hierarchical ObjectStore - noatime
Hi, we want to put some more hard drives into your Galaxy Server. And we plan to use the hierarchical ObjectStore for that purpose. The new discs will be type="distributed" id="primary" and the old disc will become type="disk" id="secondary". If I understood correctly the old disc is them in some read-only state and will not touched until the primary discs are full or not working ... Is it save to mount the old discs or all discs with noatime, to get a small performance gain? Is Galaxy using noatime? Thanks, Bjoern
On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening <bjoern.gruening@gmail.com>wrote:
The new discs will be type="distributed" id="primary" and the old disc will become type="disk" id="secondary". If I understood correctly the old disc is them in some read-only state and will not touched until the primary discs are full or not working ...
Correct -- the default HierarchicalObjectStore always writes new files to the first ObjectStore but can read through to any of them. Probably worth noting that, with this base implementation (that could easily be extended to do whatever you'd prefer), when the first objectstore gets full it still won't attempt to write to the second.
Is it save to mount the old discs or all discs with noatime, to get a small performance gain? Is Galaxy using noatime?
I do believe we're using it, but Nate would be better able to comment on the actual performance gain we see.
Hi Björn, atime is definitely not used by Galaxy, and we have generally disabled it on all filesystems we mount. --nate On Tue, Dec 3, 2013 at 8:10 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening <bjoern.gruening@gmail.com
wrote:
The new discs will be type="distributed" id="primary" and the old disc will become type="disk" id="secondary". If I understood correctly the old disc is them in some read-only state and will not touched until the primary discs are full or not working ...
Correct -- the default HierarchicalObjectStore always writes new files to the first ObjectStore but can read through to any of them. Probably worth noting that, with this base implementation (that could easily be extended to do whatever you'd prefer), when the first objectstore gets full it still won't attempt to write to the second.
Is it save to mount the old discs or all discs with noatime, to get a small performance gain? Is Galaxy using noatime?
I do believe we're using it, but Nate would be better able to comment on the actual performance gain we see.
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Thanks for the info Nate and Dannon! Bjoern
Hi Björn,
atime is definitely not used by Galaxy, and we have generally disabled it on all filesystems we mount.
--nate
On Tue, Dec 3, 2013 at 8:10 AM, Dannon Baker <dannon.baker@gmail.com> wrote: On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote: The new discs will be type="distributed" id="primary" and the old disc will become type="disk" id="secondary". If I understood correctly the old disc is them in some read-only state and will not touched until the primary discs are full or not working ...
Correct -- the default HierarchicalObjectStore always writes new files to the first ObjectStore but can read through to any of them. Probably worth noting that, with this base implementation (that could easily be extended to do whatever you'd prefer), when the first objectstore gets full it still won't attempt to write to the second.
Is it save to mount the old discs or all discs with noatime, to get a small performance gain? Is Galaxy using noatime?
I do believe we're using it, but Nate would be better able to comment on the actual performance gain we see.
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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participants (4)
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Bjoern Gruening -
Björn Grüning -
Dannon Baker -
Nate Coraor