Thank you--I looked on the man page and it is not clear to me what pe=2 does. Is that the number of threads? So if I want 16 mpi procs with 2 threads is it for 32 cores (two nodes)
mpirun -map-by core:pe=2 -n 16 ? Sorry if I mangled this. Ron --- Ron Cohen recoh...@gmail.com skypename: ronaldcohen twitter: @recohen3 On Fri, Mar 25, 2016 at 2:03 PM, Ralph Castain <r...@open-mpi.org> wrote: > Okay, what I would suggest is that you use the following cmd line: > > mpirun -map-by core:pe=2 (or 8 or whatever number you want) > > This should give you the best performance as it will tight-pack the procs and > assign them to the correct number of cores. See if that helps > >> On Mar 25, 2016, at 10:38 AM, Ronald Cohen <recoh...@gmail.com> wrote: >> >> 1.10.2 >> >> Ron >> >> --- >> Ron Cohen >> recoh...@gmail.com >> skypename: ronaldcohen >> twitter: @recohen3 >> >> >> On Fri, Mar 25, 2016 at 1:30 PM, Ralph Castain <r...@open-mpi.org> wrote: >>> Hmmm…what version of OMPI are you using? >>> >>> >>> On Mar 25, 2016, at 10:27 AM, Ronald Cohen <recoh...@gmail.com> wrote: >>> >>> --report-bindings didn't report anything >>> --- >>> Ron Cohen >>> recoh...@gmail.com >>> skypename: ronaldcohen >>> twitter: @recohen3 >>> >>> >>> On Fri, Mar 25, 2016 at 1:24 PM, Ronald Cohen <recoh...@gmail.com> wrote: >>> >>> —display-allocation an >>> didn't seem to give useful information: >>> >>> ====================== ALLOCATED NODES ====================== >>> n005: slots=16 max_slots=0 slots_inuse=0 state=UP >>> n008.cluster.com: slots=16 max_slots=0 slots_inuse=0 state=UP >>> n007.cluster.com: slots=16 max_slots=0 slots_inuse=0 state=UP >>> n006.cluster.com: slots=16 max_slots=0 slots_inuse=0 state=UP >>> ================================================================= >>> >>> for >>> mpirun -display-allocation --map-by ppr:8:node -n 32 >>> >>> Ron >>> >>> --- >>> Ron Cohen >>> recoh...@gmail.com >>> skypename: ronaldcohen >>> twitter: @recohen3 >>> >>> >>> On Fri, Mar 25, 2016 at 1:17 PM, Ronald Cohen <recoh...@gmail.com> wrote: >>> >>> Actually there was the same number of procs per node in each case. I >>> verified this by logging into the nodes while they were running--in >>> both cases 4 per node . >>> >>> Ron >>> >>> --- >>> Ron Cohen >>> recoh...@gmail.com >>> skypename: ronaldcohen >>> twitter: @recohen3 >>> >>> >>> On Fri, Mar 25, 2016 at 1:14 PM, Ralph Castain <r...@open-mpi.org> wrote: >>> >>> >>> On Mar 25, 2016, at 9:59 AM, Ronald Cohen <recoh...@gmail.com> wrote: >>> >>> It is very strange but my program runs slower with any of these >>> choices than if IO simply use: >>> >>> mpirun -n 16 >>> with >>> #PBS -l >>> nodes=n013.cluster.com:ppn=4+n014.cluster.com:ppn=4+n015.cluster.com:ppn=4+n016.cluster.com:ppn=4 >>> for example. >>> >>> >>> This command will tightly pack as many procs as possible on a node - note >>> that we may well not see the PBS directives regarding number of ppn. Add >>> —display-allocation and let’s see how many slots we think were assigned on >>> each node >>> >>> >>> The timing for the latter is 165 seconds, and for >>> #PBS -l nodes=4:ppn=16,pmem=1gb >>> mpirun --map-by ppr:4:node -n 16 >>> it is 368 seconds. >>> >>> >>> It will typically be faster if you pack more procs/node as they can use >>> shared memory for communication. >>> >>> >>> Ron >>> >>> --- >>> Ron Cohen >>> recoh...@gmail.com >>> skypename: ronaldcohen >>> twitter: @recohen3 >>> >>> >>> On Fri, Mar 25, 2016 at 12:43 PM, Ralph Castain <r...@open-mpi.org> wrote: >>> >>> >>> On Mar 25, 2016, at 9:40 AM, Ronald Cohen <recoh...@gmail.com> wrote: >>> >>> Thank you! I will try it! >>> >>> >>> What would >>> -cpus-per-proc 4 -n 16 >>> do? >>> >>> >>> This would bind each process to 4 cores, filling each node with procs until >>> the cores on that node were exhausted, to a total of 16 processes within the >>> allocation. >>> >>> >>> Ron >>> --- >>> Ron Cohen >>> recoh...@gmail.com >>> skypename: ronaldcohen >>> twitter: @recohen3 >>> >>> >>> On Fri, Mar 25, 2016 at 12:38 PM, Ralph Castain <r...@open-mpi.org> wrote: >>> >>> Add -rank-by node to your cmd line. You’ll still get 4 procs/node, but they >>> will be ranked by node instead of consecutively within a node. >>> >>> >>> >>> On Mar 25, 2016, at 9:30 AM, Ronald Cohen <recoh...@gmail.com> wrote: >>> >>> I am using >>> >>> mpirun --map-by ppr:4:node -n 16 >>> >>> and this loads the processes in round robin fashion. This seems to be >>> twice as slow for my code as loading them node by node, 4 processes >>> per node. >>> >>> How can I not load them round robin, but node by node? >>> >>> Thanks! >>> >>> Ron >>> >>> >>> --- >>> Ron Cohen >>> recoh...@gmail.com >>> skypename: ronaldcohen >>> twitter: @recohen3 >>> >>> --- >>> Ronald Cohen >>> Geophysical Laboratory >>> Carnegie Institution >>> 5251 Broad Branch Rd., N.W. >>> Washington, D.C. 20015 >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/03/28828.php >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/03/28829.php >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/03/28830.php >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/03/28831.php >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/03/28832.php >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/03/28833.php >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/03/28837.php >>> >>> >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/03/28840.php >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2016/03/28843.php > > _______________________________________________ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/03/28844.php
