I'm not sure how caffe is called, but you can use cgroups to limit CPU usage for processes on centos6 and beyond. An example of CPU usage restriction for 5 logical processors:
sudo mkdir -p /sys/fs/cgroup/cpu/fivecpus
sudo bash -c "echo 500000 > /sys/fs/cgroup/cpu/fivecpus/cpu.cfs_quota_us"
sudo bash -c "echo $$ > /sys/fs/cgroup/cpu/fivecpus/tasks"
your_command
, 500000 5 /sys/fs/cgroup/cpu/fivecpus/cpu.cfs_period_us