posix_madvise returned an error (touchMemory)

ocstx commented 1 year ago

Expected Behavior

No errors reported

Current Behavior

when I run foldseek easy-search I get the error mentioned in the title. Although it is apparently working well. Here I'm pasting a fraction of the output where this error appears: `Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out posix_madvise returned an error (touchMemory) [=================================================================] 100.00% 1 eta - Time for merging to strualn: 0h 0m 0s 0ms Time for processing: 0h 0m 0s 316ms mvdb FSTMP//3259066021161492335/search_tmp/7344007857547324109/strualn FSTMP//3259066021161492335/search_tmp/7344007857547324109/aln

Time for processing: 0h 0m 0s 0ms mvdb FSTMP//3259066021161492335/search_tmp/7344007857547324109/aln FSTMP//3259066021161492335/result -v 3 `

Steps to Reproduce (for bugs)

every time I run foldseek easy-search (search module not tested)

Foldssek Output (for bugs)

Please make sure to also post the complete output of Spacepharer. You can use gist.github.com for large output. `easy-search d1asha_ ../EXAMPLE/targetDB aln.m8 tmpFolder/

MMseqs Version: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce Seq. id. threshold 0 Coverage threshold 0 Coverage mode 0 Max reject 2147483647 Max accept 2147483647 Add backtrace false TMscore threshold 0 TMalign hit order 0 TMalign fast 1 Preload mode 0 Threads 6 Verbosity 3 LDDT threshold 0 Sort by structure bit score 1 Substitution matrix aa:3di.out,nucl:3di.out Alignment mode 3 Alignment mode 0 E-value threshold 10 Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Max sequence length 65535 Compositional bias 1 Compositional bias 1 Gap open cost aa:10,nucl:10 Gap extension cost aa:1,nucl:1 Compressed 0 Seed substitution matrix aa:3di.out,nucl:3di.out Sensitivity 9.5 k-mer length 6 k-score seq:2147483647,prof:2147483647 Max results per query 1000 Split database 0 Split mode 2 Split memory limit 0 Diagonal scoring true Exact k-mer matching 0 Mask residues 0 Mask residues probability 0.99995 Mask lower case residues 1 Minimum diagonal score 30 Selected taxa
Spaced k-mers 1 Spaced k-mer pattern
Local temporary path
Exhaustive search mode false Prefilter mode 0 Search iterations 1 Alignment type 2 Remove temporary files true MPI runner
Force restart with latest tmp false Cluster search 0 Chain name mode 0 Write mapping file 0 Mask b-factor threshold 0 Coord store mode 2 Write lookup file 1 Tar Inclusion Regex .* Tar Exclusion Regex ^$ Alignment format 0 Format alignment output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits Database output false Greedy best hits false

createdb d1asha_ tmpFolder//16337538361226239420/query --chain-name-mode 0 --write-mapping 0 --mask-bfactor-threshold 0 --coord-store-mode 2 --write-lookup 1 --tar-include '.*' --tar-exclude '^$' --threads 6 -v 3

Output file: tmpFolder//16337538361226239420/query [=================================================================] 100.00% 1 eta - Time for merging to query_ss: 0h 0m 0s 5ms Time for merging to query_h: 0h 0m 0s 5ms Time for merging to query_ca: 0h 0m 0s 5ms Time for merging to query: 0h 0m 0s 5ms Ignore 0 out of 1. Too short: 0, incorrect: 0, not proteins: 0. Time for processing: 0h 0m 0s 66ms Create directory tmpFolder//16337538361226239420/search_tmp search tmpFolder//16337538361226239420/query ../EXAMPLE/targetDB tmpFolder//16337538361226239420/result tmpFolder//16337538361226239420/search_tmp --alignment-mode 3 --comp-bias-corr 1 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 -s 9.5 -k 6 --mask 0 --mask-prob 0.99995 --remove-tmp-files 1

prefilter tmpFolder//16337538361226239420/query_ss ../EXAMPLE/targetDB_ss.idx tmpFolder//16337538361226239420/search_tmp/4262090326834439573/pref --sub-mat 'aa:3di.out,nucl:3di.out' --seed-sub-mat 'aa:3di.out,nucl:3di.out' -s 9.5 -k 6 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 1000 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 0.15 --diag-score 1 --exact-kmer-matching 0 --mask 0 --mask-prob 0.99995 --mask-lower-case 1 --min-ungapped-score 30 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 6 --compressed 0 -v 3

Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out Query database size: 1 type: Aminoacid Estimated memory consumption: 977M Target database size: 26 type: Aminoacid Process prefiltering step 1 of 1

k-mer similarity threshold: 78 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 1 Target db start 1 to 26 [=================================================================] 100.00% 1 eta -

180.292517 k-mers per position 1233 DB matches per sequence 0 overflows 26 sequences passed prefiltering per query sequence 26 median result list length 0 sequences with 0 size result lists Time for merging to pref: 0h 0m 0s 1ms Time for processing: 0h 0m 13s 650ms structurealign tmpFolder//16337538361226239420/query ../EXAMPLE/targetDB.idx tmpFolder//16337538361226239420/search_tmp/4262090326834439573/pref tmpFolder//16337538361226239420/search_tmp/4262090326834439573/strualn --tmscore-threshold 0 --lddt-threshold 0 --sort-by-structure-bits 1 --sub-mat 'aa:3di.out,nucl:3di.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 10 --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 0.5 --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:10,nucl:10 --gap-extend aa:1,nucl:1 --zdrop 40 --threads 6 --compressed 0 -v 3

Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out posix_madvise returned an error (touchMemory) [=================================================================] 100.00% 1 eta - Time for merging to strualn: 0h 0m 0s 4ms Time for processing: 0h 0m 0s 121ms mvdb tmpFolder//16337538361226239420/search_tmp/4262090326834439573/strualn tmpFolder//16337538361226239420/search_tmp/4262090326834439573/aln

Time for processing: 0h 0m 0s 3ms mvdb tmpFolder//16337538361226239420/search_tmp/4262090326834439573/aln tmpFolder//16337538361226239420/result -v 3

Time for processing: 0h 0m 0s 4ms Removing temporary files rmdb tmpFolder//16337538361226239420/search_tmp/4262090326834439573/pref -v 3

Time for processing: 0h 0m 0s 1ms aln.m8 exists and will be overwritten convertalis tmpFolder//16337538361226239420/query ../EXAMPLE/targetDB.idx tmpFolder//16337538361226239420/result aln.m8 --sub-mat 'aa:3di.out,nucl:3di.out' --format-mode 0 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits --translation-table 1 --gap-open aa:10,nucl:10 --gap-extend aa:1,nucl:1 --db-output 0 --db-load-mode 0 --search-type 0 --threads 6 --compressed 0 -v 3

Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out Index version: fs1 Generated by: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce ScoreMatrix: 3di.out [=================================================================] 100.00% 1 eta - Time for merging to aln.m8: 0h 0m 0s 1ms Time for processing: 0h 0m 0s 8ms rmdb tmpFolder//16337538361226239420/result -v 3

Time for processing: 0h 0m 0s 1ms rmdb tmpFolder//16337538361226239420/query -v 3

Time for processing: 0h 0m 0s 0ms rmdb tmpFolder//16337538361226239420/query_h -v 3

Time for processing: 0h 0m 0s 0ms rmdb tmpFolder//16337538361226239420/query_ca -v 3

Time for processing: 0h 0m 0s 0ms rmdb tmpFolder//16337538361226239420/query_ss -v 3

Time for processing: 0h 0m 0s 0ms `

Context

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Your Environment

Include as many relevant details about the environment you experienced the bug in.

Git commit used (The string after "MMseqs Version:" when you execute foldseek without any parameters): foldseek Version: 04e0ec84ce220a7f9cab9d309a8daa99ee052fce
Which foldseek version was used (Statically-compiled, self-compiled, Conda, etc.): Statically-compiled download from https://mmseqs.com/foldseek/
For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
Server specifications (especially CPU support for AVX2/SSE and amount of system memory): avx2 version: Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz sse2 version: AMD Phenom(tm) II X6 1055T Processor
Operating system and version: AlmaLinux 8.8 (Sapphire Caracal) with kernel: avx2 version: 6.3.1-2.el8.elrepo.x86_64 sse2 version: 4.18.0-477.13.1.el8_8.x86_64

milot-mirdita commented 1 year ago

Thank you for your detailed report. You can ignore the error, it shouldn't lead to any issues. We will investigate deeper and most likely disable the error message for the next release.

Rohit-Satyam commented 3 months ago

Yes I also get this when I create index and save it on my disk and try running

foldseek createdb target/ tt
foldseek createindex tt tmp
foldseek easy-complexsearch query/7nyu.pdb tt result tempagain

where tt is the database index made from two pdb complexes 1nen.pdb and 6oqr.pdb

steineggerlab / foldseek