From: Zeki Zeybek (zeki.zeybek_at_bilgiedu.net)
Date: Thu May 18 2017 - 02:27:27 CDT
I somehow figured out a more crude way of handling the problem. Simply just open a new file specifically named
as "config", file name must be config. Then add the following inside the file config. Make sure that the config file is located in your main account directory not scratch i.e. clustername/home/accountName/.ssh.
Add those into the config file,
Host *
StrictHostKeyChecking no
________________________________
From: Zeki Zeybek
Sent: 12 May 2017 10:05:13
To: Boonstra, S.; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: CHARMRUN ERROR
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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