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Subject: Re: [OMPI users] How does authentication between nodes work without password? (Newbie alert on)
From: Tena Sakai (tsakai_at_[hidden])
Date: 2011-02-14 18:45:47


Hi Gus,

Thank you very much for your help and reply.

I agree with each and every point you make. I look forward to
the day I can write 'little How To.'

Regards,

Tena

On 2/14/11 1:47 PM, "Gus Correa" <gus_at_[hidden]> wrote:

> Hi Tena
>
> Answers inline.
> This is getting big!
>
> Tena Sakai wrote:
>> Hi Gus,
>>
>> Thank you for your reply, comments, and suggestions.
>>
>> EC2 does have support, but it is with extra charge and I am
>> discouraged to use it for budgetary reasons. Also, I have
>> heard that their support is a bit toward virtualization
>> and amazon environment specific. I may have to override
>> all these and ask them for a help...
>>
>
> Ask them at least for super-saving free shipping.
> I do this all the time.
> The downside is that delivery takes 4-9 business days at least ... :)
>
>> (Incidentally, I really like openmpi mailing list. The
>> atmosphere you people generate and sustain is quite wonderful
>
> +1 4 that!
>
> The best friendly+knowledgeable+helpful combination amongst
> all 10+ mailing lists I subscribe to.
> Kudos to Jeff, Ralph, and the other developers for keeping it this way.
>
>> and I hope one day
>> I can be a contributing member.)
>>
>
> How about your bringing the world of MPI and cloud computing
> into the list with your ongoing postings?
> I think it is a sound contribution.
> When you get it to work, maybe you can write up a little 'HowTo'. :)
>
>> As to your suggestions:
>> 1) This is a good idea. I will do hostname via mpirun. Increasing
>> complexity from the simplest will probably reveal something I
>> don't know.
>> 2) I have run R serially on EC2 with this very ami. I have not seen
>> any problem and many others have done the same.
>>
>> Also, here is an idea I came up in my sleep that I want to check
>> out.
>
> I hope Amazon EC2 is not making nightmares out of your dreams.
>
>> The ami I have been using is a centos 5.5, which I have built
>> from ground up. EC2 has something called Amazon Linux ami. I
>> don't know what distribution that is and I am sure it doesn't have
>> R, nor openmpi. But I thought I would load these components I
>> need to the Amazon Linux (again as you suggest by starting the
>> simplest case) and see if I can reproduce the behavior I have
>> been experiencing on different (and Amazon "official" ami).
>>
>
> That would be a possible way to go, but given my EC2-blindness,
> I can all but wonder if it has chances to work.
> I have yet to understand whether you copy your compiled tools
> (OpenMPI, R, etc) from your local machines to EC2,
> or if you build/compile them directly on the EC2 environment.
> Also, it's not clear to me if the OS in EC2 is an image
> from your local machines' OS/Linux distro, or independent of them,
> or if you can choose to have it either way.
>
> On another posting, Ashley Pittman reported to
> be using OpenMPI in Amazon EC2 without problems,
> suggests pathway and gives several tips for that.
> That is probably a more promising path,
> which you may want to try.
>
>> I will report as I discover interesting/relevant finding.
>>
>> Regards,
>>
>> Tena
>>
>
> Best,
> Gus Correa
>
>>
>> On 2/12/11 9:42 PM, "Gustavo Correa" <gus_at_[hidden]> wrote:
>>
>>> Hi Tena
>>>
>>> Thank you for taking the time to explain the details of
>>> the EC2 procedure.
>>>
>>> I am afraid everything in my bag of tricks was used.
>>> As Ralph and Jeff suggested, this seems to be a very specific
>>> problem with EC2.
>>>
>>> The difference in behavior when you run as root vs. when you
>>> run as Tena, tells that there is some use restriction to regular users
>>> in EC2 that isn't present in common machines (Linux or other), I guess.
>>> This may be yet another 'stone to turn', as you like to say.
>>> It also suggests that there is nothing wrong in principle with your
>>> openMPI setup or with your program, otherwise root would not be able to run
>>> it.
>>>
>>> Besides Ralph suggestion of trying the EC2 mailing list archive,
>>> I wonder if EC2 has any type of user support where you could ask
>>> for help.
>>> After all, it is a paid sevice, isn't it?
>>> (OpenMPI is not paid and has a great customer service, doesn't it? :) )
>>> You have a well documented case to present,
>>> and the very peculiar fact that the program fails for normal users but runs
>>> for root.
>>> This should help the EC2 support to start looking for a solution.
>>>
>>> I am running out of suggestions of what you could try on your own.
>>> But let me try:
>>>
>>> 1) You may try to reduce the problem to its less common denominator,
>>> perhaps by trying to run non-R based MPI programs on EC2, maybe the
>>> hello_c.c,
>>> ring_c.c, and connectivity_c.c programs in the OpenMPi examples directory.
