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add path to hdf5 path in build process to allow easier testing #1642

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add path to hdf5 path in build process to allow easier testing #1642

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2 changes: 1 addition & 1 deletion gemma-cli/pom.xml
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Expand Up @@ -29,7 +29,7 @@
</program>
</programs>
<!-- this allows Log4j 2 to lookup for Log4j 1.2 configuration -->
<extraJvmArguments>${jvmOptions}</extraJvmArguments>
<extraJvmArguments>-Djava.library.path=${hdf5.libDir} ${jvmOptions}</extraJvmArguments>
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@arteymix arteymix Mar 26, 2026

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This is a very bad idea. It will be included in the Appassembler package and will literally break deployment.

If you need to make testing easier, you can add a line like this to a .env or .envrc file:

export JAVA_OPTS="-Djava.library.path=/path/to/hdf5-1.12.3/lib"

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@arteymix arteymix Mar 26, 2026

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The only place we pass this is in testJvmOptions because building and testing is done on the same machine.

<!-- Gemma CLI extensions can be dropped in that folder -->
<endorsedDir>contrib</endorsedDir>
</configuration>
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