafold2,alphafold2_ptm,alphafold2_multimer_v1,alphafold2_multimer_v2,alphafold2_multimer_v3,deepfold_v1}] [--model-order MODEL_ORDER] [--initial-guess [INITIAL_GUESS]] [--use-dropout] [--max-seq MAX_SEQ] [--max-extra-seq MAX_EXTRA_SEQ] [--max-msa MAX_MSA] [--disable-cluster-profile] [--calc-extra-ptm] [--no-use-probs-extra] [--data DATA] [--amber] [--num-relax NUM_RELAX] [--relax-max-iterations RELAX_MAX_ITERATIONS] [--relax-tolerance RELAX_TOLERANCE] [--relax-stiffness RELAX_STIFFNESS] [--relax-max-outer-iterations RELAX_MAX_OUTER_ITERATIONS] [--use-gpu-relax] [--rank {auto,plddt,ptm,iptm,multimer}] [--stop-at-score STOP_AT_SCORE] [--jobname-prefix JOBNAME_PREFIX] [--save-all] [--save-recycles] [--save-single-representations] [--save-pair-representations] [--skip-output SKIP_OUTPUT] [--overwrite-existing-results] [--zip] [--sort-queries-by {none,length,msa_depth,random}] [--host-url HOST_URL] [--disable-unified-memory] [--recompile-padding RECOMPILE_PADDING] [--use-pallas [BOOL]] [--debug-logging] [--af3-json] input results : : [illya@rockylinux test]$ cat<<_EOF_>query.fasta >sample PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK _EOF_ [saber@rockylinux test]$ colabfold_batch --amber --templates --num-recycle 3 --use-gpu-relax ./query.fasta ./out --data /apps/alphafold_params_2022-12-06 WARNING: All log messages before absl::InitializeLog() is called are written to STDERR E0000 00:00:1782411337.430049 10576 cuda_dnn.cc:8579] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered E0000 00:00:1782411337.432625 10576 cuda_blas.cc:1407] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered W0000 00:00:1782411337.439027 10576 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once. W0000 00:00:1782411337.439038 10576 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once. W0000 00:00:1782411337.439040 10576 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once. W0000 00:00:1782411337.439041 10576 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once. 2026-06-26 03:15:38,577 Running colabfold 1.6.1 (0ff4794957abbd5d476a6e1c9b3db853d2b607c9) 2026-06-26 03:15:38,817 Running on GPU W0000 00:00:1782411338.842585 10576 gpu_device.cc:2430] TensorFlow was not built with CUDA kernel binaries compatible with compute capability 12.0. CUDA kernels will be jit-compiled from PTX, which could take 30 minutes or longer. 2026-06-26 03:15:38,963 Found 9 citations for tools or databases 2026-06-26 03:15:38,963 Query 1/1: sample (length 59) COMPLETE: 100%|--------------------------------------------------------------------------| 150/150 [elapsed: 00:01 remaining: 00:00] 2026-06-26 03:15:43,190 Sequence 0 found templates: ['3mb2_C', '6bgn_C', '2fm7_B', '4fdx_A', '1otf_D', '3ry0_B', '1bjp_A', '7m59_B', '6fps_P', '6fps_R', '5cln_I', '5clo_C', '4faz_C', '7xuy_A', '3abf_B', '7puo_F', '4x1c_F', '6ogm_L', '2op8_A', '7puo_F'] 2026-06-26 03:15:43,475 Setting max_seq=512, max_extra_seq=5120 WARNING: All log messages before absl::InitializeLog() is called are written to STDERR I0000 00:00:1782411347.135745 10576 mlir_graph_optimization_pass.cc:425] MLIR V1 optimization pass is not enabled 2026-06-26 03:17:05,222 alphafold2_ptm_model_1_seed_000 recycle=0 pLDDT=97.9 pTM=0.786 2026-06-26 03:17:06,024 alphafold2_ptm_model_1_seed_000 