>>> This would be to avoid the extra layer of complexity introduced by R.
>>> Even simpler would be to run 'hostname' with mpiexec (mpiexec -np 2
>>> hostname).
>>> I.e. go in a progression of increasing complexity, see where you hit the
>>> wall.
>>> This may shed some light on what is going on.
>>>
>>> I don't know if this suggestion may really help, though.
>>> It is not clear to me where the thing fails, whether it is during program
>>> execution,
>>> or while mpiexec is setting up the environment for the program to run.
>>> If it is very early in the process, before the program starts, my suggestion
>>> won't work.
>>> Jeff and Ralph, who know OpenMPI inside out, may have better advice in this
>>> regard.
>>>
>>> 2) Another thing would be to try to run R on E2C in serial mode, without
>>> mpiexec,
>>> interactively or via script, to see who EC2 doesn't like: R or OpenMPI (but
>>> maybe it's both).
>>>
>>> Gus Correa
>>>
>>> On Feb 11, 2011, at 9:54 PM, Tena Sakai wrote:
>>>
>>>> Hi Gus,
>>>>
>>>> Thank you for your tips.
>>>>
>>>> I didn't find any smoking gun or anything comes close.
>>>> Here's the upshot:
>>>>
>>>> [tsakai_at_ip-10-114-239-188 ~]$ ulimit -a
>>>> core file size (blocks, -c) 0
>>>> data seg size (kbytes, -d) unlimited
>>>> scheduling priority (-e) 0
>>>> file size (blocks, -f) unlimited
>>>> pending signals (-i) 61504
>>>> max locked memory (kbytes, -l) 32
>>>> max memory size (kbytes, -m) unlimited
>>>> open files (-n) 1024
>>>> pipe size (512 bytes, -p) 8
>>>> POSIX message queues (bytes, -q) 819200
>>>> real-time priority (-r) 0
>>>> stack size (kbytes, -s) 8192
>>>> cpu time (seconds, -t) unlimited
>>>> max user processes (-u) 61504
>>>> virtual memory (kbytes, -v) unlimited
>>>> file locks (-x) unlimited
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$ sudo su
>>>> bash-3.2#
>>>> bash-3.2# ulimit -a
>>>> core file size (blocks, -c) 0
>>>> data seg size (kbytes, -d) unlimited
>>>> scheduling priority (-e) 0
>>>> file size (blocks, -f) unlimited
>>>> pending signals (-i) 61504
>>>> max locked memory (kbytes, -l) 32
>>>> max memory size (kbytes, -m) unlimited
>>>> open files (-n) 1024
>>>> pipe size (512 bytes, -p) 8
>>>> POSIX message queues (bytes, -q) 819200
>>>> real-time priority (-r) 0
>>>> stack size (kbytes, -s) 8192
>>>> cpu time (seconds, -t) unlimited
>>>> max user processes (-u) unlimited
>>>> virtual memory (kbytes, -v) unlimited
>>>> file locks (-x) unlimited
>>>> bash-3.2#
>>>> bash-3.2#
>>>> bash-3.2# ulimit -a > root_ulimit-a
>>>> bash-3.2# exit
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$ ulimit -a > tsakai_ulimit-a
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$ diff root_ulimit-a tsakai_ulimit-a
>>>> 14c14
>>>> < max user processes (-u) unlimited
>>>> ---
>>>>> max user processes (-u) 61504
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$ cat /proc/sys/fs/file-nr
>>>> /proc/sys/fs/file-max
>>>> 480 0 762674
>>>> 762674
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$ sudo su
>>>> bash-3.2#
>>>> bash-3.2# cat /proc/sys/fs/file-nr /proc/sys/fs/file-max
>>>> 512 0 762674
>>>> 762674
>>>> bash-3.2# exit
>>>> exit
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$ sysctl -a |grep fs.file-max
>>>> -bash: sysctl: command not found
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$ /sbin/!!
>>>> /sbin/sysctl -a |grep fs.file-max
>>>> error: permission denied on key 'kernel.cad_pid'
>>>> error: permission denied on key 'kernel.cap-bound'
>>>> fs.file-max = 762674
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>> [tsakai_at_ip-10-114-239-188 ~]$ sudo /sbin/sysctl -a | grep fs.file-max
>>>> fs.file-max = 762674
>>>> [tsakai_at_ip-10-114-239-188 ~]$
>>>>
>>>> I see a bit of difference between root and tsakai, but I cannot
>>>> believe such small difference results in somewhat a catastrophic
>>>> failure as I have reported. Would you agree with me?
>>>>
>>>> Regards,
>>>>
>>>> Tena
>>>>
>>>> On 2/11/11 6:06 PM, "Gus Correa" <gus_at_[hidden]> wrote:
>>>>
>>>>> Hi Tena
>>>>>
>>>>> Please read one answer inline.
