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Error Could not initialize class ch.systemsx.cisd.hdf5.CharacterEncoding on AffineExport on h5 file #8
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Hi @boazmohar and @StephanPreibisch , I'm getting the same error on a SLURM cluster running a standalone spark cluster. java info:
mvn:
submit command:
Using This didn't happen when running locally with |
@trautmane, do you have some time to look at that? |
@mkitti - that sounds familiar, did we discuss this? The problem that HDF5 creates a local tmp directory? |
I will check the pom this afternoon. |
thanks @mkitti! |
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The reported line number is slightly off. |
We may need to take a close look at your classpaths. Also either of you are running on Debian or Ubuntu? Is it possible that you have on old version of the |
The current pom actually imports jhdf5 14.12.6. The above source links are for 19.04. |
Line 143 lines up with older jhdf5 source at https://svnsis.ethz.ch/repos/cisd/jhdf5/trunk/source/java/ch/systemsx/cisd/hdf5/HDF5BaseReader.java
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Hi @mkitti ,
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This is @mkitti with @boazmohar: Per https://unlimited.ethz.ch/display/JHDF/JHDF5+FAQ#JHDF5FAQ-Whataretheoptionstoprovidethenativelibraries? we can provide a JVM option to point Java to a pre-extracted location of the file. In @boazmohar's case, we prepended We extracted |
Confirming the above also works on my end
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It may be useful to considering using |
Hi @StephanPreibisch,
I am trying to do an AffineExport with spark:
And get this error:
I can open it in Fiji and look at the data with BigStitcher without an issue.
The xml is in:
/groups/mousebrainmicro/mousebrainmicro/data/Lightsheet/20210812_AG/ML_Rendering-test/aligned_data.xml
Any idea what to do?
Found this, might be related.
Thanks,
Boaz
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