Expected performance for GPU e2e, seems slow #689

agenore · 2025-03-03T01:50:04Z

I'm trying to run a single colabfold_search with gpu. only one line in my fasta.

The machine is quite powerful, but it seems that it took about 9 minutes to run through all of the steps and it caught me by surprise as I expected it being a little faster.

I also tried to run it starting the GPU server beforehand, but the result was similar.
I tried both downloading and building mmseqs, but no difference.

as I wanted to run in ungapped fashion, do you think this result is expected?
any other advice?

-> % cat /colabfold/experiment/single.fasta        
>13836b2592094dd0abbe66ca1fa1f7f45c848a348e867b4c92be7336d41b739a
MAAAAQLSLTQLSSGNPVYEKYYRQVDTGNTGRVLASDAAAFLKKSGLPDLILGKIWDLADTDGKGILNKQEFFVALRLVACAQNGLEVSLSSLNLAVPPPRFHDTSSPLLISGTSAAELPWAVKPEDKAKYDAIFDSLSPVNGFLSGDKVKPVLLNSKLPVDILGRVWELSDIDHDGMLDRDEFAVAMFLVYCALEKEPVPMSLPPALVPPSKRKTWVVSPAEKAKYDEIFLKTDKDMDGFVSGLEVREIFLKTGLPSTLLAHIWSLCDTKDCGKLSKDQFALAFHLISQKLIKGIDPPHVLTPEMIPPSDRASLQKNIIGSSPVADFSAIKELDTLNNEIVDLQREKNNVEQDLKEKEDTIKQRTSEVQDLQDEVQRENTNLQKLQAQKQQVQELLDELDEQKAQLEEQLKEVRKKCAEEAQLISSLKAELTSQESQISTYEEELAKAREELSRLQQETAELEESVESGKAQLEPLQQHLQDSQQEISSMQMKLMEMKDLENHNSQLNWCSSPHSILVNGATDYCSLSTSSSETANLNEHVEGQSNLESEPIHQESPARSSPELLPSGVTDENEVTTAVTEKVCSELDNNRHSKEEDPFNVDSSSLTGPVADTNLDFFQSDPFVGSDPFKDDPFGKIDPFGGDPFKGSDPFASDCFFRQSTDPFATSSTDPFSAANNSSITSVETLKHNDPFAPGGTVVAASDSATDPFASVFGNESFGGGFADFSTLSKVNNEDPFRSATSSSVSNVVITKNVFEETSVKSEDEPPALPPKIGTPTRPCPLPPGKRSINKLDSPDPFKLNDPFQPFPGNDSPKEKDPEIFCDPFTSATTTTNKEADPSNFANFSAYPSEEDMIEWAKRESEREEEQRLARLNQQEQEDLELAIALSKSEISEA


-> % time colabfold_search --mmseqs ../MMseqs2/build/bin/mmseqs --gpu 1 --gpu-server 0 /colabfold/experiment/single.fasta /colabfold/dbs /colabfold/experiment/

INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs createdb /colabfold/experiment/query.fas /colabfold/experiment/qdb --shuffle 0
createdb /colabfold/experiment/query.fas /colabfold/experiment/qdb --shuffle 0 

Converting sequences

Time for merging to qdb_h: 0h 0m 0s 0ms
Time for merging to qdb: 0h 0m 0s 0ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs search /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db /colabfold/experiment/res /colabfold/experiment/tmp --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1
Create directory /colabfold/experiment/tmp
search /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db /colabfold/experiment/res /colabfold/experiment/tmp --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1 

ungappedprefilter /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/tmp/9697694622423327960/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
[=================================================================] 100.00% 1 eta -
Time for merging to pref_0: 0h 0m 0s 0ms
Time for processing: 0h 0m 10s 756ms
align /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/tmp/9697694622423327960/pref_0 /colabfold/experiment/tmp/9697694622423327960/aln_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 1 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Compute score only
Query database size: 1 type: Aminoacid
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 1 eta -
Time for merging to aln_0: 0h 0m 0s 0ms
10000 alignments calculated
1563 sequence pairs passed the thresholds (0.156300 of overall calculated)
1563.000000 hits per query sequence
Time for processing: 0h 0m 1s 500ms
result2profile /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/tmp/9697694622423327960/aln_0 /colabfold/experiment/tmp/9697694622423327960/profile_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 36293491 type: Aminoacid
[=================================================================] 100.00% 1 eta -
Time for merging to profile_0: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 601ms
ungappedprefilter /colabfold/experiment/tmp/9697694622423327960/profile_0 /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/tmp/9697694622423327960/pref_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
[=================================================================] 100.00% 1 eta -
Time for merging to pref_tmp_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 10s 141ms
subtractdbs /colabfold/experiment/tmp/9697694622423327960/pref_tmp_1 /colabfold/experiment/tmp/9697694622423327960/aln_0 /colabfold/experiment/tmp/9697694622423327960/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3 

