The problem here is that by default, Splunk limits the amount of disk-space a user can use while searching. This is to ensure that all resources are not consumed by one user running lots of inefficient searches, and it is documented here. This page will also tell you how to increase the quota in authorize.conf for a specific role.
Searches run in a seperate process to splunkd, so just because splunkd is killed/restarted doesn't necessarily mean that the searches themselves will also disappear.
If you want to get a view into what searches are running, you can click on the Jobs link in the top right corner and see all the current and recent searches by a user. Any jobs that persist on disk will take up space, and I believe the default lifetime of a search object is 15 minutes.
If you clear some space by deleting the jobs, the messages will cease.
The message being displayed is produced when a User tries kick off a new search. Splunk will first check the disk quota in use from previous searches to ensure that it has enough space to store results in $SPLUNK_HOME/var/run/splunk. If you run 'du -sh *' on that directory, you'll be able to identify the searches that are using so much space and manually remove them. It's likely that the directories no longer exist at this point unless you have set the retention time pretty high.
In the current version of 4.1, there is no 'self-monitoring' capability for searches, so they will continue to run and eat up disk space until finished. The disk-quota check is run just once at the beginning of the search to ensure the space exists and the search can be run. If the check finds that the quota has been reached, the new search will NOT run but previous large searches will not be finalized automatically. Also, real-time searches have specific windows and buffers to ensure that they don't take up excessive disk-space so we don't expect them to be an issue in this case, just the historic searches.
In the upcoming version, 4.2, searches will be able to monitor themselves and auto-finalize when the quota is reached and notifications will be pushed to Users via the UI and logs.
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