error while running e2spt_refine

[Maia Azubel]

iter r was running for a few weeks and finally failed.

Any advice would be greatly appreciated.

Maia

version

EMAN 2.99.54 ( GITHUB: 2023-12-05 12:49 - commit: 4e38f2525 )

Your EMAN2 is running on: Linux-4.18.0-540.el8.x86_64-x86_64-with-centos-8 4.18.0-540.el8.x86_64

Your Python version is: 3.7.9

command

e2spt_refine_new.py --ptcls sets/256ncp.lst --ref old_spt_97_threed_01.hdf --startres=15 --sym=c1 --goldstandard --iters=p3,t2,p,t,r,d --keep=0.95 --top=localwiener --parallel=thread:70 --threads=70  --maxres 5

error

Iteration 6 complete, 234:35:05

######## iter 8 ##########

### Subtilt rotational refinement....

e2spt_subtlt_local.py --ref spt_185/threed_07.hdf --path spt_185 --iter 8 --maxres 5.00 --parallel thread:70 --aliptcls3d spt_185/aliptcls3d_06.lst --smooth 100 --smoothN 15 --refine_trans --refine_rot --goldcontinue

3685466 jobs on 70 CPUs

Traceback (most recent call last):

  File "/data/maia2/miniconda3/envs/eman2/bin/e2spt_subtlt_local.py", line 481, in <module>

    main()

  File "/data/maia2/miniconda3/envs/eman2/bin/e2spt_subtlt_local.py", line 80, in main

    rets=etc.get_results(i)[1]

  File "/data/maia2/miniconda3/envs/eman2/lib/python3.7/site-packages/EMAN2PAR.py", line 197, in get_results

    return self.handler.get_results(taskid)

  File "/data/maia2/miniconda3/envs/eman2/lib/python3.7/site-packages/EMAN2PAR.py", line 818, in get_results

    task=load(open("%s/%07d"%(self.scratchdir,taskid),"rb"))

FileNotFoundError: [Errno 2] No such file or directory: '/tmp/e2tmp.1972560708/0000000'

tail .eman2log.txt

2025/02/09 10:06:01     2025/02/09 10:06:01     1790855/1790809   sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2proc3d.py spt_185/threed_07_odd.hdf spt_185/tmp_odd.hdf --multfile spt_185/mask.hdf --ppid=1790809

2025/02/09 10:06:01     incomplete              1790858/1790809   sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2proc3d.py spt_185/tmp_even.hdf spt_185/fsc_masked_07.txt --calcfsc spt_185/tmp_odd.hdf --ppid=1790809

2025/02/09 10:06:03     2025/02/09 10:06:04     1790862/1790809   sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2proc3d.py spt_185/threed_07_even.hdf spt_185/threed_even_unmasked.hdf --process filter.lowpass.tophat:cutoff_abs=0.5 --ppid=1790809

2025/02/09 10:06:04     2025/02/09 10:06:05     1790865/1790809   sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2proc3d.py spt_185/threed_07_odd.hdf spt_185/threed_odd_unmasked.hdf --process filter.lowpass.tophat:cutoff_abs=0.5 --ppid=1790809

2025/02/09 10:06:05     2025/02/09 10:09:34     1790868/1790809   sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2fsc_real_local.py spt_185/threed_even_unmasked.hdf spt_185/threed_odd_unmasked.hdf --output spt_185/fscvol_07.hdf --outfilt spt_185/threed_07.hdf --outfilte spt_185/threed_07_even.hdf --outfilto spt_185/threed_07_odd.hdf --mask spt_185/mask.hdf --threads 70 --localsizea 20 --compressbits 12 -v 1 --ppid=1790809

2025/02/09 10:09:35     2025/02/09 10:09:35     1791077/1790809   sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2proc3d.py spt_185/threed_07.hdf spt_185/threed_07.hdf --multfile spt_185/mask.hdf --process normalize.edgemean --ppid=1790809

2025/02/09 10:09:35     2025/02/09 10:09:36     1791080/1790809   sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2proc3d.py spt_185/threed_07_even.hdf spt_185/threed_07_even.hdf --multfile spt_185/mask.hdf --process normalize.edgemean --ppid=1790809

2025/02/09 10:09:36     2025/02/09 10:09:37     1791083/1790809   sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2proc3d.py spt_185/threed_07_odd.hdf spt_185/threed_07_odd.hdf --multfile spt_185/mask.hdf --process normalize.edgemean --ppid=1790809

2025/02/09 10:09:38     100%                    1791086/895807    sr20-395c92b4ea.stanford.edu  /data/maia2/miniconda3/envs/eman2/bin/e2spt_subtlt_local.py --ref spt_185/threed_07.hdf --path spt_185 --iter 8 --maxres 5.00 --parallel thread:70 --aliptcls3d spt_185/aliptcls3d_06.lst --smooth 100 --smoothN 15 --refine_trans --refine_rot --goldcontinue --ppid=895807

[Muyuan Chen]

Temporary file folder full, or get cleaned when the program is running? You can set --parallel thread:70:/ data/maia2/tmp/ to use some other paths for temporary files if you are on a shared machine. 

Muyuan

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[Maia Azubel]

Thanks for the prompt response!

One question, if I want to continue from were it failed is the following correct

e2spt_refine_new.py --path spt_185 --continuefrom 7 --iter r,d  --startres=10 --sym=c1 --keep=0.95 --top=localwiener --parallel thread:70:/ data/maia2/tmp/ --threads=70  --maxres 5

Is it --goldcontinue also needed?

Thanks, 
Maia

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From: em...@googlegroups.com <em...@googlegroups.com> on behalf of Muyuan Chen <g5v...@gmail.com>
Sent: Monday, February 24, 2025 9:32 AM
To: em...@googlegroups.com <em...@googlegroups.com>
Subject: Re: [EMAN2] error while running e2spt_refine

 

To view this discussion visit https://groups.google.com/d/msgid/eman2/CAO_0xqECz0wwqg6S6W%2BBoA-z3WtKiL%2BRZHmSdt%2Bh8piOPfjnmw%40mail.gmail.com.

[Muyuan Chen]

I don't think --goldcontinue is required, but adding it never hurt. 

Also if  you have a GPU, maybe the GMM based refinement at this point instead of the traditional one. 

https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_p22#GMM-based_refinement

The 'r' iteration there often have better result, and sometimes faster. It does not do defocus refinement though. 

Muyuan

To view this discussion visit https://groups.google.com/d/msgid/eman2/MN2PR02MB66724A09B4602FD3CD2815DCDFC02%40MN2PR02MB6672.namprd02.prod.outlook.com.