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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: 2011-02-11 21:54:42


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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