Hi Ashley,
> If you do this I would appreciate the chance to proof-read it before you go
> public...
Absolutely! I am a firm believer in two-heads-are-better-than-
one concept.
Regards,
Tena
On 2/18/11 1:29 AM, "Ashley Pittman" wrote:
>
> On 18 Feb 2011, at 09:09,
line.
>
> So, from the computer/instance-A side orted gives the first kick,
> but somehow the ball never comes back from computer/instance-B.
> It's ping- without -pong.
> The same frustrating feeling I had when I was a kid and kicked the
> soccer ball on the neighbor's s
mini "how-to openMPI on cloud".
Regards,
Tena
On 2/17/11 6:52 AM, "Jeff Squyres" wrote:
> On Feb 16, 2011, at 6:17 PM, Tena Sakai wrote:
>
>> For now, may I point out something I noticed out of the
>> DEBUG3 Output last night?
>>
>>
e ssh authenticity test, I added
UserKnownHostsFile /dev/null
StrictHostKeyChecking no
to /etc/ssh/ssh_config
Hope one of these helps.
bw
On 2/17/11 6:11 PM, Tena Sakai wrote:
Re: [OMPI users] How are IP addresses determined? Hi Barnet,
> If I understand you correctly, t
; tool for assistance.
--
10.96.197.154 - daemon did not report back when launched
[tsakai@ip-10-110-10-137 .ssh]$
[tsakai@ip-10-110-10-137 .ssh]$ # I can't figure out what more to do
[tsakai@ip-10-110-
rnal uri might be a problem.
If you try this (or anything else), I'd appreciate it if you'd post your
results.
bw
On 2/17/11 4:08 AM, Tena Sakai wrote:
Re: [OMPI users] How are IP addresses determined? Hi Barnet,
Allow me to interject.
Are you saying that you run m
Hi Barnet,
Allow me to interject.
Are you saying that you run master on your local machine and launching openMPI
process on EC2? You are saying that 1) tcp port tcp://192.168.1.101:35272 is
on your local system and 2) the ec2 instance is trying to connect your local
machine’s port 35272 , and
e I parse that line.
>
> So, from the computer/instance-A side orted gives the first kick,
> but somehow the ball never comes back from computer/instance-B.
> It's ping- without -pong.
> The same frustrating feeling I had when I was a kid and kicked the
> soccer ball on the neig
sh
> takes a look at the debug3 session log that you included.
>
> I can't see if/where/why ssh is failing for you in EC2.
>
> See other answers inline, please.
>
> Tena Sakai wrote:
>> Hi Gus,
>>
>> Thank you again for your reply.
>>
>>> A sl
n ssh
> takes a look at the debug3 session log that you included.
>
> I can't see if/where/why ssh is failing for you in EC2.
>
> See other answers inline, please.
>
> Tena Sakai wrote:
>> Hi Gus,
>>
>> Thank you again for your reply.
>>
>>&g
entions a few environmental
varialbles. SSH_ASKPASS, SSH_AUTH_SOCK, SSH_CONNECTION, etc. Do
any of these matter as far as openMPI is concerned?
Thank you, Gus.
Regards,
Tena
On 2/15/11 5:09 PM, "Gus Correa" wrote:
> Tena Sakai wrote:
>> Hi,
>>
>> I am trying to rep
Hi,
I am trying to reproduce what I was able to show last Friday on Amazon
EC2 instances, but I am having a problem. What I was able to show last
Friday as root was with this command:
mpirun –app app.ac
with app.ac being:
-H dns-entry-A –np 1 (linux command)
-H dns-entry-A –np 1 (linux comm
Hi Gus,
Please read my comments inline.
On 2/14/11 7:05 PM, "Gus Correa" wrote:
> Hi Tena
>
> Answers inline.
>
> Tena Sakai wrote:
>> Hi Gus,
>>
>>> Hence, I don't understand why the lack of symmetry in the
>>> firewall protectio
ves several tips for that.
> That is probably a more promising path,
> which you may want to try.
