Unable to start CryoSPARC v4.1.2 on standalone workstation

Install, Configure and Update
1

Hi,
I have installed Cryosparc v4.1.2 as a fresh install after formatting my standalone workstation. i installed latest CUDA and followed the steps of installation. As my is a single workstation, i followed the standalone installation guide. When i put the command “cryosparcm test install”, i get the following:
Running installation tests…
✓ Running as cryoSPARC owner
✓ Running on master node
✓ CryoSPARC is running
✓ Connected to command_core at http://smbl:39002
✓ CRYOSPARC_LICENSE_ID environment variable is set
✓ License has correct format
✓ Insecure mode is disabled
✓ License server set to “https://get.cryosparc.com”
✓ Connection to license server succeeded
✓ License server returned success status code 200
✓ License server returned valid JSON response
✓ License exists and is valid
✓ CryoSPARC is running v4.1.2
✓ Running the latest version of CryoSPARC
Could not get latest patch (status code 404)
✓ Patch update not required
✓ Admin user has been created
✕ No workers are connected to CryoSPARC. Use ‘cryosparcw connect’ to add a worker.
Now when i start cryosparcm and want to run import movies’ after i press queue it gives the message:
“Scheduler error: no scheduler lanes found. Please connect a worker using ‘cryosparcw connect’”.
In my previous installation of ver3, there was no such problem. Kindly help me with this.

2

During a --standalone installation, cryosparc_worker/install.sh and cryosparcw connect (are supposed to) happen “under the hood”, but these steps may have failed.
May I suggest you:

  • remove the existing cryosparc_worker directory
  • repeat unpacking, installation, connection of the worker software (guide)
  • report here any errors you observe in the process
3

Hi wtempel,
Yes, the cryosparc_worker should work under the hood automatically. the problem is coming in the installation of pycuda step. it terminated with following error:
compilation terminated.
error: command ‘/usr/bin/gcc’ failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pycuda

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
check_install_deps.sh: 66: ERROR: installing python failed.

I tried to solve the “/usr/bin/gcc’ failed with exit code 1”, but its not working. I am running on Ubuntu 22 and cuda 12. so can it be the reason that cryosparc v4 does not support this?

4

CUDA toolkit version 12 is not currently supported by CryoSPARC.
You could try to work around this issue by

  1. running cryosparcw install-3dflex. This would install CUDA-11.7. Before running this command, you would have to ensure that no existing CUDA toolkit files are present in PATH or LD_LIBRARY_PATH environment variable definitions (details)
  2. and then running cryosparcw connect [...] (details)
5

Well, i was able to install it finally. I downgraded my cuda to 11.4, ubuntu to 20.04 and nvidia driver 470 for rtx 3090. The worker installed automatically under the hood with no problem. Everything went well.
Thanks for the support

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