subtractdbs /colabfold/experiment/tmp/9697694622423327960/pref_tmp_1 /colabfold/experiment/tmp/9697694622423327960/aln_0 /colabfold/experiment/tmp/9697694622423327960/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3 

Remove /colabfold/experiment/tmp/9697694622423327960/aln_0 ids from /colabfold/experiment/tmp/9697694622423327960/pref_tmp_1
[=================================================================] 100.00% 1 eta -
Time for merging to pref_1: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 59ms
rmdb /colabfold/experiment/tmp/9697694622423327960/pref_tmp_1 

Time for processing: 0h 0m 0s 0ms
align /colabfold/experiment/tmp/9697694622423327960/profile_0 /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/tmp/9697694622423327960/pref_1 /colabfold/experiment/tmp/9697694622423327960/aln_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 1 eta -
Time for merging to aln_tmp_1: 0h 0m 0s 0ms
8448 alignments calculated
1015 sequence pairs passed the thresholds (0.120147 of overall calculated)
1015.000000 hits per query sequence
Time for processing: 0h 0m 1s 24ms
mergedbs /colabfold/experiment/tmp/9697694622423327960/profile_0 /colabfold/experiment/tmp/9697694622423327960/aln_1 /colabfold/experiment/tmp/9697694622423327960/aln_0 /colabfold/experiment/tmp/9697694622423327960/aln_tmp_1 

Merging the results to /colabfold/experiment/tmp/9697694622423327960/aln_1
[=================================================================] 100.00% 1 eta -
Time for merging to aln_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 1ms
rmdb /colabfold/experiment/tmp/9697694622423327960/aln_0 

Time for processing: 0h 0m 0s 0ms
rmdb /colabfold/experiment/tmp/9697694622423327960/aln_tmp_1 

Time for processing: 0h 0m 0s 0ms
result2profile /colabfold/experiment/tmp/9697694622423327960/profile_0 /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/tmp/9697694622423327960/aln_1 /colabfold/experiment/tmp/9697694622423327960/profile_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Query database size: 1 type: Profile
Target database size: 36293491 type: Aminoacid
[=================================================================] 100.00% 1 eta -
Time for merging to profile_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 735ms
ungappedprefilter /colabfold/experiment/tmp/9697694622423327960/profile_1 /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/tmp/9697694622423327960/pref_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
[=================================================================] 100.00% 1 eta -
Time for merging to pref_tmp_2: 0h 0m 0s 0ms
Time for processing: 0h 0m 9s 301ms
subtractdbs /colabfold/experiment/tmp/9697694622423327960/pref_tmp_2 /colabfold/experiment/tmp/9697694622423327960/aln_1 /colabfold/experiment/tmp/9697694622423327960/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3 

subtractdbs /colabfold/experiment/tmp/9697694622423327960/pref_tmp_2 /colabfold/experiment/tmp/9697694622423327960/aln_1 /colabfold/experiment/tmp/9697694622423327960/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3 

Remove /colabfold/experiment/tmp/9697694622423327960/aln_1 ids from /colabfold/experiment/tmp/9697694622423327960/pref_tmp_2
[=================================================================] 100.00% 1 eta -
Time for merging to pref_2: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 549ms
rmdb /colabfold/experiment/tmp/9697694622423327960/pref_tmp_2 

Time for processing: 0h 0m 0s 0ms
align /colabfold/experiment/tmp/9697694622423327960/profile_1 /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/tmp/9697694622423327960/pref_2 /colabfold/experiment/tmp/9697694622423327960/aln_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 1 eta -
Time for merging to aln_tmp_2: 0h 0m 0s 0ms
7505 alignments calculated
4597 sequence pairs passed the thresholds (0.612525 of overall calculated)
4597.000000 hits per query sequence
Time for processing: 0h 0m 1s 408ms
mergedbs /colabfold/experiment/tmp/9697694622423327960/profile_1 /colabfold/experiment/res /colabfold/experiment/tmp/9697694622423327960/aln_1 /colabfold/experiment/tmp/9697694622423327960/aln_tmp_2 

