| Out of memory [message #2395] |
Tue, 11 March 2025 16:10  |
Christophe
Messages: 34
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: 233
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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| Re: Out of memory [message #2405 is a reply to message #2404] |
Sat, 22 March 2025 17:26 |
nbehrnd
Messages: 233
Registered: June 2019
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Senior Member |
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Hello Christophe,
a bypass could be to set up a separate Linux partition on your computer because then the file in path /opt/datawarrior/datawarrior would provide you access to these parameters. Either by a double-boot (right after starting the computer, you will be asked which operating system to be used exclusively), or with a virtualization (for instance windows wsl) as a permanent change to the computer.
It equally is possible to start Linux from a USB/pen drive (e.g., https://rufus.ie/en/) provided the BIOS of the computer is set to allow to boot from USB. In principle this would provide a non-permanent access to the parameters (after launch of the OS, installation of DataWarrior, adjustment of the parameters, launch of DataWarrior) without change to the hosting computer. This tends to be a bit less performant than a true installation, though not as much with 64 Go at disposition, than e.g., 8 Go. After deconnection of the USB drive, the computer would boot as it did prior to this excursion. Which could be worth a test, too.
Best regards,
Norwid
https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux
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