3D variability analysis error



Dear cryoSPARC developer,

I’m trying to run 3D variability analysis and got this error:

Traceback (most recent call last):
  File "cryosparc2_worker/cryosparc2_compute/run.py", line 78, in cryosparc2_compute.run.main
  File "cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.py", line 164, in cryosparc2_compute.jobs.var3D.run.run
  File "cryosparc2_worker/cryosparc2_compute/engine/newengine.py", line 641, in cryosparc2_compute.engine.newengine.EngineThread.project_model
  File "cryosparc2_worker/cryosparc2_compute/engine/newcuda_kernels.py", line 2700, in cryosparc2_compute.engine.newcuda_kernels.slice_volumes
  File "cryosparc2_worker/cryosparc2_compute/engine/cuda_core.py", line 362, in cryosparc2_compute.engine.cuda_core.context_dependent_memoize.wrapper
  File "cryosparc2_worker/cryosparc2_compute/engine/newcuda_kernels.py", line 2675, in cryosparc2_compute.engine.newcuda_kernels.get_slice_volumes_kernel
  File "/storage/hyl5126/.apps/opt/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/compiler.py", line 291, in __init__
    arch, code, cache_dir, include_dirs)
  File "/storage/hyl5126/.apps/opt/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/compiler.py", line 254, in compile
    return compile_plain(source, options, keep, nvcc, cache_dir, target)
  File "/storage/hyl5126/.apps/opt/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/compiler.py", line 137, in compile_plain
    stderr=stderr.decode("utf-8", "replace"))
CompileError: nvcc compilation of /tmp/tmpRuqFRq/kernel.cu failed
[command: nvcc --cubin -arch sm_61 -I/storage/hyl5126/.apps/opt/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/pycuda/cuda kernel.cu]
kernel.cu(130): error: identifier "__shfl_down_sync" is undefined

kernel.cu(254): error: identifier "__shfl_down_sync" is undefined

kernel.cu(315): error: identifier "__shfl_down_sync" is undefined

kernel.cu(378): error: identifier "__shfl_down_sync" is undefined

4 errors detected in the compilation of "/tmp/tmpxft_0000e2c3_00000000-7_kernel.cpp1.ii".

Would you give me any advice to resolve the issue?
Thank you.



Hi @hyunwooklee,

Can you specify which version of the CUDA Toolkit you are running, which CUDA driver version, and which GPU this job was run on? Can you also specify your cryoSPARC version?


My CUDA toolkit version is 9.0.176 (It could be 8.0.61. I don’t remember which one I was on when I updated cryoSPARC.) and NVIDIA driver version is 390.48.
I’m running cryoSPARC v2.11.0 on TITAN Xp.

Thank you.


Hi @hyunwooklee,

Are you able to upgrade your CUDA Toolkit version? If you are, follow the steps in this previous post:


Upgrading CUDA version > 10 fixed the problem.
Thank you!