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.
Here’s 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.
Here’s 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
Here’s 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 don’t have.
I end up typing control-C.
Here’s 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
