Hi,
has anyone had this error in Flex 3D reconstruction?
I have successfully run 3D reconstruction with multiple box sizes.
When I run reconstruction with a box size of 600 I get the following error. There is a big lagg before actually beginning iterations (maybe 3 mins) and fails on the final 1000 particles.
The above exception was the direct cause of the following exception:
[CPU: 66.13 GB Avail: 175.82 GB]
====== High resolution flexible refinement =======
[CPU: 66.13 GB Avail: 175.82 GB]
Max num L-BFGS iterations was set to 20
[CPU: 66.13 GB Avail: 175.82 GB]
Starting L-BFGS.
[CPU: 66.13 GB Avail: 175.82 GB]
Reconstructing half-map A
[CPU: 66.13 GB Avail: 175.82 GB]
Iteration 0 : 13000 / 14000 particles
[CPU: 95.24 GB Avail: 146.55 GB]
ValueError: 0-th dimension must be fixed to 1105033884 but got 5400001180
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_compute.run.main
File “/spshared/apps/cryosparc4/cryosparc_worker/cryosparc_compute/jobs/flex_refine/run_highres.py”, line 150, in run
flexmod.do_hr_refinement_flex(numiter=params[‘flex_bfgs_num_iters’])
File “cryosparc_master/cryosparc_compute/jobs/flex_refine/flexmod.py”, line 1640, in cryosparc_compute.jobs.flex_refine.flexmod.do_hr_refinement_flex
File “/spshared/apps/cryosparc4/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_lbfgsb_py.py”, line 199, in fmin_l_bfgs_b
res = _minimize_lbfgsb(fun, x0, args=args, jac=jac, bounds=bounds,
File “/spshared/apps/cryosparc4/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/site-packages/scipy/optimize/_lbfgsb_py.py”, line 353, in _minimize_lbfgsb
_lbfgsb.setulb(m, x, low_bnd, upper_bnd, nbd, f, g, factr,
ValueError: failed in converting 10th argument `wa’ of _lbfgsb.setulb to C/Fortran array