[ome-users] OMERO with multiple data directories

[Benjamin Schmid]

Dear all,

Sorry for the lengthy mail, and thanks to those who read it fully to the 
end ;)

So far, we have been running OMERO (and the Dropbox) on an Ubuntu server 
with an attached Thecus storage array (N16000pro) with 16 TB storage 
space. The Thecus machine is connected to the server via iSCSI and hosts 
(amongst others) the users' home and OMERO Dropbox folders. These are 
shared via Samba to the microscope computers.

Because storage was filling up, we expanded the RAID volume on the 
Thecus machine. Afterwards, I also wanted to expand the iSCSI LUN. 
That's were trouble started because I realized that the maximum LUN size 
on the Thecus system is 16 TB. I can create another LUN, but this will 
basically end up as a second partition on the server. My question is now 
whether OMERO can use multiple data directories, or if there is another 
solution to this problem.


What I thought about so far:

* Put some of the users (the ones that occupy most storage sapce) on the 
2nd partition
Create symbolic links in both the Dropbox and ManagedRepository folders 
that point to the respective folders for these users on the 2nd partition:
ManagedRepository/user1 -> /partition2/ManagedRepository/user1
DropBox/user1 -> /partition2/DropBox/user1
However, it seems OMERO Dropbox does not follow symbolic links (is there 
any way to make this work?)

* Leaving the DropBox in the primary OMERO data folder, and only moving 
the ManagedRepository folder of some users to the 2nd partition
Does not work because importing from the DropBox is done via hard links 
(which I very much appreciate), and hard links cannot cross file system 
borders.

* mhddfs (https://romanrm.net/mhddfs)
I found this small Linux tool that basically joins several filesystems 
into a (virtual) large partition. However, it seems to have some impact 
on performance, and, more severely, does also not create correct hard 
links when importing via OMERO DropBox.

* LVM
This could also be used for combining several partitions into a single 
big one. Advantages over mhddfs is that it's integrated in the Linux 
kernel. Disadvantage is that the used partitions need to be formatted 
for LVM, so unlike mhddfs, it doesn't work with existing partitions 
(with existing data). I could however initialize the new partition with 
LVM, copy data from the existing LUN onto it, free the first partition 
and then add it to the LVM managed volume. Downside: data copying will 
take a lot of time, and I have no experience with LVM, in particular I 
do not know whether hard linking will work properly. Also I have no idea 
how LVM would impact performance. Maybe somebody can provide some 
information about this.

* Going away from iSCSI, instead share the entire RAID volume via NFS, 
which is then mounted on the server (and re-shared via Samba to the 
microscope computers)
However, I read a couple of times that re-sharing an NFS mount via Samba 
causes trouble and is not recommended. Can anybody confirm this?

* Giving up on the hard-linking import and make users delete their data 
in their DropBox folders once it's imported.
Not really nice.

* Giving up OMERO Dropbox and make users use OMERO.insight to import the 
acquired data.
Not really nice.


Has anybody had a similar problem in the past?
What is the preferred way to solve this?
Have I overseen anything obvious to make this work?
I'm not really happy with any of the things I outlined above.

Thank you very much in advance,

Benjamin




-- 
Optical Imaging Centre Erlangen

Hartmannstr. 14
91052 Erlangen, Germany

http://www.oice.erlangen.de