Large boxsize 1600 got a err

[wonderful]

Hi all,
When I using cryosparc to do refinement with boxsize 1600,I got a err like blew.My Gpu is rtx8000,and my memory is 256 like your recommend in website,could give me some advice howe to fix that?
thanks very much.

[CPU: 102.46 GB] Traceback (most recent call last):
  File "cryosparc_worker/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main
  File "cryosparc_worker/cryosparc_compute/jobs/refine/newrun.py", line 327, in cryosparc_compute.jobs.refine.newrun.run_homo_refine
  File "/home/spider/software/cryospooarc/cryosparc_worker/cryosparc_compute/newfourier.py", line 416, in resample_resize_real
    return ZT( ifft( ZT(fft(x, stack=stack), N_resample, stack=stack), stack=stack), M, stack=stack), psize_final
  File "/home/spider/software/cryospooarc/cryosparc_worker/cryosparc_compute/newfourier.py", line 119, in ifft
    return ifftcenter3(X, fft_threads)
  File "/home/spider/software/cryospooarc/cryosparc_worker/cryosparc_compute/newfourier.py", line 92, in ifftcenter3
    v = fftmod.irfftn(tmp, threads=th)
  File "/home/spider/software/cryospooarc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pyfftw/interfaces/numpy_fft.py", line 295, in irfftn
    calling_func, **_norm_args(norm))
  File "/home/spider/software/cryospooarc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pyfftw/interfaces/_utils.py", line 128, in _Xfftn
    FFTW_object = getattr(builders, calling_func)(*planner_args)
  File "/home/spider/software/cryospooarc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pyfftw/builders/builders.py", line 545, in irfftn
    avoid_copy, inverse, real, **_norm_args(norm))
  File "/home/spider/software/cryospooarc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/site-packages/pyfftw/builders/_utils.py", line 261, in _Xfftn
    flags, threads, normalise_idft=normalise_idft, ortho=ortho)
  File "pyfftw/pyfftw.pyx", line 1223, in pyfftw.pyfftw.FFTW.__cinit__
ValueError: ('Strides of the output array must be less than ', '2147483647')

[apunjani]

Hi @wonderful, unfortunately the error indicates that one of the libraries we use (pyFFTW) uses 32-bit numbers to store the shape of the 3D volume and can’t handle a box size of 1600. We will look into this but probably can’t fix this very soon!
Do you definitely need a box size of 1600? Do you expect to get close to the nyquist resolution?

[wonderful]

Hi,@apunjani

Thanks for your reply.I need use this boxsize is because my protein is very big,I need 2048 (bin1)boxsize actualy.If this problem can be fixed,it will a wonderful thing for me.And I using rtx8000 to do that reconstruct.I am very expect for that your team can fix that problem.

[apunjani]

Hi @wonderful,

We will definitely be looking into this but it may not be something we can fix soon!
To help us out can you provide:

• your OS version and output of uname -a
• full output of nvidia-smi
• full output of free -g

Thanks

[wonderful]

Hi @apunjani,

Thanks much for your reply.my OS version is centos7,and the command output is blew.

This maybe another question:The swap that I set to solve the RAM problem that I meet when refine withe boxsize 1024(job can complete with the swap).And I prepare to using a PCLE8 ssd to play the swap,Is this a good way to solve the prolem blew,or I need add more RAM.Looking forward your reply.Thanks very much.