>>>>>
>>>>> Tena Sakai wrote:
>>>>>> Hi Jeff,
>>>>>> Hi Gus,
>>>>>>
>>>>>> Thanks for your replies.
>>>>>>
>>>>>> I have pretty much ruled out PATH issues by setting tsakai's PATH
>>>>>> as identical to that of root. In that setting I reproduced the
>>>>>> same result as before: root can run mpirun correctly and tsakai
>>>>>> cannot.
>>>>>>
>>>>>> I have also checked out permission on /tmp directory. tsakai has
>>>>>> no problem creating files under /tmp.
>>>>>>
>>>>>> I am trying to come up with a strategy to show that each and every
>>>>>> programs in the PATH has "world" executable permission. It is a
>>>>>> stone to turn over, but I am not holding my breath.
>>>>>>
>>>>>>> ... you are running out of file descriptors. Are file descriptors
>>>>>>> limited on a per-process basis, perchance?
>>>>>> I have never heard there is such restriction on Amazon EC2. There
>>>>>> are folks who keep running instances for a long, long time. Whereas
>>>>>> in my case, I launch 2 instances, check things out, and then turn
>>>>>> the instances off. (Given that the state of California has a huge
>>>>>> debts, our funding is very tight.) So, I really doubt that's the
>>>>>> case. I have run mpirun unsuccessfully as user tsakai and immediately
>>>>>> after successfully as root. Still, I would be happy if you can tell
>>>>>> me a way to tell number of file descriptors used or remmain.
>>>>>>
>>>>>> Your mentioned file descriptors made me think of something under
>>>>>> /dev. But I don't know exactly what I am fishing. Do you have
>>>>>> some suggestions?
>>>>>>
>>>>> 1) If the environment has anything to do with Linux,
>>>>> check:
>>>>>
>>>>> cat /proc/sys/fs/file-nr /proc/sys/fs/file-max
>>>>>
>>>>>
>>>>> or
>>>>>
>>>>> sysctl -a |grep fs.file-max
>>>>>
>>>>> This max can be set (fs.file-max=whatever_is_reasonable)
>>>>> in /etc/sysctl.conf
>>>>>
>>>>> See 'man sysctl' and 'man sysctl.conf'
>>>>>
>>>>> 2) Another possible source of limits.
>>>>>
>>>>> Check "ulimit -a" (bash) or "limit" (tcsh).
>>>>>
>>>>> If you need to change look at:
>>>>>
>>>>> /etc/security/limits.conf
>>>>>
>>>>> (See also 'man limits.conf')
>>>>>
>>>>> **
>>>>>
>>>>> Since "root can but Tena cannot",
>>>>> I would check 2) first,
>>>>> as they are the 'per user/per group' limits,
>>>>> whereas 1) is kernel/system-wise.
>>>>>
>>>>> I hope this helps,
>>>>> Gus Correa
>>>>>
>>>>> PS - I know you are a wise and careful programmer,
>>>>> but here we had cases of programs that would
>>>>> fail because of too many files that were open and never closed,
>>>>> eventually exceeding the max available/permissible.
>>>>> So, it does happen.
>>>>>
>>>>>> I wish I could reproduce this (weired) behavior on a different
>>>>>> set of machines. I certainly cannot in my local environment. Sigh!
>>>>>>
>>>>>> Regards,
>>>>>>
>>>>>> Tena
>>>>>>
>>>>>>
>>>>>> On 2/11/11 3:17 PM, "Jeff Squyres (jsquyres)" <jsquyres_at_[hidden]> wrote:
>>>>>>
>>>>>>> It is concerning if the pipe system call fails - I can't think of why
>>>>>>> that
>>>>>>> would happen. Thats not usually a permissions issue but rather a deeper
>>>>>>> indication that something is either seriously wrong on your system or
>>>>>>> you
>>>>>>> are
>>>>>>> running out of file descriptors. Are file descriptors limited on a
>>>>>>> per-process
>>>>>>> basis, perchance?
>>>>>>>
>>>>>>> Sent from my PDA. No type good.
>>>>>>>
>>>>>>> On Feb 11, 2011, at 10:08 AM, "Gus Correa" <gus_at_[hidden]>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Tena
>>>>>>>>
>>>>>>>> Since root can but you can't,
>>>>>>>> is is a directory permission problem perhaps?
>>>>>>>> Check the execution directory permission (on both machines,
>>>>>>>> if this is not NFS mounted dir).
>>>>>>>> I am not sure, but IIRR OpenMPI also uses /tmp for
>>>>>>>> under-the-hood stuff, worth checking permissions there also.
>>>>>>>> Just a naive guess.
>>>>>>>>
>>>>>>>> Congrats for all the progress with the cloudy MPI!
