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
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This policy is intended to make information on the forum more searchable, findable, useful.

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

  • Inside a fresh shell, load the cryoSPARC worker environment (for execution of the following commands); substitute the actual path of the cryosparcw script:
    eval $(/path/to/cryosparc_worker/bin/cryosparcw env)
    env | grep PATH
    which nvcc
    nvcc --version
    python -c "import pycuda.driver; print(pycuda.driver.get_version())"
    /sbin/ldconfig -p | grep -i cuda
    uname -a
    free -g
  • record the output
  • exit the shell

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:

2D Classification error V2
Homogeneous refinement fails after several iterations
No job works anymore. [Errno 2] No such file or directory
Restore database from previous backup
Disconnecting of the database
Patch Motion Correction Fails
CUDA 11.4 error
Heterogeneous Refinement crash
Extract From Micrographs Job can't complete
AssertionError during Ab-initio
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?
Pycuda issues after updating from 4.0.2 to 4.1.1 - gcc related?
Extract from micrographs : skcuda_internal.cufft.cufftInternalError
Database: ERROR (spawn error)
Homogeneous refinement failed after reextract particles using original box size
Preprocessing result thumbnails are not shown
Preprocessing result thumbnails are not shown
2D classification error: cryosparc_compute.skcuda_internal.cufft.cufftAllocFailed
3D flex Reconstruction stalling at iteration 0
Patch motion correction problem
Patch motion correction cuMemAlloc failed: out of memory
CUDA memory error during 2D classification
Error during 2D class of manual picked particles
HELP! I have trouble in negative stain data processing
Patch motion correction multi error
2D classification failed at the very end
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
New cluster nodes, CUDA detection error
Installing Cryosparc on HPC
Pycuda install error
Motion Corr fails after update to v4.0.1
Patch motion correction job completed immediately after launching
V4 upgrade - cuInit failed: no CUDA-capable device is detected
pycuda._driver.LogicError: cuStreamSynchronize failed: an illegal memory access was encountered
2d classification kernel error
Import failed after updating from version 4.0 to version 4.1
Import failed after updating from version 4.0 to version 4.1
Cryosparc crashing - sock file
Problem with PyTorch
Cryosparc crashing - sock file
Extract particle skcuda error
Can't run Patch CTF Estimation with cryoSPARC v4.1.1
Import project after migrating files between filesystems (on different cryosparc installations)
cuStreamSynchronize failed during reconstruction
Cryosparc2relion2cryosparc_ rextraction problem
Worker test failed. Kill signal sent by unknown user
Particle Extraction failed: cufftInternalError
Patch CTF won't run
AssertionError: Child process has terminated unexpectedly
DeepPicker error: Input number of GPUs must be less than or equal to number of available GPUs
Import particles between projects
2D classification fails!
3D Flex Training error (library not found)
Blob Picker Job Error cannot open shared object file
Get error: pycuda._driver.MemoryError: cuArray3DCreate failed: out of memory
TOPAZ not using GPU
Workspace not showing
Fail to build wheel for pycuda on fresh worker install
LogicError: cuMemHostAlloc failed: OS call failed or operation not supported on this OS
O-EM batch size (per class)
Error in Deep Enhancer
Job is terminated abnormally after reading some headers
3dflex job failed with ""
Undefined symbol: cuIpcOpenMemHandle_v2
Undefined symbol: cuIpcOpenMemHandle_v2
Unable to connect standalone worker after reinstalling
3D flex Reconstruction stalling at iteration 0
Import Micrograph error
AssertionError: Not enough patches to constrain spline fit (Patch CTF Estimation)
Patch CTF won't run
Running cryosparc on simulated images
Long job fails due to fopen error
pycuda._driver.MemoryError: cuMemHostAlloc failed: out of memory in v3.0
Refinements fail after SSD caching
All jobs are in queue forever, The new build job failed to run
Error using motioncor
Error trying to exec 'cc1plus': execvp: No such file or directory\nnvcc fatal
Installing "3dflex" got failed
Local Refinement Error
cryoSPARC v2.11 Stuck at Database Migration
Bin micrographs
cufftInternalError during 2d classification
Patch motion correction multi error
Could not get database status
Webapp connection refused on CentOS
Exporting mrc format back to cryosparc is missing one file
Issues with local CTF estimation
ValueError: total size of new array must be unchanged
Homogeneous Refinement failed abnormally
About the Troubleshooting category