rosalindfranklininstitute / parakeet

Phantom generator
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Resources temporary unavailable #54

Closed MohamadHarastani closed 10 months ago

MohamadHarastani commented 1 year ago

Hello James I was having an error related to h5py when running parakeet.run -c config.yaml --steps all. The error said "Resources temporary unavailable" and is related to a "locked" file. Something is not freeing the the h5 files, or maybe is a bug in the h5py. I worked around this error by pip install h5py==3.8.0 Cheers

jmp1985 commented 1 year ago

Hi Mohamad

That's really weird. I tried running the same command on a generic config file and I didn't have any issues. Can you send me the config file that showed this error?

I am also running h5py==3.8.0 at the moment but I will try updating and see if that breaks anything!

Best wishes James

MohamadHarastani commented 1 year ago

Hi James

Sorry for the late reply. I used to run this command with no issue, I reinstalled Parakeet and I was getting this problem sometimes (it's a tricky one). I have some config files that contain a lot of local structures that can reproduce the error, at least on my computer :-). If you wish, I can share them with you on email. But since I downgraded h5py everything is working fine. I'll keep this issue here just in case someone else faced this problem.

Cheers Mohamad

jmp1985 commented 1 year ago

Hi Mohamad

Sure, if you can, send me the config files. I will try with the latest h5py on my machine and try and figure it out! But yes, until this is sorted it is best to keep the issue open!

Best wishes James

jmp1985 commented 10 months ago

Hi Mohamad

I'm just going through trying to clear up a few issues. I decided to update all my packages and so now I am running with h5py 3.10. Everything seems to be working for me so I will close this issue.

If you get the issue again and find a way of reproducing it then we can re-open the issue.

Best wishes James