Error on tensor proto size

[rkflygaard]

Hi,
I'm getting an error when trying to run alphafold on a particular sequence, that tensor proto cannot exceed 2GB (see attached file with the error log). I have successfully run alphafold on many other sequences without any problem, but for this particular sequence I am getting this tensor proto error no matter what I try (e.g. running with full database vs reduced one, different gpu nodes to not hit out of memory).

Any help on what I can try would be much appreciated!
Thanks a lot!

AF2_slurm_56393_snoke5_alphafold_56393_4294967294.txt

[yzyw0702]

Same issue took place in my case, when the input sequence is very long (>1500).

[rkflygaard]

Same issue took place in my case, when the input sequence is very long (>1500).

The strange thing for me though is that I have successfully run sequences of >2000 residues without getting any errors or problems, but this single input sequence always gives an error on tensor proto size.

[Augustin-Zidek]

Hi, this is most likely because the MSA is too big. There is a suggested workaround (reducing the size of the MSA) in: #71

[yzyw0702]

Thanks Zidek, and new things to update: I found that AF2 uses TF2.compat.v1 to call Tensor, and we may switch it to TF2 native Tensor or other packages as alternative way to solve the issue.

[Augustin-Zidek]

Addressed in 0be2b30.