Is this a VPS or dedicated?
Is this a VPS or a dedicated server? How you proceed will depend on the answer to this.
If it is a dedicated server, what is the output of the following commands?
There need to be partitions mounted with quota support. If there are, then try the following command:
If there are no partitions mounted with quotas, then /etc/fstab needs to be edited and the partition that contains /home, at least, needs to be remounted with quota support, then fixquotas run after it is remounted.
If this is a VPS, second-level quota support needs to be enabled for the VPS. This is done in the hardware node. The following guide explains how to enable second-level quotas for a Virtuozzo or OpenVZ VPS:
Turning On and Off Second-Level Quotas for Container