Prevent box sizes to be of the same value

[JorMaister]

Reported by DSheperd.

Command:

Protocol failed: Command ' mpirun -np 3 which relion_refine_mpi --ios Runs/007241_ProtRelionRefineSubtomograms/extra/_optimisation_set.star --i Runs/009538_ProtRelionRefineSubtomograms/extra/inSubtomos.star --o Runs/009538_ProtRelionRefineSubtomograms/extra/ --j 2 --ctf --particle_diameter 450 --pool 10 --dont_combine_weights_via_disc --gpu "0" --oversampling 1 --auto_refine --split_random_halves --low_resol_join_halves 40 --norm --scale --flatten_solvent --ref Runs/006998_ProtRelionResizeVolume/extra/volume_rescaled_001.mrc --firstiter_cc --ini_high 40.00 --sym C13 --zero_mask --healpix_order 4 --offset_range 5 --offset_step 2 --auto_local_healpix_order 4 --pad 2 ' returned non-zero exit status 1.

Error:

I did a relionsubtomo classification run and one of the classes always gives me the following error whenever I try to do a refine job

00017: DIRECT_A1D_ELEM(sigma2, i)= 5.3654e-11
00018: in: /home/doulin/software/em/relion-4.0/src/backprojector.cpp, line 1088
00019: ERROR:
00020: BackProjector::reconstruct: ERROR: unexpectedly small, yet non-zero sigma2 value, this should not happen...
00021: === Backtrace ===
00022: /home/doulin/scipion_installation/software/em/relion-4.0/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x7d) [0x5564383b93cd]
00023: /home/doulin/scipion_installation/software/em/relion-4.0/bin/relion_refine_mpi(+0x5d89c) [0x55643833689c]
00024: /home/doulin/scipion_installation/software/em/relion-4.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi12maximizationEv+0x5ee) [0x5564383f243e]
00025: /home/doulin/scipion_installation/software/em/relion-4.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi7iterateEv+0x53f) [0x5564383f470f]
00026: /home/doulin/scipion_installation/software/em/relion-4.0/bin/relion_refine_mpi(main+0x79) [0x5564383a3f99]
00027: /lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f1aeb029d90]
00028: /lib/x86_64-linux-gnu/libc.so.6(libc_start_main+0x80) [0x7f1aeb029e40]
00029: /home/doulin/scipion_installation/software/em/relion-4.0/bin/relion_refine_mpi(_start+0x25) [0x5564383a7595]
00030: ==================
00031: ERROR:
00032: BackProjector::reconstruct: ERROR: unexpectedly small, yet non-zero sigma2 value, this should not happen...
00033: --------------------------------------------------------------------------
00034: MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
00035: with errorcode 1.
00036:
00037: NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
00038: You may or may not see output from other processes, depending on
00039: exactly when Open MPI kills them.

Solution he found:

After much mucking about I finally resolved the error. My box size and cropped were the same so I changed my box size to 124 but kept my cropped boxsize at 56 and it seems to work now.