I have a feeling that I will be in need of more help
from her.
Regards,
Tena
On 2/14/11 3:46 PM, "Gus Correa" wrote:
> Tena Sakai wrote:
>> Hi Kevin,
>>
>
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" wrote:
> Hi Tena
>
> Answers inline.
> This is getting
Thank you, Jeff. That's good to know, but for now
I am going to stick to -app option. For this old
dog can't learn new tricks so fast.
Regards,
Tena
On 2/14/11 6:18 AM, "Jeff Squyres" wrote:
> On Feb 13, 2011, at 10:54 PM, Tena Sakai wrote:
>
>> I have
/config file. I will
update the ami, relaunch and will report back.
Regards,
Tena
On 2/14/11 6:16 AM, "Jeff Squyres" wrote:
> On Feb 13, 2011, at 2:37 PM, Tena Sakai wrote:
>
>> Also, here is an idea I came up in my sleep that I want to check
>> out. The ami I h
Many thanks to you.
Also, thanks to Reuti who raised this possibility in the
first place.
Regards,
Tena
On 2/14/11 1:37 PM, "Ashley Pittman" wrote:
>
> On 14 Feb 2011, at 21:10, Tena Sakai wrote:
>> Regarding firewall, they are different:
>
>>
>> I don
Hi Kevin,
Thanks for your reply.
Dasher is physically located under my desk and vixen is in a
cecure data center.
> does dasher have any network interfaces that vixen does not?
No, I don't think so.
Here is more definitive info:
[tsakai@dasher Rmpi]$ ifconfig
eth0 Link encap:Ethernet
annot run mpirun with the app file:
-H dasher.egcrc.org -np 1 hostname
-H dasher.egcrc.org -np 1 hostname
-H vixen.egcrc.org -np 1 hostname
-H vixen.egcrc.org -np 1 hostname
Many thanks.
Tena
On 2/14/11 11:15 AM, "Gus Correa" wrote:
> Tena Sakai wrote:
>> Hi Reut
i" wrote:
> Hi,
>
> Am 14.02.2011 um 04:54 schrieb Tena Sakai:
>
>> I have digressed and started downward descent...
>>
>> I was trying to make a simple and clear case. Everything
>> I write in this very mail is about local machines. There
>> is no virtua
our own or no password. su is a command to allow you to run commands
> as another user using their password. What sudo su is doing is running a
> command as root which is then running a shell as root, "sudo -s" is a much
> better way of achieving the same effect.
>
> Ashle
ho 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 C
Thank you, Ashley, for your comments.
I do have a question.
I was using 'sudo su' to document the problem I am running
into for people who read this mailing list, as well as for
my own record. Why would you say I shouldn't be doing so?
Regards,
Tena
On 2/13/11 1:29 PM, "Ashley Pittman" wrote
> 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,
>
is, or
> at least a contact point for someone who is already running in that
> environment.
>
> IIRC, there are some unique problems with running on that platform.
>
>
> On Feb 12, 2011, at 12:38 AM, Tena Sakai wrote:
>
>> Hi Gus,
>>
>> Thank you for all your sugge
age with the MPI failure/errors.
> Not sure if I understand which computers we're talking about,
> or where these computers are (at Amazon?),
> or if they change depending on each session you use to run your programs,
> if they are identical machines with the same limits or if they d
674
[tsakai@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" wrote:
> Hi
oot 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 perm
ught 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
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 Reu
mmand: 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" wrote:
> Hi,
>
> Am 10.02.2011 um 19:11 schrieb Tena Sakai:
&
7;re doing things
correctly. I'm almost sure you've done all of the following, but just to be
sure:
having the ssh public keys in other computer's authorized_key file.
ssh keys generated without passphrases
On Wed, Feb 9, 2011 at 10:08 PM, Tena Sakai wrote:
Hi,
I have made a bit
not an option.
Regards,
Tena
On 2/10/11 2:27 AM, "Reuti" 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-
you.