recycle=1 pLDDT=97.8 pTM=0.789 tol=0.121 2026-06-26 03:17:06,780 alphafold2_ptm_model_1_seed_000 recycle=2 pLDDT=97.9 pTM=0.791 tol=0.0317 2026-06-26 03:17:07,537 alphafold2_ptm_model_1_seed_000 recycle=3 pLDDT=97.8 pTM=0.789 tol=0.0202 2026-06-26 03:17:07,537 alphafold2_ptm_model_1_seed_000 took 80.0s (3 recycles) 2026-06-26 03:17:08,297 alphafold2_ptm_model_2_seed_000 recycle=0 pLDDT=97.8 pTM=0.795 2026-06-26 03:17:09,056 alphafold2_ptm_model_2_seed_000 recycle=1 pLDDT=97.8 pTM=0.798 tol=0.0616 2026-06-26 03:17:09,816 alphafold2_ptm_model_2_seed_000 recycle=2 pLDDT=97.9 pTM=0.801 tol=0.0364 2026-06-26 03:17:10,576 alphafold2_ptm_model_2_seed_000 recycle=3 pLDDT=97.8 pTM=0.8 tol=0.0309 2026-06-26 03:17:10,576 alphafold2_ptm_model_2_seed_000 took 3.0s (3 recycles) 2026-06-26 03:17:34,557 alphafold2_ptm_model_3_seed_000 recycle=0 pLDDT=97.3 pTM=0.775 2026-06-26 03:17:35,323 alphafold2_ptm_model_3_seed_000 recycle=1 pLDDT=97.4 pTM=0.781 tol=0.312 2026-06-26 03:17:36,090 alphafold2_ptm_model_3_seed_000 recycle=2 pLDDT=97.4 pTM=0.784 tol=0.094 2026-06-26 03:17:36,857 alphafold2_ptm_model_3_seed_000 recycle=3 pLDDT=97.4 pTM=0.783 tol=0.0427 2026-06-26 03:17:36,858 alphafold2_ptm_model_3_seed_000 took 26.3s (3 recycles) 2026-06-26 03:17:37,628 alphafold2_ptm_model_4_seed_000 recycle=0 pLDDT=97.2 pTM=0.772 2026-06-26 03:17:38,397 alphafold2_ptm_model_4_seed_000 recycle=1 pLDDT=97.2 pTM=0.78 tol=0.271 2026-06-26 03:17:39,166 alphafold2_ptm_model_4_seed_000 recycle=2 pLDDT=97.1 pTM=0.78 tol=0.0482 2026-06-26 03:17:39,936 alphafold2_ptm_model_4_seed_000 recycle=3 pLDDT=96.9 pTM=0.779 tol=0.0405 2026-06-26 03:17:39,936 alphafold2_ptm_model_4_seed_000 took 3.1s (3 recycles) 2026-06-26 03:17:40,708 alphafold2_ptm_model_5_seed_000 recycle=0 pLDDT=96.8 pTM=0.779 2026-06-26 03:17:41,478 alphafold2_ptm_model_5_seed_000 recycle=1 pLDDT=96.4 pTM=0.779 tol=0.314 2026-06-26 03:17:42,249 alphafold2_ptm_model_5_seed_000 recycle=2 pLDDT=96.4 pTM=0.781 tol=0.0963 2026-06-26 03:17:43,019 alphafold2_ptm_model_5_seed_000 recycle=3 pLDDT=96.5 pTM=0.78 tol=0.0618 2026-06-26 03:17:43,019 alphafold2_ptm_model_5_seed_000 took 3.1s (3 recycles) 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_seed_000 pLDDT=97.8 pTM=0.8 2026-06-26 03:17:45,677 Relaxation took 0.9s 2026-06-26 03:17:45,677 rank_002_alphafold2_ptm_model_1_seed_000 pLDDT=97.8 pTM=0.789 2026-06-26 03:17:46,360 Relaxation took 0.7s 2026-06-26 03:17:46,361 rank_003_alphafold2_ptm_model_3_seed_000 pLDDT=97.4 pTM=0.783 2026-06-26 03:17:47,207 Relaxation took 0.8s 2026-06-26 03:17:47,207 rank_004_alphafold2_ptm_model_4_seed_000 pLDDT=96.9 pTM=0.779 2026-06-26 03:17:47,901 Relaxation took 0.7s 2026-06-26 03:17:47,901 rank_005_alphafold2_ptm_model_5_seed_000 pLDDT=96.5 pTM=0.78 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問題ないのですが、そうでない場合、そのまま実行するとその計算機にある全てのGPUを使って計算を行うみたい. &size(10){全てのGPUを使っているように見えるが実際には１つのGPUで処理しているみたい}; ２枚刺しGPUマシンで、cryoSPARCを流して、localcolabfoldを流すとたぶんcryoSPARCが使っているGPUにもそのジョブが回る。せっかく２枚あるならすみ分けてほしい. その場合は環境変数 CUDA_VISIBLE_DEVICES を使って使用するGPUを指定することが出来るっぽい #code(nonumber){{ CUDA_VISIBLE_DEVICES=1 colabfold_batch --amber --templates --num-recycle 3 --use-gpu-relax ./query.fasta ./out }} CUDA_VISIBLE_DEVICESは0から始まるようで、２枚目は「１」となる。この0とか1とかは、nvidia-smiで表示される GPU 番号と同じっぽい。
