The strange thing happens when I ssh to remote hpc cluster.

Discussion in 'Linux Networking' started by Hongyi Zhao, Jun 10, 2015.

  1. Hongyi Zhao

    Hongyi Zhao Guest

    Hi all,

    I've a count on the hpc cluster of my university. Recently, when I ssh
    into it, I often can meet the strange things as follows:

    [1].

    $ ssh zhaohongsheng@202.201.128.36
    Password:
    Last login: Wed Jun 10 05:47:21 2015 from 60.6.238.7
    generating ssh file /public/home/zhaohongsheng/.ssh/id_rsa ...
    Generating public/private rsa key pair.
    Your identification has been saved in /public/home/zhaohongsheng/.ssh/
    id_rsa.
    Your public key has been saved in /public/home/zhaohongsheng/.ssh/
    id_rsa.pub.
    The key fingerprint is:
    51:8a:00:74:2e:eb:26:48:ac:88:de:7a:ec:08:32:bc zhaohongsheng@node32
    adding id to ssh file /public/home/zhaohongsheng/.ssh/authorized_keys
    adding StrictHostKeyChecking=no to ssh config file /public/home/
    zhaohongsheng/.ssh/config
    zhaohongsheng@node32:~>

    [2].

    zhaohongsheng@node32:~> cd bin/

    [3].

    zhaohongsheng@node32:~/bin> ls
    /bin/ls: transiesta.3.2.4: No such file or directory
    /bin/ls: get_forces: No such file or directory
    /bin/ls: lev00: No such file or directory
    /bin/ls: siesta.3.2.4: No such file or directory
    /bin/ls: siesta.458: No such file or directory
    /bin/ls: tetr: No such file or directory
    /bin/ls: vasp.5.2.12.gamma: No such file or directory
    /bin/ls: transiesta.458: No such file or directory
    /bin/ls: vasp.5.2.12.noncollinear.vtst.3.1: No such file or directory
    /bin/ls: vasp.5.2.12.gamma.vtst.3.1: No such file or directory
    /bin/ls: vasp.5.2.12.half.vtst.3.1: No such file or directory
    /bin/ls: vasp.5.2.12.tbdyn: No such file or directory
    /bin/ls: vaspkit: No such file or directory
    /bin/ls: vasp.5.2.12: No such file or directory
    aux-tools subcastep vasp.5.2.12.half vasp.5.2.12.noncollinear

    [4].

    zhaohongsheng@node32:~/bin> ls -la
    total 166728
    drwxr-xr-x 4 zhaohongsheng users 4096 2015-05-13 11:38 .
    drwxr-xr-x 20 zhaohongsheng users 4096 2015-06-11 10:11 ..
    drwxr-xr-x 11 zhaohongsheng users 4096 2014-03-12 07:05 aux-tools
    -rwxr-xr-x 1 zhaohongsheng users 819391 2014-05-17 04:42 get_forces
    -rwxr-xr-x 1 zhaohongsheng users 2777140 2014-05-15 23:39 lev00
    -rwxr-xr-x 1 zhaohongsheng users 10166932 2014-03-27 01:33 siesta.3.2.4
    -rwxr-xr-x 1 zhaohongsheng users 12184268 2014-03-27 01:34 siesta.458
    drwxr-xr-x 2 zhaohongsheng users 4096 2014-03-27 00:31 subcastep
    -rwxr-xr-x 1 zhaohongsheng users 4066871 2014-05-17 04:42 tetr
    -rwxr-xr-x 1 zhaohongsheng users 10689914 2014-03-27 01:33
    transiesta.3.2.4
    -rwxr-xr-x 1 zhaohongsheng users 12717300 2014-03-27 01:34 transiesta.458
    lrwxrwxrwx 1 zhaohongsheng users 16 2015-05-13 11:38 vasp.5.2.12 -
    -rwxr-xr-x 1 zhaohongsheng users 16323410 2014-03-27 00:52
    vasp.5.2.12.gamma
    -rwxr-xr-x 1 zhaohongsheng users 17012609 2014-04-05 03:23
    vasp.5.2.12.gamma.vtst.3.1
    -rwxr-xr-x 1 zhaohongsheng users 16286845 2014-03-27 00:52
    vasp.5.2.12.half
    -rwxr-xr-x 1 zhaohongsheng users 16981927 2014-04-05 03:23
    vasp.5.2.12.half.vtst.3.1
    -rwxr-xr-x 1 zhaohongsheng users 16227084 2015-05-13 11:27
    vasp.5.2.12.noncollinear
    -rwxr-xr-x 1 zhaohongsheng users 16925025 2014-04-05 03:23
    vasp.5.2.12.noncollinear.vtst.3.1
    -rwxr-xr-x 1 zhaohongsheng users 16235019 2014-03-27 00:53
    vasp.5.2.12.tbdyn
    -rwxr-xr-x 1 zhaohongsheng users 1025246 2014-04-03 08:48 vaspkit


