Comments (4)
I do have the same problem when I try to allocate 32G of data in 2 A30 GPUs (with 24GB each), either using both GPUs or single one. So I get around by using CPU instead, although it's certainly slower.
You can put at the very beginning of your code:
import jax
jax.config.update('jax_platform_name', 'cpu')
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Thank you! I tried that (I also have Colab pro) but it now says "Your session crashed after using all available RAM." Is the only workaround this to purchase more RAM through Colab?
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Unfortunately... Unless you get a GPU with larger amounts of memory, there isn't an easy to reduce memory usage :(
We tried implementating crops during design, but this didn't work too well.
Final option would be to use "design_semigreedy" or "_design_mcmc" (the later might be broken, it was something I implemented but haven't tested yet). This does not backprop through the model (which requires 2X more memory).
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@sokrypton I think you can use partial hallucination with template to crop the target protein, then use the resulting protein to design binder by providing hotspots away from hallucinated regions. Although it needs to set template=True in all steps.
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Related Issues (20)
- critical typo in kmeans.py (simport instead of import) HOT 1
- Can we see generated sequences other than final one? HOT 1
- The sequence in design.fasta is different from the sequence in best.pdb HOT 5
- How to predict the Cyclic Peptide's structure by a given sequence HOT 3
- Problem in designability_test.py HOT 2
- WARNING: 'model_1_ptm' not found HOT 1
- Using RFdiffusion to design a binder, with some parts of the binder fixed HOT 6
- where is the output file when finish the model.design_3stage() run? HOT 1
- atom index in af.prep.prep_pdb HOT 1
- Any plans to add af2seq to the colab design
- MPNN designed sequence not separated correctly with multiple targets and multiple binders HOT 2
- Patch fix_partial_contigs when residue numbering in PDB has a gap HOT 2
- Allow to select the Complex_beta_ckpt model in RFdiffusion colab?
- Translate colab for RFdiffusion to a jupyter notebook?
- How to get PAE files when running RFdiffusion
- Is it possible to bypass the design step of AfDesign?
- Do the soft iterations in pssm_semigreedy obey the bias matrix
- fix_pos in af/fixbb HOT 2
- Partially folding a structure using AF
- How to continue a design run?
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