On Apr 3, 2011, at 5:25 PM, Laurence Marks wrote: > Thanks. I will test this tomorrow. > > Many people run Wien2k with openmpi as you say, I only became aware of > the issue of Wien2k (and perhaps other codes) leaving orphaned > processes still running a few days ago. I also know someone who wants > to run Wien2k on a system where both rsh and ssh are banned.
Sorry to hear that policy - as I said, that is not the norm in the community. > Personally, as I don't want to be banned from the supercomputers I use > I want to find a adequate patch for myself --- and then try and > persuade the developers to adopt it. It will be interesting to see what they say. Using ssh to launch mpirun for this purpose seems a bad idea to me, and unnecessary given the use pattern you described. I don't think any of the MPIs out there would recommend that approach. Good luck! > > On Sun, Apr 3, 2011 at 6:13 PM, Ralph Castain <r...@open-mpi.org> wrote: >> >> On Apr 3, 2011, at 4:37 PM, Laurence Marks wrote: >> >>> On Sun, Apr 3, 2011 at 5:08 PM, Reuti <re...@staff.uni-marburg.de> wrote: >>>> Am 03.04.2011 um 23:59 schrieb David Singleton: >>>> >>>>> On 04/04/2011 12:56 AM, Ralph Castain wrote: >>>>>> >>>>>> What I still don't understand is why you are trying to do it this way. >>>>>> Why not just run >>>>>> >>>>>> time mpirun -v -x LD_LIBRARY_PATH -x PATH -np 2 -machinefile .machineN >>>>>> /home/lma712/src/Virgin_10.1/lapw1Q_mpi lapw1Q_1.def >>>>>> >>>>>> where machineN contains the names of the nodes where you want the MPI >>>>>> apps to execute? mpirun will only execute apps on those nodes, so this >>>>>> accomplishes the same thing as your script - only with a lot less pain. >>>>>> >>>>>> Your script would just contain a sequence of these commands, each with >>>>>> its number of procs and machinefile as required. >>>>>> >>>>> >>>>> Maybe I missed why this suggestion of forgetting about the ssh/pbsdsh >>>>> altogether >>>>> was not feasible? Just use mpirun (with its great tm support!) to >>>>> distribute >>>>> MPI jobs. >>>> >>>> Wien2k has a two stage startup, e.g. for 16 slots: >>>> >>>> a) start 4 times `ssh` in the background to go to some of the granted nodes >>>> b) use there on each node `mpirun` to start processes on the remaining >>>> nodes, 3 for each call >>>> >>>> Problems: >>>> >>>> 1) control `ssh` under Torque >>>> 2) provide a partially hostlist to `mpirun`, maybe by disabling the >>>> default tight integration >>>> >>>> -- Reuti >>>> >>> >>> 1) The mpi tasks can be started on only one node (Reuti, "setenv >>> MPI_REMOTE 0" in parallel_options which was introduced for other >>> reasons in 9.3 and later releases). That seems to be safe and maybe >>> the only viable method with OMPI as pbsdsh appears to be unable to >>> launch mpi tasks correctly (or needs some environmental variables that >>> I don't know about). >>> 2) This is already done (Reuti, this is .machine0, .machine1 etc. If >>> you need information about setting up the Wien2k file under qsub in >>> general, contact me offline or look for Machines2W on the mailing list >>> which may be part of the next release, I'm not sure and I don't make >>> those decisions). >>> >>> However, there is another layer that Ruedi did not mention for this >>> code which is that some processes also need to be remotely launched to >>> ensure that the correct scratch directories are used (i.e. local >>> storage which is faster rather than nfs or similar). Maybe pbsdsh can >>> be used for this, I am still testing and I am not sure. It may be >>> enough to create a script with all important environmental variables >>> exported (as they may not all be in .bashrc or .cshrc) although there >>> might be issues making this fully portable. Since there are > 1000 >>> licenses of Wien2k, it has to be able to cope with different OS's, and >>> not just OMPI. >>> >> >> Here is what I would do, based on my knowledge of OMPI's internals (and I >> wrote the launchers :-)): >> >> 1. do not use your script - you don't want all those PBS envars to confuse >> OMPI >> >> 2. mpirun -mca plm rsh -launch-agent pbsdsh -mca ras ^tm --machinefile m1.... >> >> This cmd line tells mpirun to use the "rsh/ssh" launcher, but to substitute >> "pbsdsh" for "ssh". It also tells it to ignore the PBS_NODEFILE and just use >> the machinefile for the nodes to be used for that job. >> >> I can't swear this will work as I have never verified that pbsdsh and ssh >> have the same syntax, but I -think- that was true. If so, then this might do >> what you are attempting. >> >> >> I