Merging the results to /colabfold/experiment/res
[=================================================================] 100.00% 1 eta -
Time for merging to res: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
rmdb /colabfold/experiment/tmp/9697694622423327960/aln_1 

Time for processing: 0h 0m 0s 0ms
rmdb /colabfold/experiment/tmp/9697694622423327960/aln_tmp_2 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs mvdb /colabfold/experiment/tmp/latest/profile_1 /colabfold/experiment/prof_res
mvdb /colabfold/experiment/tmp/latest/profile_1 /colabfold/experiment/prof_res 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs lndb /colabfold/experiment/qdb_h /colabfold/experiment/prof_res_h
lndb /colabfold/experiment/qdb_h /colabfold/experiment/prof_res_h 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs expandaln /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res_exp --db-load-mode 0 --threads 64 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95
expandaln /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res_exp --db-load-mode 0 --threads 64 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
[=================================================================] 100.00% 1 eta -
Time for merging to res_exp: 0h 0m 0s 4ms
Time for processing: 0h 1m 45s 269ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs align /colabfold/experiment/prof_res /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res_exp /colabfold/experiment/res_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a
align /colabfold/experiment/prof_res /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res_exp /colabfold/experiment/res_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 350950053 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 1 eta -
Time for merging to res_exp_realign: 0h 0m 0s 0ms
50815 alignments calculated
44816 sequence pairs passed the thresholds (0.881944 of overall calculated)
44816.000000 hits per query sequence
Time for processing: 0h 1m 11s 416ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs filterresult /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res_exp_realign /colabfold/experiment/res_exp_realign_filter --db-load-mode 0 --qid 0 --qsc 0.8 --diff 0 --threads 64 --max-seq-id 1.0 --filter-min-enable 100
filterresult /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res_exp_realign /colabfold/experiment/res_exp_realign_filter --db-load-mode 0 --qid 0 --qsc 0.8 --diff 0 --threads 64 --max-seq-id 1.0 --filter-min-enable 100 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 350950053 type: Aminoacid
[=================================================================] 100.00% 1 eta -
Time for merging to res_exp_realign_filter: 0h 0m 0s 0ms
Time for processing: 0h 0m 7s 961ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs result2msa /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res_exp_realign_filter /colabfold/experiment/uniref.a3m --msa-format-mode 6 --db-load-mode 0 --threads 64 --filter-msa 1 --filter-min-enable 1000 --diff 3000 --qid 0.0,0.2,0.4,0.6,0.8,1.0 --qsc 0 --max-seq-id 0.95
result2msa /colabfold/experiment/qdb /colabfold/dbs/uniref30_2302_db.idx /colabfold/experiment/res_exp_realign_filter /colabfold/experiment/uniref.a3m --msa-format-mode 6 --db-load-mode 0 --threads 64 --filter-msa 1 --filter-min-enable 1000 --diff 3000 --qid 0.0,0.2,0.4,0.6,0.8,1.0 --qsc 0 --max-seq-id 0.95 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out


Query database size: 1 type: Aminoacid
Target database size: 350950053 type: Aminoacid
[=================================================================] 100.00% 1 eta -
Time for merging to uniref.a3m: 0h 0m 0s 0ms
Time for processing: 0h 1m 3s 707ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/res_exp_realign_filter
rmdb /colabfold/experiment/res_exp_realign_filter 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/res_exp_realign
rmdb /colabfold/experiment/res_exp_realign 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/res_exp
rmdb /colabfold/experiment/res_exp 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/res
rmdb /colabfold/experiment/res 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs search /colabfold/experiment/prof_res /colabfold/dbs/colabfold_envdb_202108_db /colabfold/experiment/res_env /colabfold/experiment/tmp3 --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1
Create directory /colabfold/experiment/tmp3
search /colabfold/experiment/prof_res /colabfold/dbs/colabfold_envdb_202108_db /colabfold/experiment/res_env /colabfold/experiment/tmp3 --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1 

