[ome-users] OMERO and NFS (was: NullPointerException in FileMaker)

[Niko Ehrenfeuchter]

Hi all,

On 07.08.2012 09:59, Chris Allan wrote:
> Hi Harri,
>
> On 6 Aug 2012, at 15:42, Harri Jäälinoja wrote:
>
>> Hi all,
>> I think I've solved this. Some googling points to NFS locking issues:
>> https://forums.oracle.com/forums/thread.jspa?threadID=2232128&tstart=0&messageID=9907997
>>
>> This makes sense, because in our new environment, the big data drive is a NFS share.
>>
>> I did this:
>> service nfslock start
>>
>> and after that, I haven't seen the errors anymore.
>
> We'll certainly try and add that to the startup script tests in the future so that it's obvious when there is a complete lack of locking.
>
>>
>> Do you have any comments in general about having OMERO store data on NFS (speed for example)? We have also the PostgreSQL data directory there. In our case we got this 4T storage area for free from a national computing center, and I don't think we have much say about how we receive it, but it would be good to know if there are any possible issues.
>
> Really that heavily depends on the performance of your NFS data store. One of the classical problems with NFS is locking semantics, and really this applies to any distributed or network filesystem. OMERO makes fairly heavy use of POSIX locking, especially on the Files and Index portions of the binary repository. You may wish to store your Index on local disk, it will be faster, less prone to corruption and should be small anyway. Storing your PostgreSQL data directory on NFS is probably a very bad idea unless you have a really good understanding of the semantics of the NFS data store you're using.

I'd like to pick up this older thread again...

We're currently planning a somewhat bigger OMERO installation for our 
imaging facility and the groups we're servicing. During the discussions 
with our IT department (they're going to provide the server space plus 
the storage), they mentioned that storage will be delivered as an NFS 
share - so I'm a bit worried now what decisions to take on which 
hardware to buy for the server running OMERO.

My current idea is as follows:
   - rather more Gigahertz than cores, so kind of a quad-core CPU with 
2.8 GHz preferred over a six-core 2.4
   - keep I/O paths as separate as possible, e.g. one RAID1 for the OS 
and one for the database (the latter maybe even on SSD if that makes sense)
   - my personal preference for storage (speaking of the binary 
repository) would definitely be a dedicated storage network like iSCSI 
or FibreChannel (first of all for performance reasons and congestion 
fears on the regular network), but this currently seems to be unavailable

...hence my question about any concerns regarding NFS as the storage 
provider for the binary repository? Is locking a real issue on NFS or 
can this be thoroughly solved using the "nfslock" service as stated 
above? Don't worry, putting the Postgres on NFS has never been an option 
(and it never will ;)).

Any help and thoughts are greatly appreciated!

Niko