atop package has been updated few days ago. The problem is that $INTARVAL value does not includes from /etc/sysconfig/atop anymore, it is hardcoded in /usr/share/atop/atop.daily to 600 (10 minutes). The value of 5-10 seconds better for any investigation purposes, but it is not configurable after last update.
Thank you, will investigate.
atop-2.3.0-6.el7 has been submitted as an update to Fedora EPEL 7. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2017-1716b12298
atop-2.3.0-6.el7 has been pushed to the Fedora EPEL 7 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2017-1716b12298
*** Bug 1524445 has been marked as a duplicate of this bug. ***
atop-2.3.0-7.el7 has been submitted as an update to Fedora EPEL 7. https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2017-3fc29cb70f
atop-2.3.0-7.el7 has been pushed to the Fedora EPEL 7 testing repository. If problems still persist, please make note of it in this bug report. See https://fedoraproject.org/wiki/QA:Updates_Testing for instructions on how to install test updates. You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-EPEL-2017-3fc29cb70f
atop-2.3.0-7.el7 has been pushed to the Fedora EPEL 7 stable repository. If problems still persist, please make note of it in this bug report.
This is still an issue in atop-2.4.0-1.el7.x86_64