ungappedprefilter /colabfold/experiment/prof_res /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/tmp3/8856241292126032855/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
[=================================================================] 100.00% 1 eta -
Time for merging to pref_0: 0h 0m 0s 0ms
Time for processing: 0h 0m 58s 502ms
align /colabfold/experiment/prof_res /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/tmp3/8856241292126032855/pref_0 /colabfold/experiment/tmp3/8856241292126032855/aln_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 1 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Compute score only
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 1 eta -
Time for merging to aln_0: 0h 0m 0s 0ms
10000 alignments calculated
6989 sequence pairs passed the thresholds (0.698900 of overall calculated)
6989.000000 hits per query sequence
Time for processing: 0h 0m 4s 74ms
result2profile /colabfold/experiment/prof_res /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/tmp3/8856241292126032855/aln_0 /colabfold/experiment/tmp3/8856241292126032855/profile_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
[=================================================================] 100.00% 1 eta -
Time for merging to profile_0: 0h 0m 0s 0ms
Time for processing: 0h 0m 3s 102ms
ungappedprefilter /colabfold/experiment/tmp3/8856241292126032855/profile_0 /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
[=================================================================] 100.00% 1 eta -
Time for merging to pref_tmp_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 13s 263ms
subtractdbs /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_1 /colabfold/experiment/tmp3/8856241292126032855/aln_0 /colabfold/experiment/tmp3/8856241292126032855/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3 

subtractdbs /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_1 /colabfold/experiment/tmp3/8856241292126032855/aln_0 /colabfold/experiment/tmp3/8856241292126032855/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3 

Remove /colabfold/experiment/tmp3/8856241292126032855/aln_0 ids from /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_1
[=================================================================] 100.00% 1 eta -
Time for merging to pref_1: 0h 0m 0s 1ms
Time for processing: 0h 0m 0s 93ms
rmdb /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_1 

Time for processing: 0h 0m 0s 0ms
align /colabfold/experiment/tmp3/8856241292126032855/profile_0 /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/tmp3/8856241292126032855/pref_1 /colabfold/experiment/tmp3/8856241292126032855/aln_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 1 eta -
Time for merging to aln_tmp_1: 0h 0m 0s 0ms
4099 alignments calculated
2499 sequence pairs passed the thresholds (0.609661 of overall calculated)
2499.000000 hits per query sequence
Time for processing: 0h 0m 3s 82ms
mergedbs /colabfold/experiment/tmp3/8856241292126032855/profile_0 /colabfold/experiment/tmp3/8856241292126032855/aln_1 /colabfold/experiment/tmp3/8856241292126032855/aln_0 /colabfold/experiment/tmp3/8856241292126032855/aln_tmp_1 

Merging the results to /colabfold/experiment/tmp3/8856241292126032855/aln_1
[=================================================================] 100.00% 1 eta -
Time for merging to aln_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
rmdb /colabfold/experiment/tmp3/8856241292126032855/aln_0 

Time for processing: 0h 0m 0s 0ms
rmdb /colabfold/experiment/tmp3/8856241292126032855/aln_tmp_1 

Time for processing: 0h 0m 0s 0ms
result2profile /colabfold/experiment/tmp3/8856241292126032855/profile_0 /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/tmp3/8856241292126032855/aln_1 /colabfold/experiment/tmp3/8856241292126032855/profile_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
[=================================================================] 100.00% 1 eta -
Time for merging to profile_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 3s 921ms
ungappedprefilter /colabfold/experiment/tmp3/8856241292126032855/profile_1 /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
[=================================================================] 100.00% 1 eta -
Time for merging to pref_tmp_2: 0h 0m 0s 0ms
Time for processing: 0h 0m 15s 488ms
subtractdbs /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_2 /colabfold/experiment/tmp3/8856241292126032855/aln_1 /colabfold/experiment/tmp3/8856241292126032855/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3 

subtractdbs /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_2 /colabfold/experiment/tmp3/8856241292126032855/aln_1 /colabfold/experiment/tmp3/8856241292126032855/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3 

Remove /colabfold/experiment/tmp3/8856241292126032855/aln_1 ids from /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_2
[=================================================================] 100.00% 1 eta -
Time for merging to pref_2: 0h 0m 0s 1ms
Time for processing: 0h 0m 0s 86ms
rmdb /colabfold/experiment/tmp3/8856241292126032855/pref_tmp_2 

