3D Refinement Error

[Emre Firlar]

Hi, 

My name is Emre Firlar, working at Rutgers CryoEM & Nanoimaging Facility. I have been using EMAN2 v2.91 for my tomography projects, and in my latest project, I ran the 3D refinement job using the GUI with the following code: 

/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_refine.py sets/tomobox_0707a.lst --reference=sptsgd_00/output.hdf --niter=5 --sym=c1 --mass=3000.0 --goldstandard=30 --pkeep=0.8 --maxtilt=95.0 --threads=18 --ppid=-2

I see the output and progress in the job:

NOT Writing notes, ppid=-2

e2proc3d.py sptsgd_00/output.hdf spt_09/model_input.hdf --process mask.soft:outer_radius=-1 --first 0 --last 0

e2spt_align.py sets/tomobox_0707a.lst spt_09/alignref.hdf --parallel thread:18 --path spt_09 --iter 1 --sym c1 --minres 200 --maxres 22.5  --goldcontinue

59439 jobs on 18 CPUs

Error running task :  7

e2spt_average.py --parallel thread:18 --path spt_09 --sym c1 --keep 0.800 --iter 1 --skippostp 

Cannot find a spt_09/particle_parms* file

Traceback (most recent call last):

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_refine.py", line 357, in <module>

    main()

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_refine.py", line 262, in main

    data=EMData(combine)

  File "/data/k/efirlar/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 400, in db_emd_init

    self.__initc(*parms)

RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615309007099/work/libEM/io/hdfio2.cpp:464: error with 'spt_09/threed_01.hdf': 'cannot access file 'spt_09/threed_01.hdf'' caught

Could you please help me understand what could be wrong here. I also run the same code with --maxtilt=90.0 and have same/similar error.

Thanks.

Best regards,

Emre Firlar, PhD

Rutgers CryoEM & Nanoimaging Facility 

Rutgers University

[Ludtke, Steven J.]

Often this indicates a problem with running out of RAM. How much RAM does the machine have, and what is the box size of the 3-D particles?

Another possibility is your /tmp folder is mounted as a limited space ramdisk and it's getting filled up. You can use 'df' to see if /tmp is getting full. If there are issues with that, there is an optional 3rd argument for --parallel so you can explicitly specify a scratch folder (put it somewhere on a hard drive), eg - --parallel=thread:18:/home/yourname/tmp or somesuch.

If those aren't the problem check the thread.out file in the folder where you ran the job. If there are errors in running threads, you should see them there.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Emre Firlar]

Hi Steven,

Thanks for getting back about this so quickly.  Our system has 128GB RAM. Box size is 192 pixels.

I will try the code with edited /tmp folder location as you suggested. 

Thanks

Best regards,

Emre Firlar, PhD

Rutgers CryoEM & Nanoimaging Facility 

Rutgers University

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/01A9C5D0-0117-46F1-96A8-C4459820ED7E%40bcm.edu.

[Muyuan Chen]

Since e2spt_align died in the first place, it may also be useful to look into the thread.out file and see what’s the actual error message...

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAA10iu5fuJvO2fzKkRc9_8%2ByvrjxASJhb2KLpYOLh_H7iFh0xQ%40mail.gmail.com.

[Emre Firlar]

Hi, I copied and pasted the thread.out file here: 

Thanks

Best regards,

Emre

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
    main()
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_align.py", line 625, in execute
    c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)

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[Muyuan Chen]

This seems more likely to be an issue of memory or disk space like Steve mentioned at the beginning. Does it always fail or does it run on a small subset of particles (or the tutorial ribosome dataset)? How long does it take to crash? How does the memory usage look like before it crashes? 

I don't know your box size, but the idea of having 60k particles on 18 cpus seems a bit odd too. Unless the particles are tiny, this would take forever to run and strange things can happen during the infinitely long run time I guess...

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[Emre Firlar]

Box size is 192pixels.

I will check timing for fail as well. 

Best regards,

Emre

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[Emre Firlar]

Hi,

Currently I managed to move to sub-tilt refinement with box size 96(shrink2 from 192 pixels) and used  sub-tilt refinement from GUI with the following code:

/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py --ptclin spt_13_00/ali_ptcls_00_odd.lst --ptclout spt_13_00/ali_ptcls_01_odd.lst --ref spt_13_00/threed_00_odd.hdf --threedout spt_13_00/threed_01_odd.hdf --keep 0.8 --threads 12 --parallel thread:12 --refineastep 1.0 --refinentry 8 --maxshift 8 --padby 1.5 --sym c1 --ppid=33416

thread.out did not update for this run. 

However, I am having the following error in the terminal:  OSError: spt_13_00/fsc_masked_01.txt not found.

doesn't exist spt_13_00/fscvol_00.hdf 

Is this also memory relevant? All of what is given in the terminal is attached below. Thanks.

TERMINAL:

e2spt_tiltrefine_oneiter.py --ptclin spt_13_00/ali_ptcls_00_odd.lst --ptclout spt_13_00/ali_ptcls_01_odd.lst --ref spt_13_00/threed_00_odd.hdf --threedout spt_13_00/threed_01_odd.hdf --keep 0.8 --threads 12 --parallel thread:12 --refineastep 1.0 --refinentry 8 --maxshift 8 --padby 1.5 --sym c1 

Initializing parallelism...

