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 virtual machines involved. I am talking about two > machines, vixen and dasher, which share the same file > structure. Vixen is a nfs server and dasher is an nfs > client. I have just installed openmpi 1.4.3 on dasher, > which is the same version I have on vixen. > > I have a file app.ac3, which looks like: > [tsakai@vixen Rmpi]$ cat app.ac3 > -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 > [tsakai@vixen Rmpi]$ > > Vixen can run this without any problem: > [tsakai@vixen Rmpi]$ mpirun -app app.ac3 > vixen.egcrc.org > vixen.egcrc.org > dasher.egcrc.org > dasher.egcrc.org > [tsakai@vixen Rmpi]$ > > But I can't run this very command from dasher: > [tsakai@vixen Rmpi]$ > [tsakai@vixen Rmpi]$ ssh dasher > Last login: Sun Feb 13 19:26:57 2011 from vixen.egcrc.org > [tsakai@dasher ~]$ > [tsakai@dasher ~]$ cd Notes/R/parallel/Rmpi/ > [tsakai@dasher Rmpi]$ > [tsakai@dasher Rmpi]$ mpirun -app app.ac3 > mpirun: killing job... a) can you ssh from dasher to vixen? b) firewall on vixen? -- Reuti > -------------------------------------------------------------------------- > 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. > -------------------------------------------------------------------------- > vixen.egcrc.org - daemon did not report back when launched > [tsakai@dasher Rmpi]$ > > After I issue the mpirun command, it hangs and I had to Cntrol-C out > of it at which point it generated all lines " mpirun: killing job..." > and below. > > A strange thing is that dahser has no problem executing the same > thing via ssh: > [tsakai@dasher Rmpi]$ ssh vixen.egcrc.org hostname > vixen.egcrc.org > [tsakai@dasher Rmpi]$ > > In fact, dasher can run it via mpirun so long as no foreign machine > is present in the app file. Ie., > [tsakai@dasher Rmpi]$ cat app.ac4 > -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 > [tsakai@dasher Rmpi]$ > [tsakai@dasher Rmpi]$ mpirun -app app.ac4 > dasher.egcrc.org > dasher.egcrc.org > [tsakai@dasher Rmpi]$ > > Can you please tell me why I can go one way (from vixen to dasher) > and not the other way (dasher to vixen)? > > Thank you. > > Tena > > > On 2/12/11 9:42 PM, "Gustavo Correa" <g...@ldeo.columbia.edu> 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@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@ip-10-114-239-188 ~]$ >>> [tsakai@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@ip-10-114-239-188 ~]$ >>> [tsakai@ip-10-114-239-188 ~]$ ulimit -a > tsakai_ulimit-a >>> [tsakai@ip-10-114-239-188 ~]$ >>> [tsakai@ip-10-114-239-188 ~]$ diff root_ulimit-a tsakai_ulimit-a >>> 14c14 >>> < max user processes (-u) unlimited >>> --- >>>> max user processes (-u) 61504 >>> [tsakai@ip-10-114-239-188 ~]$ >>> [tsakai@ip-10-114-239-188 ~]$ cat /proc/sys/fs/file-nr >>> /proc/sys/fs/file-max >>> 480 0 762674 >>> 762674 >>> [tsakai@ip-10-114-239-188 ~]$ >>> [tsakai@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@ip-10-114-239-188 ~]$ >>> [tsakai@ip-10-114-239-188 ~]$ >>> [tsakai@ip-10-114-239-188 ~]$ sysctl -a |grep fs.file-max >>> -bash: sysctl: command not found >>> [tsakai@ip-10-114-239-188 ~]$ >>> [tsakai@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@ip-10-114-239-188 ~]$ >>> [tsakai@ip-10-114-239-188 ~]$ sudo /sbin/sysctl -a | grep fs.file-max >>> fs.file-max = 762674 >>> [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" <g...@ldeo.columbia.edu> 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)" <jsquy...@cisco.com> 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" <g...