Time for processing: 0h 0m 0s 0ms
align /colabfold/experiment/tmp3/8856241292126032855/profile_1 /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/tmp3/8856241292126032855/pref_2 /colabfold/experiment/tmp3/8856241292126032855/aln_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 1 eta -
Time for merging to aln_tmp_2: 0h 0m 0s 0ms
2222 alignments calculated
715 sequence pairs passed the thresholds (0.321782 of overall calculated)
715.000000 hits per query sequence
Time for processing: 0h 0m 2s 861ms
mergedbs /colabfold/experiment/tmp3/8856241292126032855/profile_1 /colabfold/experiment/res_env /colabfold/experiment/tmp3/8856241292126032855/aln_1 /colabfold/experiment/tmp3/8856241292126032855/aln_tmp_2 

Merging the results to /colabfold/experiment/res_env
[=================================================================] 100.00% 1 eta -
Time for merging to res_env: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
rmdb /colabfold/experiment/tmp3/8856241292126032855/aln_1 

Time for processing: 0h 0m 0s 0ms
rmdb /colabfold/experiment/tmp3/8856241292126032855/aln_tmp_2 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs expandaln /colabfold/experiment/prof_res /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env_exp -e inf --expansion-mode 0 --db-load-mode 0 --threads 64
expandaln /colabfold/experiment/prof_res /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env_exp -e inf --expansion-mode 0 --db-load-mode 0 --threads 64 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
[=================================================================] 100.00% 1 eta -
Time for merging to res_env_exp: 0h 0m 0s 1ms
Time for processing: 0h 1m 29s 33ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs align /colabfold/experiment/tmp3/latest/profile_1 /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env_exp /colabfold/experiment/res_env_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a
align /colabfold/experiment/tmp3/latest/profile_1 /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env_exp /colabfold/experiment/res_env_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 738695581 type: Aminoacid
Calculation of alignments
[=================================================================] 100.00% 1 eta -
Time for merging to res_env_exp_realign: 0h 0m 0s 0ms
78521 alignments calculated
57383 sequence pairs passed the thresholds (0.730798 of overall calculated)
57383.000000 hits per query sequence
Time for processing: 0h 0m 20s 9ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs filterresult /colabfold/experiment/qdb /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env_exp_realign /colabfold/experiment/res_env_exp_realign_filter --db-load-mode 0 --qid 0 --qsc 0.8 --diff 0 --max-seq-id 1.0 --threads 64 --filter-min-enable 100
filterresult /colabfold/experiment/qdb /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env_exp_realign /colabfold/experiment/res_env_exp_realign_filter --db-load-mode 0 --qid 0 --qsc 0.8 --diff 0 --max-seq-id 1.0 --threads 64 --filter-min-enable 100 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 738695581 type: Aminoacid
[=================================================================] 100.00% 1 eta -
Time for merging to res_env_exp_realign_filter: 0h 0m 0s 0ms
Time for processing: 0h 0m 11s 394ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs result2msa /colabfold/experiment/qdb /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env_exp_realign_filter /colabfold/experiment/bfd.mgnify30.metaeuk30.smag30.a3m --msa-format-mode 6 --db-load-mode 0 --threads 64 --filter-msa 1 --filter-min-enable 1000 --diff 3000 --qid 0.0,0.2,0.4,0.6,0.8,1.0 --qsc 0 --max-seq-id 0.95
result2msa /colabfold/experiment/qdb /colabfold/dbs/colabfold_envdb_202108_db.idx /colabfold/experiment/res_env_exp_realign_filter /colabfold/experiment/bfd.mgnify30.metaeuk30.smag30.a3m --msa-format-mode 6 --db-load-mode 0 --threads 64 --filter-msa 1 --filter-min-enable 1000 --diff 3000 --qid 0.0,0.2,0.4,0.6,0.8,1.0 --qsc 0 --max-seq-id 0.95 

Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Index version: 16
Generated by:  16.747c6
ScoreMatrix:  VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 738695581 type: Aminoacid
[=================================================================] 100.00% 1 eta -
Time for merging to bfd.mgnify30.metaeuk30.smag30.a3m: 0h 0m 0s 0ms
Time for processing: 0h 0m 42s 981ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/res_env_exp_realign_filter
rmdb /colabfold/experiment/res_env_exp_realign_filter 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/res_env_exp_realign
rmdb /colabfold/experiment/res_env_exp_realign 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/res_env_exp
rmdb /colabfold/experiment/res_env_exp 

Time for processing: 0h 0m 0s 1ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/res_env
rmdb /colabfold/experiment/res_env 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs mergedbs /colabfold/experiment/qdb /colabfold/experiment/final.a3m /colabfold/experiment/uniref.a3m /colabfold/experiment/bfd.mgnify30.metaeuk30.smag30.a3m
mergedbs /colabfold/experiment/qdb /colabfold/experiment/final.a3m /colabfold/experiment/uniref.a3m /colabfold/experiment/bfd.mgnify30.metaeuk30.smag30.a3m 

