ARIA - FAQ

 

We will update this FAQ regularly, when new postings to our mailing list show up. If anyone wants to add a paragraph, please email us. Thanks.

 

1. How to set up ARIA on several machines in parallel using ssh:

If you want to use ARIA on multiple machines, the easiest way is to use ssh
to connect and run the job on another machine.
In run.cns you can use the queue command:
"ssh other_computer nice csh" (with or without nice) instead of just "csh"

However, you have to prevent the shell from asking you the password every
time you log in. Here comes a short tutorial how to set up ssh accordingly.


how to ssh from A to B without providing a password
----------------------------------------------------

in 3 steps

*) generate a identity file on A
**) copy it over to B
***) add this file to the list of authorized login

let's do it:

*) on A:
you just need to <press return> after all questions asked (3 times)

- using ssh version 1

[tru@betty ~]$ ssh-keygen
Generating public/private rsa1 key pair.
Enter file in which to save the key (/home/tru/.ssh/identity): <press
return>
Enter passphrase (empty for no passphrase): <press
return>
Enter same passphrase again: <press
return>
Your identification has been saved in /home/tru/.ssh/identity.
Your public key has been saved in /home/tru/.ssh/identity.pub.

- using ssh2 (default on our machines redhat 7.1)
There are two crypt algorithms RSA and DSA, do it for both!
I think one is enough, just is case....

[tru@betty ~]$ ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/home/tru/.ssh/id_rsa): <press
return>
Created directory '/home/tru/.ssh'.
Enter passphrase (empty for no passphrase): <press
return>
Enter same passphrase again: <press
return>
Your identification has been saved in /home/tru/.ssh/id_rsa.
Your public key has been saved in /home/tru/.ssh/id_rsa.pub.
[tru@betty ~]$ ssh-keygen -t dsa
Generating public/private dsa key pair.
Enter file in which to save the key (/home/tru/.ssh/id_dsa): <press
return>
Enter passphrase (empty for no passphrase): <press
return>
Enter same passphrase again: <press
return>
Your identification has been saved in /home/tru/.ssh/id_dsa.
Your public key has been saved in /home/tru/.ssh/id_dsa.pub.

[tru@betty ~/.ssh]$ ls -l
total 24
-rw------- 1 tru Genopole 668 Sep 26 18:37 id_dsa
-rw-r--r-- 1 tru Genopole 614 Sep 26 18:37 id_dsa.pub
-rw------- 1 tru Genopole 539 Sep 26 18:41 identity
-rw-r--r-- 1 tru Genopole 343 Sep 26 18:41 identity.pub
-rw------- 1 tru Genopole 883 Sep 26 18:36 id_rsa
-rw-r--r-- 1 tru Genopole 234 Sep 26 18:36 id_rsa.pub

**) on A copying to B the required files
since you $HOME is nfs mounted you can use cp otherwise use scp
to transfer the *.pub files (ATTN don't overwrite existing ones)

cp id_dsa.pub id_dsa.pub-Bis
cp identity.pub identity.pub-Bis
cp id_rsa.pub id_rsa.pub-Bis

***) on B "authorize" login from A
since you $HOME is nfs mounted you can skip the ssh step :)

ssh to B
cd $HOME/.ssh (you might need to create it )

[on machine B]
[tru@betty ~/.ssh]$ cat identity.pub-Bis >> authorized_keys
[tru@betty ~/.ssh]$ cat id_rsa.pub-Bis id_dsa.pub-Bis >>
authorized_keys2

That is it!
you can now ssh FROM A to B without password
In our case (shared nfs mounted $HOME) this means that you can freely
ssh from/to any workstation.

 

2. Numerical problems using Torsion Angle Dynamics:

"When trying using TAD in aria, I get errors messages that prevent cns from finishing its jobs. These errors appear totally randomly, i.e. they can happen on any structure generated between it0 and it8. What happens is that sometimes cns is not able to find coordinates to work with. The errors are as follow:

%ATMCHK-ERR: unknown coordinates for atom " -14 -LEU -CA "
....
and the .out file keeps growing non-stop with the error
ERROR: matrix is not a rotation matrix
"

Both errors indicate that there is simply a numeric problem during the dynamics in CNS, usually do to the dynamics time step being too long. if everything is fine in cartesian dynamics, you can reduce the "tadfactor" in run.cns.

 

 


contact: Jens Linge, Michael Nilges