know people have run Wien2k with OMPI before - but I have never heard of >> the problems you are reporting. >> >> >>>> >>>>> A simple example: >>>>> >>>>> vayu1:~/MPI > qsub -lncpus=24,vmem=24gb,walltime=10:00 -wd -I >>>>> qsub: waiting for job 574900.vu-pbs to start >>>>> qsub: job 574900.vu-pbs ready >>>>> >>>>> [dbs900@v250 ~/MPI]$ wc -l $PBS_NODEFILE >>>>> 24 >>>>> [dbs900@v250 ~/MPI]$ head -12 $PBS_NODEFILE > m1 >>>>> [dbs900@v250 ~/MPI]$ tail -12 $PBS_NODEFILE > m2 >>>>> [dbs900@v250 ~/MPI]$ mpirun --machinefile m1 ./a2a143 120000 30 & mpirun >>>>> --machinefile m2 ./pp143 >>>>> >>>>> >>>>> Check how the processes are distributed ... >>>>> >>>>> vayu1:~ > qps 574900.vu-pbs >>>>> Node 0: v250: >>>>> PID S RSS VSZ %MEM TIME %CPU COMMAND >>>>> 11420 S 2104 10396 0.0 00:00:00 0.0 -tcsh >>>>> 11421 S 620 10552 0.0 00:00:00 0.0 pbs_demux >>>>> 12471 S 2208 49324 0.0 00:00:00 0.9 /apps/openmpi/1.4.3/bin/mpirun >>>>> --machinefile m1 ./a2a143 120000 30 >>>>> 12472 S 2116 49312 0.0 00:00:00 0.0 /apps/openmpi/1.4.3/bin/mpirun >>>>> --machinefile m2 ./pp143 >>>>> 12535 R 270160 565668 1.0 00:00:02 82.4 ./a2a143 120000 30 >>>>> 12536 R 270032 565536 1.0 00:00:02 81.4 ./a2a143 120000 30 >>>>> 12537 R 270012 565528 1.0 00:00:02 87.3 ./a2a143 120000 30 >>>>> 12538 R 269992 565532 1.0 00:00:02 93.3 ./a2a143 120000 30 >>>>> 12539 R 269980 565516 1.0 00:00:02 81.4 ./a2a143 120000 30 >>>>> 12540 R 270008 565516 1.0 00:00:02 86.3 ./a2a143 120000 30 >>>>> 12541 R 270008 565516 1.0 00:00:02 96.3 ./a2a143 120000 30 >>>>> 12542 R 272064 567568 1.0 00:00:02 91.3 ./a2a143 120000 30 >>>>> Node 1: v251: >>>>> PID S RSS VSZ %MEM TIME %CPU COMMAND >>>>> 10367 S 1872 40648 0.0 00:00:00 0.0 orted -mca ess env -mca >>>>> orte_ess_jobid 1444413440 -mca orte_ess_vpid 1 -mca orte_ess_num_procs 2 >>>>> --hnp-uri "1444413440.0;tcp://10.1.3.58:37339" >>>>> 10368 S 1868 40648 0.0 00:00:00 0.0 orted -mca ess env -mca >>>>> orte_ess_jobid 1444347904 -mca orte_ess_vpid 1 -mca orte_ess_num_procs 3 >>>>> --hnp-uri "1444347904.0;tcp://10.1.3.58:39610" >>>>> 10372 R 271112 567556 1.0 00:00:04 74.5 ./a2a143 120000 30 >>>>> 10373 R 271036 567564 1.0 00:00:04 71.5 ./a2a143 120000 30 >>>>> 10374 R 271032 567560 1.0 00:00:04 66.5 ./a2a143 120000 30 >>>>> 10375 R 273112 569612 1.1 00:00:04 68.5 ./a2a143 120000 30 >>>>> 10378 R 552280 840712 2.2 00:00:04 100 ./pp143 >>>>> 10379 R 552280 840708 2.2 00:00:04 100 ./pp143 >>>>> 10380 R 552328 841576 2.2 00:00:04 100 ./pp143 >>>>> 10381 R 552788 841216 2.2 00:00:04 99.3 ./pp143 >>>>> Node 2: v252: >>>>> PID S RSS VSZ %MEM TIME %CPU COMMAND >>>>> 10152 S 1908 40780 0.0 00:00:00 0.0 orted -mca ess env -mca >>>>> orte_ess_jobid 1444347904 -mca orte_ess_vpid 2 -mca orte_ess_num_procs 3 >>>>> --hnp-uri "1444347904.0;tcp://10.1.3.58:39610" >>>>> 10156 R 552384 840200 2.2 00:00:07 99.3 ./pp143 >>>>> 10157 R 551868 839692 2.2 00:00:06 99.3 ./pp143 >>>>> 10158 R 551400 839184 2.2 00:00:07 100 ./pp143 >>>>> 10159 R 551436 839184 2.2 00:00:06 98.3 ./pp143 >>>>> 10160 R 551760 839692 2.2 00:00:07 100 ./pp143 >>>>> 10161 R 551788 839824 2.2 00:00:07 97.3 ./pp143 >>>>> 10162 R 552256 840332 2.2 00:00:07 100 ./pp143 >>>>> 10163 R 552216 840340 2.2 00:00:07 99.3 ./pp143 >>>>> >>>>> >>>>> You would have to do something smarter to get correct process binding etc. >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>> >>> >>> >>> -- >>> Laurence Marks >>> Department of Materials Science and Engineering >>> MSE Rm 2036 Cook Hall >>> 2220 N Campus Drive >>> Northwestern University >>> Evanston, IL 60208, USA >>> Tel: (847) 491-3996 Fax: (847) 491-7820 >>> email: L-marks at northwestern dot edu >>> Web: www.numis.northwestern.edu >>> Chair, Commission on Electron Crystallography of IUCR >>> www.numis.northwestern.edu/ >>> Research is to see what everybody else has seen, and to think what >>> nobody else has thought >>> Albert Szent-Gyorgi >>> >>> _______________________________________________ >>> 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 >> > > > > -- > Laurence Marks > Department of Materials Science and Engineering > MSE Rm 2036 Cook Hall > 2220 N Campus Drive > Northwestern University > Evanston, IL 60208, USA > Tel: (847) 491-3996 Fax: (847) 491-7820 > email: L-marks at northwestern dot edu > Web: www.numis.northwestern.edu > Chair, Commission on Electron Crystallography of IUCR > www.numis.northwestern.edu/ > Research is to see what everybody else has seen, and to think what > nobody else has thought > Albert Szent-Gyorgi > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
