OMERO Reader crashes KNIME

KNIME Extensions
1

Hi,

when I click "start OMERO insight" in the OMERO Reader node, KNIME crashes entirely (see below whats printed into the terminal).

I am running Knime 3.1.2 on linux mint 17.3.

If it helps I'd glady provide the error report file that is mentioned below.

Thanks for your help!

-----------------------------------

# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fbaab201eaf, pid=2663, tid=140439585056512
#
# JRE version: Java(TM) SE Runtime Environment (8.0_60-b27) (build 1.8.0_60-b27)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.60-b23 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libgdk-x11-2.0.so.0+0x4ceaf]  gdk_display_open+0x3f
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
hs_err_pid2663.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.

2

Dear Kai,

sorry for the trouble and thanks for letting us know. We will try to reproduce the problem and come back with a solution asap.

Best,

Christian

PS: Which OMERO Version are you using on the Server side? Just out of curiosity and to make sure that KNIME can connect.
PPS: We are working on a more flexible solution (based on imagej) to read/write images from and to OMERO.

3

Dear Christian,

thanks for the quick reply!

we are currently using OMERO 5.1.2 but are also in the process of upgrading to a more recent version.

Thanks for your help and cheers,

Kai

4

Hi Kai,

I was able to reproduce the problem. No I will work on a fix. ;-)

Thanks again for reporting,

Christian

5

Hi Kai,

I opened an issue in our GitHub Repo. We will tackle the problem next week.

https://github.com/knime-ip/knip-omero/issues/3

Christian

6

HI Christian,

 

thanks for the update! I'll stay tuned for next week then :)

 

Cheers,

Kai

7

Dear Christian,

many thanks for the feedback and the issue tracker link!

 

Cheers

Niko

8

Hi Niko & Kai,

we fixed the Client for OMERO 5.2.x (available via our nightly build). We will also provide a version for OMERO 5.1.x (probably only via nightly build, hopefully next week).

However, as mentoined above, we want to redesign our OMERO integration and offer a new Reader/Writer based on imagej-omero / scifio. It would be great, as we don't have too much experience with OMERO, if you could provide us some feedback what are "must haves" and/or "nice-to-haves" of such new nodes (e.g. you want to read a complete dataset and then write back the results, or ...).  We opened a GitHub issue for further discussion:

https://github.com/knime-ip/knip-omero/issues/5

I hope this helps,

Christian

 

9

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