+1 on what Ralph is saying. You need to talk to your local administrators and ask them why Torque is killing your job. Perhaps you're submitting to a queue that only allows jobs to run for a few seconds, or something like that.
On Mar 27, 2011, at 3:08 PM, Ralph Castain wrote: > It means that Torque is unhappy with your job - either you are running longer > than it permits, or you exceeded some other system limit. > > Talk to your sys admin about imposed limits. Usually, there are flags you can > provide to your job submission that allow you to change limits for your > program. > > > On Mar 27, 2011, at 12:59 PM, Jack Bryan wrote: > >> Hi, I have figured out how to run the command. >> >> OMPI_RANKFILE=$HOME/$PBS_JOBID.ranks >> >> mpirun -np 200 -rf $OMPI_RANKFILE --mca btl self,sm,openib >> -output-filename 700g200i200p14ye ./myapplication >> >> Each process print out to a distinct file. >> >> But, the program is terminated by the error : >> --------------------------------------------------------------------------------------------------------------------- >> =>> PBS: job killed: node 18 (n314) requested job terminate, 'EOF' (code >> 1099) - received SISTER_EOF attempting to communicate with sister MOM's >> mpirun: Forwarding signal 10 to job >> mpirun: killing job... >> >> -------------------------------------------------------------------------- >> 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. >> -------------------------------------------------------------------------- >> n341 >> n338 >> n337 >> n336 >> n335 >> n334 >> n333 >> n332 >> n331 >> n329 >> n328 >> n326 >> n324 >> n321 >> n318 >> n316 >> n315 >> n314 >> n313 >> n312 >> n309 >> n308 >> n306 >> n305 >> >> -------------------------------------------------------------------- >> >> After searching, I find that the error is probably related to the highly >> frequent I/O activities. >> >> I have also run valgrind to do mem check in order to find the possible >> reason for the original >> signal 9 (SIGKILL) problem. >> >> mpirun -np 200 -rf $OMPI_RANKFILE --mca btl self,sm,openib >> /usr/bin/valgrind --tool=memcheck --error-limit=no --leak-check=yes >> --log-file=nsga2b_g700_pop200_p200_valg_cystorm_mpi.log ./myapplication >> >> But, I got the similar error as the above. >> >> What does the error mean ? >> I cannot change the file system of the cluster. >> >> I only want to find a way to find the bug, which only appears in the case >> that the problem size is very large. >> >> But, I am stucked by the SIGKILL and then the above MOM_SISTER issues now. >> >> Any help is really appreciated. >> >> thanks >> >> Jack >> >> -------------------------------------------------------------------------------------------------------- >> From: r...@open-mpi.org >> Date: Sat, 26 Mar 2011 20:47:19 -0600 >> To: us...@open-mpi.org >> Subject: Re: [OMPI users] OMPI error terminate w/o reasons >> >> That command line cannot possibly work. Both the -rf and --output-filename >> options require arguments. >> >> PLEASE read the documentation? mpirun -h, or "man mpirun" will tell you how >> to correctly use these options. >> >> >> On Mar 26, 2011, at 6:35 PM, Jack Bryan wrote: >> >> Hi, I used : >> >> mpirun -np 200 -rf --output-filename /mypath/myapplication >> But, no files are printed out. >> >> Can "--debug" option help me hear ? >> >> When I tried : >> >> -bash-3.2$ mpirun -debug >> -------------------------------------------------------------------------- >> A suitable debugger could not be found in your PATH. Check the values >> specified in the orte_base_user_debugger MCA parameter for the list of >> debuggers that was searched. >> -------------------------------------------------------------------------- >> Any help is really appreciated. >> >> thanks >> >> From: r...@open-mpi.org >> Date: Sat, 26 Mar 2011 15:45:39 -0600 >> To: us...@open-mpi.org >> Subject: Re: [OMPI users] OMPI error terminate w/o reasons >> >> If you use that mpirun option, mpirun will place the output from each rank >> into a -separate- file for you. Give it: >> >> mpirun --output-filename /myhome/debug/run01 >> >> and in /myhome/debug, you will find files: >> >> run01.0 >> run01.1 >> ... >> >> each with the output from the indicated rank. >> >> >> >> On Mar 26, 2011, at 3:41 PM, Jack Bryan wrote: >> >> The cluster can print out all output into one file. >> >> But, checking them for bugs is very hard. >> >> The cluster also print out possible error messages into one file. >> >> But, sometimes the error file is empty , sometimes it is signal 9. >> >> If I only run dummy tasks on worker nodes, no errors. >> >> If I run real task, sometimes processes are terminated w/o any errors before >> the program normally exit. >> Sometimes, the program get signal 9 but no other error messages. >> >> It is weird. >> >> Any help is really appreciated. >> >> Jack >> From: r...@open-mpi.org >> Date: Sat, 26 Mar 2011 15:18:53 -0600 >> To: us...