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Alphafold2 v/s Parafold timings #21

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adi1bioinfo opened this issue Apr 29, 2022 · 1 comment
Open

Alphafold2 v/s Parafold timings #21

adi1bioinfo opened this issue Apr 29, 2022 · 1 comment

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@adi1bioinfo
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adi1bioinfo commented Apr 29, 2022 •
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I have a fundamental doubt about the difference between Alphafold2 and Parafold running procedure, how to determine whether Parafold is doing Parallel task unlike sequential tasks performed by Alphafold2 for the first step involving Jackhmmer, Jackhmmer and HHblits searches.

Snippets of log files obtained from running Alphafold2 and Parafold

Alphafold2 log:

I0409 14:04:28.020900 139865793787712 run_alphafold.py:376] Have 5 models: ['model_1_pred_0', 'model_2_pred_0', 'model_3_pred_0', 'model_4_pred_0', 'model_5_pred_0']
I0409 14:04:28.021180 139865793787712 run_alphafold.py:393] Using random seed 1420247507508611084 for the data pipeline
I0409 14:04:28.021463 139865793787712 run_alphafold.py:161] Predicting seq1
I0409 14:04:28.037414 139865793787712 jackhmmer.py:133] Launching subprocess "/.conda/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmpm1u84thu/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1/fasta_files/seq1.fasta /alphafold_data//uniref90/uniref90.fasta"
I0409 14:04:28.111756 139865793787712 utils.py:36] Started Jackhmmer (uniref90.fasta) query
I0409 14:10:17.276236 139865793787712 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 349.164 seconds
I0409 14:10:17.462168 139865793787712 jackhmmer.py:133] Launching subprocess "/.conda/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmpub1qi595/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /fasta_files/seq1.fasta /alphafold_data//mgnify/mgy_clusters_2018_12.fa"
I0409 14:10:17.513182 139865793787712 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query
I0409 14:16:32.112656 139865793787712 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 374.599 seconds
I0409 14:16:33.369129 139865793787712 hhsearch.py:85] Launching subprocess "/.conda/envs/alphafold/bin/hhsearch -i /tmp/tmpyot74k7r/query.a3m -o /tmp/tmpyot74k7r/output.hhr -maxseq 1000000 -d /alphafold_data//pdb70/pdb70"
I0409 14:16:33.466009 139865793787712 utils.py:36] Started HHsearch query
I0409 14:22:32.148045 139865793787712 utils.py:40] Finished HHsearch query in 358.682 seconds
I0409 14:22:32.838686 139865793787712 hhblits.py:128] Launching subprocess "/.conda/envs/alphafold/bin/hhblits -i /fasta_files/seq1.fasta -cpu 4 -oa3m /tmp/tmpedyoxta1/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /alphafold_data//bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /alphafold_data//uniclust30/uniclust30_2018_08/uniclust30_2018_08"
I0409 14:22:32.926801 139865793787712 utils.py:36] Started HHblits query
I0409 18:56:30.223437 139865793787712 utils.py:40] Finished HHblits query in 16437.296 seconds

Parafold log:

I0427 21:17:27.915049 140305630689088 run_alphafold.py:397] Have 5 models: ['model_1_pred_0', 'model_2_pred_0', 'model_3_pred_0', 'model_4_pred_0', 'model_5_pred_0']
I0427 21:17:27.915312 140305630689088 run_alphafold.py:414] Using random seed 1534697036303804749 for the data pipeline
I0427 21:17:27.915629 140305630689088 run_alphafold.py:165] Predicting seq2
I0427 21:17:27.925500 140305630689088 jackhmmer.py:133] Launching subprocess "/.conda/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmp5fo28348/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /fasta_files/seq2.fasta /alphafold_data//uniref90/uniref90.fasta"
I0427 21:17:27.996705 140305630689088 utils.py:36] Started Jackhmmer (uniref90.fasta) query
I0427 21:23:54.643056 140305630689088 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 386.646 seconds
I0427 21:23:54.829476 140305630689088 jackhmmer.py:133] Launching subprocess "/.conda/envs/alphafold/bin/jackhmmer -o /dev/null -A /tmp/tmprs3za6w_/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --incE 0.0001 -E 0.0001 --cpu 8 -N 1 /fasta_files/seq2.fasta /alphafold_data//mgnify/mgy_clusters_2018_12.fa"
I0427 21:23:54.875119 140305630689088 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query
I0427 21:31:38.409492 140305630689088 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 463.534 seconds
I0427 21:31:39.768360 140305630689088 hhsearch.py:85] Launching subprocess "/.conda/envs/alphafold/bin/hhsearch -i /tmp/tmpjgr58ebb/query.a3m -o /tmp/tmpjgr58ebb/output.hhr -maxseq 1000000 -d /alphafold_data//pdb70/pdb70"
I0427 21:31:39.850885 140305630689088 utils.py:36] Started HHsearch query
I0427 21:39:23.420352 140305630689088 utils.py:40] Finished HHsearch query in 463.569 seconds
I0427 21:39:24.173583 140305630689088 hhblits.py:128] Launching subprocess "/.conda/envs/alphafold/bin/hhblits -i /fasta_files/seq2.fasta -cpu 4 -oa3m /tmp/tmpmzl5arhr/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /alphafold_data//bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /alphafold_data//uniclust30/uniclust30_2018_08/uniclust30_2018_08"
I0427 21:39:24.259592 140305630689088 utils.py:36] Started HHblits query
I0428 01:34:31.302148 140305630689088 utils.py:40] Finished HHblits query in 14107.042 seconds

They look similar to me, and both use 8cpus, 8cpus, and 4cpus, respectively.
Please clarify this for me.

Thank you
Aditi
@Serious-Huang
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I'm also confused about this. When I use top to view a node's status, it seems MSA searches on CPUs are not running in parallel...

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@adi1bioinfo @Serious-Huang