java heap space error
RichardCorbett opened this issue · 5 comments
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?
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
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.
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.
No problem. I really appreciate your responsiveness. Best of luck!
Thanks! It's almost dinner here, so for this tiny bloop of space time, all is well! haha ;)