>>>>>>>>
>>>>>>>> Gus Correa
>>>>>>>>
>>>>>>>> Tena Sakai wrote:
>>>>>>>>> Hi,
>>>>>>>>> I have made a bit more progress. I think I can say ssh authenti-
>>>>>>>>> cation problem is behind me now. I am still having a problem running
>>>>>>>>> mpirun, but the latest discovery, which I can reproduce, is that
>>>>>>>>> I can run mpirun as root. Here's the session log:
>>>>>>>>> [tsakai_at_vixen ec2]$ 2ec2 ec2-184-73-104-242.compute-1.amazonaws.com
>>>>>>>>> Last login: Fri Feb 11 00:41:11 2011 from 10.100.243.195
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ ll
>>>>>>>>> total 8
>>>>>>>>> -rw-rw-r-- 1 tsakai tsakai 274 Feb 11 00:47 app.ac
>>>>>>>>> -rwxr-xr-x 1 tsakai tsakai 379 Feb 11 00:48 fib.R
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ ll .ssh
>>>>>>>>> total 16
>>>>>>>>> -rw------- 1 tsakai tsakai 232 Feb 5 23:19 authorized_keys
>>>>>>>>> -rw------- 1 tsakai tsakai 102 Feb 11 00:34 config
>>>>>>>>> -rw-r--r-- 1 tsakai tsakai 1302 Feb 11 00:36 known_hosts
>>>>>>>>> -rw------- 1 tsakai tsakai 887 Feb 8 22:03 tsakai
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ ssh ip-10-100-243-195.ec2.internal
>>>>>>>>> Last login: Fri Feb 11 00:36:20 2011 from 10.195.198.31
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$ # I am on machine B
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$ hostname
>>>>>>>>> ip-10-100-243-195
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$ ll
>>>>>>>>> total 8
>>>>>>>>> -rw-rw-r-- 1 tsakai tsakai 274 Feb 11 00:44 app.ac
>>>>>>>>> -rwxr-xr-x 1 tsakai tsakai 379 Feb 11 00:47 fib.R
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$ cat app.ac
>>>>>>>>> -H ip-10-195-198-31.ec2.internal -np 1 Rscript /home/tsakai/fib.R 5
>>>>>>>>> -H ip-10-195-198-31.ec2.internal -np 1 Rscript /home/tsakai/fib.R 6
>>>>>>>>> -H ip-10-100-243-195.ec2.internal -np 1 Rscript /home/tsakai/fib.R 7
>>>>>>>>> -H ip-10-100-243-195.ec2.internal -np 1 Rscript /home/tsakai/fib.R 8
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$ # go back to machine A
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$
>>>>>>>>> [tsakai_at_ip-10-100-243-195 ~]$ exit
>>>>>>>>> logout
>>>>>>>>> Connection to ip-10-100-243-195.ec2.internal closed.
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ hostname
>>>>>>>>> ip-10-195-198-31
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ # Execute mpirun
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ mpirun -app app.ac
>>>>>>>>>
>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>> --
>>>>>>>>> --
>>>>>>>>> mpirun was unable to launch the specified application as it
>>>>>>>>> encountered
>>>>>>>>> an
>>>>>>>>> error:
>>>>>>>>> Error: pipe function call failed when setting up I/O forwarding
>>>>>>>>> subsystem
>>>>>>>>> Node: ip-10-195-198-31
>>>>>>>>> while attempting to start process rank 0.
>>>>>>>>>
>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>> --
>>>>>>>>> --
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ # try it as root
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ sudo su
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# pwd
>>>>>>>>> /home/tsakai
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# ls -l /root/.ssh/config
>>>>>>>>> -rw------- 1 root root 103 Feb 11 00:56 /root/.ssh/config
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# cat /root/.ssh/config
>>>>>>>>> Host *
>>>>>>>>> IdentityFile /root/.ssh/.derobee/.kagi
>>>>>>>>> IdentitiesOnly yes
>>>>>>>>> BatchMode yes
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# pwd
>>>>>>>>> /home/tsakai
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# ls -l
>>>>>>>>> total 8
>>>>>>>>> -rw-rw-r-- 1 tsakai tsakai 274 Feb 11 00:47 app.ac
>>>>>>>>> -rwxr-xr-x 1 tsakai tsakai 379 Feb 11 00:48 fib.R
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# # now is the time for mpirun
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# mpirun --app ./app.ac
>>>>>>>>> 13 ip-10-100-243-195
>>>>>>>>> 21 ip-10-100-243-195
>>>>>>>>> 5 ip-10-195-198-31
>>>>>>>>> 8 ip-10-195-198-31
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# # It works (being root)!
