Re: CHARMRUN ERROR

From: Zeki Zeybek (zeki.zeybek_at_bilgiedu.net)
Date: Fri May 12 2017 - 02:05:13 CDT

Thank you for your help and also for explaining the cause behind the problem but interestingly the problem is somehow solved by itself. I tried to start the simulation just after an hour or so it worked like a charm. Once again thank you for the insight about the issue.

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________________________________
From: Boonstra, S. <s.boonstra_at_rug.nl>
Sent: Thursday, May 11, 2017 11:03:38 PM
To: namd-l_at_ks.uiuc.edu; Zeki Zeybek
Subject: Re: namd-l: CHARMRUN ERROR

Hi Zeki,

I dealt with the same problem on our cluster just yesterday.

Possibly, the RSA fingerprint of the node(s) has changed.
See also http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/2465.html
and
https://askubuntu.com/questions/45679/ssh-connection-problem-with-host-key-verification-failed-error

You can renew the fingerprints (they end up in .ssh/known_hosts) of all the nodes (or nodes in $server_list)
with a (bash) script like

server_list=`sinfo -N --format="%N" | sort -u | grep tcn1[67]` #slurm specific
for h in $server_list; do
    printf "$h " #verbose
    ip=$(dig +search +short $h)
    ssh-keygen -R $h
    ssh-keygen -R $ip
    ssh-keyscan -H $ip >> ~/.ssh/known_hosts
    ssh-keyscan -H $h >> ~/.ssh/known_hosts
done
print #verbose

On Thu, May 11, 2017 at 9:39 AM, Zeki Zeybek <zeki.zeybek_at_bilgiedu.net<mailto:zeki.zeybek_at_bilgiedu.net>> wrote:

Hi!

Everything has been running smoothly till today. I did not change anything in the script or in the config file. The error output is;

sardalya>> name of the partition in which I am trying to use the nodes

ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed.^M
Charmrun> Error 255 returned from remote shell (sardalya78:0)
Charmrun> Reconnection attempt 1 of 3
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed.^M
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed.^M
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed.^M
Charmrun> Error 255 returned from remote shell (sardalya79:1)
Charmrun> Reconnection attempt 1 of 3
Charmrun> Error 255 returned from remote shell (sardalya80:2)
Charmrun> Reconnection attempt 1 of 3
Charmrun> Error 255 returned from remote shell (sardalya81:3)
Charmrun> Reconnection attempt 1 of 3
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed.^M
Charmrun> Error 255 returned from remote shell (sardalya78:0)
Charmrun> Reconnection attempt 2 of 3
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed.^M
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed.^M
Charmrun> Error 255 returned from remote shell (sardalya79:1)
Charmrun> Reconnection attempt 2 of 3
Charmrun> Error 255 returned from remote shell (sardalya80:2)
Charmrun> Reconnection attempt 2 of 3
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed.^M
Host key verification failed.^M
Charmrun> Error 255 returned from remote shell (sardalya81:3)
Charmrun> Reconnection attempt 2 of 3
Charmrun> Error 255 returned from remote shell (sardalya78:0)
Charmrun> Reconnection attempt 3 of 3
ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory^M
Host key verification failed
Charmrun> Error 255 returned from remote shell (sardalya81:3)
Charmrun> Reconnection attempt 3 of 3
Charmrun> Error 255 returned from remote shell (sardalya78:0)
Charmrun> Too many reconnection attempts; bailing out

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