CryoSPARC#
“CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.”
Access to CryoSPARC on M3#
A General Access (GA) CryoSPARC is available upon request to any user of M3. Please submit a request via this form.
sbatch: error: Required nodes outside of the reservation (setting a job’s time limit)#
If a maintenance period is approaching, you may see the following error message in CryoSPARC:
sbatch: error: Required nodes outside of the reservation
sbatch: error: Batch job submission failed: Requested node configuration is not available
This occurs if your job’s runtime would overlap with the maintenance period. A workaround is to reduce your CryoSPARC job’s time limit such that it can complete before the maintenance period begins. Click on “Cluster submission script variables” when you are queuing a job, and modify the job_walltime field for “This job”. This value should be of any format accepted by SLURM’s sbatch command for the --time` field (see https://slurm.schedmd.com/sbatch.html#OPT_time).
As the maintenance period draws closer, this workaround will eventually stop working. At this point, you will simply have to wait until the maintenance is completed before you can submit any new jobs to CryoSPARC. Note that even if, for example, the maintenance begins in 8 hours and you set the time limit to only 1 hour, you may still see the above error message since other jobs (including those from other users) could still be in the job queue.
Example job submission with the time limit set to 2 hours via job_walltime.#