>>>>>>>>> bash-3.2#
>>>>>>>>> bash-3.2# exit
>>>>>>>>> exit
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ # try it one more time as tsakai
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ mpirun --app app.ac
>>>>>>>>>
>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>> --
>>>>>>>>> --
>>>>>>>>> mpirun was unable to launch the specified application as it
>>>>>>>>> encountered
>>>>>>>>> an
>>>>>>>>> error:
>>>>>>>>> Error: pipe function call failed when setting up I/O forwarding
>>>>>>>>> subsystem
>>>>>>>>> Node: ip-10-195-198-31
>>>>>>>>> while attempting to start process rank 0.
>>>>>>>>>
>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>> --
>>>>>>>>> --
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ # I don't get it.
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$
>>>>>>>>> [tsakai_at_ip-10-195-198-31 ~]$ exit
>>>>>>>>> logout
>>>>>>>>> [tsakai_at_vixen ec2]$
>>>>>>>>> So, why does it say "pipe function call failed when setting up
>>>>>>>>> I/O forwarding subsystem Node: ip-10-195-198-31" ?
>>>>>>>>> The node it is referring to is not the remote machine. It is
>>>>>>>>> What I call machine A. I first thought maybe this is a problem
>>>>>>>>> With PATH variable. But I don't think so. I compared root's
>>>>>>>>> Path to that of tsaki's and made them identical and retried.
>>>>>>>>> I got the same behavior.
>>>>>>>>> If you could enlighten me why this is happening, I would really
>>>>>>>>> Appreciate it.
>>>>>>>>> Thank you.
>>>>>>>>> Tena
>>>>>>>>> On 2/10/11 4:12 PM, "Tena Sakai" <tsakai_at_[hidden]> wrote:
>>>>>>>>>> Hi jeff,
>>>>>>>>>>
>>>>>>>>>> Thanks for the firewall tip. I tried it while allowing all tip
>>>>>>>>>> traffic
>>>>>>>>>> and got interesting and preplexing result. Here's what's interesting
>>>>>>>>>> (BTW, I got rid of "LogLevel DEBUG3" from ./ssh/config on this run):
>>>>>>>>>>
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ mpirun --app app.ac2
>>>>>>>>>> Host key verification failed.
>>>>>>>>>>
>>>>>>>>>>
>>>> ------------------------------------------------------------------------->>
>>>> >>
>>>> -
>>>>>>>>>> A daemon (pid 2743) died unexpectedly with status 255 while
>>>>>>>>>> attempting
>>>>>>>>>> to launch so we are aborting.
>>>>>>>>>>
>>>>>>>>>> There may be more information reported by the environment (see
>>>>>>>>>> above).
>>>>>>>>>>
>>>>>>>>>> This may be because the daemon was unable to find all the needed
>>>>>>>>>> shared
>>>>>>>>>> libraries on the remote node. You may set your LD_LIBRARY_PATH to
>>>>>>>>>> have
>>>>>>>>>> the
>>>>>>>>>> location of the shared libraries on the remote nodes and this will
>>>>>>>>>> automatically be forwarded to the remote nodes.
>>>>>>>>>>
>>>>>>>>>>
>>>> ------------------------------------------------------------------------->>
>>>> >>
>>>> -
>>>>>>>>>>
>>>> ------------------------------------------------------------------------->>
>>>> >>
>>>> -
>>>>>>>>>> mpirun noticed that the job aborted, but has no info as to the
>>>>>>>>>> process
>>>>>>>>>> that caused that situation.
>>>>>>>>>>
>>>>>>>>>>
>>>> ------------------------------------------------------------------------->>
>>>> >>
>>>> -
>>>>>>>>>> mpirun: clean termination accomplished
>>>>>>>>>>
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ env | grep LD_LIB
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ # Let's set LD_LIBRARY_PATH to
>>>>>>>>>> /usr/local/lib
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ export LD_LIBRARY_PATH='/usr/local/lib'
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ # I better to this on machine B as well
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ ssh -i tsakai ip-10-195-171-159
>>>>>>>>>> Warning: Identity file tsakai not accessible: No such file or
>>>>>>>>>> directory.
>>>>>>>>>> Last login: Thu Feb 10 18:31:20 2011 from 10.203.21.132
>>>>>>>>>> [tsakai_at_ip-10-195-171-159 ~]$
>>>>>>>>>> [tsakai_at_ip-10-195-171-159 ~]$ export
>>>>>>>>>> LD_LIBRARY_PATH='/usr/local/lib'
>>>>>>>>>> [tsakai_at_ip-10-195-171-159 ~]$
>>>>>>>>>> [tsakai_at_ip-10-195-171-159 ~]$ env | grep LD_LIB
>>>>>>>>>> LD_LIBRARY_PATH=/usr/local/lib
>>>>>>>>>> [tsakai_at_ip-10-195-171-159 ~]$
>>>>>>>>>> [tsakai_at_ip-10-195-171-159 ~]$ # OK, now go bak to machine A
>>>>>>>>>> [tsakai_at_ip-10-195-171-159 ~]$ exit
>>>>>>>>>> logout
>>>>>>>>>> Connection to ip-10-195-171-159 closed.
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ hostname
>>>>>>>>>> ip-10-203-21-132
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ # try mpirun again
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ mpirun --app app.ac2
>>>>>>>>>> Host key verification failed.
>>>>>>>>>>
>>>>>>>>>>
>>>> ------------------------------------------------------------------------->>
>>>> >>
>>>> -
>>>>>>>>>> A daemon (pid 2789) died unexpectedly with status 255 while
>>>>>>>>>> attempting
>>>>>>>>>> to launch so we are aborting.
>>>>>>>>>>
>>>>>>>>>> There may be more information reported by the environment (see
>>>>>>>>>> above).
>>>>>>>>>>
>>>>>>>>>> This may be because the daemon was unable to find all the needed
>>>>>>>>>> shared
>>>>>>>>>> libraries on the remote node. You may set your LD_LIBRARY_PATH to
>>>>>>>>>> have
>>>>>>>>>> the
>>>>>>>>>> location of the shared libraries on the remote nodes and this will
>>>>>>>>>> automatically be forwarded to the remote nodes.
>>>>>>>>>>
>>>>>>>>>>
>>>> ------------------------------------------------------------------------->>
>>>> >>
>>>> -
>>>>>>>>>>
>>>> ------------------------------------------------------------------------->>
>>>> >>
>>>> -
>>>>>>>>>> mpirun noticed that the job aborted, but has no info as to the
>>>>>>>>>> process
>>>>>>>>>> that caused that situation.
>>>>>>>>>>
>>>>>>>>>>
>>>> ------------------------------------------------------------------------->>
>>>> >>
>>>> -
>>>>>>>>>> mpirun: clean termination accomplished
>>>>>>>>>>
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ # I thought openmpi library was in
>>>>>>>>>> /usr/local/lib...
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ ll -t /usr/local/lib | less
>>>>>>>>>> total 16604
>>>>>>>>>> lrwxrwxrwx 1 root root 16 Feb 8 23:06 libfuse.so ->
>>>>>>>>>> libfuse.so.2.8.5
>>>>>>>>>> lrwxrwxrwx 1 root root 16 Feb 8 23:06 libfuse.so.2 ->
>>>>>>>>>> libfuse.so.2.8.5
>>>>>>>>>> lrwxrwxrwx 1 root root 25 Feb 8 23:06 libmca_common_sm.so ->
>>>>>>>>>> libmca_common_sm.so.1.0.0
>>>>>>>>>> lrwxrwxrwx 1 root root 25 Feb 8 23:06 libmca_common_sm.so.1 ->
>>>>>>>>>> libmca_common_sm.so.1.0.0
>>>>>>>>>> lrwxrwxrwx 1 root root 15 Feb 8 23:06 libmpi.so ->
>>>>>>>>>> libmpi.so.0.0.2
>>>>>>>>>> lrwxrwxrwx 1 root root 15 Feb 8 23:06 libmpi.so.0 ->
>>>>>>>>>> libmpi.so.0.0.2
>>>>>>>>>> lrwxrwxrwx 1 root root 19 Feb 8 23:06 libmpi_cxx.so ->
>>>>>>>>>> libmpi_cxx.so.0.0.1
>>>>>>>>>> lrwxrwxrwx 1 root root 19 Feb 8 23:06 libmpi_cxx.so.0 ->
>>>>>>>>>> libmpi_cxx.so.0.0.1
>>>>>>>>>> lrwxrwxrwx 1 root root 19 Feb 8 23:06 libmpi_f77.so ->
>>>>>>>>>> libmpi_f77.so.0.0.1
>>>>>>>>>> lrwxrwxrwx 1 root root 19 Feb 8 23:06 libmpi_f77.so.0 ->
>>>>>>>>>> libmpi_f77.so.0.0.1
>>>>>>>>>> lrwxrwxrwx 1 root root 19 Feb 8 23:06 libmpi_f90.so ->
>>>>>>>>>> libmpi_f90.so.0.0.1
>>>>>>>>>> lrwxrwxrwx 1 root root 19 Feb 8 23:06 libmpi_f90.so.0 ->
>>>>>>>>>> libmpi_f90.so.0.0.1
>>>>>>>>>> lrwxrwxrwx 1 root root 20 Feb 8 23:06 libopen-pal.so ->
>>>>>>>>>> libopen-pal.so.0.0.0
>>>>>>>>>> lrwxrwxrwx 1 root root 20 Feb 8 23:06 libopen-pal.so.0 ->
>>>>>>>>>> libopen-pal.so.0.0.0
>>>>>>>>>> lrwxrwxrwx 1 root root 20 Feb 8 23:06 libopen-rte.so ->
>>>>>>>>>> libopen-rte.so.0.0.0
>>>>>>>>>> lrwxrwxrwx 1 root root 20 Feb 8 23:06 libopen-rte.so.0 ->
>>>>>>>>>> libopen-rte.so.0.0.0
>>>>>>>>>> lrwxrwxrwx 1 root root 26 Feb 8 23:06 libopenmpi_malloc.so ->
>>>>>>>>>> libopenmpi_malloc.so.0.0.0
