Topaz Train Error version

Particle Picking
1

Dear all,

I was not able to find a dicussion on this problem. If already exists, my apologies.
I have a recurrent problem with Topaz Train. I tried to reinstall it but it always gives me the same error and I’m not able to solve it.

Do you have any suggestions?
I’m using cryoSPARC3.4.0.

Thank you for your help and attention.
Best,
Andrea

Traceback (most recent call last):
  File "cryosparc_worker/cryosparc_compute/run.py", line 85, in cryosparc_compute.run.main
  File "/home/agwilson/Software/cryosparcuser/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py", line 112, in run_topaz_wrapper_train
    topaz_version = utils.get_topaz_version(topaz_exec_path)
  File "/home/agwilson/Software/cryosparcuser/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/topaz_utils.py", line 136, in get_topaz_version
    f'Cannot determine topaz version, command "{topaz_exec_path} --version" did not produce valid output: "{topaz_version}"'
AssertionError: Cannot determine topaz version, command "/home/agwilson/Software/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/topaz/bin/topaz --version" did not produce valid output: "Current thread 0x00007f50b72a3740 (most recent call first):"
2

Hi Andrea,

Have you tried using a wrapper script for the Path to Topaz executable?

3

Hi @wtempel,

Thank you for your kind and prompt reply.

I prepared the wrapper script, but now I obtained a different error on topaz version:

 File "cryosparc_worker/cryosparc_compute/run.py", line 85, in cryosparc_compute.run.main
  File "/home/agwilson/Software/cryosparcuser/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/run_topaz.py", line 112, in run_topaz_wrapper_train
    topaz_version = utils.get_topaz_version(topaz_exec_path)
  File "/home/agwilson/Software/cryosparcuser/cryosparc/cryosparc_worker/cryosparc_compute/jobs/topaz/topaz_utils.py", line 136, in get_topaz_version
    f'Cannot determine topaz version, command "{topaz_exec_path} --version" did not produce valid output: "{topaz_version}"'
AssertionError: Cannot determine topaz version, command "/home/agwilson/Software/cryosparcuser/topaz.sh --version" did not produce valid output: "ImportError: /home/agwilson/Software/cryosparcuser/cryosparc/cryosparc_master/deps/anaconda/envs/topaz/lib/python2.7/site-packages/torch/lib/libmkldnn.so.0: undefined symbol: cblas_sgemm_alloc"

Do you have any suggestions?
Thank you,
Andrea

4

You can find a discussion of this error and a potential solution under this topic: cryoSPARC v.3.1.0 and Topaz - #13 by zybo