Docker on different platforms, running containers differently?

[Patrick]

Here is a strange one.

When working on a new Ubuntu Docker image for GROMACS benchmarking, I am noticing some strange behavior. Namely that if I run the Docker container on Ubuntu 14,04, 16.04 or 17.04 the container will not kill the benchmark process after 6 minutes as it is supposed to. I let it run overnight.

Fedora works as expected.

If you want to try:

docker run -it linuxbench/gromacs:zesty

If anyone has a RHEL, SUSE, or CentOS 7.3 box up, I would love to see how it goes. I am trying to figure out why it is not terminating the process with Docker.

 

[Gary Gapinski]

I don't have an RHEL system handy atm. Just tried this on an Ubuntu 17.04 system. Timed the second of two runs. Both ended after 10 minutes or so.

The second ended with the following (the first also ended with the same "Run time exceeded 0.099 hours").

gapinski@NUC7i7BNH:~$ time docker run -it linuxbench/gromacs:zesty
$numthreads is empty
Threads is 2
--2017-06-28 07:37:54-- http://files.linux-bench.com/lb/gromacs-bench.tar.gz
Resolving files.linux-bench.com (files.linux-bench.com)... 65.19.142.22
Connecting to files.linux-bench.com (files.linux-bench.com)|65.19.142.22|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2543040 (2.4M) [application/octet-stream]
Saving to: 'gromacs-bench.tar.gz'
… [snip much verbosity] …
starting mdrun 'Protein in water'
500000 steps, 1000.0 ps.

Step 16080: Run time exceeded 0.099 hours, will terminate the run

Core t (s) Wall t (s) (%)
Time: 714.216 357.108 200.0
(ns/day) (hour/ns)
Performance: 7.791 3.080

GROMACS reminds you: "If everything seems under control, you're just not going fast enough." (Mario Andretti)


real 12m23.982s
user 0m0.112s
sys 0m0.100s
gapinski@NUC7i7BNH:~$

 

[Patrick]

Ok that is going to drive me crazy now. What you are seeing is the correct behavior.

 

[nitrobass24]

Don't get me started on Docker Strangeness Following to see what happens.

 

[epicurean]

Would a docker image also work different on say a synology system, vis a vis Ubuntu or Centos?

 

[Patrick]

In theory no