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RuntimeError: Error compiling objects for extension

2

Please help me. How to solve this problem. I have no idea：：：： /data/lwq/openfold-main/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/cloneable.h:57:59: 错误：从类型‘const torch::OrderedDict’到类型‘torch::OrderedDict&’中的 static_cast 无效 /data/lwq/openfold-main/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/cloneable.h:69:61: 错误：从类型‘const torch::OrderedDict’到类型‘torch::OrderedDict&’中的 static_cast 无效 /data/lwq/openfold-main/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/nn/cloneable.h: In instantiation of ‘std::shared_ptr torch::nn::Cloneable::clone(const c10::optional&) const...

liweiqing1997

seq_length dimension different to AlphaFold-multimer

2

In case of the original AlphaFold pipeline, the "seq_length" array in the feature_dict seems to get flattened in multimer mode (in monomer mode it stays a 1-D array). As far...

georgkempf

DeepSpeed and Illegal Instruction

1

Hello, I am currently trying to run a training on a SLURM environment. The IT-support of the cluster I am using is currently working on it (let's call it `cluster...

DA-L3

Question regarding Openfold Colab's max residue input

1

Hello! I have been able to use the Openfold Colab with success following an upgrade to colab pro+ in order to connect to a machine with more RAM (50 GB)....

Cweb118

Can l run without cuda or GPU?

4

l am running the instance on VMare. It could not install cuda, or the whole machine breaks. So can l run the instance without cuda? Regardless of speed.

bzjf

Is pytorch1.7 supported ？

1

I want to use a lower version of PyTorch, such as 1.7 instead of 10(Openfold default), has anyone tested this before ？

gofreelee

error in python3 setup.py install:"TypeError: expected string or bytes-like object"

2

can you help me ! I ran it according to the instructions, I don't know why I get an error (openfold_venv) [lwq@alphafold2-1 openfold-main]$ python3 setup.py install No CUDA runtime is...

liweiqing1997

UnboundLocalError in generate_chain_data_cache.py

2

Hi, I sucessfully generated the mmcif cache, but ran into an issue while trying to generate the chain data cache: ``` python3 scripts/generate_chain_data_cache.py /data/openfold/data/pdb_mmcif/mmcif_files_new/ chain_data_cache.json --cluster_file clusters-by-entity-40.txt --no_workers 16 10%|███████▋...

calmasri

--trace_model error when running inferencing

2

Hi @gahdritz, Here are a bit more details about my error when adding --trace_model option while doing inferencing. Here is the commands I run: ``` python3 run_pretrained_openfold.py \ /mnt/sampledata/fasta_T1044 \...

shangz-ai

Alignment taking too long

4

I was trying to generate new alignments using the `precompute_alignments_mmseqs.py ` script: ``` python3 scripts/precompute_alignments_mmseqs.py /fasta_dir/query_seqs.fasta \ data/mmseqs_dbs \ uniref30_2103_db \ /fasta_dir \ /data/MMseqs2/build/bin/mmseqs \ --hhsearch_binary_path /usr/bin/hhsearch \ --env_db colabfold_envdb_202108_db...

calmasri