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YoshitakaMo / localcolabfold

ColabFold on your local PC
MIT License
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Question: After updating from cuda 11.5 to 11.8+, do I need to re-install localcolabfold? #213

Open dbolser opened 9 months ago

dbolser commented 9 months ago

I'm cautiously updating cuda from the package managers version (11.5) to the required minimum (11.8+ ... I think I'm getting 12.3.2...).

I'm first removing cuda like this:

sudo apt-get --purge remove "*cuda*" "*cublas*" "*cufft*" "*curand*" "*cusolver*" "*cusparse*" "*npp*" "*nvjpeg*" "nsight*" "*nvvm*"

Then adding the package here: https://developer.nvidia.com/cuda-downloads?target_os=Linux&target_arch=x86_64&Distribution=Ubuntu&target_version=22.04&target_type=deb_local

I'll try this obviously, but do I need to re-install the localcolabfold from scratch after updating cuda?

Thanks

dbolser commented 9 months ago

Seems to be working...

However, I set --use-gpu-relax as a test on a /similar/ run to one that finished in about 30 mins... this one seems to be taking forever...

First run, without gpu-relax:

$ time colabfold_batch --templates --amber P0DPD7-P68104.fasta P0DPD7-P68104/
2024-02-13 12:43:27,725 Running colabfold 1.5.5 (0cf2621921f2e79a1da9db7ba2ed072291f68e45)
2024-02-13 12:43:27,890 Running on GPU
2024-02-13 12:43:28,180 Found 9 citations for tools or databases
2024-02-13 12:43:28,180 Query 1/1: EEF1AKMT4_EEF1A1_complex (length 717)
COMPLETE: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 300/300 [elapsed: 00:27 remaining: 00:00]
2024-02-13 12:47:09,200 Sequence 0 found templates: ['2pxx_A', '3bus_A', '3bus_A', '3bkw_A', '6uv6_B', '2avn_A', '5gm2_L', '2gs9_A', '5gm2_N', '5gm1_L', '3sm3_A', '3mgg_A', '4ine_A', '4ine_B', '1ve3_A', '1ve3_A', '6uak_A', '3l8d_A', '5wp5_B', '5wp4_A']
2024-02-13 12:47:28,352 Sequence 1 found templates: ['6ra9_B', '4c0s_A', '8g5z_EF', '4c0s_A', '1ije_A', '4cxg_A', '5lzy_jj', '1jny_A', '1jny_B', '3wy9_B', '7csl_A', '3j5y_B', '3wya_A', '4d61_i', '4crn_P', '5w75_A', '5w75_B', '5w75_D', '1r5o_A', '1r5n_A']
COMPLETE: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 300/300 [elapsed: 00:05 remaining: 00:00]
2024-02-13 12:47:35,906 Setting max_seq=508, max_extra_seq=2048
2024-02-13 12:49:02,999 alphafold2_multimer_v3_model_1_seed_000 recycle=0 pLDDT=85.1 pTM=0.757 ipTM=0.758
2024-02-13 12:49:51,358 alphafold2_multimer_v3_model_1_seed_000 recycle=1 pLDDT=87.2 pTM=0.812 ipTM=0.805 tol=1.99
2024-02-13 12:50:38,197 alphafold2_multimer_v3_model_1_seed_000 recycle=2 pLDDT=86.8 pTM=0.803 ipTM=0.815 tol=1.13
2024-02-13 12:51:24,919 alphafold2_multimer_v3_model_1_seed_000 recycle=3 pLDDT=87.4 pTM=0.804 ipTM=0.834 tol=0.435
2024-02-13 12:51:24,920 alphafold2_multimer_v3_model_1_seed_000 took 224.6s (3 recycles)
2024-02-13 12:52:11,971 alphafold2_multimer_v3_model_2_seed_000 recycle=0 pLDDT=87.2 pTM=0.821 ipTM=0.766