    [5].

    zhaohongsheng@node32:~/bin> ls
    aux-tools tetr vasp.5.2.12.half
    get_forces transiesta.3.2.4 vasp.5.2.12.half.vtst.3.1
    lev00 transiesta.458 vasp.5.2.12.noncollinear
    siesta.3.2.4 vasp.5.2.12
    vasp.5.2.12.noncollinear.vtst.3.1
    siesta.458 vasp.5.2.12.gamma vasp.5.2.12.tbdyn
    subcastep vasp.5.2.12.gamma.vtst.3.1 vaspkit
    zhaohongsheng@node32:~/bin>


    Here I meet two issues:

    [1] ``generating ssh file'' file issue as showed in the step [1]. Why
    does this happen?

    [2] The ``ls'' will failed when I first issued this command, as showed in
    step [3]. But after I issue the ``ls -la'' command in step [4], as you
    can see, the ``ls'' will then successfully work again just as showed in
    step [5].

    ps. The hpc cluster using NFS for hosting the home directories for all
    users on it.

    Any hints on these issues?

    Regards
     
    Hongyi Zhao, Jun 10, 2015
    #1
    1. Advertisements

  2. That looks like something your local site has done. AFAICS it’s not
    part of OpenSSH.
    No idea. Something broken about the cluster’s NFS setup perhaps.
     
    Richard Kettlewell, Jun 10, 2015
    #2
    1. Advertisements

  3. You posted the same thing in comp.unix.shell under a different
    message-id. That's called multiposting and you should not do it.
    Next time the internet morality police will come for you :)
     
    Ian Zimmerman, Jun 10, 2015
    #3
  4. Hongyi Zhao

    Marc Haber Guest

    Because you'll partition the answers in two parts which will cause
    wasted time with the people who will answer you. That's impolite. I
    think there's an Emily Postnews Article giving more explanation.

    Greetings
    Marc
     
    Marc Haber, Jun 10, 2015
    #4
  5. Hongyi Zhao

    Rick Jones Guest

    Some old boiler-plate I used to trot-out when newnews was busier:

    One can specify more than one newsgroup in the Newsgroups: line. The
    format would look like this:

    Newsgroups: group1,group2,group3

    with no spaces in the grouplist. This has several advantages (so long
    as it is not abused by posting messages to inappropriate groups). Only
    one copy of your message must traverse the Internet, saving network
    bandwidth; only one copy of your message must be stored on each news
    server on the Internet, saving many MB of space world-wide; you only
    have to enter the news posting once, saving you time; people only have
    to read/skip your post once, saving them time; all responses in any
    group can be seen in all groups, keeping everyone up to date with the
    conversation.

    Also, you can add a Followup-to: header line which will direct all the
    follow-ups to a particular group, making it easier for you to look for
    responses.

    I hope you find this helpful. If you do, please pass it along to your
    peers as you see them needing the same advice.

    sincerely,

    rick jones
     
    Rick Jones, Jun 10, 2015
    #5
    1. Advertisements

Ask a Question

Want to reply to this thread or ask your own question?

You'll need to choose a username for the site, which only take a couple of moments (here). After that, you can post your question and our members will help you out.