Merging the results to /colabfold/experiment/final.a3m
[=================================================================] 100.00% 1 eta -
Time for merging to final.a3m: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 17ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/bfd.mgnify30.metaeuk30.smag30.a3m
rmdb /colabfold/experiment/bfd.mgnify30.metaeuk30.smag30.a3m 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/uniref.a3m
rmdb /colabfold/experiment/uniref.a3m 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs unpackdb /colabfold/experiment/final.a3m /colabfold/experiment --unpack-name-mode 0 --unpack-suffix .a3m
unpackdb /colabfold/experiment/final.a3m /colabfold/experiment --unpack-name-mode 0 --unpack-suffix .a3m 

[=================================================================] 100.00% 1 eta -
Time for processing: 0h 0m 0s 29ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/final.a3m
rmdb /colabfold/experiment/final.a3m 

Time for processing: 0h 0m 0s 1ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/prof_res
rmdb /colabfold/experiment/prof_res 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/prof_res_h
rmdb /colabfold/experiment/prof_res_h 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/qdb
rmdb /colabfold/experiment/qdb 

Time for processing: 0h 0m 0s 0ms
INFO:colabfold.mmseqs.search:Running ../MMseqs2/build/bin/mmseqs rmdb /colabfold/experiment/qdb_h
rmdb /colabfold/experiment/qdb_h 

Time for processing: 0h 0m 0s 0ms
colabfold_search --mmseqs ../MMseqs2/build/bin/mmseqs --gpu 1 --gpu-server 0   142.16s user 317.81s system 82% cpu 9:18.38 total
(colabfold) mark@x86_64-conda-linux-gnu [01:15:53 PM] [/colabfold/ColabFold] 
-> % 
(colabfold) mark@x86_64-conda-linux-gnu [01:15:53 PM] [/colabfold/ColabFold] 
-> % 
(colabfold) mark@x86_64-conda-linux-gnu [01:15:53 PM] [/colabfold/ColabFold] 
-> % cat /colabfold/experiment/single.fasta
>13836b2592094dd0abbe66ca1fa1f7f45c848a348e867b4c92be7336d41b739a
MAAAAQLSLTQLSSGNPVYEKYYRQVDTGNTGRVLASDAAAFLKKSGLPDLILGKIWDLADTDGKGILNKQEFFVALRLVACAQNGLEVSLSSLNLAVPPPRFHDTSSPLLISGTSAAELPWAVKPEDKAKYDAIFDSLSPVNGFLSGDKVKPVLLNSKLPVDILGRVWELSDIDHDGMLDRDEFAVAMFLVYCALEKEPVPMSLPPALVPPSKRKTWVVSPAEKAKYDEIFLKTDKDMDGFVSGLEVREIFLKTGLPSTLLAHIWSLCDTKDCGKLSKDQFALAFHLISQKLIKGIDPPHVLTPEMIPPSDRASLQKNIIGSSPVADFSAIKELDTLNNEIVDLQREKNNVEQDLKEKEDTIKQRTSEVQDLQDEVQRENTNLQKLQAQKQQVQELLDELDEQKAQLEEQLKEVRKKCAEEAQLISSLKAELTSQESQISTYEEELAKAREELSRLQQETAELEESVESGKAQLEPLQQHLQDSQQEISSMQMKLMEMKDLENHNSQLNWCSSPHSILVNGATDYCSLSTSSSETANLNEHVEGQSNLESEPIHQESPARSSPELLPSGVTDENEVTTAVTEKVCSELDNNRHSKEEDPFNVDSSSLTGPVADTNLDFFQSDPFVGSDPFKDDPFGKIDPFGGDPFKGSDPFASDCFFRQSTDPFATSSTDPFSAANNSSITSVETLKHNDPFAPGGTVVAASDSATDPFASVFGNESFGGGFADFSTLSKVNNEDPFRSATSSSVSNVVITKNVFEETSVKSEDEPPALPPKIGTPTRPCPLPPGKRSINKLDSPDPFKLNDPFQPFPGNDSPKEKDPEIFCDPFTSATTTTNKEADPSNFANFSAYPSEEDMIEWAKRESEREEEQRLARLNQQEQEDLELAIALSKSEISEA
(colabfold) mark@x86_64-conda-linux-gnu [01:16:56 PM] [/colabfold/ColabFold]

