Docker on different platforms, running containers differently?

Discussion in 'Docker and Containers' started by Patrick, Jun 27, 2017.

  1. Patrick

    Patrick Administrator
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    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:
    Code:
    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.
     
    #1
  2. Gary Gapinski

    Gary Gapinski New Member

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    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:~$
     
    #2
  3. Patrick

    Patrick Administrator
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    Ok that is going to drive me crazy now. What you are seeing is the correct behavior.
     
    #3
  4. nitrobass24

    nitrobass24 Moderator

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    Don't get me started on Docker Strangeness :) Following to see what happens.
     
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  5. epicurean

    epicurean Member

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

    Patrick Administrator
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    In theory no
     
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