12 total CPUs available

101609 jobs

Error running task :  4

e2proc3d.py spt_13_00/threed_01_odd.hdf spt_13_00/threed_raw_odd.hdf

Traceback (most recent call last):

  File "/data/k/efirlar/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 657, in db_get_image_count

    ret = EMUtil.get_image_count_c(fsp)

RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615309007099/work/libEM/io/hdfio2.cpp:464: error with 'spt_13_00/threed_01_odd.hdf': 'cannot access file 'spt_13_00/threed_01_odd.hdf'' caught

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2proc3d.py", line 890, in <module>

    main()

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2proc3d.py", line 308, in main

    else : nimg = EMUtil.get_image_count(infile)

  File "/data/k/efirlar/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 660, in db_get_image_count

    raise Exception(fsp)

Exception: spt_13_00/threed_01_odd.hdf

e2refine_postprocess.py --even spt_13_00/threed_01_even.hdf --odd spt_13_00/threed_01_odd.hdf --output spt_13_00/threed_01.hdf --iter 1 --restarget 12.05083524339072 --threads 12 --sym c1 --mass 3000.0  --setsf None --tophat localwiener

Sat Sep 11 12:22:11 2021: e2proc3d.py spt_13_00/threed_01_even.hdf spt_13_00/fsc_unmasked_01.txt --calcfsc=spt_13_00/threed_01_odd.hdf

Traceback (most recent call last):

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2proc3d.py", line 890, in <module>

    main()

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2proc3d.py", line 464, in main

    datafsc=EMData(options.calcfsc)

  File "/data/k/efirlar/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 400, in db_emd_init

    self.__initc(*parms)

RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615309007099/work/libEM/io/hdfio2.cpp:464: error with 'spt_13_00/threed_01_odd.hdf': 'cannot access file 'spt_13_00/threed_01_odd.hdf'' caught

Error running:  e2proc3d.py spt_13_00/threed_01_even.hdf spt_13_00/fsc_unmasked_01.txt --calcfsc=spt_13_00/threed_01_odd.hdf

Traceback (most recent call last):

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_tiltrefine.py", line 539, in <module>

    main()

  File "/data/k/efirlar/eman2-sphire-sparx/bin/e2spt_tiltrefine.py", line 460, in main

    fsc=np.loadtxt(os.path.join(path, "fsc_masked_{:02d}.txt".format(itr+1)))

  File "/data/k/efirlar/eman2-sphire-sparx/lib/python3.7/site-packages/numpy/lib/npyio.py", line 968, in loadtxt

    fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)

  File "/data/k/efirlar/eman2-sphire-sparx/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 269, in open

    return ds.open(path, mode, encoding=encoding, newline=newline)

  File "/data/k/efirlar/eman2-sphire-sparx/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 623, in open

    raise IOError("%s not found." % path)

OSError: spt_13_00/fsc_masked_01.txt not found.

doesn't exist spt_13_00/fscvol_00.hdf

[Muyuan Chen]

Does that mean the _even part of the subtilt refinement runs successfully without errors?

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[Ludtke, Steven J.]

That isn't really a command you would normally run manually. Presumably there was a higher level command you ran, which ran this as one of its component subprocesses. The error here is quite clear:

On Sep 13, 2021, at 4:13 PM, Emre Firlar <efi...@gmail.com> wrote:

cannot access file 'spt_13_00/threed_01_odd.hdf'

usually meaning that the file doesn't exist because something went wrong earlier in the process (before the command you sent). I assume, if you check, that the file in question doesn't exist?

[Emre Firlar]

Thanks for replies. The command I wrote is what I copied from notebook. 

Also even and odd components ran one time only and then it crashed.

Best regards

Emre

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[Emre Firlar]

On GUI/Command Tab, the code used was

e2spt_tiltrefine.py --path=spt_13 --iter=-1 --niters=4 --keep=0.8 --maxalt=45.0 --mask=auto --threads=12 --parallel=thread:12 --tophat=localwiener

I can see maps on threed_01_even.hdf, threed_00_even.hdf, threed_00_odd.hdf but not threed_01_odd.hdf.

Best regards,

Emre

[Muyuan Chen]

That's interesting... I would suspect there is something wrong with one of the particles in the _odd subset.  How long does it take for e2spt_tiltrefine_oneiter to throw out the error? If it happens quickly and is reproducible, you can run with the --debug option and see if it says anything meaningful.  

e2spt_tiltrefine_oneiter.py --ptclin spt_13_00/ali_ptcls_00_odd.lst --ptclout spt_13_00/ali_ptcls_01_odd.lst --ref spt_13_00/threed_00_odd.hdf --threedout spt_13_00/threed_01_odd.hdf --keep 0.8 --threads 12 --parallel thread:12 --refineastep 1.0 --refinentry 8 --maxshift 8 --padby 1.5 --sym c1 --debug

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[Emre Firlar]

Thanks.
Situation still persists. Debug code gave the following:

Initializing parallelism...

12 total CPUs available

96 jobs

0

0.0

12.5

25.0

37.5

50.0

62.5

75.0

87.5

I also picked other set of particles and moved the data to cluster from local workstation and still have the same error.

Thanks.

Best regards,

Emre

[Muyuan Chen]

I don’t know what happened. It seems a random thing if it works on one half of the data but not the other half. I guess you may bypass this by add —transonly to spt_tiltrefine command so it will skip the local rotational refinement and may avoid the mysterious bug too. The rotation in subtilt refinement should not do much in general. And if you want to try, there is also the e2spt_refine_new program that can refine it in a more integrated way. It also has less c++ code any may be easier to debug if anything goes wrong.

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