| Out of memory [message #2395] |
Tue, 11 March 2025 16:10  |
Christophe
Messages: 32
Registered: January 2022
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Member |
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Hello everyone,
I am currently working with a quite big dataset (~25000 molecules) and I try to make a UMAP vizualisation after the calculation of some data warrior fingerprints.
Each time I try to create a UMAP vizualization I get the following message:
"Out of memory. Launch DataWarrior with Java option -Xms???m or -Xmx???m"
How can I get around this problem?
I run DW on Intel core i5 at 2.7 GHz with 64 Go RAM
Thank you for any clarification you may be able to provide
Christophe
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| Re: Out of memory [message #2396 is a reply to message #2395] |
Wed, 12 March 2025 23:07  |
nbehrnd
Messages: 230
Registered: June 2019
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Senior Member |
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Hello Christophe,
the line you report is very close to the BASH script of DataWarrior's installer and launcher script in Linux. As an example, it can contain the line reading
/opt/datawarrior/jre/bin/java -Xms512m -Xmx4096m -splash:/opt/datawarrior/loading.png --add-exports java.base/jdk.internal.module=ALL-UNNAMED -Dfile.encoding=UTF-8 -cp $DWJAR/datawarriorlauncher.jar:$DWJAR/capka.jar org.openmolecules.datawarrior.launcher.DataWarriorLauncher $*
This example reads as "allocate DataWarrior 512 MByte RAM to start, provide up to 4 GO/GByte maximum" to allow other programs than DataWarrior to process concurrently. However, if you manage a larger data set on a more powerful computer, it is possible to manually adjust (i.e., increase) these thresholds. Try to work with e.g., `-Xmx60g`.
Best regards,
Norwid
https://www.star.bris.ac.uk/mbt/stilts/sun256/jvmArgs.html
[Updated on: Wed, 12 March 2025 23:08] Report message to a moderator |
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