fix PepQuery2 memory #722
fix PepQuery2 memory #722
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| @@ -32,7 +32,7 @@ | |||
| #end if | |||
| ## PepQuery command | |||
| pepquery | |||
| -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g | |||
| -Xmx\$(( \${GALAXY_MEMORY_MB:-8192} - 256 - (\${GALAXY_SLOTS:-1} / 5) - \${GALAXY_MEMORY_MB:-8192} * (1 / 20) ))m | |||
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How do you arrive at this formula?
If you want to make the memory depend on the number of available threads use it may be better to use \$GALAXY_MEMORY_MB_PER_SLOT?
Wouldn't it be a simple solution to let the admin just give more memory to the application?
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If you want to make the memory depend on the number of available threads use it may be better to use $GALAXY_MEMORY_MB_PER_SLOT?
Yes I should use that one indeed
Wouldn't it be a simple solution to let the admin just give more memory to the application?
-8192 sets a default value. The change is needed because I had the case when the JVM used all mem specified in Galaxy for the heap (-Xmx), which leads to a run out of memory error, becuase the JVM needs memory also for the stack and other overhead. The formula is not super precise but follows a recommendation for JVM memory settings, from this source
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Here is what I do on my instance. In each destination of the job_conf I add
<env id="_JAVA_OPTIONS">-Xmx@JAVAMEM@ -Xms256m</env>
and set @JAVAMEM@ to something lower than the available memory (roughly 33%). I guess this does not work here because the bioconda recipe seems not to respect _JAVA_OPTIONS, but I might be wrong. If I'm right it would be good to adapt the recipe .. a grep _JAVA_OPTIONS in the bioconda recipes should guide you.
Would be interesting to ask the TPV / admin community how they handle java memory.
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Wouln't it be cleaner to substract that 33% already in the wrapper and not later. Otherwise all admins would need to think of it (like me for example) and we would need an additional destination and configuration lines
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Test 2 is failing for me on the main branch with --docker, could someone check if it is just for me or in general?
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@mira-miracoli we have now something similar in the default tool. Do we need this PR still? |
I changed the Java options, because the JVM overhead can lead to failing jobs, when the tool uses the full amount defined in GALAXY_MEMORY_MB as stack.