cufftAllocFailed in 2D classification

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#1

Hi all,

After the particle extraction in CryoSparc, I did the 2D classification. There was an error as belows:

Traceback (most recent call last):
File “cryosparc2_compute/jobs/runcommon.py”, line 1481, in run_with_except_hook
run_old(*args, **kw)
File “cryosparc2_worker/cryosparc2_compute/engine/cuda_core.py”, line 110, in cryosparc2_compute.engine.cuda_core.GPUThread.run
File “cryosparc2_worker/cryosparc2_compute/engine/cuda_core.py”, line 111, in cryosparc2_compute.engine.cuda_core.GPUThread.run
File “cryosparc2_worker/cryosparc2_compute/engine/engine.py”, line 991, in cryosparc2_compute.engine.engine.process.work
File “cryosparc2_worker/cryosparc2_compute/engine/engine.py”, line 109, in cryosparc2_compute.engine.engine.EngineThread.load_image_data_gpu
File “cryosparc2_worker/cryosparc2_compute/engine/gfourier.py”, line 33, in cryosparc2_compute.engine.gfourier.fft2_on_gpu_inplace
File “/data/home/cryosparc_user/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/skcuda/fft.py”, line 126, in init
onembed, ostride, odist, self.fft_type, self.batch)
File “/data/home/cryosparc_user/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/skcuda/cufft.py”, line 741, in cufftMakePlanMany
cufftCheckStatus(status)
File “/data/home/cryosparc_user/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/skcuda/cufft.py”, line 116, in cufftCheckStatus
raise e
cufftAllocFailed

What can I do to fix this?

Thanks
Shasha


#2

Hi @Shasha,

What was the box size of the particles, and the number of classes?

The error means that the GPU is running out of GPU memory during 2D classification. This would happen if the box size is very very large (unlikely) or if there is another process using the GPU at the same time (e.g Relion, etc).

You can check for other processes using the command line tool

nvidia-smi