[ome-devel] Problem when importing >1000 images

[Josh Moore]

Hi Andrii,

On Tue, Apr 26, 2016 at 10:56 AM, Andrii Iudin <andrii at ebi.ac.uk> wrote:
> Dear Josh,
>
> Please find attached the import script. For each EMDB entry it performs an
> import of six images - three sides and their thumbnails.

Thanks for this. And where's the definition of `run_command`?


> To stop OMERO we use "omero web stop" and then "omero admin stop" commands.
> After this it is necessary to remove
> var/OMERO.data/.omero/repository/*/.lock files before starting OMERO again.
> The system is NFS.

I'd assume then that disconnections & the .lock files are unrelated.
Please see https://www.openmicroscopy.org/site/support/omero5.2/sysadmins/unix/server-binary-repository.html#locking-and-remote-shares
regarding using remote shares.

Cheers,
~Josh.



> Best regards,
> Andrii
>
>
> On 25/04/2016 16:21, Josh Moore wrote:
>>
>> On Fri, Apr 22, 2016 at 12:41 PM, Andrii Iudin <andrii at ebi.ac.uk> wrote:
>>>
>>> Dear OMERO developers,
>>>
>>> We are experiencing an issue when importing a large number of images in a
>>> single consequent go. This usually happens after importing more than a
>>> thousand images. Please see below excerpts from the logs. Increasing a
>>> time
>>> period between each import seemed to helped a bit, however this issue
>>> ultimately happened anyway.
>>
>> Is this script available publicly? It would be useful to see how it's
>> working.
>>
>>
>>> To get OMERO server working after this happens,
>>> it is necessary to stop it, remove .lock files and start the server
>>> again.
>>> It would be much appreciated if you could point out to a possible way to
>>> solve this issue.
>>
>> How did you stop OMERO? Is your file system on NFS or another remote
>> share?
>>
>>
>>> Thank you and with best regards,
>>> Andrii
>>
>> Cheers,
>> ~Josh.