2024-02-13 12:52:58,632 alphafold2_multimer_v3_model_2_seed_000 recycle=1 pLDDT=87.4 pTM=0.819 ipTM=0.805 tol=1.39
2024-02-13 12:53:45,287 alphafold2_multimer_v3_model_2_seed_000 recycle=2 pLDDT=87.2 pTM=0.794 ipTM=0.798 tol=0.587
2024-02-13 12:54:32,967 alphafold2_multimer_v3_model_2_seed_000 recycle=3 pLDDT=87.1 pTM=0.78 ipTM=0.799 tol=0.149
2024-02-13 12:54:32,968 alphafold2_multimer_v3_model_2_seed_000 took 187.8s (3 recycles)
2024-02-13 12:55:21,764 alphafold2_multimer_v3_model_3_seed_000 recycle=0 pLDDT=84 pTM=0.687 ipTM=0.686
2024-02-13 12:56:11,831 alphafold2_multimer_v3_model_3_seed_000 recycle=1 pLDDT=87.4 pTM=0.811 ipTM=0.819 tol=3.34
2024-02-13 12:57:00,742 alphafold2_multimer_v3_model_3_seed_000 recycle=2 pLDDT=88.1 pTM=0.828 ipTM=0.829 tol=1.3
2024-02-13 12:57:49,461 alphafold2_multimer_v3_model_3_seed_000 recycle=3 pLDDT=87.8 pTM=0.803 ipTM=0.804 tol=0.439
2024-02-13 12:57:49,462 alphafold2_multimer_v3_model_3_seed_000 took 196.2s (3 recycles)
2024-02-13 12:58:38,175 alphafold2_multimer_v3_model_4_seed_000 recycle=0 pLDDT=80.8 pTM=0.59 ipTM=0.605
2024-02-13 12:59:26,725 alphafold2_multimer_v3_model_4_seed_000 recycle=1 pLDDT=86.6 pTM=0.789 ipTM=0.811 tol=13.1
2024-02-13 13:00:14,884 alphafold2_multimer_v3_model_4_seed_000 recycle=2 pLDDT=87.9 pTM=0.796 ipTM=0.83 tol=1.22
2024-02-13 13:01:03,023 alphafold2_multimer_v3_model_4_seed_000 recycle=3 pLDDT=86.8 pTM=0.759 ipTM=0.782 tol=0.274
2024-02-13 13:01:03,023 alphafold2_multimer_v3_model_4_seed_000 took 193.3s (3 recycles)
2024-02-13 13:01:51,901 alphafold2_multimer_v3_model_5_seed_000 recycle=0 pLDDT=86.7 pTM=0.807 ipTM=0.747
2024-02-13 13:02:39,922 alphafold2_multimer_v3_model_5_seed_000 recycle=1 pLDDT=86.9 pTM=0.804 ipTM=0.784 tol=0.808
2024-02-13 13:03:28,248 alphafold2_multimer_v3_model_5_seed_000 recycle=2 pLDDT=87.2 pTM=0.817 ipTM=0.813 tol=0.424
2024-02-13 13:03:28,249 alphafold2_multimer_v3_model_5_seed_000 took 144.9s (2 recycles)
2024-02-13 13:03:28,532 reranking models by 'multimer' metric
2024-02-13 13:03:28,963 Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
2024-02-13 13:05:17,822 Relaxation took 109.3s
2024-02-13 13:05:17,822 rank_001_alphafold2_multimer_v3_model_1_seed_000 pLDDT=87.4 pTM=0.804 ipTM=0.834
2024-02-13 13:12:25,391 Relaxation took 427.6s
2024-02-13 13:12:25,391 rank_002_alphafold2_multimer_v3_model_5_seed_000 pLDDT=87.2 pTM=0.817 ipTM=0.813
2024-02-13 13:14:36,916 Relaxation took 131.5s
2024-02-13 13:14:36,916 rank_003_alphafold2_multimer_v3_model_3_seed_000 pLDDT=87.8 pTM=0.803 ipTM=0.804
2024-02-13 13:21:36,510 Relaxation took 419.6s
2024-02-13 13:21:36,510 rank_004_alphafold2_multimer_v3_model_2_seed_000 pLDDT=87.1 pTM=0.78 ipTM=0.799
2024-02-13 13:23:18,092 Relaxation took 101.6s
2024-02-13 13:23:18,092 rank_005_alphafold2_multimer_v3_model_4_seed_000 pLDDT=86.8 pTM=0.759 ipTM=0.782
2024-02-13 13:23:19,178 Done

real    39m56.113s
user    572m40.031s
sys 8m35.583s

Second run, /with/ gpu-relax:

