Hi Gus, Thank you for your reply, comments, and suggestions.
EC2 does have support, but it is with extra charge and I am discouraged to use it for budgetary reasons. Also, I have heard that their support is a bit toward virtualization and amazon environment specific. I may have to override all these and ask them for a help... (Incidentally, I really like openmpi mailing list. The atmosphere you people generate and sustain is quite wonderful and I hope one day I can be a contributing member.) As to your suggestions: 1) This is a good idea. I will do hostname via mpirun. Increasing complexity from the simplest will probably reveal something I don't know. 2) I have run R serially on EC2 with this very ami. I have not seen any problem and many others have done the same. Also, here is an idea I came up in my sleep that I want to check out. The ami I have been using is a centos 5.5, which I have built from ground up. EC2 has something called Amazon Linux ami. I don't know what distribution that is and I am sure it doesn't have R, nor openmpi. But I thought I would load these components I need to the Amazon Linux (again as you suggest by starting the simplest case) and see if I can reproduce the behavior I have been experiencing on different (and Amazon "official" ami). I will report as I discover interesting/relevant finding. Regards, 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. >>>>>>>>>>>> >>>>>>>>>>>> Here¹s 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. >>>>>>>>>>>> >>>>>>>>>>>> Here¹s 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 >>>>>>>>>>>> >>>>>>>>>>>> Here¹s 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 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 >>>>>>>>>>>> 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
