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
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
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:
&
nk you.
Tena Sakai
tsa...@gallo.ucsf.edu
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
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
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
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
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
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
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, 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
ow I can do what I describe?
Thank you.
Tena Sakai
tsa...@gallo.ucsf.edu
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
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:
>
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
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
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
/
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-
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
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:
&
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
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
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
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
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
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
> 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,
>
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
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
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
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
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
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
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
/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
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
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
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,
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
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
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
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
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
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
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
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
; 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-
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
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?
>>
>>
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
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,
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