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I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.i2pc.es
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Do relion 2D classification report file doesn't exist #2071

Open liz18 opened 4 years ago

liz18 commented 4 years ago

Scipion 2.0 was installed on Ubuntu 18.04.

When doing 2D classification by relion, it kept on reporting error "File Runs/xxxxx_RrotRelionClassify2D/logs/run.stdous doesn't exist", this sentence repeat again and again then the program failed.

This bug was the same when I tried eman2 auto_ctf program.

What could be the problem?

pconesa commented 4 years ago

Thanks @liz18 . .. if it happens with two different plugins might be something in the core or the computer.

Can you try to run scipion but activating debugging?

export SCIPION_DEBUG=1

And then run scipion

Checkout the terminal output

liz18 commented 4 years ago

@pconesa I did as what you said and run scipion again, the terminal output was as following: image

liz18 commented 4 years ago

Should I reinstall the OS to Centos?

pconesa commented 4 years ago

I'm afraid the log does not help much.

Does it happen with any protocol? Do other protocols work fine?

El sáb., 4 ene. 2020 12:47, liz18 notifications@github.com escribió:

Should I reinstall the OS to Centos?

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liz18 commented 4 years ago

The xmipp manual picking doesn't work sometimes. I have not tried the protocols after 2D classification yet. Scipion 2.0 was installed on Ubuntu 19.10 before the reinstalled 18.04. Problem happened when doing RELION 2D classification, but with openmpi problem. So I changed to the 18.04, but the other problem described above happened.

Maybe I should try Centos.

azazellochg commented 4 years ago

Hello @liz18, let's start from basic checks. Could you please run 'scipion run mpirun -np 3 hostname' command and post the output here?