Before You Post: Troubleshooting Guidelines

Dear cryoSPARC users,

Thank you for communicating with us on the discussion forum.

Before you post your topic, check the following items:

  • Are you on the latest version of cryoSPARC? cryosparcm update and see Software Updates in the cryoSPARC Guide
  • Have you tried restarting cryoSPARC? cryosparcm restart
  • Has this issue already been posted on the discussion forum? Search here
  • Have you removed any personal/identifiable information from your post?

When posting, use this template to provide as much information as possible about your issue:

To make it easier for us to understand and troubleshoot issues and errors encountered, please use the following template to provide as much information as possible about your issue:

cryoSPARC instance information

  • Type: single workstation, master-worker, or cluster
  • Software version from cryosparcm status
  • Output of
    uname -a && free -g
    on master node

cryoSPARC worker environment

  • Load the cryoSPARC worker environment (for execution of the following commands):
    eval $(<path-to-cryosparc_worker>/bin/cryosparcw env)
  • CUDA toolkit path:
  • CUDA toolkit version:
    ${CRYOSPARC_CUDA_PATH}/bin/nvcc --version
  • pycuda information (run command in same shell):
    python -c "import pycuda.driver; print(pycuda.driver.get_version())"
  • Output of
    uname -a && free -g && nvidia-smi

on relevant worker node(s)


  • Type of Issue (Installation Error, Job Error: Motion Correction, etc)
  • Explain the problem in as much detail as possible
  • Include the full error message/traceback, if you received any
  • Relevant logs:
  • backend: cryosparcm log command_core
  • jobs: cryosparcm joblog Px Jx
  • webapp: cryosparcm log webapp
  • database: cryosparcm log database
  • For job-related errors:
  • Name of job
  • Inputs to job
  • Any non-default parameters specified in the job
  • Copy-paste the text of any error messages for future searchability by other users
  • Include any relevant screenshots of the UI that can help explain your issue

Steps to Reproduce

  • How can a developer/user reproduce this issue?
  • If you have received different results from what you expected, please explain what you were expecting

Thank you! :grinning:

Homogeneous refinement fails after several iterations
2D Classification error V2
No job works anymore. [Errno 2] No such file or directory
Restore database from previous backup
Disconnecting of the database
ValueError: total size of new array must be unchanged
Issues with local CTF estimation
Homogeneous Refinement failed abnormally
CUDA 11.4 error
About the Troubleshooting category
Extract From Micrographs Job can't complete
Patch Motion Correction Fails
ImportError after update to 3.3.2
"list index out of range" error when trying to run jobs
Why do I need to refresh my browser to see progress on jobs?
Database: ERROR (spawn error)
Webapp connection refused on CentOS
Preprocessing result thumbnails are not shown
Preprocessing result thumbnails are not shown
2D classification error: cryosparc_compute.skcuda_internal.cufft.cufftAllocFailed
Error using motioncor
Bin micrographs
Patch motion correction problem
Patch motion correction cuMemAlloc failed: out of memory
CUDA memory error during 2D classification
Heterogeneous Refinement crash
Error during 2D class of manual picked particles
HELP! I have trouble in negative stain data processing
Patch motion correction multi error
cryoSPARC v2.11 Stuck at Database Migration
2D classification failed at the very end
Local Refinement Error
2D classification can't be run
2D Classification Error after Template Picker
Cuda_runtime.h: No such file or directory
Reintroducing subtracted volume
Error in running homogeneous refinement