@ldeo.columbia.edu> >>>>>> 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@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@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@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@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@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@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@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@ip-10-100-243-195 ~]$ >>>>>>>> [tsakai@ip-10-100-243-195 ~]$ # I am on machine B >>>>>>>> [tsakai@ip-10-100-243-195 ~]$ hostname >>>>>>>> ip-10-100-243-195 >>>>>>>> [tsakai@ip-10-100-243-195 ~]$ >>>>>>>> [tsakai@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@ip-10-100-243-195 ~]$ >>>>>>>> [tsakai@ip-10-100-243-195 ~]$ >>>>>>>> [tsakai@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@ip-10-100-243-195 ~]$ >>>>>>>> [tsakai@ip-10-100-243-195 ~]$ # go back to machine A >>>>>>>> [tsakai@ip-10-100-243-195 ~]$ >>>>>>>> [tsakai@ip-10-100-243-195 ~]$ exit >>>>>>>> logout >>>>>>>> Connection to ip-10-100-243-195.ec2.internal closed. >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ hostname >>>>>>>> ip-10-195-198-31 >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ # Execute mpirun >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@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@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ # try it as root >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@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@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ # try it one more time as tsakai >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@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@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ # I don't get it. >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ >>>>>>>> [tsakai@ip-10-195-198-31 ~]$ exit >>>>>>>> logout >>>>>>>> [tsakai@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" <tsa...@gallo.ucsf.edu> 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@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@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@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ env | grep LD_LIB >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ # Let's set LD_LIBRARY_PATH to >>>>>>>>> /usr/local/lib >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ export LD_LIBRARY_PATH='/usr/local/lib' >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ # I better to this on machine B as well >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@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@ip-10-195-171-159 ~]$ >>>>>>>>> [tsakai@ip-10-195-171-159 ~]$ export LD_LIBRARY_PATH='/usr/local/lib' >>>>>>>>> [tsakai@ip-10-195-171-159 ~]$ >>>>>>>>> [tsakai@ip-10-195-171-159 ~]$ env | grep LD_LIB >>>>>>>>> LD_LIBRARY_PATH=/usr/local/lib >>>>>>>>> [tsakai@ip-10-195-171-159 ~]$ >>>>>>>>> [tsakai@ip-10-195-171-159 ~]$ # OK, now go bak to machine A >>>>>>>>> [tsakai@ip-10-195-171-159 ~]$ exit >>>>>>>>> logout >>>>>>>>> Connection to ip-10-195-171-159 closed. >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ hostname >>>>>>>>> ip-10-203-21-132 >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ # try mpirun again >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@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@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ # I thought openmpi library was in >>>>>>>>> /usr/local/lib... >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@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@ip-10-203-21-132 ~]$ >>>>>>>>> [tsakai@ip-10-203-21-132 ~]$ # Now, I am really confused... >>>>>>>>> [tsakai@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" <jsquy...