Error with too many open files

[sonnyarora]

I am running higlass through docker on CentOS 7.7.1908. I ran into an issue when I had several files loaded in HiGlass. In particular, when I have 8 bigWigs and an mcool file in HiGlass, after zooming in and out, I see the following error in the higlass container in /data/log/hgs.log :

[Errno 24] Too many open files: '/data/media/mm10.tsv'

Running some tests: With no loaded files, I check how many open files all the uwsgi processes have open:

lsof -p 2640,2649,2651,2652,2653 | wc -l

I get 553. After loading a single big wig, the number rises to: 1020. As I zoom in, the number keeps increasing: 1020,1031,1259. Passing this input to grep to search only for the names of the bigWig I have loaded in higlass, I see more lines appear as I zoom. I see the same pattern of the number of open files increasing as I zoom in different locations with all 8 bigWigs and the mcool file loaded until I get the above error.

The limit on number of open files for a single process set by default for my CentOS is 1024. If I increase this limit, I don't run into the same problem. Setting this limit high enough is a good enough solution for me for this problem.

[nvictus]

Thanks for reporting this! This seems to be caused by resource leakage when pybbi raises exceptions internally. Will work on a fix here: nvictus/pybbi#10

[nvictus]

This is now fixed in pybbi 0.2.2

[sonnyarora]

Thanks for taking care of that! What are the next steps to get higlass-server to use the new version of pybbi?

[nvictus]

If you're using the docker image, it will be distributed in the next release, probably in the next day or so. If you're running higlass-server in a local environment, you just need to upgrade pybbi via pip.

[pkerpedjiev]

Should be updated in v0.6.39 of the Docker container 👍 Please let us know if you still encounter this issue.

And thanks for reporting it :-)

[sonnyarora]

Hey, thanks for taking care of that! I'm not seeing any open bigwigs in lsof anymore. Also, extra file handles don't appear to be opened when zooming. Marking this as closed.