NAMD running on a Cluster of Ubuntu Linux

From: Marisol Oswald (marisoloswald1988_at_gmail.com)
Date: Sun Oct 09 2016 - 18:37:55 CDT

Hi all,

I am trying to run NAMD on a Ubuntu 16.0 cluster. My setup does allow to
SSH login without any password, but
I am still getting some kind of permission errors. Please help.

******* Error Using Linux-x86_64 (64-bit Intel/AMD with ethernet) using
Version 2.11 (2015-12-22)

sudo ./charmrun namd2 ++verbose +idlepoll +p8 p_run.conf >> p_run.log
Charmrun> charmrun started...
Charmrun> using /home/user1/.nodelist as nodesfile
Charmrun> remote shell (192.168.1.7:0) started
Charmrun> node programs all started
Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).
Charmrun> Error 255 returned from remote shell (192.168.1.7:0)
Charmrun> Reconnection attempt 1 of 3
Charmrun> remote shell (192.168.1.7:0) started
Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).
Charmrun> Error 255 returned from remote shell (192.168.1.7:0)
Charmrun> Reconnection attempt 2 of 3
Charmrun> remote shell (192.168.1.7:0) started
Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).
Charmrun> Error 255 returned from remote shell (192.168.1.7:0)
Charmrun> Reconnection attempt 3 of 3
Charmrun> remote shell (192.168.1.7:0) started
Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).
Charmrun> Error 255 returned from remote shell (192.168.1.7:0)
Charmrun> Too many reconnection attempts; bailing out

****** Error using Linux-x86_64-TCP using Version 2.10

​~/NAMD_2.10_Linux-x86_64-TCP$ sudo ./charmrun namd2 ++verbose +idlepoll
+p8 p_run.conf >> p_run.log
[sudo] password for user1:
Charmrun> charmrun started...
Charmrun> using /home/user1/.nodelist as nodesfile
Charmrun> remote shell (192.168.1.10:0) started
Charmrun> remote shell (192.168.1.10:1) started
Charmrun> remote shell (192.168.1.10:2) started
Charmrun> remote shell (192.168.1.10:3) started
Charmrun> remote shell (192.168.1.10:4) started
Charmrun> remote shell (192.168.1.10:5) started
Charmrun> remote shell (192.168.1.10:6) started
Charmrun> remote shell (192.168.1.10:7) started
Charmrun> node programs all started
root_at_192.168.1.10's password: root_at_192.168.1.10's password:
root_at_192.168.1.10's password: root_at_192.168.1.10's password:
root_at_192.168.1.10's password: root_at_192.168.1.10's password:
root_at_192.168.1.10's password:root_at_192.168.1.10's password:
Permission denied, please try again.
root_at_192.168.1.10's password:

****** Error using Linux-x86_64-TCP using Version 2.11

~/NAMD_2.11_Linux-x86_64-TCP$ sudo ./charmrun namd2 ++verbose +idlepoll
+p8 p_run.conf >> p_run.log
Charmrun> charmrun started...
Charmrun> using /home/user1/.nodelist as nodesfile
Charmrun> remote shell (192.168.1.10:0) started
Charmrun> node programs all started
Permission denied (publickey,password).
Charmrun> Error 255 returned from remote shell (192.168.1.10:0)
Charmrun> Reconnection attempt 1 of 3
Charmrun> remote shell (192.168.1.10:0) started
Permission denied (publickey,password).
Charmrun> Error 255 returned from remote shell (192.168.1.10:0)
Charmrun> Reconnection attempt 2 of 3
Charmrun> remote shell (192.168.1.10:0) started
Permission denied (publickey,password).
Charmrun> Error 255 returned from remote shell (192.168.1.10:0)
Charmrun> Reconnection attempt 3 of 3
Charmrun> remote shell (192.168.1.10:0) started
Permission denied (publickey,password).
Charmrun> Error 255 returned from remote shell (192.168.1.10:0)
Charmrun> Too many reconnection attempts; bailing out

Thanks,
Marisol

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