[ome-devel] batch import into OME 5.0.2

[Yanling Liu]

Josh,

I have increased ulimit nofile to 65000 and the "file doesn't exist
problem" seems to be fixed!

Will try to import more images into OME...

Thanks,
Yanling


On Mon, Jun 16, 2014 at 3:55 PM, Josh Moore <josh at glencoesoftware.com>
wrote:

> Hi Yanling,
>
> my apologies for not getting to this sooner. (There are people to hit me
> with a stick when I forget to reply to a mailing list email, but not when
> it goes only to me)
>
> On Jun 12, 2014, at 6:17 PM, Yanling Liu wrote:
>
> > Josh,
> >
> > bin/omero fs repos
> > ...
> > the repo did *not* recently move locations.
>
> Yup, looks very healthy.
>
>
> > I was trying to import a dataset including 161 folders and 8514 images. I
> > have created a python script to iterate these 161 folders and import each
> > folder as one dataset in OMERO.
> >
> > As I indicated in previous message, I would get "file not existing error"
> > during the import process. Also after the import process, I am having
> > problem to do anything to OMERO including new imports and deletions. If I
> > start new import I will get "Too many open files" error message. And
> OMERO
> > will not be able to accept more TCP connections.
>
> Thanks for these. I'll take a look first thing tomorrow. If configuring
> ulimit to get rid of the "Too many open files" fixes the problem, please
> let me know.
>
> Cheers,
> ~Josh.
>
>
>
> > I have attached complete import log message, along with my python script.
> >
> > My python script is simply a wrapper to iteratively call omero import
> > command.
> >
> > Thanks,
> > Yanling
> >
> >
> > On Tue, Jun 10, 2014 at 11:51 AM, Josh Moore <josh at glencoesoftware.com>
> > wrote:
> >
> >> Hi Yanling,
> >>
> >> On Jun 10, 2014, at 5:44 PM, Yanling Liu wrote:
> >>
> >>> Server configuration: Ubuntu 12.04 VM with 3TB NFS storage attached.
> OME5
> >>> is installed and the ManagedRepository is located on the 3TB NFS
> storage.
> >>>
> >>> When using command line import tool to inject one user folder plus its
> >>> subfolders to one dataset in OME, I have got following error on certain
> >>> TIFF images (file path removed from log info)  :
> >>
> >> Would you mind sending the full log (via private email if you'd prefer)?
> >> Also having the command-line as you executed it would be useful.
> >>
> >>
> >>> I have verified the file 51-11.tif exists as
> >>> ManagedRepository/acharyaj_52/2014-06/06/16-43-40.589/51-11.tif. Tried
> >> run
> >>> tiffinfo tool again the image file and found no problem. Don't know why
> >> OME
> >>> report an existing file as non-exist...
> >>
> >> Could you send the output of:
> >>
> >>  bin/omero fs repos
> >>
> >> and:
> >>
> >>  bin/omero config get | grep omero.data.dir
> >>
> >> Did the repo recently move locations?
> >>
> >>
> >>> Thanks,
> >>> Yanling
> >>
> >> Cheers,
> >> ~Josh
> > <output.txt><importSingleUserImages_s.py>
>
>
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