@cisco.com> 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" <re...@staff.uni-marburg.de> 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" <re...@staff.uni-marburg.de> 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@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 >>>>>>>>>>>>> tsa...@gallo.ucsf.edu >>>>>>>>>>>>> >>>>>>>>>>>>> On 2/9/11 7:52 PM, "Tena Sakai" <tsa...@gallo.ucsf.edu> 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 >>>>>>>>>>>>> /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R 6 >>>>>>>>>>>>> -H blitzen.egcrc.org -np 1 Rscript >>>>>>>>>>>>> /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R 7 >>>>>>>>>>>>> -H blitzen.egcrc.org -np 1 Rscript >>>>>>>>>>>>> /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R 8 >>>>>>>>>>>>> >>>>>>>>>>>>> The program I run is >>>>>>>>>>>>> Rscript /Users/tsakai/Notes/R/parallel/Rmpi/local/fib.R x >>>>>>>>>>>>> Where x is [5..8]. The machines vixen and blitzen each run 2 >>>>>>>>>>>>> runs. >>>>>>>>>>>>> >>>>>>>>>>>>> Here’s the program fib.R: >>>>>>>>>>>>> [ tsakai@vixen local]$ cat fib.R >>>>>>>>>>>>> # fib() computes, given index n, fibonacci number iteratively >>>>>>>>>>>>> # here's the first dozen sequence (indexed from 0..11) >>>>>>>>>>>>> # 1, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89 >>>>>>>>>>>>> >>>>>>>>>>>>> fib <- function( n ) { >>>>>>>>>>>>> a <- 0 >>>>>>>>>>>>> b <- 1 >>>>>>>>>>>>> for ( i in 1:n ) { >>>>>>>>>>>>> t <- b >>>>>>>>>>>>> b <- a >>>>>>>>>>>>> a <- a + t >>>>>>>>>>>>> } >>>>>>>>>>>>> a >>>>>>>>>>>>> >>>>>>>>>>>>> arg <- commandArgs( TRUE ) >>>>>>>>>>>>> myHost <- system( 'hostname', intern=TRUE ) >>>>>>>>>>>>> cat( fib(arg), myHost, '\n' ) >>>>>>>>>>>>> >>>>>>>>>>>>> It reads an argument from command line and produces a fibonacci >>>>>>>>>>>>> number >>>>>>>>>>>>> that >>>>>>>>>>>>> corresponds to that index, followed by the machine name. Pretty >>>>>>>>>>>>> simple >>>>>>>>>>>>> stuff. >>>>>>>>>>>>> >>>>>>>>>>>>> Here’s the run output: >>>>>>>>>>>>> [tsakai@vixen local]$ mpirun -app app.ac1 >>>>>>>>>>>>> 5 vixen.egcrc.org >>>>>>>>>>>>> 8 vixen.egcrc.org >>>>>>>>>>>>> 13 blitzen.egcrc.org >>>>>>>>>>>>> 21 blitzen.egcrc.org >>>>>>>>>>>>> >>>>>>>>>>>>> Which is exactly what I expect. So far so good. >>>>>>>>>>>>> >>>>>>>>>>>>> Now I want to run the same thing on cloud. I launch 2 instances >>>>>>>>>>>>> of >>>>>>>>>>>>> the >>>>>>>>>>>>> same >>>>>>>>>>>>> virtual machine, to which I get to by: >>>>>>>>>>>>> [tsakai@vixen local]$ ssh –A I ~/.ssh/tsakai >>>>>>>>>>>>> machine-instance-A-public-dns >>>>>>>>>>>>> >>>>>>>>>>>>> Now I am on machine A: >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ # and I can go to machine B >>>>>>>>>>>>> without >>>>>>>>>>>>> password authentication, >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ # i.e., use public/private key >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ hostname >>>>>>>>>>>>> domU-12-31-39-00-D1-F2 >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ ssh -i .ssh/tsakai >>>>>>>>>>>>> domU-12-31-39-0C-C8-01 >>>>>>>>>>>>> Last login: Wed Feb 9 20:51:48 2011 from 10.254.214.4 >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ # I am now on machine B >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ hostname >>>>>>>>>>>>> domU-12-31-39-0C-C8-01 >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ # now show I can get to machine >>>>>>>>>>>>> A >>>>>>>>>>>>> without using password >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ ssh -i .ssh/tsakai >>>>>>>>>>>>> domU-12-31-39-00-D1-F2 >>>>>>>>>>>>> The authenticity of host 'domu-12-31-39-00-d1-f2 (10.254.214.4)' >>>>>>>>>>>>> can't >>>>>>>>>>>>> be established. >>>>>>>>>>>>> RSA key fingerprint is >>>>>>>>>>>>> e3:ad:75:b1:a4:63:7f:0f:c4:0b:10:71:f3:2f:21:81. >>>>>>>>>>>>> Are you sure you want to continue connecting (yes/no)? yes >>>>>>>>>>>>> Warning: Permanently added 'domu-12-31-39-00-d1-f2' (RSA) to the >>>>>>>>>>>>> list >>>>>>>>>>>>> of >>>>>>>>>>>>> known hosts. >>>>>>>>>>>>> Last login: Wed Feb 9 20:49:34 2011 from 10.215.203.239 >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ hostname >>>>>>>>>>>>> domU-12-31-39-00-D1-F2 >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ exit >>>>>>>>>>>>> logout >>>>>>>>>>>>> Connection to domU-12-31-39-00-D1-F2 closed. >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-0C-C8-01 ~]$ exit >>>>>>>>>>>>> logout >>>>>>>>>>>>> Connection to domU-12-31-39-0C-C8-01 closed. >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ # back at machine A >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ hostname >>>>>>>>>>>>> domU-12-31-39-00-D1-F2 >>>>>>>>>>>>> >>>>>>>>>>>>> As you can see, neither machine uses password for authentication; >>>>>>>>>>>>> it >>>>>>>>>>>>> uses >>>>>>>>>>>>> public/private key pairs. There is no problem (that I can see) >>>>>>>>>>>>> for >>>>>>>>>>>>> ssh >>>>>>>>>>>>> invocation >>>>>>>>>>>>> from one machine to the other. This is so because I have a copy >>>>>>>>>>>>> of >>>>>>>>>>>>> public >>>>>>>>>>>>> key >>>>>>>>>>>>> and a copy of private key on each instance. >>>>>>>>>>>>> >>>>>>>>>>>>> The app.ac file is identical, except the node names: >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ cat app.ac1 >>>>>>>>>>>>> -H domU-12-31-39-00-D1-F2 -np 1 Rscript /home/tsakai/fib.R 5 >>>>>>>>>>>>> -H domU-12-31-39-00-D1-F2 -np 1 Rscript /home/tsakai/fib.R 6 >>>>>>>>>>>>> -H domU-12-31-39-0C-C8-01 -np 1 Rscript /home/tsakai/fib.R 7 >>>>>>>>>>>>> -H domU-12-31-39-0C-C8-01 -np 1 Rscript /home/tsakai/fib.R 8 >>>>>>>>>>>>> >>>>>>>>>>>>> Here’s what happens with mpirun: >>>>>>>>>>>>> >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ mpirun -app app.ac1 >>>>>>>>>>>>> tsakai@domu-12-31-39-0c-c8-01's password: >>>>>>>>>>>>> Permission denied, please try again. >>>>>>>>>>>>> tsakai@domu-12-31-39-0c-c8-01's password: mpirun: killing job... >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> -----------------------------------------------------------------------> >>>>>>>>>> >>>>>>>>>> >>>>>>>> - >>>>>>>>>>>>> -- >>>>>>>>>>>>> mpirun noticed that the job aborted, but has no info as to the >>>>>>>>>>>>> process >>>>>>>>>>>>> that caused that situation. >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> -----------------------------------------------------------------------> >>>>>>>>>> >>>>>>>>>> >>>>>>>> - >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> mpirun: clean termination accomplished >>>>>>>>>>>>> >>>>>>>>>>>>> [tsakai@domU-12-31-39-00-D1-F2 ~]$ >>>>>>>>>>>>> >>>>>>>>>>>>> Mpirun (or somebody else?) asks me password, which I don’t have. >>>>>>>>>>>>> I end up typing control-C. >>>>>>>>>>>>> >>>>>>>>>>>>> Here’s my question: >>>>>>>>>>>>> How can I get past authentication by mpirun where there is no >>>>>>>>>>>>> password? >>>>>>>>>>>>> >>>>>>>>>>>>> I would appreciate your help/insight greatly. >>>>>>>>>>>>> >>>>>>>>>>>>> Thank you. >>>>>>>>>>>>> >>>>>>>>>>>>> Tena Sakai >>>>>>>>>>>>> tsa...@gallo.ucsf.edu >>>> _______________________________________________ >>>> users mailing list >>>> us...@open-mpi.org >>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
