<div dir="ltr"><div><div><div>Josh,<br><br></div>I have increased ulimit nofile to 65000 and the "file doesn't exist problem" seems to be fixed!<br><br></div>Will try to import more images into OME...<br><br>
Thanks,<br></div>Yanling<br><div><div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jun 16, 2014 at 3:55 PM, Josh Moore <span dir="ltr"><<a href="mailto:josh@glencoesoftware.com" target="_blank">josh@glencoesoftware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Yanling,<br>
<br>
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)<br>
<br>
On Jun 12, 2014, at 6:17 PM, Yanling Liu wrote:<br>
<br>
> Josh,<br>
><br>
> bin/omero fs repos<br>
> ...<br>
<div class="">> the repo did *not* recently move locations.<br>
<br>
</div>Yup, looks very healthy.<br>
<div class=""><br>
<br>
> I was trying to import a dataset including 161 folders and 8514 images. I<br>
> have created a python script to iterate these 161 folders and import each<br>
> folder as one dataset in OMERO.<br>
><br>
> As I indicated in previous message, I would get "file not existing error"<br>
> during the import process. Also after the import process, I am having<br>
> problem to do anything to OMERO including new imports and deletions. If I<br>
> start new import I will get "Too many open files" error message. And OMERO<br>
> will not be able to accept more TCP connections.<br>
<br>
</div>Thanks for these. I'll take a look first thing tomorrow. If configuring<br>
ulimit to get rid of the "Too many open files" fixes the problem, please<br>
let me know.<br>
<br>
Cheers,<br>
~Josh.<br>
<div><div class="h5"><br>
<br>
<br>
> I have attached complete import log message, along with my python script.<br>
><br>
> My python script is simply a wrapper to iteratively call omero import<br>
> command.<br>
><br>
> Thanks,<br>
> Yanling<br>
><br>
><br>
> On Tue, Jun 10, 2014 at 11:51 AM, Josh Moore <<a href="mailto:josh@glencoesoftware.com">josh@glencoesoftware.com</a>><br>
> wrote:<br>
><br>
>> Hi Yanling,<br>
>><br>
>> On Jun 10, 2014, at 5:44 PM, Yanling Liu wrote:<br>
>><br>
>>> Server configuration: Ubuntu 12.04 VM with 3TB NFS storage attached. OME5<br>
>>> is installed and the ManagedRepository is located on the 3TB NFS storage.<br>
>>><br>
>>> When using command line import tool to inject one user folder plus its<br>
>>> subfolders to one dataset in OME, I have got following error on certain<br>
>>> TIFF images (file path removed from log info) :<br>
>><br>
>> Would you mind sending the full log (via private email if you'd prefer)?<br>
>> Also having the command-line as you executed it would be useful.<br>
>><br>
>><br>
>>> I have verified the file 51-11.tif exists as<br>
>>> ManagedRepository/acharyaj_52/2014-06/06/16-43-40.589/51-11.tif. Tried<br>
>> run<br>
>>> tiffinfo tool again the image file and found no problem. Don't know why<br>
>> OME<br>
>>> report an existing file as non-exist...<br>
>><br>
>> Could you send the output of:<br>
>><br>
>> bin/omero fs repos<br>
>><br>
>> and:<br>
>><br>
>> bin/omero config get | grep omero.data.dir<br>
>><br>
>> Did the repo recently move locations?<br>
>><br>
>><br>
>>> Thanks,<br>
>>> Yanling<br>
>><br>
>> Cheers,<br>
>> ~Josh<br>
</div></div>> <output.txt><importSingleUserImages_s.py><br>
<br>
</blockquote></div><br></div></div></div></div></div></div>