search

flatironinstitute / ftk

Factorization of the translation kernel for fast rigid image alignment
Apache License 2.0
3 stars 1 forks source link

crash on laptop #2

Closed ahbarnett closed 4 years ago

ahbarnett commented 4 years ago

it crashed on the last size! I'm using IDP python on i7 w/ 32 GB RAM. Does it require > 32 GB? I'll add that to README.

Going fine until... ... delta_range = 25 BFT, precomp = 91.027 s BFT, comp = 14.758 s Traceback (most recent call last): File "src/benchmark.py", line 105, in main() File "src/benchmark.py", line 100, in main benchmark(2) File "src/benchmark.py", line 68, in benchmark prods_ftk, tm_ftk = ftk.ftk_execute(plan, Mhat, Shat) File "/home/alex/SCDA/cryoEM/rangan/frtalign/ftk/src/ftk.py", line 659, in ftk_execute all_rnks, BigMul_left) File "/home/alex/SCDA/cryoEM/rangan/frtalign/ftk/src/ftk.py", line 137, in svd_decomposition_alignment dtype=np.complex128) numpy.core._exceptions.MemoryError: Unable to allocate array with shape (10, 53, 384, 300) and data type complex128

I checked the size of said array is <1 GB.

Even if I cut the loop from range(n_tries) to range(2), the oversampling=4 case fails:

File "/home/alex/SCDA/cryoEM/rangan/frtalign/ftk/src/ftk.py", line 513, in rotations_brute_force inner_prods = pyfftw.zeros_aligned((n_templates, n_images, n_gamma, Nfine, Nfine), dtype='complex128') File "pyfftw/utils.pxi", line 217, in pyfftw.pyfftw.zeros_aligned File "pyfftw/utils.pxi", line 229, in pyfftw.pyfftw.zeros_aligned File "pyfftw/utils.pxi", line 204, in pyfftw.pyfftw.empty_aligned numpy.core._exceptions.MemoryError: Unable to allocate array with shape (12582912032,) and data type int8

Could be RAM again. THat's a large array!

Other than that, plotting for oversample=2 works great. Thanks!