$ time colabfold_batch --templates --amber --use-gpu-relax Q8N6R0-P68104.fasta Q8N6R0-P68104
2024-02-13 14:09:50,144 Running colabfold 1.5.5 (0cf2621921f2e79a1da9db7ba2ed072291f68e45)
2024-02-13 14:09:50,317 Running on GPU
2024-02-13 14:09:50,600 Found 9 citations for tools or databases
2024-02-13 14:09:50,600 Query 1/1: METTL13_EEF1A1_complex (length 1161)
COMPLETE: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████| 300/300 [elapsed: 00:35 remaining: 00:00]
2024-02-13 14:12:02,878 Sequence 0 found templates: ['5wcj_A', '2pxx_A', '3gjy_A', '6qmm_B', '7xih_A', '6o65_C', '2q41_A', '2q41_A', '6o64_A', '6o63_A', '6o64_H', '6o63_B', '6o63_D', '6o64_E', '6o65_H', '6o64_B', '6o64_D', '6o64_C', '1ve3_A', '1ve3_A']
2024-02-13 14:12:21,853 Sequence 1 found templates: ['6ra9_B', '4c0s_A', '8g5z_EF', '4c0s_A', '1ije_A', '4cxg_A', '5lzy_jj', '1jny_A', '1jny_B', '3wy9_B', '7csl_A', '3j5y_B', '3wya_A', '4d61_i', '4crn_P', '5w75_A', '5w75_B', '5w75_D', '1r5o_A', '1r5n_A']
COMPLETE: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████| 300/300 [elapsed: 00:08 remaining: 00:00]
2024-02-13 14:12:33,854 Setting max_seq=508, max_extra_seq=2048
2024-02-13 14:15:58,537 alphafold2_multimer_v3_model_1_seed_000 recycle=0 pLDDT=78.1 pTM=0.526 ipTM=0.19
2024-02-13 14:18:45,568 alphafold2_multimer_v3_model_1_seed_000 recycle=1 pLDDT=78.8 pTM=0.517 ipTM=0.243 tol=4.13
2024-02-13 14:21:27,262 alphafold2_multimer_v3_model_1_seed_000 recycle=2 pLDDT=78.6 pTM=0.482 ipTM=0.259 tol=3.36
2024-02-13 14:24:14,520 alphafold2_multimer_v3_model_1_seed_000 recycle=3 pLDDT=78.5 pTM=0.481 ipTM=0.369 tol=2.63
2024-02-13 14:27:01,185 alphafold2_multimer_v3_model_1_seed_000 recycle=4 pLDDT=78.4 pTM=0.477 ipTM=0.41 tol=2.72
2024-02-13 14:29:50,727 alphafold2_multimer_v3_model_1_seed_000 recycle=5 pLDDT=79.2 pTM=0.476 ipTM=0.459 tol=3.2
2024-02-13 14:32:33,657 alphafold2_multimer_v3_model_1_seed_000 recycle=6 pLDDT=79.2 pTM=0.479 ipTM=0.477 tol=2.16
2024-02-13 14:35:24,475 alphafold2_multimer_v3_model_1_seed_000 recycle=7 pLDDT=78.9 pTM=0.469 ipTM=0.478 tol=1.61
2024-02-13 14:38:24,367 alphafold2_multimer_v3_model_1_seed_000 recycle=8 pLDDT=79.1 pTM=0.471 ipTM=0.495 tol=1.12
2024-02-13 14:41:29,017 alphafold2_multimer_v3_model_1_seed_000 recycle=9 pLDDT=79.5 pTM=0.473 ipTM=0.505 tol=0.61
2024-02-13 14:44:48,524 alphafold2_multimer_v3_model_1_seed_000 recycle=10 pLDDT=78.8 pTM=0.465 ipTM=0.482 tol=0.773
2024-02-13 14:47:28,409 alphafold2_multimer_v3_model_1_seed_000 recycle=11 pLDDT=79.1 pTM=0.47 ipTM=0.488 tol=0.899
2024-02-13 14:50:10,124 alphafold2_multimer_v3_model_1_seed_000 recycle=12 pLDDT=78.9 pTM=0.469 ipTM=0.496 tol=0.857
2024-02-13 14:52:50,813 alphafold2_multimer_v3_model_1_seed_000 recycle=13 pLDDT=79.4 pTM=0.475 ipTM=0.5 tol=0.999
