Hi,
I’ve been failing to run Homogeneous Refinement when full dataset (23k) was applied in the process of Optimizing FSC Mask…
Anybody has a clue to fix the problem?
Thanks,
Xiangan
– Iteration 3
Using Full Dataset (split 11316 in A, 11316 in B)
Using Max Alignment Radius 36.122 (13.842A)
– DEV 1 THR 1 NUM 5816 TOTAL 3175.9082 ELAPSED 5394.2277 –
set_models : 0.000357151
set_data_preparation : 0.318315983
load_image_data_allocate : 0.612573624
load_image_data_cpu_arrange : 3157.665030718
load_image_data_download : 0.697479725
load_image_data_real_prepare : 0.084305763
load_image_data_transform : 0.302505016
setup_current_data_and_ctf_xys : 0.070070028
setup_current_data_and_ctf_datactf : 0.788176775
setup_current_noise : 0.039562941
compute_image_power : 0.012027025
setup_current_poses_and_shifts_poses : 1.514653921
setup_current_poses_and_shifts_shifts : 0.035112143
setup_current_poses_and_shifts_cpu : 0.179729223
compute_resid_pow : 3.726548672
compute_error : 1.044440031
cull_candidates : 1.635835409
subdivide : 0.149050236
find_and_set_best_pose_shift_minargmin : 0.006273746
find_and_set_best_pose_shift_findbest : 0.001963854
find_and_set_best_pose_shift_set : 0.180496216
normalize_and_set_posterior_thresh : 0.019851446
backproject : 6.823891640
Processed 22632.000 images in 5400.482s.
Computing FSCs…
Done in 143.446s
Optimizing FSC Mask…
Traceback (most recent call last):
File “/ssd/cryosparc/cryosparc-compute/sparcjob.py”, line 552, in
superspeed = job_type==‘superrefine’)
File “/ssd/cryosparc/cryosparc-compute/refinement.py”, line 382, in refine
fsc_info = sigproc.find_best_fsc(rMA, rMB, radwn_bp, psize)
File “/ssd/cryosparc/cryosparc-compute/sigproc.py”, line 743, in find_best_fsc
tight_near_ang=near, tight_far_ang=far)
File “/ssd/cryosparc/cryosparc-compute/sigproc.py”, line 719, in compute_all_fscs
radwns, fsc_true, fsc_noisesub = noise_sub_fsc (rMA, rMB, mask, radwn_noisesub_start, radwn_max)
File “/ssd/cryosparc/cryosparc-compute/sigproc.py”, line 603, in noise_sub_fsc
fMBrand = fourier.fft(fourier.ifft(randomphases(fourier.fft(MB), radwn_ns)) * mask)
File “/ssd/cryosparc/cryosparc-compute/sigproc.py”, line 596, in randomphases
randphases = 1.0 * n.random.randn(*fM.shape) + 1.0j * n.random.randn(*fM.shape)
MemoryError