Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / aqlaboratory/openfold issues and pull requests
#490 - [pl_upgrades] OpenFold not configured to support compute capability 9.0
Issue -
State: open - Opened by reedharrison 10 days ago
#489 - AttributeError: 'AlphaFold' object has no attribute 'template_pair_embedder' when using long_sequence_inference=True
Issue -
State: open - Opened by Lix1993 11 days ago
#488 - Openfold multimer model weights
Issue -
State: open - Opened by johnny-rodriguez 12 days ago
#487 - fix typo in config.py
Pull Request -
State: open - Opened by Lix1993 15 days ago
#486 - Training on Multi-GPUs
Issue -
State: closed - Opened by abhinavb22 21 days ago
- 1 comment
#485 - Bug Fix: Preserve full FASTA ID in alignment directory parsing to prevent truncation errors
Pull Request -
State: open - Opened by juliocesar-io 22 days ago
#484 - OpenFold Local Jupyter Notebook 📔 | Metrics, Plots, Concurrent Inference
Pull Request -
State: open - Opened by juliocesar-io about 1 month ago
#483 - OpenFold Multimer Training Status
Issue -
State: open - Opened by ecalfee about 1 month ago
#482 - Fix for docs on deepspeed inference
Pull Request -
State: open - Opened by josemduarte about 1 month ago
- 1 comment
#481 - Example training set fails with CUDA out of memory on CUDA 12.1 and PyTorch 2.1
Issue -
State: open - Opened by RJ3 about 1 month ago
#480 - inconsistency in tests/compare_utils.py, AssertionError: Scalars are not close!
Issue -
State: open - Opened by RJ3 about 1 month ago
#479 - Update Installation.md - fix pl_upgrades clone instructions
Pull Request -
State: open - Opened by vaclavhanzl about 1 month ago
#478 - Update Inference.md - missing backslash
Pull Request -
State: open - Opened by vaclavhanzl about 1 month ago
#477 - Unspecified Numpy version causing installation issue
Issue -
State: open - Opened by RJ3 about 1 month ago
- 1 comment
#476 - using alphafold weights - Expected hasRecord("Version") to be true
Issue -
State: closed - Opened by maartensandbox about 2 months ago
- 1 comment
#475 - AttributeError: 'dict' object has no attribute 'new_ones'
Issue -
State: open - Opened by cpplyqz about 2 months ago
#474 - No support for `aarch64`
Issue -
State: open - Opened by wahabk 2 months ago
- 1 comment
#473 - CUDA out of memory during training with A100 GPUs
Issue -
State: open - Opened by abhinavb22 2 months ago
- 3 comments
#472 - Random crop during training
Issue -
State: open - Opened by VarunUllanat 2 months ago
- 1 comment
#471 - RuntimeError: cusolver error: CUSOLVER_STATUS_INTERNAL_ERROR
Issue -
State: open - Opened by abhinavb22 2 months ago
#470 - Remove unnecessary double-load of config_json.
Pull Request -
State: closed - Opened by rkosai 2 months ago
#469 - NVIDIA Corporation TU117GL not compatible with FA2
Issue -
State: open - Opened by fapirro 2 months ago
#468 - Output issue on H100 with memory-efficient kernel
Issue -
State: open - Opened by psohani 3 months ago
- 12 comments
#467 - tests.test_primitives.TestLMA: torch.cuda.OutOfMemoryError: CUDA out of memory
Issue -
State: open - Opened by rafaeltiveron 3 months ago
- 3 comments
#466 - Has the self-distillation database with 270,000 structures been provided, and where can I find it? Or do I need to generate it myself?
Issue -
State: closed - Opened by muuu23333 3 months ago
- 1 comment
#465 - why the training loss is strange
Issue -
State: open - Opened by yzb123789 3 months ago
#464 - Fix 3-to-1 letter conversion to use extended mapping
Pull Request -
State: closed - Opened by ljarosch 3 months ago
- 1 comment
#463 - How to emphasize on the structure?
Issue -
State: open - Opened by bzhousd 3 months ago
- 1 comment
#462 - installation error
Issue -
State: open - Opened by abhinavb22 3 months ago
- 3 comments
#461 - Uniprot hits for Open Protein Set
Issue -
State: open - Opened by abhinavb22 3 months ago
#460 - why target_feat is with shape (N,22), not same as alphafold2 paper (N,21)
Issue -
State: open - Opened by Paulie-ai 4 months ago
#459 - The flatten_roda.sh has problems.
