Refine3D——ERROR: Array_by_array: different shapes (+)

[jiaz6985]

Hello,

In the previous stage, I completed the processing in WarpEM. After converting the obtained data into the format required by RELION, I successfully ran the InitialModel step in RELION 4.0. However, I encountered some issues during the Refine3D step. Could you please assist me in resolving these problems? Thank you very much.

mpirun -n 3 $(which relion_refine_mpi) --o Refine3D/job001/run --auto_refine --split_random_halves --ios relion_pix10_2d_optimisation_set.star --ref initial.mrc --firstiter_cc --trust_ref_size --ini_high 60 --dont_combine_weights_via_disc --pool 30 --pad 2 --ctf --particle_diameter 230 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --auto_local_healpix_order 3 --offset_range 5 --offset_step 2 --sym C6 --low_resol_join_halves 40 --norm --scale --j 2 --gpu "0" --pipeline_control Refine3D/job001/
failed to open /dev/dri/renderD128: Permission denied
failed to open /dev/dri/renderD129: Permission denied
failed to open /dev/dri/renderD130: Permission denied
failed to open /dev/dri/renderD131: Permission denied
failed to open /dev/dri/renderD128: Permission denied
failed to open /dev/dri/renderD129: Permission denied
failed to open /dev/dri/renderD130: Permission denied
failed to open /dev/dri/renderD131: Permission denied
RELION version: 4.0.2
Precision: BASE=double

WARNING: No reference mask filename was found in file relion_pix10_2d_optimisation_set.star. Continuing without mask.
WARNING: No reference mask filename was found in file relion_pix10_2d_optimisation_set.star. Continuing without mask.
WARNING: No reference mask filename was found in file relion_pix10_2d_optimisation_set.star. Continuing without mask.
=== RELION MPI setup ===

• Number of MPI processes = 3
• Number of threads per MPI process = 2
• Total number of threads therefore = 6
• Leader (0) runs on host = cryoema100
• Follower 1 runs on host = cryoema100
• Follower 2 runs on host = cryoema100
  =================
  uniqueHost cryoema100 has 2 ranks.
  Follower 1 will distribute threads over devices 0
  Thread 0 on follower 1 mapped to device 0
  Thread 1 on follower 1 mapped to device 0
  Follower 2 will distribute threads over devices 0
  Thread 0 on follower 2 mapped to device 0
  Thread 1 on follower 2 mapped to device 0
  Device 0 on cryoema100 is split between 2 followers
• WARNING: will ignore (but maintain) values for the unknown label: rlnTomoVisibleFrames
• WARNING: will ignore (but maintain) values for the unknown label: rlnTomoVisibleFrames
• WARNING: will ignore (but maintain) values for the unknown label: rlnTomoVisibleFrames
  Running CPU instructions in double precision.
• WARNING: will ignore (but maintain) values for the unknown label: rlnTomoVisibleFrames
  Estimating initial noise spectra from at most 5000 particles
  000/??? sec ~~(,_,"> [oo] Size(Y,X): 40x40 i=[-20..19] j=[-20..19]
  Number of images = 41 Size(Y,X): 40x40 i=[-20..19] j=[-20..19]
  ERROR:
  Array_by_array: different shapes (+)
  ERROR:
  Array_by_array: different shapes (+)

---

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.