Particle stack size variable for cluster -l tmp_free


Is there a variable for particle stacks size to use for -l tmp_free?:

ex: #$ -l tmp_free {{particle_stack_size}}

or is there a workaround for this? It would be nice to specify the tmp_free per job on the cluster.

Cryosparc does check the stack size:

[CPU: 779.6 MB] SSD cache : cache successfuly synced in_use
[CPU: 779.6 MB] SSD cache : cache successfuly synced, found 0.00MB of files on SSD.
[CPU: 779.6 MB] SSD cache : cache successfuly requested to check 4338 files.
[CPU: 781.4 MB] SSD cache : cache requires 15718.45MB more on the SSD for files to be downloaded.
[CPU: 781.4 MB] SSD cache : cache has enough available space.

So can it be easily sent to the cluster as a variable? With different scratch sizes on each cluster node and different stack sizes for each job, setting an arbitrary value for tmp_free wouldn’t make sense.


Hi Matt, unfortunately there’s no easy way to get this information from cryoSPARC before you submit the job. The amount of space required is calculated from the connected particle stack(s) after the job is queued and running.

In future releases of cryoSPARC, we may be able to calculate and expose this information for the submitted job before it runs. I’ve recorded this in our tracker and will keep you posted on its status here.

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Alright, thanks for the response @nfrasser. If it’s an easy fix that would be great, but if not, no worries.