Question: Galaxy crashing, running out of memory (database upload?)
0
gravatar for danielfortin86
2.8 years ago by
United States
danielfortin86110 wrote:

Hi,

 

For some reason my Galaxy process gets killed because it runs out of memory after a few seconds (running with 64Gb on a VM). I'm using postgres and notice that while Galaxy is running that it uses 100% CPU, while the Galaxy processes' memory quickly rises until the process gets killed. Using the Galaxy reports framework it looks like there is a running job related to uploading. Could this job be what's causing this memory failure? If so, how do I kill this job? Can I manually remove this from the postgres database? How would I do this? Any suggestions would be greatly appreciated! Please see below for the error message

 

Thanks!!

 

Out of memory: Kill process 3616 (python) score 986 or sacrifice child

Killed process 3616, UID 551, (python) total-vm:68426688kB, anon-rss:65019188kB, file-rss:4kB

crash postgres • 801 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by danielfortin86110
0
gravatar for danielfortin86
2.8 years ago by
United States
danielfortin86110 wrote:

In case anyone runs into this issue, apparently the last job in the postgres database was causing these issues. This job was related to adding files to a shared data library. Loosely following the instructions in Section 8.2 below solved the issue:

http://ihpe.univ-perp.fr/methods/methods/Galaxy_production_mode_installation_walkthrough.html

After deletion of all database entries related to the last job, galaxy again runs without issues. 

 

 

 

ADD COMMENTlink written 2.8 years ago by danielfortin86110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour