本家様 https://github.com/YoshitakaMo/localcolabfold

localcolabfoldは、ColabFold様の「ColabFold: AlphaFold2 using MMseqs2」をlocal(自分の計算機)で実現できる代物でございます.
ColabFold様による「ColabFold」のご説明はこちら
https://docs.google.com/presentation/d/1mnffk23ev2QMDzGZ5w1skXEadTe54l8-Uei6ACce8eI/edit#slide=id.p

version 1.5.2 がリリースされました. それに伴いここの内容を書き換えてます

インストール

計算機に入っているCUDAのライブラリバージョンとGCCのバージョンをチェックします
サイトから 「Cuda compiler driver is 11.1 or later」で「GNU compiler version is 9.0 or later」とある.

[root@rockylinux ~]# cat /etc/redhat-release
Rocky Linux release 8.9 (Green Obsidian)
 
[root@rockylinux ~]#
[root@rockylinux ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module  535.146.02  Sun Dec  3 14:06:14 UTC 2023
GCC version:  gcc version 8.5.0 20210514 (Red Hat 8.5.0-18) (GCC)
 
[root@rockylinux ~]#
[root@rockylinux ~]# /usr/local/cuda/bin/nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Tue_Feb__7_19:32:13_PST_2023
Cuda compilation tools, release 12.1, V12.1.66
Build cuda_12.1.r12.1/compiler.32415258_0
 
[root@rockylinux ~]#

と、ここまで要件に合格しているのだが、gccはRockylinux8では8.5.0系なので要件には合わない

[root@rockylinux ~]# gcc --version
gcc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
[root@rockylinux ~]#

なので「gcc-toolset」で上げてみる

[root@rockylinux ~]# dnf install gcc-toolset-12
[root@rockylinux ~]# source scl_source enable gcc-toolset-12
[root@rockylinux ~]# gcc --version
gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-7)
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
[root@rockylinux ~]#

で一応達成できる.
っが、「GLIBCXX_3.4.26」が含まれることと書かれている.

[root@rockylinux ~]# strings /usr/lib64/libstdc++.so.6.0.25 |grep GLIBCXX
GLIBCXX_3.4
GLIBCXX_3.4.1
(略
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_DEBUG_MESSAGE_LENGTH
GA+GLIBCXX_ASSERTIONS
[root@rockylinux ~]#

と「GLIBCXX_3.4.26」は持っていないのだが....

一応これで作ってみる

githubからソースを取得して展開したい場所の上でインストーラーを実行します

[root@rockylinux ~]# mkdir -p /apps/src
[root@rockylinux ~]# cd /apps/src/
 
[root@rockylinux src]# git clone https://github.com/YoshitakaMo/localcolabfold
 
[root@rockylinux src]# cd localcolabfold/
 
[root@rockylinux localcolabfold]# git log -1
commit 6dde12ee16a7f8fa240be8a6c4a88a31f81ec16b (HEAD -> main, origin/main, origin/HEAD)
Author: YoshitakaMo <virgospica93@gmail.com>
Date:   Thu Jan 11 19:05:25 2024 +0900
 
    fix missing dependencies
 
[root@rockylinux localcolabfold]# cd /apps/
 
[root@rockylinux apps]# ./src/localcolabfold/install_colabbatch_linux.sh

EnvironmentModules

[root@rockylinux ~]# vi /apps/modulefiles/localcolabfold
#%Module1.0
set colabfold /apps/localcolabfold/colabfold-conda
prepend-path PATH $colabfold/bin
 
[root@rockylinux ~]#

テスト

予測対象の配列は別途ファイルで用意するみたい

[illya@rockylinux test]$ module load localcolabfold
 
[illya@rockylinux test]$ colabfold_batch -h
usage: colabfold_batch [-h] [--msa-only] [--msa-mode {mmseqs2_uniref_env,mmseqs2_uniref,single_sequence}]
                       [--pair-mode {unpaired,paired,unpaired_paired}] [--pair-strategy {complete,greedy}] [--templates]
                       [--custom-template-path CUSTOM_TEMPLATE_PATH] [--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]
 :
 :
[illya@rockylinux test]$ vi query.fasta
>sample
PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK
[illya@rockylinux test]$
 
[saber@rockylinux test]$ colabfold_batch --amber --templates --num-recycle 3 --use-gpu-relax ./query.fasta ./out
2024-01-12 01:21:44,537 Running colabfold 1.5.5 (941feece178db14c9af1580eefbf4a8fe4e5b5af)
2024-01-12 01:21:44,643 Unable to initialize backend 'rocm': NOT_FOUND: Could not find registered platform with name: "rocm". Available platform names are: CUDA
2024-01-12 01:21:44,644 Unable to initialize backend 'tpu': INTERNAL: Failed to open libtpu.so: libtpu.so: cannot open shared object file: No such file or directory
2024-01-12 01:21:44.817720: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:9261] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2024-01-12 01:21:44.817758: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:607] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2024-01-12 01:21:44.818446: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1515] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2024-01-12 01:21:45.386170: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-01-12 01:21:45,738 Running on GPU
2024-01-12 01:21:46,612 Failed to extract font properties from /usr/share/fonts/google-noto-emoji/NotoColorEmoji.ttf: In FT2Font: Can not load face (unknown file format; error code 0x2)
2024-01-12 01:21:47,008 generated new fontManager
 :
[illya@rockylinux test]$ ls -CF
out/  query.fasta
 
[illya@rockylinux test]$ ls -CF out/
cite.bibtex          sample_predicted_aligned_error_v1.json                       sample_scores_rank_004_alphafold2_ptm_model_4_seed_000.json
config.json          sample_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb  sample_scores_rank_005_alphafold2_ptm_model_5_seed_000.json
log.txt              sample_relaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb  sample_template_domain_names.json
sample.a3m           sample_relaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb  sample_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
sample_coverage.png  sample_relaxed_rank_004_alphafold2_ptm_model_4_seed_000.pdb  sample_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
sample.done.txt      sample_relaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb  sample_unrelaxed_rank_003_alphafold2_ptm_model_3_seed_000.pdb
sample_env/          sample_scores_rank_001_alphafold2_ptm_model_2_seed_000.json  sample_unrelaxed_rank_004_alphafold2_ptm_model_4_seed_000.pdb
sample_pae.png       sample_scores_rank_002_alphafold2_ptm_model_1_seed_000.json  sample_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
sample_plddt.png     sample_scores_rank_003_alphafold2_ptm_model_3_seed_000.json
 
[illya@rockylinux test]$

ログには「colabfold 1.5.5」とあるがlocalcolabfold としては1.5.2って事かな?
openmmに「GLIBCXX_3.4.26」が必要とあるが、なくてもなんか行けているみたい

入力ファイルはソースコードを拝見すると、a3m形式(拡張子が[.a3m])、fasta形式(拡張子が[.fasta]、[.faa]、[.fa])の他に
csvやtsvでも対応みたい.

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Last-modified: 2024-01-12 (金) 01:47:58