Hi Reuti,
> your local machine is Linux like, but the execution hosts
> are Macs? I saw the /Users/tsakai/... in your output.
No, my environment is entirely linux. The path to my home
directory on one host (blitzen) has been known as /Users/tsakai,
despite it is an nfs mount from vixen (which is known to
itself as /home/tsakai). For historical reasons, I have
chosen to give a symbolic link named /Users to vixen's /Home,
so that I can use consistent path for both vixen and blitzen.
> Is this a private cluster (or at least private interfaces)?
> It would also be an option to use hostbased authentication,
> which will avoid setting any known_hosts file or passphraseless
> ssh-keys for each user.
No, it is not a private cluster. It is Amazon EC2. When I
Ssh from my local machine (vixen) I use its public interface,
but to address from one amazon cluster node to the other I
use nodes' private dns names: domU-12-31-39-07-35-21 and
domU-12-31-39-06-74-E2. Both public and private dns names
change from a launch to another. I am using passphrasesless
ssh-keys for authentication in all cases, i.e., from vixen to
Amazon node A, from amazon node A to amazon node B, and from
Amazon node B back to A. (Please see my initail post. There
is a session dialogue for this.) They all work without authen-
tication dialogue, except a brief initial dialogue:
The authenticity of host 'domu-xx-xx-xx-xx-xx-x (10.xx.xx.xx)'
can't be established.
RSA key fingerprint is e3:ad:75:b1:a4:63:7f:0f:c4:0b:10:71:f3:2f:21:81.
Are you sure you want to continue connecting (yes/no)?
to which I say "yes."
But I am unclear with what you mean by "hostbased authentication"?
Doesn't that mean with password? If so, it is not an option.
Regards,
Tena
On 2/10/11 2:27 AM, "Reuti" <re...@staff.uni-marburg.de> wrote:
> Hi,
>
> your local machine is Linux like, but the execution hosts are Macs? I saw the
> /Users/tsakai/... in your output.
>
> a) executing a command on them is also working, e.g.: ssh
> domU-12-31-39-07-35-21 ls
>
> Am 10.02.2011 um 07:08 schrieb Tena Sakai:
>
>> Hi,
>>
>> I have made a bit of progress(?)...
>> I made a config file in my .ssh directory on the cloud. It looks like:
>> # machine A
>> Host domU-12-31-39-07-35-21.compute-1.internal
>
> This is just an abbreviation or nickname above. To use the specified settings,
> it's necessary to specify exactly this name. When the settings are the same
> anyway for all machines, you can use:
>
> Host *
> IdentityFile /home/tsakai/.ssh/tsakai
> IdentitiesOnly yes
> BatchMode yes
>
> instead.
>
> Is this a private cluster (or at least private interfaces)? It would also be
> an option to use hostbased authentication, which will avoid setting any
> known_hosts file or passphraseless ssh-keys for each user.
>
> -- Reuti
>
>
>> HostName domU-12-31-39-07-35-21
>> BatchMode yes
>> IdentityFile /home/tsakai/.ssh/tsakai
>> ChallengeResponseAuthentication no
>> IdentitiesOnly yes
>>
>> # machine B
>> Host domU-12-31-39-06-74-E2.compute-1.internal
>> HostName domU-12-31-39-06-74-E2
>> BatchMode yes
>> IdentityFile /home/tsakai/.ssh/tsakai
>> ChallengeResponseAuthentication no
>> IdentitiesOnly yes
>>
>> This file exists on both machine A and machine B.
>>
>> Now When I issue mpirun command as below:
>> [tsakai@domU-12-31-39-06-74-E2 ~]$ mpirun -app app.ac2
>>
>> It hungs. I control-C out of it and I get:
>> mpirun: killing job...
>>
>>
>> --------------------------------------------------------------------------
>> mpirun noticed that the job aborted, but has no info as to the process
>> that caused that situation.
>>
>> --------------------------------------------------------------------------
>>
>> --------------------------------------------------------------------------
>> mpirun was unable to cleanly terminate the daemons on the nodes shown
>> below. Additional manual cleanup may be required - please refer to
>> the "orte-clean" tool for assistance.
>>
>> --------------------------------------------------------------------------
>> domU-12-31-39-07-35-21.compute-1.internal - daemon did not report
>> back when launched
>>
>> Am I making progress?
>>
>> Does this mean I am past authentication and something else is the problem?
>> Does someone have an example .ssh/config file I can look at? There are so
>> many keyword-argument paris for this config file and I would like to look at
>> some very basic one that works.
>>
>> Thank you.
>>
>> Tena Sakai
>> tsa...@gallo.ucsf.edu
>>
>> On 2/9/11 7:52 PM, "Tena Sakai" <tsa...@gallo.ucsf.edu> wrote:
>>
>>> Hi
>>>
>>> I have an app.ac1 file like below:
>>> [tsakai@vixen local]$ cat app.ac1
>>> -H vixen.egcrc.org -np 1 Rscript
>>> /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R 5
>>> -H vixen.egcrc.org -np 1 Rscript
>>> /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R 6
>>> -H blitzen.egcrc.org -np 1 Rscript
>>> /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R 7
>>> -H blitzen.egcrc.org -np 1 Rscript
>>> /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R 8
>>>
>>> The program I run is
>>> Rscript /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R x
>>> Where x is [5..8]. The machines vixen and blitzen each run 2 runs.
