[biomart-users] "file descriptors" problem on RedHat 7

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

[biomart-users] "file descriptors" problem on RedHat 7

zhilianghu
I have set up the most recent Biomart on a RedHat 7 system with
  > git clone https://github.com/biomart/BioMart.git --branch 0.9.0

compiled with 'ant' and started as in
  > cd dist
  > ./scripts/biomart-server.sh

Immediately it generates tons of open files (before any data is set up):

  > lsof | grep java | wc -l
15745
  > lsof | grep biomart | wc -l
282

... I was telling the story in a reverse way - the problem initially was
there were often system complains that a process could not write to "/tmp"
from time to time.  A "lsof | wc -l" shows it's over 19,000. I didn't
want to blindly raise the limit. That led me to dig deeper to find not
that it was caused by not enough file descriptors left on the system. When
stop Biomart it went down to ~3,000, comparable to our other servers.

This is consistantly repeatable.

Biomart runs well on RedHat 6 on our old server.  Anything special for
RH7 that makes Biomart loops out too many open files?

Zhiliang