>>>>>>>>>> lrwxrwxrwx 1 root root 26 Feb 8 23:06 libopenmpi_malloc.so.0
>>>>>>>>>> ->
>>>>>>>>>> libopenmpi_malloc.so.0.0.0
>>>>>>>>>> lrwxrwxrwx 1 root root 20 Feb 8 23:06 libulockmgr.so ->
>>>>>>>>>> libulockmgr.so.1.0.1
>>>>>>>>>> lrwxrwxrwx 1 root root 20 Feb 8 23:06 libulockmgr.so.1 ->
>>>>>>>>>> libulockmgr.so.1.0.1
>>>>>>>>>> lrwxrwxrwx 1 root root 16 Feb 8 23:06 libxml2.so ->
>>>>>>>>>> libxml2.so.2.7.2
>>>>>>>>>> lrwxrwxrwx 1 root root 16 Feb 8 23:06 libxml2.so.2 ->
>>>>>>>>>> libxml2.so.2.7.2
>>>>>>>>>> -rw-r--r-- 1 root root 385912 Jan 26 01:00 libvt.a
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$ # Now, I am really confused...
>>>>>>>>>> [tsakai_at_ip-10-203-21-132 ~]$
>>>>>>>>>>
>>>>>>>>>> Do you know why it's complaining about shared libraries?
>>>>>>>>>>
>>>>>>>>>> Thank you.
>>>>>>>>>>
>>>>>>>>>> Tena
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 2/10/11 1:05 PM, "Jeff Squyres" <jsquyres_at_[hidden]> wrote:
>>>>>>>>>>
>>>>>>>>>>> Your prior mails were about ssh issues, but this one sounds like you
>>>>>>>>>>> might
>>>>>>>>>>> have firewall issues.
>>>>>>>>>>>
>>>>>>>>>>> That is, the "orted" command attempts to open a TCP socket back to
>>>>>>>>>>> mpirun
>>>>>>>>>>> for
>>>>>>>>>>> various command and control reasons. If it is blocked from doing so
>>>>>>>>>>> by
>>>>>>>>>>> a
>>>>>>>>>>> firewall, Open MPI won't run. In general, you can either disable
>>>>>>>>>>> your
>>>>>>>>>>> firewall or you can setup a trust relationship for TCP connections
>>>>>>>>>>> within
>>>>>>>>>>> your
>>>>>>>>>>> cluster.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Feb 10, 2011, at 1:03 PM, Tena Sakai wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Reuti,
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks for suggesting "LogLevel DEBUG3." I did so and complete
>>>>>>>>>>>> session is captured in the attached file.
>>>>>>>>>>>>
>>>>>>>>>>>> What I did is much similar to what I have done before: verify
>>>>>>>>>>>> that ssh works and then run mpirun command. In my a bit lengthy
>>>>>>>>>>>> session log, there are two responses from "LogLevel DEBUG3." First
>>>>>>>>>>>> from an scp invocation and then from mpirun invocation. They both
>>>>>>>>>>>> say
>>>>>>>>>>>> debug1: Authentication succeeded (publickey).
>>>>>>>>>>>>
>>>>>>>>>>>> From mpirun invocation, I see a line:
>>>>>>>>>>>> debug1: Sending command: orted --daemonize -mca ess env -mca
>>>>>>>>>>>> orte_ess_jobid 3344891904 -mca orte_ess_vpid 1 -mca
>>>>>>>>>>>> orte_ess_num_procs
>>>>>>>>>>>> 2 --hnp-uri "3344891904.0;tcp://10.194.95.239:54256"
>>>>>>>>>>>> The IP address at the end of the line is indeed that of machine B.
>>>>>>>>>>>> After that there was hanging and I controlled-C out of it, which
>>>>>>>>>>>> gave me more lines. But the lines after
>>>>>>>>>>>> debug1: Sending command: orted bla bla bla
>>>>>>>>>>>> doesn't look good to me. But, in truth, I have no idea what they
>>>>>>>>>>>> mean.
>>>>>>>>>>>>
>>>>>>>>>>>> If you could shed some light, I would appreciate it very much.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards,
>>>>>>>>>>>>
>>>>>>>>>>>> Tena
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 2/10/11 10:57 AM, "Reuti" <reuti_at_[hidden]> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> Am 10.02.2011 um 19:11 schrieb Tena Sakai:
>>>>>>>>>>>>
>>>>>>>>>>>> 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.
