sokrypton / sokrypton/ColabFold

Failed to mmap memory dataSize

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Description

I've been using colabfold_search smoothly for a long time. Then all of a sudden the below error came.
Versions:

colabfold                   1.6.1            pypi_0                pypi
mmseqs2                     18.8cc5c         hd6d6fdc_0            bioconda

Here is the log:

INFO:colabfold.mmseqs.search:Running mmseqs createdb msas_spy_af3/query.fas msas_spy_af3/qdb --shuffle 0 --dbtype 1
msas_spy_af3/qdb exists and will be overwritten
createdb msas_spy_af3/query.fas msas_spy_af3/qdb --shuffle 0 --dbtype 1 

Converting sequences
[
Time for merging to qdb_h: 0h 0m 0s 57ms
Time for merging to qdb: 0h 0m 0s 71ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 196ms
INFO:colabfold.mmseqs.search:Running mmseqs search msas_spy_af3/qdb .../local/ColabFold/dbs/uniref30_2302_db msas_spy_af3/res msas_spy_af3/tmp --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1
Failed to mmap memory dataSize=244437757952 File=.../local/ColabFold/dbs/uniref30_2302_db.idx. Error 12.
Traceback (most recent call last):
  File ".../miniconda3/envs/cf/bin/colabfold_search", line 6, in <module>
    sys.exit(main())
             ~~~~^^
  File ".../miniconda3/envs/cf/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 481, in main
    mmseqs_search_monomer(
    ~~~~~~~~~~~~~~~~~~~~~^
        mmseqs=args.mmseqs,
        ^^^^^^^^^^^^^^^^^^^
    ...<19 lines>...
        unpack=args.unpack,
        ^^^^^^^^^^^^^^^^^^^
    )
    ^
  File ".../miniconda3/envs/cf/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 131, in mmseqs_search_monomer
    run_mmseqs(mmseqs, ["search", base.joinpath("qdb"), dbbase.joinpath(uniref_db), base.joinpath("res"), base.joinpath("tmp"), "--threads", str(threads)] + search_param)
    ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File ".../miniconda3/envs/cf/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 47, in run_mmseqs
    subprocess.check_call([mmseqs] + params)
    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
  File ".../miniconda3/envs/cf/lib/python3.13/subprocess.py", line 419, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '[PosixPath('mmseqs'), 'search', PosixPath('msas_spy_af3/qdb'), PosixPath('.../local/ColabFold/dbs/uniref30_2302_db'), PosixPath('msas_spy_af3/res'), PosixPath('msas_spy_af3/tmp'), '--threads', '64', '--num-iterations', '3', '--db-load-mode', '0', '-a', '-e', '0.1', '--max-seqs', '10000', '--gpu', '1', '--prefilter-mode', '1']' returned non-zero exit status 1.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading colabfold/mmseqs/search.py, especially mmseqs_search_monomer and run_mmseqs, then reproduce the logged mmseqs search command using the stated versions and database path. Done means determining why the uniref30_2302_db search fails to mmap and making the same search complete or documenting the confirmed environmental limitation.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
35/100

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