Dear all,
I've encountered a strange error when using Relion for 3D classification. The job ran for days with many iterations, and died (stalled not crashed) with an error message:
Error in askMemory: Memory allocation size requested is zero!
File: src/memory.cpp line: 27
In thread 6
I've tried to resubmit the job, but encountered the same error - just died/stalled at different cycle of iterations. However, one thing is consistent among the failing runs - they all died at when they were ending the iteration while writing files (the Relion mouse almost ate the whole cheese!!).
My data set has ~100,000 particles with a image size of 64x64 and a pixel size of 4.88. This is probably not an out-of-memory issue - the memory usage is supposed to be not that intensive as the stdout at the 33rd iteration reported (before my job died):
Estimated memory for expectation step > 1.52443 Gb, available memory = 24 Gb.
Estimated memory for maximization step > 0.0414566 Gb, available memory = 24 Gb.
Expectation iteration 33 of 50
Here is my Relion command line:
mpirun -map-by node -x OMP_NUM_THREADS -x PATH -x LD_LIBRARY_PATH -n $relion_mpi_tasks `which relion_refine_mpi` --o Class3D/run1 --i 2D_class_filtered_160420.star --particle_diameter 200 --angpix 4.88 --ref CryoComplex_Hsp90_Dmut.mrc --firstiter_cc --ini_high 40 --ctf --iter 50 --tau2_fudge 4 --K 3 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 8 --offset_step 2 --sym C1 --norm --scale --j 8 --memory_per_thread 3
Has anyone encountered this? Are there obvious mistakes I've made in the command line? Also - are there ways to trigger "--verbose" mode or compile a debug mode of RELION?
Thanks for the help in advance!
Cheers,
Ray