Tena Sakai
tsa...@gallo.ucsf.edu
On 2/9/11 7:52 PM, "Tena Sakai" 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
/
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
solve my science. (And I haven't forgotten to look
into Torque.)
Regards,
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/13/11 4:18 PM, "Gus Correa" wrote:
> Tena Sakai wrote:
>> Fantastic, Gus! Now I think I got framework pretty much done.
>> The rest is to work on
Fantastic, Gus! Now I think I got framework pretty much done.
The rest is to work on 'problem solving' end with R.
Many thanks for your insight and kindness. I really appreciate it.
Regards,
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/13/11 2:40 PM, "Gus Correa" wrote:
>
Thank you, Hicham. I will check out bash man page.
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/13/11 12:38 PM, "Hicham Mouline" wrote:
> I have some old memory of this where the .bashrc file and the .profile are
> distinguishing login and non-login.
> Also something to do
ow I can do what I describe?
Thank you.
Tena Sakai
tsa...@gallo.ucsf.edu
Thank you, Jeff.
I just commented the stty line out and it doesn't seem to have
any ill effect with interactive shells. I guess my
stty erase ^\?
was superfluous to begin with. I have hard time remembering
which rc file invokes/chains what other rc file.
Regards,
Tena Saka
Thank you, Gus. I am encouraged. I will look into Torque
in a day or two or three.
Regards,
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/12/11 6:49 PM, "Gus Correa" wrote:
> Tena Sakai wrote:
>> Hi,
>>
>> I can execute the command below:
>>$ mpirun -H vix
Thank you, David. That did it!
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/12/11 6:40 PM, "David Zhang" wrote:
I think you just make a hostfile with
vixen
compute-0-0
...
and load the file in the first -H before the colon.
On Wed, Jan 12, 2011 at 6:23 PM, Tena Sakai wrote:
Hi,
I c
hat I can use to do mpi resource
control, but I don't know enough about mpi and don't want to bite more
than I can chew. What I want to do at the moment is to get to know openMpi
to the best I can.
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/12/11 6:30 PM, "Gus Correa" wrote:
> Tena
correct in concluding that –H and —hostfile cannot be issued in the
same mpirun command which contains a colon (:)? Or is there any trick
or work-around to have both –H and —hostfile?
Thank you.
Tena Sakai
tsa...@gallo.ucsf.edu
Thank you, Gus.
I agree with what you say about location of OpenMPI software.
Indeed, /usr/local is nfs-mounted to all cluster nodes, albeit
a bit unfortunate name "local." If/when I have a chance to
Set up machines, I will make local really local to each node.
Regards,
Tena
Thank you, Gus.
I grep'ed "stty" in all . in my home directory and found
that I had a line
stty erase ^\?
in .bashrc. When I commented out the line, the error message
"stty: standard input: Invalid argument" went away.
I appreciate your tip.
Tena Sakai
tsa...@gall
directory /usr/local/lib/openmpi was generated
(with many
files in it). Given that, do I set D_LIBRARY_PATH to /usr/local/lib or do I set
it to /usr/local/lib/openmpi?
Thank you.
Tena Sakai
tsa...@gallo.ucsf.edu
nk you.
Tena Sakai
tsa...@gallo.ucsf.edu
ots=4
Is the first field (dummyX) machine/node name? What is the definition
of slots? (Max number of processes to spawn?)
Am I missing a different man page? Can you please shed some light?
Thank you.
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/10/11 11:38 PM, "Siegmar Gross"
wrote:
&
me?
Thank you in advance.
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/10/11 8:14 PM, "pooja varshneya" wrote:
You can use mpirun.
On Mon, Jan 10, 2011 at 8:04 PM, Tena Sakai wrote:
Hi,
I am an mpi newbie. My open MPI is v 1.4.3, which I compiled
on a linux machine.
I am using a langu
but I had notion that open MPI
is to have functionalities of all. Is this a wrong impression?
Thank you for your help.
Tena Sakai
tsa...@gallo.ucsf.edu
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