problem running KNIME on a cluster via qsub (Sun Grid Engine)

Hey there!

I am trying to run KNIME workflows on a cluster by submitting jobs to nodes using qsub. I have a local KNIME 2.11.3 folder and upon qsub submission, KNIME gets executed. However, around 10 seconds into operation (when loading Weka nodes) I get a fatal error and a crash. The head of the error log is as follows:

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 A fatal error has been detected by the Java Runtime Environment:

  SIGSEGV (0xb) at pc=0x00002abbb993ac4c, pid=114327, tid=46988475459328

 JRE version: Java(TM) SE Runtime Environment (7.0_60-b19) (build 1.7.0_60-b19)
 Java VM: Java HotSpot(TM) 64-Bit Server VM (24.60-b09 mixed mode linux-amd64 compressed oops)
 Problematic frame:
 C  [libc.so.6+0x7fc4c]  cfree+0x1c

 Core dump written. Default location: /exports/eddie3_homes_local/pgrabows/core or core.114327

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Do you know what is a possible culprit here ? I never encountered this and can't find anything on Google. I would really appreciate any hints.

 

 

Best,

Piotr

Hi Piotr,

Not really sure how to debug this one, but my first suggestion would be to upgrade to the latest version of KNIME.

Best,

Jon

I didn't upgrade KNIME, but I did manage to solve this problem. It was actually extremely easy, I had to ask the cluster for a node with 8GB of RAM minimum (-l h_vmem=8G). For some awkward reason, any value below that was giving me this crash.

It might be that it's a problem that was specific to our cluster system, but somebody might stumble upon this thread in the future...