Issue -
State: open - Opened by smallfishabc 4 months ago
#458 - Unable to install OpenFold within Anaconda
Issue -
State: open - Opened by jimmyz100 4 months ago
#457 - MMseqs precomputing alignment too slow
Issue -
State: open - Opened by hanrthu 4 months ago
#456 - Unable to install OpenFold in Google Colaboratory
Issue -
State: open - Opened by nickraisgit 4 months ago
#455 - Docker container AttributeError: Did you mean: 'linear_a_p'? when trying to run multimer inference
Issue -
State: open - Opened by DieHof 4 months ago
#454 - fix: support flash-attention v2
Pull Request -
State: closed - Opened by jnooree 4 months ago
- 1 comment
#453 - Multimer predicting a homomer
Issue -
State: closed - Opened by agustin-ormazabal 4 months ago
- 2 comments
#452 - RuntimeError: Error building extension 'evoformer_attn'
Issue -
State: closed - Opened by agustin-ormazabal 4 months ago
- 1 comment
#451 - ModuleNotFoundError: No module named 'attn_core_inplace_cuda'
Issue -
State: closed - Opened by agustin-ormazabal 4 months ago
- 1 comment
#450 - Remove manual -std=c++14 flag for compatibility
Pull Request -
State: open - Opened by jnooree 4 months ago
#449 - Questions about the meaning of folder naming conventions in OpenProteinSet
Issue -
State: closed - Opened by lonelycrab888 4 months ago
- 1 comment
#448 - Update Aux_seq_files.md
Pull Request -
State: closed - Opened by jnwei 4 months ago
#447 - Fixes and improvements to the installation instructions
Pull Request -
State: open - Opened by jkosinski 4 months ago
#446 - Enable Dropout in inference
Issue -
State: open - Opened by tkramer-motion 4 months ago
- 1 comment
#445 - ModuleNotFoundError: No module named 'attn_core_inplace_cuda'
Issue -
State: closed - Opened by pikruse 4 months ago
- 3 comments
#443 - Fix formatting in installation.md
Pull Request -
State: closed - Opened by jnwei 4 months ago
#442 - added threading and Colabfold-like plots generation
Pull Request -
State: open - Opened by jflucier 5 months ago
#441 - Alignment error during inference
Issue -
State: closed - Opened by dthorburn 5 months ago
- 1 comment
#440 - Link OpenFold repo from the docs
Pull Request -
State: closed - Opened by vaclavhanzl 5 months ago
- 1 comment
#439 - Adds Documentation and minor quality of life fixes
Pull Request -
State: closed - Opened by jnwei 5 months ago
#438 - Upgrades pl_upgrades to match main branch changes.
Pull Request -
State: closed - Opened by jnwei 5 months ago
#437 - Adds mkl version to environment.yml
Pull Request -
State: closed - Opened by jnwei 5 months ago
#437 - Adds mkl version to environment.yml
Pull Request -
State: closed - Opened by jnwei 5 months ago
#436 - Question: Can the geometry module and rigid_utils be converted to each other?
Issue -
State: open - Opened by wtni-gidle 5 months ago
#436 - Question: Can the geometry module and rigid_utils be converted to each other?
Issue -
State: open - Opened by wtni-gidle 5 months ago
#435 - OS.Environ for LMA default chunk_sizes
Pull Request -
State: open - Opened by jyaacoub 5 months ago
#435 - OS.Environ for LMA default chunk_sizes
Pull Request -
State: open - Opened by jyaacoub 5 months ago
#434 - Docker build broken
Issue -
State: closed - Opened by vaclavhanzl 5 months ago
- 4 comments
#433 - Colab broken by version skew
Issue -
State: closed - Opened by vaclavhanzl 5 months ago
- 1 comment
#432 - Fix Colab by using OF commit from pl_upgrades
Pull Request -
State: closed - Opened by vaclavhanzl 5 months ago
- 1 comment
#431 - Rigid.from_3_points comment
Issue -
State: open - Opened by Zhu-Siqi 5 months ago
- 1 comment
#430 - Fix `atom37_to_atom14` tensor shape errors in `all_atom_multimer.py`
Pull Request -
State: open - Opened by amorehead 5 months ago
#429 - Frequently failed in training.
Issue -
State: open - Opened by C-de-Furina 5 months ago
- 2 comments
#428 - I notice there is only instructions for a Linux Install, can I run this on my Windows laptop?
