@wtempel I am having same issue in Topaz extract.
Please can you post the
- CryoSPARC version
- context (attempted processing activity)
- text of error message(s) in your specific case.
- cryospac version v4…4.0+231114
- topaz extract, (topaz validation with same executable file was ok).
- Error : Failed to enqueue P6 J34 : Job has builder error. Path to Topaz executable: Invalid path specified: /programs/x86_64-linux/system/sbgrid_bin/topaz directory allowed: false; file allowed.:Ture; glob allowed false.
Please can you post the output of these commands
cryosparcm cli "get_job('P6', 'J34', 'params_spec')"
stat /programs/x86_64-linux/system/sbgrid_bin/topaz
/full/path/to/cryosparc_worker/bin/cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz --version
cryosparcm cli “get_job(‘P6’, ‘J34’, ‘params_spec’)”
_id : 655f6eaesf534434’, ‘project_uid’ : ‘P6’, ‘uid’: 'J34,}
/full/path/to/cryosparc_worker/bin/cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz --versionCryoSPARC System master node installed at
/home/cryosparc/cryosparc/cryosparc_master
Current cryoSPARC version: v4.4.0+231114
I am connected using ssh on a machine on same network for remote execution of commands.
@vijayverma Unfortunately, I have not tested this kind of setup and would need to see the output of the remaining commands
to provide additional suggestions.
Alternatively, you might:
- Install topaz as described at cryosparcm cli reference - CryoSPARC Guide.
- Create a wrapper script
topaz.sh. - Point the Path to Topaz executable parameter to that wrapper script.
@wtempel , I did these command you mentioned in linux that is on master node.
cryosparcm cli "get_job('P6', 'J34', 'params_spec')"
stat /programs/x86_64-linux/system/sbgrid_bin/topaz
/full/path/to/cryosparc_worker/bin/cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz --version
for the command/full/path/to/cryosparc_worker/bin/cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz --version
I do not get worker path- [cryosparc@hermes ~]$ which cryosparcw
/usr/bin/which: no cryosparcw in (/programs/x86_64-linux/system/sbgrid_bin:/usr/local/cuda/bin:/home/cryosparc/cryosparc/cryosparc_master/bin:/home/cryosparc/.local/bin:/home/cryosparc/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/programs/share/bin:/programs/share/sbgrid/bin:/programs/x86_64-linux/sbgrid_installer/latest)
cryosparcm cli “get_job(‘P6’, ‘J34’, ‘params_spec’)”
_id : 655f6eaesf534434’, ‘project_uid’ : ‘P6’, ‘uid’: 'J34,}/full/path/to/cryosparc_worker/bin/cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz --version
I do not get worker path-
[cryosparc@hermes ~]$ which cryosparcw
/usr/bin/which: no cryosparcw in (/programs/x86_64-linux/system/sbgrid_bin:/usr/local/cuda/bin:/home/cryosparc/cryosparc/cryosparc_master/bin:/home/cryosparc/.local/bin:/home/cryosparc/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/programs/share/bin:/programs/share/sbgrid/bin:/programs/x86_64-linux/sbgrid_installer/latest)
Hope this is more clear now.
Could it be
/home/cryosparc/cryosparc/cryosparc_worker/bin/cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz --version
?
This is just a guess based on the path to your cryosparc_master/ directory.
@wtempel , Thank You , I will try this
/home/cryosparc/cryosparc/cryosparc_worker/bin/cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz –version
should I write the version of cryosparc v4.4.0+231114
and this command from master node or remote node.
I assumed that your CryoSPARC installation is a single-node, combined master/worker instance, but I failed to confirm this assumption.
If you know that this CryoSPARC installation is a single-node, combined master/worker instance, please run the command
/home/cryosparc/cryosparc/cryosparc_worker/bin/cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz --version
on the CryoSPARC master node without specifying a version, and post here the output of that command.
If you are not sure that this CryoSPARC installation is a single-node, combined master/worker instance, please run the commands, also on the master node
cryosparcm status | grep HOSTNAME
cryosparcm cli "get_scheduler_targets()"
**@wtempel **
/home/cryosparc/cryosparc/cryosparc_worker//cryosparcw call /programs/x86_64-linux/system/sbgrid_bin/topaz --version
/home/cryosparc/cryosparc/cryosparc_worker/bincryosparcw: line 272
Usage:Topaz {-h} {version} …
Topaz: error: the following arguments are required:
cryosparcm status | grep HOSTNAME
/home/cryosparc/cryosparc/cryosparc_master
export CRYOSPARC_DB_PATH="/home/cryosparc/cryosparc/cryosparc_database
cryosparcm cli “get_scheduler_targets()”
Thanks @vijayverma for trying that. What is the output when you run the following command on hermes?
cryosparcm cli "get_project('P6', 'project_params_pdef')"
To avoid miscommunication due to transcription errors, you may want to both
[cryosparc@hermes ~]$ cryosparcm cli “get_project(‘P6’, ‘project_params_pdef’)”
{‘_id’: ‘655cff1078fe5da1a12d3383’, ‘project_params_pdef’: {}}
Interesting. It seems that Path to Topaz executable was not set project-wide. Was it defined at the job level?
Please can you post terminal text and screenshot also for this command:
cryosparcm cli "get_job('P6', 'J34', 'job_type', 'params_spec')"
For this command, I assumed that the project and job identifiers that you posted in Topaz and deepemhancer not working in version 4.1.2 - #12 by vijayverma.
[cryosparc@hermes ~]$ cryosparcm cli “get_job(‘P6’, ‘J34’, ‘job_type’, ‘params_spec’)”
{‘_id’: ‘655f6ea56d00817e2ec62154’, ‘job_type’: ‘topaz_extract’, ‘params_spec’: {‘exec_path’: {‘value’: ‘/home/cryosparc/anaconda2/envs/topaz/bin/topaz’}}, ‘project_uid’: ‘P6’, ‘uid’: ‘J34’}
Thanks. On hermes, what are the outputs of the commands:
/home/cryosparc/anaconda2/envs/topaz/bin/topaz --version
stat /home/cryosparc/anaconda2/envs/topaz/bin/topaz
[cryosparc@hermes ~] /home/cryosparc/anaconda2/envs/topaz/bin/topaz
-bash: /home/cryosparc/anaconda2/envs/topaz/bin/topaz: No such file or directory
[cryosparc@hermes ~] stat /home/cryosparc/anaconda2/envs/topaz/bin/topaz
stat: cannot statx ‘/home/cryosparc/anaconda2/envs/topaz/bin/topaz’: No such file or directory
[cryosparc@hermes ~]$