java heap space error

[RichardCorbett]

Links

• container collection: https://singularity-hub.org/containers/12557/log
• GitHub repository or recipe file: https://github.com/RichardCorbett/PROFYLE_TMB

Version of Singularity

Write here

Behavior when Building Locally

Hi folks I can build this locally on my network without any special switches. ie: sudo singularity build --force PROFYLE_TMB PROFYLE_TMB.recipe

Error on Singularity Hub

my build is failing when some java code is supposed to run to reformat some files after they are downloaded.

...
00:01:07 Loading interactions from : /usr/TMB/snpEff/./data/GRCh37.75/interactions.bin
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3332)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:124)
...

What do you think is going on?

It looks like the java command is asking for 16Gb, perhaps that is more than is allocated to the build jobs on singularityhub?

[vsoch]

Yes, unfortunately the Singularity Hub instances only have about 3.75 GB of memory. You can try:

• decreasing the requested amount, and I'd give it some buffer
• building some base on Docker Hub and pulling said base after the memory operation is done
• using sylabs cloud

[RichardCorbett]

Thanks. I tried a build locally using only 3Gb but ran out of RAM and it crashed. I'll take a look into using sylabs.

[vsoch]

Great! Sorry I can't offer more than that, I've been running this for almost 4 years now, and also procuring funding, refactoring when needed, responding to issues, and the thing that I definitely can't do is give total freedom to use expensive resources. Good luck with Sylabs Cloud, closing issue.

[RichardCorbett]

No problem. I really appreciate your responsiveness. Best of luck!

[vsoch]

Thanks! It's almost dinner here, so for this tiny bloop of space time, all is well! haha ;)