>>>>>>>>>>>> okay. Sometimes the protection of the home directory must be
>>>>>>>>>>>> adjusted
>>>>>>>>>>>> too,
>>>>>>>>>>>> but
>>>>>>>>>>>> as you can do it from the command line this shouldn't be an issue.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 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.
>>>>>>>>>>>> No. It's convenient inside a private cluster as it won't fill each
>>>>>>>>>>>> users'
>>>>>>>>>>>> known_hosts file and you don't need to create any ssh-keys. But
>>>>>>>>>>>> when
>>>>>>>>>>>> the
>>>>>>>>>>>> hostname changes every time it might also create new hostkeys. It
>>>>>>>>>>>> uses
>>>>>>>>>>>> hostkeys (private and public), this way it works for all users.
>>>>>>>>>>>> Just
>>>>>>>>>>>> for
>>>>>>>>>>>> reference:
>>>>>>>>>>>>
>>>>>>>>>>>> http://arc.liv.ac.uk/SGE/howto/hostbased-ssh.html
>>>>>>>>>>>>
>>>>>>>>>>>> You could look into it later.
>>>>>>>>>>>>
>>>>>>>>>>>> ==
>>>>>>>>>>>>
>>>>>>>>>>>> - Can you try to use a command when connecting from A to B? E.g.
>>>>>>>>>>>> ssh
>>>>>>>>>>>> `domU-12-31-39-06-74-E2 ls`. Is this working too?
>>>>>>>>>>>>
>>>>>>>>>>>> - What about putting:
>>>>>>>>>>>>
>>>>>>>>>>>> LogLevel DEBUG3
>>>>>>>>>>>>
>>>>>>>>>>>> In your ~/.ssh/config. Maybe we can see what he's trying to
>>>>>>>>>>>> negotiate
>>>>>>>>>>>> before
>>>>>>>>>>>> it fails in verbose mode.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> -- Reuti
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Regards,
>>>>>>>>>>>>
>>>>>>>>>>>> Tena
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 2/10/11 2:27 AM, "Reuti" <reuti_at_[hidden]> 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_at_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
>>>>>>>>>>>> tsakai_at_[hidden]
>>>>>>>>>>>>
>>>>>>>>>>>> On 2/9/11 7:52 PM, "Tena Sakai" <tsakai_at_[hidden]> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> Hi
>>>>>>>>>>>>
>>>>>>>>>>>> I have an app.ac1 file like below:
>>>>>>>>>>>> [tsakai_at_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_at_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_at_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_at_vixen local]$ ssh ­A I ~/.ssh/tsakai
>>>>>>>>>>>> machine-instance-A-public-dns
>>>>>>>>>>>>
>>>>>>>>>>>> Now I am on machine A:
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$ # and I can go to machine B
>>>>>>>>>>>> without
>>>>>>>>>>>> password authentication,
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$ # i.e., use public/private key
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$ hostname
>>>>>>>>>>>> domU-12-31-39-00-D1-F2
>>>>>>>>>>>> [tsakai_at_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_at_domU-12-31-39-0C-C8-01 ~]$
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-0C-C8-01 ~]$ # I am now on machine B
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-0C-C8-01 ~]$ hostname
>>>>>>>>>>>> domU-12-31-39-0C-C8-01
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-0C-C8-01 ~]$
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-0C-C8-01 ~]$ # now show I can get to machine
>>>>>>>>>>>> A
>>>>>>>>>>>> without using password
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-0C-C8-01 ~]$
>>>>>>>>>>>> [tsakai_at_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_at_domU-12-31-39-00-D1-F2 ~]$
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$ hostname
>>>>>>>>>>>> domU-12-31-39-00-D1-F2
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$ exit
>>>>>>>>>>>> logout
>>>>>>>>>>>> Connection to domU-12-31-39-00-D1-F2 closed.
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-0C-C8-01 ~]$
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-0C-C8-01 ~]$ exit
>>>>>>>>>>>> logout
>>>>>>>>>>>> Connection to domU-12-31-39-0C-C8-01 closed.
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$
>>>>>>>>>>>> [tsakai_at_domU-12-31-39-00-D1-F2 ~]$ # back at machine A
>>>>>>>>>>>> [tsakai_at_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_at_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_at_domU-12-31-39-00-D1-F2 ~]$ mpirun -app app.ac1
>>>>>>>>>>>> tsakai_at_domu-12-31-39-0c-c8-01's password:
>>>>>>>>>>>> Permission denied, please try again.
>>>>>>>>>>>> tsakai_at_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_at_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
>>>>>>>>>>>> tsakai_at_[hidden]
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