is it possible to continue gmm refinement from last iteration?

[Maia Azubel]

Hi

I'm using EMAN 2.99.66 ( GITHUB: 2025-03-13 19:17 - commit: ce0afb465-dirty )

Your EMAN2 is running on: Linux-4.18.0-540.el8.x86_64-x86_64-with-glibc2.28 4.18.0-540.el8.x86_64

Your Python version is: 3.12.9

Due to a power outage the computers crashes when I was running 

e2gmm_spt_refine.py spt_23/threed_09.hdf --startres 15 --sym c1 --initpts spt_23/threed_09_seg.pdb --iters r,p,r --threads=8 --parallel threads:8

It completed iterations r,p, so I'm wondering if there is a way to restart the job from where it failed. 

And (maybe) on a related note,  when/how is --startiter STARTITER option used

Thanks,

Maia

[Muyuan Chen]

I think if you use the same command, adding --path with the existing path, --startres to be the resolution of the last successful iteration, and --startiter to be the last iteration number (so 2 here I think), it should work. Do backup the existing folder. I only used this function once or twice after power outages too...

Muyuan

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[Steve Ludtke]

Is there really an advantage to resuming, rather than just starting a new iteration with --startres set higher than the resolution already achieved? Seems like that would be pretty equivalent...

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[Muyuan Chen]

There is no real advantage other than maybe better book keeping… 

On Feb 23, 2026, at 5:16 PM, Steve Ludtke <slud...@gmail.com> wrote:

Is there really an advantage to resuming, rather than just starting a new iteration with --startres set higher than the resolution already achieved? Seems like that would be pretty equivalent...

To view this discussion visit https://groups.google.com/d/msgid/eman2/6BDD9B92-86C0-4521-B7E9-31AD223F8479%40gmail.com.

[Maia Azubel]

Thanks for the response. 

Would the second alternative look like this?

e2gmm_spt_refine.py gmm_3/threed_02.hdf --startres 7.5 --sym c1 --initpts spt_23/threed_09_seg.pdb --iters r --threads=8 --parallel threads:8

Maia

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From: em...@googlegroups.com <em...@googlegroups.com> on behalf of Muyuan Chen <g5v...@gmail.com>
Sent: Monday, February 23, 2026 5:21 PM
To: em...@googlegroups.com <em...@googlegroups.com>
Subject: Re: [EMAN2] is it possible to continue gmm refinement from last iteration?

 

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[Muyuan Chen]

Yes, I think..

On Feb 27, 2026, at 4:28 AM, 'Maia Azubel' via EMAN2 <em...@googlegroups.com> wrote:



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