The machine should be quite powerful


-> % nvidia-smi
Sat Mar  1 13:43:41 2025       
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 550.144             Driver Version: 550.144     CUDA Version: 12.4     |
|-----------------------------------------+------------------------+----------------------+
| GPU  Name                 Persistence-M | Bus-Id          Disp.A | Volatile Uncorr. ECC |
| Fan  Temp   Perf          Pwr:Usage/Cap |           Memory-Usage | GPU-Util  Compute M. |
|                                         |                        |               MIG M. |
|=========================================+========================+======================|
|   0  NVIDIA RTX A6000               Off |   00000000:1B:00.0 Off |                  Off |
| 30%   31C    P8             25W /  300W |    7419MiB /  49140MiB |      0%      Default |
|                                         |                        |                  N/A |
+-----------------------------------------+------------------------+----------------------+
|   1  NVIDIA RTX A6000               Off |   00000000:1C:00.0 Off |                  Off |
| 30%   30C    P8             26W /  300W |    7411MiB /  49140MiB |      0%      Default |
|                                         |                        |                  N/A |
+-----------------------------------------+------------------------+----------------------+
|   2  NVIDIA RTX A6000               Off |   00000000:1D:00.0 Off |                  Off |
| 30%   32C    P8             29W /  300W |    7395MiB /  49140MiB |      0%      Default |
|                                         |                        |                  N/A |
+-----------------------------------------+------------------------+----------------------+
|   3  NVIDIA RTX A6000               Off |   00000000:1E:00.0 Off |                  Off |
| 30%   31C    P8             22W /  300W |    7389MiB /  49140MiB |      0%      Default |
|                                         |                        |                  N/A |
+-----------------------------------------+------------------------+----------------------+
|   4  NVIDIA RTX A6000               Off |   00000000:3D:00.0 Off |                  Off |
| 30%   29C    P8             23W /  300W |    7377MiB /  49140MiB |      0%      Default |
|                                         |                        |                  N/A |
+-----------------------------------------+------------------------+----------------------+
|   5  NVIDIA RTX A6000               Off |   00000000:3F:00.0 Off |                  Off |
| 30%   32C    P8             21W /  300W |    7375MiB /  49140MiB |      0%      Default |
|                                         |                        |                  N/A |
+-----------------------------------------+------------------------+----------------------+
                                                                                         
+-----------------------------------------------------------------------------------------+
| Processes:                                                                              |
|  GPU   GI   CI        PID   Type   Process name                              GPU Memory |
|        ID   ID                                                               Usage      |
|=========================================================================================|
|    0   N/A  N/A   4128828      C   ../MMseqs2/build/bin/mmseqs                  5550MiB |
|    0   N/A  N/A   4128829      C   ../MMseqs2/build/bin/mmseqs                  1842MiB |
|    1   N/A  N/A   4128828      C   ../MMseqs2/build/bin/mmseqs                  5542MiB |
|    1   N/A  N/A   4128829      C   ../MMseqs2/build/bin/mmseqs                  1842MiB |
|    2   N/A  N/A   4128828      C   ../MMseqs2/build/bin/mmseqs                  5530MiB |
|    2   N/A  N/A   4128829      C   ../MMseqs2/build/bin/mmseqs                  1838MiB |
|    3   N/A  N/A   4128828      C   ../MMseqs2/build/bin/mmseqs                  5524MiB |
|    3   N/A  N/A   4128829      C   ../MMseqs2/build/bin/mmseqs                  1838MiB |
|    4   N/A  N/A   4128828      C   ../MMseqs2/build/bin/mmseqs                  5514MiB |
|    4   N/A  N/A   4128829      C   ../MMseqs2/build/bin/mmseqs                  1836MiB |
|    5   N/A  N/A   4128828      C   ../MMseqs2/build/bin/mmseqs                  5512MiB |
|    5   N/A  N/A   4128829      C   ../MMseqs2/build/bin/mmseqs                  1836MiB |
+-----------------------------------------------------------------------------------------+

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Expected performance for GPU e2e, seems slow #689

Expected performance for GPU e2e, seems slow #689

agenore commented Mar 3, 2025

Expected performance for GPU e2e, seems slow #689

Expected performance for GPU e2e, seems slow #689

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agenore commented Mar 3, 2025