2024-02-13 14:55:30,049 alphafold2_multimer_v3_model_1_seed_000 recycle=14 pLDDT=79.2 pTM=0.477 ipTM=0.509 tol=0.833
2024-02-13 14:58:10,432 alphafold2_multimer_v3_model_1_seed_000 recycle=15 pLDDT=79.1 pTM=0.47 ipTM=0.492 tol=0.749
2024-02-13 15:00:48,313 alphafold2_multimer_v3_model_1_seed_000 recycle=16 pLDDT=79.1 pTM=0.471 ipTM=0.491 tol=0.962
2024-02-13 15:03:27,536 alphafold2_multimer_v3_model_1_seed_000 recycle=17 pLDDT=79 pTM=0.47 ipTM=0.488 tol=0.752
2024-02-13 15:06:06,636 alphafold2_multimer_v3_model_1_seed_000 recycle=18 pLDDT=79.1 pTM=0.472 ipTM=0.496 tol=1.01
2024-02-13 15:08:43,932 alphafold2_multimer_v3_model_1_seed_000 recycle=19 pLDDT=79.4 pTM=0.472 ipTM=0.501 tol=0.664
2024-02-13 15:11:22,060 alphafold2_multimer_v3_model_1_seed_000 recycle=20 pLDDT=79.4 pTM=0.476 ipTM=0.502 tol=0.832
2024-02-13 15:11:22,062 alphafold2_multimer_v3_model_1_seed_000 took 3525.1s (20 recycles)
2024-02-13 15:14:00,965 alphafold2_multimer_v3_model_2_seed_000 recycle=0 pLDDT=78.4 pTM=0.506 ipTM=0.192
2024-02-13 15:16:39,157 alphafold2_multimer_v3_model_2_seed_000 recycle=1 pLDDT=77.4 pTM=0.49 ipTM=0.185 tol=9.77
2024-02-13 15:19:52,330 alphafold2_multimer_v3_model_2_seed_000 recycle=2 pLDDT=79.4 pTM=0.467 ipTM=0.178 tol=4.96
2024-02-13 15:23:01,521 alphafold2_multimer_v3_model_2_seed_000 recycle=3 pLDDT=79.1 pTM=0.458 ipTM=0.172 tol=3.54
2024-02-13 15:26:48,664 alphafold2_multimer_v3_model_2_seed_000 recycle=4 pLDDT=79.5 pTM=0.457 ipTM=0.172 tol=1.8
2024-02-13 15:30:36,407 alphafold2_multimer_v3_model_2_seed_000 recycle=5 pLDDT=79.4 pTM=0.445 ipTM=0.167 tol=2.47
2024-02-13 15:33:23,117 alphafold2_multimer_v3_model_2_seed_000 recycle=6 pLDDT=79.6 pTM=0.451 ipTM=0.166 tol=0.865
2024-02-13 15:36:15,044 alphafold2_multimer_v3_model_2_seed_000 recycle=7 pLDDT=79.1 pTM=0.437 ipTM=0.167 tol=3.26
2024-02-13 15:39:21,990 alphafold2_multimer_v3_model_2_seed_000 recycle=8 pLDDT=79.1 pTM=0.44 ipTM=0.165 tol=0.992
2024-02-13 15:42:35,155 alphafold2_multimer_v3_model_2_seed_000 recycle=9 pLDDT=79.1 pTM=0.433 ipTM=0.166 tol=0.88
2024-02-13 15:45:49,030 alphafold2_multimer_v3_model_2_seed_000 recycle=10 pLDDT=79.2 pTM=0.439 ipTM=0.168 tol=0.878
2024-02-13 15:48:33,548 alphafold2_multimer_v3_model_2_seed_000 recycle=11 pLDDT=78.9 pTM=0.433 ipTM=0.167 tol=0.887
2024-02-13 15:51:19,187 alphafold2_multimer_v3_model_2_seed_000 recycle=12 pLDDT=79.1 pTM=0.433 ipTM=0.164 tol=0.746
2024-02-13 15:54:03,934 alphafold2_multimer_v3_model_2_seed_000 recycle=13 pLDDT=79.3 pTM=0.437 ipTM=0.165 tol=0.381
2024-02-13 15:54:03,935 alphafold2_multimer_v3_model_2_seed_000 took 2561.1s (13 recycles)
2024-02-13 15:57:23,288 alphafold2_multimer_v3_model_3_seed_000 recycle=0 pLDDT=80.5 pTM=0.499 ipTM=0.16
