[ome-users] Import error

[Douglas Russell]

I'd checked master logs files and there was nothing of interest in there.
dmesg is more promising though, good idea. It looks like a memory issue.
I've increased the amount of memory available to 20GBs from 4GBs and now it
does not fail in the same way. Not sure why so much RAM is needed when each
image in the screen is only 2.6MBs. Now there is a nice new error.

Going by the error that I see when the database tries to rollback, I think
it is timeout related.

The import log: https://s3.amazonaws.com/dpwr/pat/import_log.txt
The server logs (I tried the import twice):
https://s3.amazonaws.com/dpwr/pat/omero_logs.zip

There are a couple of these in the database logs as you'd expect for the
two import attempts, but nothing else of interest.

LOG: unexpected EOF on client connection with an open transaction

Cheers,

Douglas

On Fri, 22 Dec 2017 at 12:20 Josh Moore <josh at glencoesoftware.com> wrote:

> On Fri, Dec 22, 2017 at 1:33 AM, Douglas Russell
> <douglas_russell at hms.harvard.edu> wrote:
> > Sure, here is the Blitz log.
>
> Thanks. Yeah, here there looks to be a panic of some form:
>
> 2017-12-21 23:54:54,179 INFO  [
> ome.security.basic.CurrentDetails] (l.Server-3) Adding
> log:INSERT,class ome.model.core.OriginalFile,7932
> 2017-12-21 23:54:54,253 INFO  [
> ome.security.basic.CurrentDetails] (l.Server-3) Adding
> log:INSERT,class ome.model.core.OriginalFile,7933
> 2017-12-21 23:54:54,318 INFO  [
> ome.security.basic.CurrentDetails] (l.Server-3) Adding
> log:INSERT,class ome.model.core.OriginalFile,7934
> 2017-12-21 23:54:54,400 INFO  [
> ome.security.basic.CurrentDetails] (l.Server-3) Adding
> log:INSERT,class ome.model.core.OriginalFile,7935
> ---> here <---
> 2017-12-21 23:54:56,129 INFO  [
> ome.services.blitz.Entry] (      main) Creating OMERO.blitz. Please
> wait...
> 2017-12-21 23:54:56,955 INFO
> [.s.ShutdownSafeEhcacheManagerFactoryBean] (      main) Initializing
> EHCache CacheManager
> 2017-12-21 23:54:57,303 INFO  [
> ome.services.util.DBPatchCheck] (      main) Verified database patch:
> OMERO5.4__0
> 2017-12-21 23:54:57,337 INFO  [
> ome.services.util.DBUserCheck] (      main) User root.id = 0
> 2017-12-21 23:54:57,338 INFO  [
> ome.services.util.DBUserCheck] (      main) User guest.id = 1
> 2017-12-21 23:54:57,338 INFO  [
> ome.services.util.DBUserCheck] (      main) Group system.id = 0
> 2017-12-21 23:54:57,338 INFO  [
> ome.services.util.DBUserCheck] (      main) Group user.id = 1
>
>
>
> > I'm afraid it's not very informative. It looks like whatever causes it to
> > fail is causing blitz to die and be restarted, going by the logs and the
> ps
> > output. Most of the services are from when OMERO was started around
> 18:22,
> > but then at the bottom we see the new services started as 23:54 which is
> > when I was doing the import.
>
>
> Was there anything in master.out or master.err? What about dmesg?
> ~J.
>
>
> > Cheers,
> >
> > Douglas
>
> >
> >
> >
> > On Thu, 21 Dec 2017 at 12:45 Josh Moore <josh at glencoesoftware.com>
> wrote:
> >>
> >> Hi Douglas,
> >>
> >> On Wed, Dec 20, 2017 at 2:25 AM, Douglas Russell
> >> <douglas_russell at hms.harvard.edu> wrote:
> >> > Has anyone seen this import error? It's pretty vague. I imported a
> test
> >> > jpg
> >> > to make sure import was working in general and it was fine. I updated
> to
> >> > the
> >> > latest OMERO and still seeing the problem.
> >> >
> >> > Any ideas?
> >>
> >> Since it's an unexpected error, Ice is unfortunately swallowing all
> >> the good stuff. Can you send us the related Blitz and/or import logs?
> >>
> >> Cheers,
> >> ~Josh.
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