Training Dataset

[dptech-corp]

Training Dataset

[lhatsk]

In the mean time, it would be great if you could upload the scripts to generate the training features. Unfortunately, AFAICT they are missing. I'm especially interested in training the multimer variant. Thanks!

[guolinke]

The multimer features mostly are the same as monomer ones, except the assembly of multiple chains.
You can refer this script https://github.com/dptech-corp/Uni-Fold/blob/main/scripts/get_pdb_assembly.py to generate the "pdb_assembly.json" we used.

[guolinke]

The dataset is very large, and we are looking for a solution for data hosting. Last week we submitted the request to "AWS Open Data Sponsorship Application", but didn't receive any response yet.

[DimaMolod]

I am trying to download the "Full training dataset" using modelscope but the MsDataset.load() doesn't work for me because the connection gets broken by peer. The latest message I get is:
File "/home/dmolodenskiy/.conda/envs/py38/lib/python3.8/site-packages/requests/models.py", line 818, in generate raise ChunkedEncodingError(e) requests.exceptions.ChunkedEncodingError: ("Connection broken: ConnectionResetError(104, 'Connection reset by peer')", ConnectionResetError(104, 'Connection reset by peer'))

[guolinke]

@DimaMolod did it happen at the beginning, or already in-progress?

[DimaMolod]

hi @guolinke
it happens after 10-20 minutes of hanging. Seems like it is trying to connect during this time and finally the error message pops up, after the connection time is out.
The modelscope directory has been created with the following structure:

 modelscope/
    hub/
            datasets/
                downloads/
                    DPTech/
                        Uni-Fold-Data/
                            master/
                                Uni-Fold-Data.json
                                dataset_infos.json

thanks for you help!

(I'll also copy the last few messages from python here just in case you find it useful)

>>> ds = MsDataset.load(dataset_name='Uni-Fold-Data', namespace='DPTech', split='train')
2022-11-18 09:49:40,975 - modelscope - WARNING - Reusing dataset Uni-Fold-Data's python file (modelscope/hub/datasets/downloads/DPTech/Uni-Fold-Data/master/Uni-Fold-Data.json)
2022-11-18 09:49:41,498 - modelscope - WARNING - Reusing dataset Uni-Fold-Data's python file (modelscope/hub/datasets/downloads/DPTech/Uni-Fold-Data/master/dataset_infos.json)
2022-11-18 09:49:41,499 - modelscope - INFO - No subset_name specified, defaulting to the default

[lhatsk]

I have the same issue. After re-trying I get now:

RequestError: {'status': -2, 'x-oss-request-id': '', 'details': "RequestError: HTTPSConnectionPool(host='dataset-hub.oss-cn-hangzhou.aliyuncs.com', port=443): Max retries exceeded with url: /public-unzip-dataset%2FDPTech%2FUni-Fold-Data%2Fmaster%2Fdatasets%2Fpdb_features%2F1e0z_A.feature.pkl.gz (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2b2f5d9bdd50>: Failed to establish a new connection: [Errno -2] Name or service not known'))"}

Does this include the training data for multimer?

[guolinke]

We will report the issues to the modelscope. And yes, the multimer data is included.

[guolinke]

The problem is due to the unstable network, as the data is hosted in China. The modelscope team promised they would fix it in the next 2 weeks.

[DimaMolod]

Thanks! Maybe meanwhile you could provide a script to generate the training dataset directory from scratch (from the downloaded databases)? I couldn't find it in the scripts directory.

[guolinke]

@DimaMolod The data generation code is almost the same as the one used in inference, except for the label extraction from mmcif. @ZiyaoLi maybe we can add a script for the mmcif processing.

BTW, our data generation code highly relies on the cloud services (mostly Ali-cloud), because it is impossible to generate the data by a single machine. In particular, it takes us several months by hundreds of machines to generate these data. Therefore, we think it is less realistic to generate these data from scratch.

[lhatsk]

Any news?

[guolinke]

@lhatsk we are waiting for the fix from modelscope team. will post the updates here.

[WeianMao]

i fix the bug, please refer to this link modelscope/modelscope#51
@guolinke @lhatsk

[lhatsk]

Thanks! Unfortunately, it still doesn't work for me.

RequestError: {'status': -2, 'x-oss-request-id': '', 'details': "RequestError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))"}

[WeianMao]

@lhatsk @guolinke i succuss yesterday, but failed today. it seems like the sever is unstable. is it possible to download the dataset from baidu drive? the issue exists too long.

[DimaMolod]

@DimaMolod The data generation code is almost the same as the one used in inference, except for the label extraction from mmcif. @ZiyaoLi maybe we can add a script for the mmcif processing.

BTW, our data generation code highly relies on the cloud services (mostly Ali-cloud), because it is impossible to generate the data by a single machine. In particular, it takes us several months by hundreds of machines to generate these data. Therefore, we think it is less realistic to generate these data from scratch.

Thank you, it would be very useful if you could upload a script for the label extraction from mmcif files.

[guolinke]

@DimaMolod The data generation code is almost the same as the one used in inference, except for the label extraction from mmcif. @ZiyaoLi maybe we can add a script for the mmcif processing.
BTW, our data generation code highly relies on the cloud services (mostly Ali-cloud), because it is impossible to generate the data by a single machine. In particular, it takes us several months by hundreds of machines to generate these data. Therefore, we think it is less realistic to generate these data from scratch.

Thank you, it would be very useful if you could upload a script for the label extraction from mmcif files.

@teslacool can you merge the code into this repo?

[dingquanyu]

Hi,

I managed to resolve the 104 error shown above but then this ReadTimeoutError was reported. Could you maybe increase your default timeout from 60s to something longer?

Thanks a lot.

HTTPConnectionPool(host='www.modelscope.cn', port=80): Max retries exceeded with url: /api/v1/datasets/DPTech/Uni-Fold-Data/oss/tree/?MaxLimit=-1&Revision=master&Recursive=True&FilterDir=True (Caused by ReadTimeoutError("HTTPConnectionPool(host='www.modelscope.cn', port=80): Read timed out. (read timeout=60)"))

I am trying to download the "Full training dataset" using modelscope but the MsDataset.load() doesn't work for me because the connection gets broken by peer. The latest message I get is: File "/home/dmolodenskiy/.conda/envs/py38/lib/python3.8/site-packages/requests/models.py", line 818, in generate raise ChunkedEncodingError(e) requests.exceptions.ChunkedEncodingError: ("Connection broken: ConnectionResetError(104, 'Connection reset by peer')", ConnectionResetError(104, 'Connection reset by peer'))

[guolinke]

@henrywotton you can report the issue to https://github.com/modelscope/modelscope