Ecosyste.ms: Issues

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GitHub / aqlaboratory/openfold issues and pull requests

#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

#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

#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

#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

#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

#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

#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

#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

#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

#429 - Frequently failed in training.

Issue - State: open - Opened by C-de-Furina 5 months ago - 2 comments

#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

#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

#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