sokrypton / sokrypton/ColabFold
localcolabfold raise error "malloc(): invalid size (unsorted)" during expandaln
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Description
I was testing localcolabfold 1.5.5 with a list of protein complexes. colabfold_search with GPU seems to produce all a3m files without any issues but when I tried to use CPU, I got errors "corrupted size vs. prev_size".
Then I tried individual complexes and some worked while others didn't. I got error message "malloc(): invalid size (unsorted)" during expandaln. I've tried with or without indices, indices built with different hardware configurations and mmseqs15 but none of them resolved the issue. An example is attached.
colabfold_search-62781089.txt
complex2.txt
localcolabfold_msa.txt
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Research direction
Start by reviewing the attached colabfold_search-62781089.txt and localcolabfold_msa.txt logs alongside complex2.txt, then reproduce the CPU failure during expandaln and compare it with the successful GPU run. Done means identifying the cause of the malloc or corrupted-size error and confirming that the affected complex completes successfully on CPU.
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Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100