milot-mirdita
commented
1 year ago If you want to run MMseqs2 with MPI, you have to compile it yourself. The bioconda version does not include MPI support.
See: https://github.com/soedinglab/MMseqs2/wiki#how-to-run-mmseqs2-on-multiple-servers-using-mpi
Expected Behavior
Current Behavior
Steps to Reproduce (for bugs)
Please make sure to execute the reproduction steps with newly recreated and empty tmp folders.
MMseqs Output (for bugs)
Please make sure to also post the complete output of MMseqs. You can use gist.github.com for large output.
Context
I am getting error when running mmseqs search mmseqs_U90_out/mmseqs-81_queryDB ../MH2_mappingFiles/mmseqsUniref90DB mmseqs_U90_out/mmseqs-81_resultDB tmp --db-load-mode 2 --threads 40 --max-seqs 25 -s 1 -a -e 1e-5 > /dev/null 2>&1
The error:
Time for merging to q_orfs_aa_h: 0h 0m 40s 360ms Time for merging to q_orfs_aa: 0h 0m 42s 543ms Time for processing: 0h 2m 43s 735ms prefilter tmp/4045178716233794437/q_orfs_aa ../MH2_mappingFiles/mmseqsUniref90DB tmp/4045178716233794437/search/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -k 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 65535 --max-seqs 25 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 2 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 40 --compressed 0 -v 3 -s 1.0
Query database size: 29993837 type: Aminoacid Target split mode. Searching through 2 splits Estimated memory consumption: 194G Target database size: 91903251 type: Aminoacid Process prefiltering step 1 of 2
slurmstepd: error: poll(): Bad address tmp/4045178716233794437/blastp.sh: line 99: 220560 Killed $RUNNER "$MMSEQS" prefilter "$INPUT" "$TARGET" "$TMPPATH/pref$STEP" $PREFILTER_PAR -s "$SENS" Error: Prefilter died Error: Search step died
Your Environment
Include as many relevant details about the environment you experienced the bug in. MMseqs2 Version: 14.7e284 I install it using: $module load miniconda $conda create --prefix /project/winter_pea_endophytes_2022/MMseqs $source activate /project/winter_pea_endophytes_2022/MMseqs $conda install -c conda-forge -c bioconda mmseqs2 and run it as environment $conda activate /project/winter_pea_endophytes_2022/MMseqs
Server: ceres.scinet.usda resources allocation $salloc -p short -N 2 -n 80 -t 12:00:00