Errors in CryoSPARC during installation on a new cluster

Troubleshooting
1

Hi all users!!

I´m installing CryoSPARC into a new cluster and the installation didn´t get any issue but when i´ve started to test it i´m getting the follow errors. Anyone here knows something or can help us about these errors?

    Import movies:
              ´================= CRYOSPARCW =======  2026-02-23 10:08:52.223332  =========
Project P70 Job J56
Master amy02.service.local Port 61002
===========================================================================
MAIN PROCESS PID 103258
========= now starting main process at 2026-02-23 10:08:52.223733
MONITOR PROCESS PID 103260
========= monitor process now waiting for main process
========= sending heartbeat at 2026-02-23 10:08:54.621990
imports.run cryosparc_compute.jobs.jobregister
ElectronCountedFramesDecompressor: reading using TIFF-EER mode.
========= sending heartbeat at 2026-02-23 10:09:04.635596
ElectronCountedFramesDecompressor::prepareRead: found 1442 frames in EER-TIFF file.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 65100 (0xfe4c) encountered.
WARNING: io_uring support disabled (not supported by kernel), I/O performance may degrade
ElectronCountedFramesDecompressor: reading using TIFF-EER mode.
ElectronCountedFramesDecompressor::prepareRead: found 1442 frames in EER-TIFF file.
========= sending heartbeat at 2026-02-23 10:09:14.649592
/programas/cryosparc/cryosparc_worker/bin/cryosparcw: line 150: 103258 Killed                  python -c "import cryosparc_compute.run as run; run.run()" "$@"



     2D classification:
             io_uring support disabled (not supported by kernel), I/O performance may degrade
             HOST ALLOCATION FUNCTION: using numba.cuda.pinned_array
/programas/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.10/site-packages/numba/cuda/cudadrv/nvrtc.py:257: UserWarning: NVRTC log messages whilst compiling kernel:

kernel(35): warning #68-D: integer conversion resulted in a change of sign

kernel(44): warning #68-D: integer conversion resulted in a change of sign

kernel(17): warning #177-D: variable "N_I" was declared but never referenced


  warnings.warn(msg)
========= sending heartbeat at 2026-02-19 19:01:44.120373
========= sending heartbeat at 2026-02-19 19:01:54.135393
========= sending heartbeat at 2026-02-19 19:02:04.150064
<string>:1: UserWarning: Cannot manually free CUDA array; will be freed when garbage collected

              RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.  fig = plt.figure(figsize=figsize)

2D classification doesn´t stop but end after 6hours when usually takes around 30minutes.

Thanks a lot for all and waiting for any idea!!

Maria

2

Welcome @maria2177 to the forum.
Please can you let us know

  1. the CryoSPARC version
  2. whether the cluster uses a workload manager, like slurm.
  3. whether the CryoSPARC master services run within or outside a cluster job allocation
  4. whether the amy02.service.local computer is a compute node or login node on the cluster
  5. the output of the
    free -h command on the amy02 computer
  6. details about the 2D classification jobs that ran 6 hours and 30 minutes, respectively. Did they
    • have the same input data
    • run with the same job parameters
    • run on the same computer
    • run on the same CryoSPARC version
3

Good Morning wtempel,

 Thanks a lot for your answer. After to review all the detail you said we resolved all the issues that we had. 
Again thanks a lot for everything
Have a good day
Marisa
1 Like