Put subcategories under "Run only the selected applications" in the GPUGRID preferences, and let the volunteers pick and choose which subcategories they went to run.

An example would be under the "ACEMD long runs (8-12 hours on fastest GPU)" put the following:

ADRIA_2OV5
GERARD_FXCXCL12RX
GERARD_MO
GIANNI_A2
GIANNI_D3C36bCHL

When implementing this, for example, if the volunteer clicked "yes" for the long runs then all the subcategories would be "yes", until the volunteer logs in and changes them. When a new subcategory is introduced, its default setting would be "yes", until the volunteer changes it. Once the volunteer makes any changes they would stay that way, until the volunteer wants to change it back.

This would allow people with slower GPUs to avoid the longer tasks without the need to abort them, among other things.

Seconded. Something like this has been needed for a long time.

Agreed, if it can be implemented, it needs to be.

Is there a way this functionality could be configured in the cc_config or app_config manually until/unless this cannot be or won't be implemented?

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Ephesians 6:18-20, please ;-)
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Is there a way this functionality could be configured in the cc_config or app_config manually until/unless this cannot be or won't be implemented?

That must be don in the Shceduler server. Either configuration or code modification.