@open-mpi.org >> Subject: Re: [OMPI users] OMPI error terminate w/o reasons >> >> I don't know, but Ashley may be able to help - or you can see his web site >> for instructions. >> >> Alternatively, since you can put print statements into your code, have you >> considered using mpirun's option to direct output from each rank into its >> own file? Look at "mpirun -h" for the options. >> >> -output-filename|--output-filename <arg0> >> Redirect output from application processes into >> filename.rank >> >> >> On Mar 26, 2011, at 2:48 PM, Jack Bryan wrote: >> >> Is it possible to enable padb to print out the stack trace and other program >> execute information into a file ? >> >> I can run the program in gdb as this: >> >> mpirun -np 200 -e gdb ./myapplication >> >> How to make gdb print out the debug information to a file ? >> So that I can check it when the program is terminated. >> >> thanks >> >> Jack >> >> From: r...@open-mpi.org >> Date: Sat, 26 Mar 2011 13:56:13 -0600 >> To: us...@open-mpi.org >> Subject: Re: [OMPI users] OMPI error terminate w/o reasons >> >> You don't need to install anything on a system folder - you can just install >> it in your home directory, assuming that is accessible on the remote nodes. >> >> As for the script - unless you can somehow modify it to allow you to run >> under a debugger, I am afraid you are completely out of luck. >> >> >> On Mar 26, 2011, at 12:54 PM, Jack Bryan wrote: >> >> Hi, >> >> I am working on a cluster, where I am not allowed to install software on >> system folder. >> >> My Open MPI is 1.3.4. >> >> I have a very quick of the padb on http://padb.pittman.org.uk/ . >> >> Does it require some software install on the cluster in order to use it ? >> >> I cannot use command-line to run job on the lcuster , but only script. >> >> thanks >> >> From: r...@open-mpi.org >> Date: Sat, 26 Mar 2011 12:12:11 -0600 >> To: us...@open-mpi.org >> Subject: Re: [OMPI users] OMPI error terminate w/o reasons >> >> Have you tried a parallel debugger such as padb? >> >> On Mar 26, 2011, at 10:34 AM, Jack Bryan wrote: >> >> Hi, >> >> I have tried this. But, the printout from 200 parallel processes make it >> very hard to locate the possible bug. >> >> They may not stop at the same point when the program got signal 9. >> >> So, even though I can figure out the print out statements from all >> 200 processes, so many different locations where the processes >> are stopped make it harder to find out some hints about the bug. >> >> Are there some other programming tricks, which can help me >> narrow down to the doubt points ASAP. >> Any help is appreciated. >> >> Jack >> >> From: r...@open-mpi.org >> Date: Sat, 26 Mar 2011 07:53:40 -0600 >> To: us...@open-mpi.org >> Subject: Re: [OMPI users] OMPI error terminate w/o reasons >> >> Try adding some print statements so you can see where the error occurs. >> >> On Mar 25, 2011, at 11:49 PM, Jack Bryan wrote: >> >> Hi , All: >> >> I running a Open MPI (1.3.4) program by 200 parallel processes. >> >> But, the program is terminated with >> >> -------------------------------------------------------------------------- >> mpirun noticed that process rank 0 with PID 77967 on node n342 exited on >> signal 9 (Killed). >> -------------------------------------------------------------------------- >> >> After searching, the signal 9 means: >> >> the process is currently in an unworkable state and should be terminated >> with extreme prejudice >> >> If a process does not respond to any other termination signals, sending it >> a SIGKILL signal will almost always cause it to go away. >> >> The system will generate SIGKILL for a process itself under some unusual >> conditions where the program cannot possibly continue to run (even to run a >> signal handler). >> >> But, the error message does not indicate any possible reasons for the >> termination. >> >> There is a FOR loop in the main() program, if the loop number is small (< >> 200), the program works well, >> but if it becomes lager and larger, the program will got SIGKILL. >> >> The cluster where I am running the MPI program does not allow running debug >> tools. >> >> If I run it on a workstation, it will take a very very long time (for > 200 >> loops) in order to >> get the error occur again. >> >> What can I do to find the possible bugs ? >> >> Any help is really appreciated. >> >> thanks >> >> Jack >> >> >> >> >> >> _______________________________________________ >> 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 >> _______________________________________________ >> 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 >> _______________________________________________ >> 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 >> _______________________________________________ >> 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 -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
