Re: [AMBER] problem with using amber

From: Feng Su <feng.su.tandemai.com>
Date: Thu, 7 Apr 2022 00:52:16 +0000

Hi David

Thank you for your answer.
And we confirmed it caused by our custom development in amber.

Thanks again.

--

Su Feng
Best Regards,
--------------------------------------------
Tel: +86 186 5107 0620
E-Mail: feng.su.tandemai.com
Address: Room 2102-2103, Block C, Suzhou Center,
Suzhou Industry Park, Jiangsu, China

在 2022/3/31 下午8:06,“David A Case”<dacase1.gmail.com> 写入:

    On Thu, Mar 31, 2022, Feng Su wrote:
>
>I found some problem when using Amber with MPI in Slurm GPU Cluster.
>We deployed the Docker service in our Computing nodes.
>The new interface docker0 was add before default interface ens3 and it caused the failure.
>
>-----------------------------------------------------------------
>docker0: flags=4163<UP,BROADCAST,RUNNING,MULTICAST> mtu 1500
> inet 172.17.0.1 netmask 255.255.0.0 broadcast 172.17.255.255
> inet6 fe80::42:75ff:fecd:fbaa prefixlen 64 scopeid 0x20<link>
>...
>ens3: flags=4163<UP,BROADCAST,RUNNING,MULTICAST> mtu 1500
> inet 192.168.100.16 netmask 255.255.255.0 broadcast 192.168.100.255
> inet6 fe80::f652:14ff:fe89:24d0 prefixlen 64 scopeid 0x20<link>
>...
>-----------------------------------------------------------------
>
>When we disable the interface docker0, it back to normal.
>It seem amber use “172.17.0.1” as the communication IP instead of “192.168.100.16”.

    I'm pretty sure that this is related to your MPI stack, and not to any code in
    Amber. Amber relies on MPI to handle communications between nodes. Can you
    run other MPI jobs (e.g. just some of the MPI examples) in the docker mode?

    Others on the list may have ideas, but this problem seems pretty specific to
    your setup, and (probably) not related to any particular code in Amber itself.

    ....good luck....dac


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Received on Wed Apr 06 2022 - 18:00:02 PDT
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