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WangPeng-Lab / scGCO

Single-cell Graph Cuts Optimization
MIT License
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Tutorial execution stucked #2

Open davidecrs opened 3 years ago

davidecrs commented 3 years ago

Hi,

I have cloned this repo, installed the dependencies and I am trying scGCO package through the tutorial jupyter notebook, however there seems to be a problem with the execution. In particular, it happens to me that step 2 of that file is stucked in an infinite execution loop (on the function gmmDict = multiGMM (data_norm)). This seems to be confirmed by the HTOP panel where the scGCO processes are in the S state.

Coke-Zhang commented 3 years ago

Hello. Enen. We havn't the issue. Thanks your 'problem'. Please show your whole pipeline and the error message.

Hi,

I have cloned this repo, installed the dependencies and I am trying scGCO package through the tutorial jupyter notebook, however there seems to be a problem with the execution. In particular, it happens to me that step 2 of that file is stucked in an infinite execution loop (on the function gmmDict = multiGMM (data_norm)). This seems to be confirmed by the HTOP panel where the scGCO processes are in the S state.

Hello. Enen. We havn't the issue. Thanks your 'problem'. Please show your whole pipeline and the error message.

davidecrs commented 3 years ago

The code doesn't show any error message. It remains running for a long (too) long time, probably for an infinite time given the S state of the processes shown in the HTOP panel.

I simply executed the code in this tutorial without changing it https://github.com/WangPeng-Lab/scGCO/blob/master/code/Tutorial/scGCO_tutorial.ipynb . The execution get stuck when running the fifth iteration (when tqdm progress bar shows 4/8 ) of gmmDict=multiGMM(data_norm) (in step 2).

Coke-Zhang commented 3 years ago

The code doesn't show any error message. It remains running for a long (too) long time, probably for an infinite time given the S state of the processes shown in the HTOP panel.

I simply executed the code in this tutorial without changing it https://github.com/WangPeng-Lab/scGCO/blob/master/code/Tutorial/scGCO_tutorial.ipynb . The execution get stuck when running the fifth iteration (when tqdm progress bar shows 4/8 ) of gmmDict=multiGMM(data_norm) (in step 2).

enen. Do you run our scGCO on windows ? Maybe the parallel have poor compatibility on windows. You can direct run gmmDict = gmm_model(data_norm). without parallel. In addition, You can save time gmmDict = gmm_model(data_norm.loc[:,your_geneList]).

davidecrs commented 3 years ago

I run scGCO on Ubuntu 20.04 with python 3.8.5. Thanks for your help, with gmmDict = gmm_model(data_norm) it works !