localcolabfold

[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 ~]#

[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

[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

[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 ~]#

[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]$

CUDA_VISIBLE_DEVICES=1 colabfold_batch --amber --templates --num-recycle 3 --use-gpu-relax ./query.fasta ./out