>>>
>>> Here¹s the program fib.R:
>>> [ tsakai@vixen local]$ cat fib.R
>>> # fib() computes, given index n, fibonacci number iteratively
>>> # here's the first dozen sequence (indexed from 0..11)
>>> # 1, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89
>>>
>>> fib <- function( n ) {
>>> a <- 0
>>> b <- 1
>>> for ( i in 1:n ) {
>>> t <- b
>>> b <- a
>>> a <- a + t
>>> }
>>> a
>>>
>>> arg <- commandArgs( TRUE )
>>> myHost <- system( 'hostname', intern=TRUE )
>>> cat( fib(arg), myHost, '\n' )
>>>
>>> It reads an argument from command line and produces a fibonacci number that
>>> corresponds to that index, followed by the machine name. Pretty simple
>>> stuff.
>>>
>>> Here¹s the run output:
>>> [tsakai@vixen local]$ mpirun -app app.ac1
>>> 5 vixen.egcrc.org
>>> 8 vixen.egcrc.org
>>> 13 blitzen.egcrc.org
>>> 21 blitzen.egcrc.org
>>>
>>> Which is exactly what I expect. So far so good.
>>>
>>> Now I want to run the same thing on cloud. I launch 2 instances of the same
>>> virtual machine, to which I get to by:
>>> [tsakai@vixen local]$ ssh A I ~/.ssh/tsakai
>>> machine-instance-A-public-dns
>>>
>>> Now I am on machine A:
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ # and I can go to machine B without
>>> password authentication,
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ # i.e., use public/private key
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ hostname
>>> domU-12-31-39-00-D1-F2
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ ssh -i .ssh/tsakai
>>> domU-12-31-39-0C-C8-01
>>> Last login: Wed Feb 9 20:51:48 2011 from 10.254.214.4
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ # I am now on machine B
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ hostname
>>> domU-12-31-39-0C-C8-01
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ # now show I can get to machine A
>>> without using password
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ ssh -i .ssh/tsakai
>>> domU-12-31-39-00-D1-F2
>>> The authenticity of host 'domu-12-31-39-00-d1-f2 (10.254.214.4)' can't
>>> be established.
>>> RSA key fingerprint is e3:ad:75:b1:a4:63:7f:0f:c4:0b:10:71:f3:2f:21:81.
>>> Are you sure you want to continue connecting (yes/no)? yes
>>> Warning: Permanently added 'domu-12-31-39-00-d1-f2' (RSA) to the list of
>>> known hosts.
>>> Last login: Wed Feb 9 20:49:34 2011 from 10.215.203.239
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ hostname
>>> domU-12-31-39-00-D1-F2
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ exit
>>> logout
>>> Connection to domU-12-31-39-00-D1-F2 closed.
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$
>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ exit
>>> logout
>>> Connection to domU-12-31-39-0C-C8-01 closed.
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ # back at machine A
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ hostname
>>> domU-12-31-39-00-D1-F2
>>>
>>> As you can see, neither machine uses password for authentication; it uses
>>> public/private key pairs. There is no problem (that I can see) for ssh
>>> invocation
>>> from one machine to the other. This is so because I have a copy of public
>>> key
>>> and a copy of private key on each instance.
>>>
>>> The app.ac file is identical, except the node names:
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ cat app.ac1
>>> -H domU-12-31-39-00-D1-F2 -np 1 Rscript /home/tsakai/fib.R 5
>>> -H domU-12-31-39-00-D1-F2 -np 1 Rscript /home/tsakai/fib.R 6
>>> -H domU-12-31-39-0C-C8-01 -np 1 Rscript /home/tsakai/fib.R 7
>>> -H domU-12-31-39-0C-C8-01 -np 1 Rscript /home/tsakai/fib.R 8
>>>
>>> Here¹s what happens with mpirun:
>>>
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ mpirun -app app.ac1
>>> tsakai@domu-12-31-39-0c-c8-01's password:
>>> Permission denied, please try again.
>>> tsakai@domu-12-31-39-0c-c8-01's password: mpirun: killing job...
>>>
>>>
>>> --------------------------------------------------------------------------
>>> mpirun noticed that the job aborted, but has no info as to the process
>>> that caused that situation.
>>>
>>> --------------------------------------------------------------------------
>>>
>>> mpirun: clean termination accomplished
>>>
>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$
>>>
>>> Mpirun (or somebody else?) asks me password, which I don¹t have.
>>> I end up typing control-C.
>>>
>>> Here¹s my question:
>>> How can I get past authentication by mpirun where there is no password?
>>>
>>> I would appreciate your help/insight greatly.
>>>
>>> Thank you.
>>>
>>> Tena Sakai
>>> tsa...@gallo.ucsf.edu
>>>
>>>
>>>
>>>
>>>
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