Bug found!

[yx0516]

When i use the following yaml file, i get the complex structure sucessfully.

sequences:

• protein:
  id: A
  sequence: MNACPHSDTLTIDPMITDLAGETSRLRAAGPLTRIDLLGVPALAVTGHTLARQLLTDTRLVKDINAWSLWQSGTVTRQWPLIGMIDVDRSMFTVDGPEHRRLRIKTTQALTRRRLDALKPTIERYVAELLDDLERAGADGAVVDLKSVFAYPLPMRVISALMGVPSEDQEQLLTWYKAFFSILTPQDERLRVIDEMHGYFTEMVRRKTAEPGDDLTSALIYATDGETPLTEEEVIGNLQALVAAGHETTVSLILTAVRALLSHPEQLRLVRDGEIGWETAIEETLRWDGPVIHLLMRFATEDIDLGDAVIPRGEGVVMSYRAIGRDITVHGADADDFDITRATAARHISFGHGPHICPGAALARLEAAIALPALFTRFPHLHPALPLDQIPNLPVLTQNDLSHFPIHLGR
• dna:
  id: B
  sequence: GGGAATGGCAGTATTCATCCACAATG
• dna:
  id: C
  sequence: CCATTGTGGATGAATACTGCCATTCC
• rna:
  id: D
  sequence: GGGUCUCGCGGAACCGGUGAGUACACCGGAAUCCAGGAAACUGGAUUUGGGCGUGCCCCCGCGAGACC
  version: 1

However, when i use only the protein sequence in the yaml file, i got no results with "| WARNING: ran out of memory, skipping batch"
under the same free GPU card with no other runing process. The yaml file as following:

sequences:

• protein:
  id: A
  sequence: MNACPHSDTLTIDPMITDLAGETSRLRAAGPLTRIDLLGVPALAVTGHTLARQLLTDTRLVKDINAWSLWQSGTVTRQWPLIGMIDVDRSMFTVDGPEHRRLRIKTTQALTRRRLDALKPTIERYVAELLDDLERAGADGAVVDLKSVFAYPLPMRVISALMGVPSEDQEQLLTWYKAFFSILTPQDERLRVIDEMHGYFTEMVRRKTAEPGDDLTSALIYATDGETPLTEEEVIGNLQALVAAGHETTVSLILTAVRALLSHPEQLRLVRDGEIGWETAIEETLRWDGPVIHLLMRFATEDIDLGDAVIPRGEGVVMSYRAIGRDITVHGADADDFDITRATAARHISFGHGPHICPGAALARLEAAIALPALFTRFPHLHPALPLDQIPNLPVLTQNDLSHFPIHLGR
  version: 1

[xinyu-dev]

Same issue here.

My instance: 1xA10 (24GB)
Input:

version: 1
sequences:
  - protein:
      id: A
      sequence: DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKAPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQRYNRAPYTFGQGTKVEIK
  - protein:
      id: B
      sequence: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSAITWNSGHIDYADSVEGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCAKVSYLSTASSLDYWGQGTLVTVSS

Memory usage is low but it still outputs | WARNING: ran out of memory, skipping batch error and the prediction fails

[xinyu-dev]

My command is:

boltz predict input/adalimumab.yaml --out_dir output --devices 1 --output_format pdb --use_msa_server

With version 0.3.0, it generated the out of memory issue above

The I uninstalled 0.3.0 and reinstalled 0.2.1, the issue is gone

[yx0516]

@jwohlwend Hi, would you help with this issue? Thanks a lot.

[jwohlwend]

We just released v0.3.2 which should address some of these issues. You can update with pip install boltz -U When testing, please remove any existing output folder for your input and run again! Please let us know.