Issue -
State: closed - Opened by emilyrkang 5 months ago
- 1 comment
#427 - Unable to create conda environment
Issue -
State: closed - Opened by AlejandroSanchezCano 6 months ago
- 5 comments
#426 - Finetune from AF_Multimer parameters
Issue -
State: open - Opened by tpdmskim 6 months ago
- 7 comments
#426 - Finetune from AF_Multimer parameters
Issue -
State: open - Opened by tpdmskim 6 months ago
#426 - Finetune from AF_Multimer parameters
Issue -
State: open - Opened by tpdmskim 6 months ago
#425 - Refactor shell setup code & update CUDA build
Pull Request -
State: open - Opened by afairley 6 months ago
#425 - Refactor shell setup code & update CUDA build
Pull Request -
State: open - Opened by afairley 6 months ago
#424 - Is the pdb_mmcif.zip from OpenProteinSet on AWS suitable for RODA training data?
Issue -
State: closed - Opened by zouzh14 6 months ago
- 1 comment
#423 - Pickling error in Docker?
Issue -
State: open - Opened by tonyageall 6 months ago
- 1 comment
#422 - Inference error using precomputed alignments
Issue -
State: open - Opened by xuagu37 6 months ago
- 1 comment
#421 - Finetune from AF parameters
Issue -
State: open - Opened by C-de-Furina 6 months ago
- 11 comments
#420 - Fix resolution field in mmcif_parsing
Pull Request -
State: closed - Opened by ljarosch 6 months ago
#419 - Duplicate expansion support
Pull Request -
State: closed - Opened by ljarosch 6 months ago
#418 - Fix distributed seeding behavior
Pull Request -
State: closed - Opened by ljarosch 6 months ago
#417 - Question : Any plans to support apple silicon Mac M1/M2/M3 ?
Issue -
State: open - Opened by DomML 7 months ago
- 2 comments
#416 - Unable to load openfold packages
Issue -
State: open - Opened by Lucie02Rose 7 months ago
- 3 comments
#415 - Distributed training and `max_recycling_iters`
Issue -
State: open - Opened by pujaltes 7 months ago
#414 - How to use *ckpt in run_pretrained_openfold.py as model npz / finetuning ckpt
Issue -
State: closed - Opened by vetmax7 7 months ago
- 2 comments
#413 - ModuleNotFoundError: No module named 'tree'
Issue -
State: closed - Opened by tonyageall 7 months ago
- 2 comments
#412 - Command throw errors in scripts/flatten_roda.sh
Issue -
State: open - Opened by Minys233 7 months ago
- 1 comment
#411 - Bug in Reading FASTAs for `precompute_alignments_mmseqs.py`
Issue -
State: open - Opened by brucejwittmann 7 months ago
- 1 comment
#410 - Timeline for Multimer Training
Issue -
State: open - Opened by jozhang97 7 months ago
- 2 comments
#409 - Soloseq inference - can't fold using ESM-1b alone
Issue -
State: open - Opened by amardeepranu 7 months ago
- 6 comments
#408 - Add use_custom_templates option
Pull Request -
State: closed - Opened by rostro36 7 months ago
- 10 comments
#407 - Pytorch lightning upgrades
Pull Request -
State: closed - Opened by jnwei 7 months ago
- 1 comment
#406 - Update multi-chain permutation and permutation unittest
Pull Request -
State: closed - Opened by dingquanyu 8 months ago
- 2 comments
#405 - Full multimer merge
Pull Request -
State: closed - Opened by christinaflo 8 months ago
#405 - Full multimer merge
Pull Request -
State: closed - Opened by christinaflo 8 months ago
#404 - Type fixes and README changes for multimer branch
Pull Request -
State: closed - Opened by jnwei 8 months ago
#404 - Type fixes and README changes for multimer branch
Pull Request -
State: closed - Opened by jnwei 8 months ago
#403 - Build openfold with newer ppytorch + cuda
Issue -
State: open - Opened by chunhui-shi 8 months ago
- 14 comments
#403 - Build openfold with newer ppytorch + cuda
Issue -
State: open - Opened by chunhui-shi 8 months ago
- 8 comments
#402 - Fix Miniforge3 download link in Dockerfile
Pull Request -
State: closed - Opened by controny 8 months ago
- 1 comment
#401 - Adding multimer support to OpenFold notebook
Pull Request -
State: closed - Opened by jnwei 8 months ago
#400 - Docker build fails
Issue -
State: closed - Opened by goran-mh 8 months ago
#399 - multimer installation weird behaviour
Issue -
State: open - Opened by eguarnera 8 months ago
- 1 comment