Nathan, Now I remove strip_prefix stuff, which was applied to the other versions of OpenMPI. I still have the same problem with msubrun command.
knteran@mzlogin01:~> msub -lnodes=2:ppn=16 -I qsub: waiting for job 7754058.sdb to start qsub: job 7754058.sdb ready knteran@mzlogin01:~> cd test-openmpi/ knteran@mzlogin01:~/test-openmpi> !mp mpicc cpi.c -o cpi knteran@mzlogin01:~/test-openmpi> mpirun -np 4 ./cpi -------------------------------------------------------------------------- There are not enough slots available in the system to satisfy the 4 slots that were requested by the application: ./cpi Either request fewer slots for your application, or make more slots available for use. -------------------------------------------------------------------------- I set PATH and LD_LIBRARY_PATH to match with my own OpenMPI installation. knteran@mzlogin01:~/test-openmpi> which mpirun /home/knteran/openmpi/bin/mpirun Thanks, --------------------------------------------------------------------------- -- Keita Teranishi Principal Member of Technical Staff Scalable Modeling and Analysis Systems Sandia National Laboratories Livermore, CA 94551 +1 (925) 294-3738 On 11/26/13 12:52 PM, "Nathan Hjelm" <hje...@lanl.gov> wrote: >Weird. That is the same configuration we have deployed on Cielito and >Cielo. Does >it work under an msub allocation? > >BTW, with that configuration you should not set >plm_base_strip_prefix_from_node_names >to 0. That will confuse orte since the node hostname will not match what >was >supplied by alps. > >-Nathan > >On Tue, Nov 26, 2013 at 08:38:51PM +0000, Teranishi, Keita wrote: >> Nathan, >> >> (Please forget about the segfault. It was my mistake). >> I use OpenMPI-1.7.2 (build with gcc-4.7.2) to run the program. I used >> contrib/platform/lanl/cray_xe6/optimized_lustre and >> --enable-mpirun-prefix-by-default for configuration. As I said, it >>works >> fine with aprun, but fails with mpirun/mpiexec. >> >> >> knteran@mzlogin01:~/test-openmpi> ~/openmpi/bin/mpirun -np 4 ./a.out >> >>------------------------------------------------------------------------- >>- >> There are not enough slots available in the system to satisfy the 4 >>slots >> that were requested by the application: >> ./a.out >> >> Either request fewer slots for your application, or make more slots >> available >> for use. >> >> >>------------------------------------------------------------------------- >>-- >> - >> >> Thanks, >> >> >>------------------------------------------------------------------------- >>-- >> -- >> Keita Teranishi >> Principal Member of Technical Staff >> Scalable Modeling and Analysis Systems >> Sandia National Laboratories >> Livermore, CA 94551 >> +1 (925) 294-3738 >> >> >> >> >> >> On 11/25/13 12:55 PM, "Nathan Hjelm" <hje...@lanl.gov> wrote: >> >> >Ok, that should have worked. I just double-checked it to me sure. >> > >> >ct-login1:/lscratch1/hjelmn/ibm/collective hjelmn$ mpirun -np 32 >>./bcast >> >App launch reported: 17 (out of 3) daemons - 0 (out of 32) procs >> >ct-login1:/lscratch1/hjelmn/ibm/collective hjelmn$ >> > >> > >> >How did you configure Open MPI and what version are you using? >> > >> >-Nathan >> > >> >On Mon, Nov 25, 2013 at 08:48:09PM +0000, Teranishi, Keita wrote: >> >> Hi Natan, >> >> >> >> I tried qsub option you >> >> >> >> mpirun -np 4 --mca plm_base_strip_prefix_from_node_names= 0 ./cpi >> >> >> >>>>----------------------------------------------------------------------- >>>>-- >> >>- >> >> There are not enough slots available in the system to satisfy the 4 >> >>slots >> >> that were requested by the application: >> >> ./cpi >> >> >> >> Either request fewer slots for your application, or make more slots >> >> available >> >> for use. >> >> >> >>>>----------------------------------------------------------------------- >>>>-- >> >>- >> >> >> >> >> >> Here is I got from aprun >> >> aprun -n 32 ./cpi >> >> Process 8 of 32 is on nid00011 >> >> Process 5 of 32 is on nid00011 >> >> Process 12 of 32 is on nid00011 >> >> Process 9 of 32 is on nid00011 >> >> Process 11 of 32 is on nid00011 >> >> Process 13 of 32 is on nid00011 >> >> Process 0 of 32 is on nid00011 >> >> Process 6 of 32 is on nid00011 >> >> Process 3 of 32 is on nid00011 >> >> : >> >> >> >> : >> >> >> >> Also, I found a strange error in the end of the program >>(MPI_Finalize?) >> >> Can you tell me what is wrong with that? >> >> [nid00010:23511] [ 0] /lib64/libpthread.so.0(+0xf7c0) >>[0x2aaaacbbb7c0] >> >> [nid00010:23511] [ 1] >> >> >> >>>>/home/knteran/openmpi/lib/libmpi.so.0(opal_memory_ptmalloc2_int_free+0x >>>>57 >> >>) >> >> [0x2aaaaaf38ec7] >> >> [nid00010:23511] [ 2] >> >> >>/home/knteran/openmpi/lib/libmpi.so.0(opal_memory_ptmalloc2_free+0xc3) >> >> [0x2aaaaaf3b6c3] >> >> [nid00010:23511] [ 3] >> >> /home/knteran/openmpi/lib/libmpi.so.0(mca_pml_base_close+0xb2) >> >> [0x2aaaaae717b2] >> >> [nid00010:23511] [ 4] >> >> /home/knteran/openmpi/lib/libmpi.so.0(ompi_mpi_finalize+0x333) >> >> [0x2aaaaad7be23] >> >> [nid00010:23511] [ 5] ./cpi() [0x400e23] >> >> [nid00010:23511] [ 6] /lib64/libc.so.6(__libc_start_main+0xe6) >> >> [0x2aaaacde7c36] >> >> [nid00010:23511] [ 7] ./cpi() [0x400b09] >> >> >> >> >> >> >> >> Thanks, >> >> >> >> >> >>>>----------------------------------------------------------------------- >>>>-- >> >>-- >> >> -- >> >> Keita Teranishi >> >> >> >> Principal Member of Technical Staff >> >> Scalable Modeling and Analysis Systems >> >> Sandia National Laboratories >> >> Livermore, CA 94551 >> >> +1 (925) 294-3738 >> >> >> >> >> >> >> >> >> >> >> >> On 11/25/13 12:28 PM, "Nathan Hjelm" <hje...