2024-02-13 16:00:40,529 alphafold2_multimer_v3_model_3_seed_000 recycle=1 pLDDT=78.9 pTM=0.489 ipTM=0.196 tol=14.6
2024-02-13 16:04:00,135 alphafold2_multimer_v3_model_3_seed_000 recycle=2 pLDDT=78.6 pTM=0.468 ipTM=0.175 tol=6.95
2024-02-13 16:06:44,090 alphafold2_multimer_v3_model_3_seed_000 recycle=3 pLDDT=78.6 pTM=0.448 ipTM=0.17 tol=1.54
2024-02-13 16:09:27,018 alphafold2_multimer_v3_model_3_seed_000 recycle=4 pLDDT=78.6 pTM=0.454 ipTM=0.167 tol=2.06
2024-02-13 16:12:33,353 alphafold2_multimer_v3_model_3_seed_000 recycle=5 pLDDT=78.8 pTM=0.446 ipTM=0.166 tol=1.37
2024-02-13 16:15:20,836 alphafold2_multimer_v3_model_3_seed_000 recycle=6 pLDDT=78.8 pTM=0.452 ipTM=0.175 tol=2.95
2024-02-13 16:18:05,085 alphafold2_multimer_v3_model_3_seed_000 recycle=7 pLDDT=79.1 pTM=0.451 ipTM=0.17 tol=3.52
2024-02-13 16:20:46,356 alphafold2_multimer_v3_model_3_seed_000 recycle=8 pLDDT=78.7 pTM=0.438 ipTM=0.166 tol=2.12
2024-02-13 16:23:29,049 alphafold2_multimer_v3_model_3_seed_000 recycle=9 pLDDT=79.2 pTM=0.455 ipTM=0.168 tol=2.75
2024-02-13 16:26:11,654 alphafold2_multimer_v3_model_3_seed_000 recycle=10 pLDDT=78.8 pTM=0.434 ipTM=0.163 tol=2.46
2024-02-13 16:28:54,762 alphafold2_multimer_v3_model_3_seed_000 recycle=11 pLDDT=78.9 pTM=0.455 ipTM=0.161 tol=2.44
2024-02-13 16:31:38,416 alphafold2_multimer_v3_model_3_seed_000 recycle=12 pLDDT=78.7 pTM=0.434 ipTM=0.166 tol=2.91
2024-02-13 16:34:23,148 alphafold2_multimer_v3_model_3_seed_000 recycle=13 pLDDT=79.2 pTM=0.455 ipTM=0.164 tol=2.83
2024-02-13 16:37:05,185 alphafold2_multimer_v3_model_3_seed_000 recycle=14 pLDDT=78.6 pTM=0.444 ipTM=0.172 tol=2.86
2024-02-13 16:39:44,853 alphafold2_multimer_v3_model_3_seed_000 recycle=15 pLDDT=78.9 pTM=0.46 ipTM=0.168 tol=1.49
2024-02-13 16:42:26,276 alphafold2_multimer_v3_model_3_seed_000 recycle=16 pLDDT=77.9 pTM=0.445 ipTM=0.177 tol=2.18
2024-02-13 16:45:07,437 alphafold2_multimer_v3_model_3_seed_000 recycle=17 pLDDT=78.9 pTM=0.463 ipTM=0.167 tol=2.7
2024-02-13 16:47:49,107 alphafold2_multimer_v3_model_3_seed_000 recycle=18 pLDDT=78.3 pTM=0.443 ipTM=0.166 tol=1.8
2024-02-13 16:50:30,455 alphafold2_multimer_v3_model_3_seed_000 recycle=19 pLDDT=78.7 pTM=0.454 ipTM=0.163 tol=1.55
2024-02-13 16:53:12,160 alphafold2_multimer_v3_model_3_seed_000 recycle=20 pLDDT=78.4 pTM=0.444 ipTM=0.171 tol=1.75
2024-02-13 16:53:12,162 alphafold2_multimer_v3_model_3_seed_000 took 3547.5s (20 recycles)
2024-02-13 16:55:51,744 alphafold2_multimer_v3_model_4_seed_000 recycle=0 pLDDT=79.4 pTM=0.493 ipTM=0.166
2024-02-13 16:58:29,576 alphafold2_multimer_v3_model_4_seed_000 recycle=1 pLDDT=78 pTM=0.491 ipTM=0.163 tol=3.05
...

I guess I should just be patient?