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RELION 3.1, incorrect image size error #519

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davidmbelnap opened this issue Oct 18, 2019 · 11 comments
Closed

RELION 3.1, incorrect image size error #519

davidmbelnap opened this issue Oct 18, 2019 · 11 comments

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@davidmbelnap
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davidmbelnap commented Oct 18, 2019 •
edited by biochem-fan
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Describe your problem
I have three particle data sets that I am combining in version 3.1. Two have the same pixel size (1.404 angs.) and box size (392 pixels). One does not (1.782 angs. and 308 pixels). I joined them with the Join star files function as described here, https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Pixel_size_issues. However, when I run a 2D classification job, I get an "incorrect image size" error. I got this twice at different images in the middle of the small box size set.

Environment:

  • OS: CentOS Linux 7 (Core)
  • MPI runtime: Intel MPI 2019.5.281
  • RELION version: RELION 3.1-beta (3.1-beta-commit-a6aaa5)
  • Memory: two nodes with 128 GB each
  • GPU: using CPUs

Dataset:

  • Box size: two small sets of 392 pixels, one very large set of 308 pixels
  • Pixel size: 1.404 and 1.782, respectively, for 392 and 308 sets
  • Number of particles: 39,649
  • Description: an icosahedral assembly of a viral capsid protein

Job options:

  • Type of job: Class2D
  • Number of MPI processes: 24
  • Number of threads: 2
  • Full command (see note.txt in the job directory):
    which relion_refine_mpi --o Class2D/job024/run --i JoinStar/job022/join_particles.star --dont_combine_weights_via_disc --no_parallel_disc_io --pool 3 --pad 2 --ctf --iter 25 --tau2_fudge 2 --particle_diameter 300 --K 10 --flatten_solvent --zero_mask --oversampling 1 --psi_step 12 --offset_range 5 --offset_step 2 --norm --scale --j 2 --pipeline_control Class2D/job024/

Error message:

 fn_img= 000025@Extract/job016/micrographs/081kx/RDS_0047.mrcs XSIZE(img())= 308 YSIZE(img())= 308
 while XSIZE(exp_imagedata)= 392 and YSIZE(exp_imagedata)= 392
in: /uufs/chpc.utah.edu/sys/srcdir/relion/3.1-beta-101519/src/ml_optimiser.cpp, line 9051
ERROR: 
MlOptimiser::getMetaAndImageDataSubset ERROR: incorrect image size
master encountered error: === Backtrace  ===
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x48) [0x443d48]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN11MlOptimiser25getMetaAndImageDataSubsetEllb+0x2cfe
) [0x78dc4e]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi11expectationEv+0x1973) [0x49a343]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(_ZN14MlOptimiserMpi7iterateEv+0x18b) [0x48870b]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi(main+0x7f) [0x43792f]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2ad41c2ad3d5]
/uufs/chpc.utah.edu/sys/installdir/relion/3.1-beta-cpu/bin/relion_refine_mpi() [0x4377e9]
==================
ERROR: 
MlOptimiser::getMetaAndImageDataSubset ERROR: incorrect image size
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
@biochem-fan
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Can you paste your optics group table here?

@davidmbelnap
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davidmbelnap commented Oct 18, 2019 via email

@biochem-fan
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I could not reproduce your problem.

fn_img= 000025@Extract/job016/micrographs/081kx/RDS_0047.mrcs XSIZE(img())= 308 YSIZE(img())= 308

This means that 000025@Extract/job016/micrographs/081kx/RDS_0047.mrcs should belong to opticsGroup1. Can you make sure values in the rlnOpticsGroup column is correct?

@davidmbelnap
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davidmbelnap commented Oct 21, 2019 via email

@davidmbelnap
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davidmbelnap commented Oct 21, 2019 via email

@davidmbelnap
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You were not able to repeat my problem with the same version I was using (3.1-beta-commit-a6aaa5) or are you using a later version? I see that a later or different version was used by the person reporting error 524 (v3.1-beta-b86482c).

@davidmbelnap
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I can send my full STAR file and image files if that would help.

@biochem-fan
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#524 is a different issue, where lack of rlnImageSize caused a problem. In your case, you have correct values in the column.

@biochem-fan biochem-fan mentioned this issue Oct 27, 2019
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@biochem-fan
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Does this happen when you disable preread particles to RAM and copy particles to scratch?

@biochem-fan
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OK, I finally found a reproducible case.

Meanwhile, if you set Use parallel disc I/O: Yes, the problem should disappear.

@biochem-fan
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I close this, since this is the same problem as #530. Please continue discussion there.

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@biochem-fan @davidmbelnap