@lanl.gov> wrote: >> >> >> >> >Just talked with our local Cray rep. Sounds like that torque syntax >>is >> >> >broken. You can continue >> >> >to use qsub (though qsub use is strongly discouraged) if you use the >> >>msub >> >> >options. >> >> > >> >> >Ex: >> >> > >> >> >qsub -lnodes=2:ppn=16 >> >> > >> >> >Works. >> >> > >> >> >-Nathan >> >> > >> >> >On Mon, Nov 25, 2013 at 01:11:29PM -0700, Nathan Hjelm wrote: >> >> >> Hmm, this seems like either a bug in qsub (torque is full of >>serious >> >> >>bugs) or a bug >> >> >> in alps. I got an allocation using that command and alps only >>sees 1 >> >> >>node: >> >> >> >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: Trying ALPS >> >> >>configuration file: "/etc/sysconfig/alps" >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: parser_ini >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: Trying ALPS >> >> >>configuration file: "/etc/alps.conf" >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: >> >> >>parser_separated_columns >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: Located ALPS >> >>scheduler >> >> >>file: "/ufs/alps_shared/appinfo" >> >> >> [ct-login1.localdomain:06010] >> >> >>ras:alps:orte_ras_alps_get_appinfo_attempts: 10 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: begin processing >> >> >>appinfo file >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: file >> >> >>/ufs/alps_shared/appinfo read >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: 47 entries in >>file >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3492 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3492 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3541 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3541 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3560 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3560 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3561 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3561 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3566 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3566 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3573 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3573 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3588 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3588 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3598 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3598 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3599 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3599 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3622 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3622 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3635 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3635 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3640 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3640 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3641 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3641 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3642 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3642 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3647 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3647 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3651 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3651 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3653 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3653 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3659 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3659 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3662 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3662 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3665 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3665 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: read data for >>resId >> >> >>3668 - myId 3668 >> >> >> [ct-login1.localdomain:06010] ras:alps:read_appinfo(modern): >> >>processing >> >> >>NID 29 with 16 slots >> >> >> [ct-login1.localdomain:06010] ras:alps:allocate: success >> >> >> [ct-login1.localdomain:06010] [[15798,0],0] ras:base:node_insert >> >> >>inserting 1 nodes >> >> >> [ct-login1.localdomain:06010] [[15798,0],0] ras:base:node_insert >> >>node 29 >> >> >> >> >> >> ====================== ALLOCATED NODES ====================== >> >> >> >> >> >> Data for node: 29 Num slots: 16 Max slots: 0 >> >> >> >> >> >> ================================================================= >> >> >> >> >> >> >> >> >> Torque also shows only one node with 16 PPN: >> >> >> >> >> >> $ env | grep PBS >> >> >> ... >> >> >> PBS_NUM_PPN=16 >> >> >> >> >> >> >> >> >> $ cat /var/spool/torque/aux//915289.sdb >> >> >> login1 >> >> >> >> >> >> Which is wrong! I will have to ask Cray what is going on here. I >> >> >>recommend you switch to >> >> >> msub to get an allocation. Moab has fewer bugs. I can't even get >> >>aprun >> >> >>to work: >> >> >> >> >> >> $ aprun -n 2 -N 1 hostname >> >> >> apsched: claim exceeds reservation's node-count >> >> >> >> >> >> $ aprun -n 32 hostname >> >> >> apsched: claim exceeds reservation's node-count >> >> >> >> >> >> >> >> >> To get an interactive session 2 nodes with 16 ppn on each run: >> >> >> >> >> >> msub -I -lnodes=2:ppn=16 >> >> >> >> >> >> Open MPI should then work correctly. >> >> >> >> >> >> -Nathan Hjelm >> >> >> HPC-5, LANL >> >> >> >> >> >> On Sat, Nov 23, 2013 at 10:13:26PM +0000, Teranishi, Keita wrote: >> >> >> > Hi, >> >> >> > I installed OpenMPI on our small XE6 using the configure >>options >> >> >>under >> >> >> > /contrib directory. It appears it is working fine, but it >> >>ignores >> >> >>MCA >> >> >> > parameters (set in env var). So I switched to mpirun (in >> >>OpenMPI) >> >> >>and it >> >> >> > can handle MCA parameters somehow. However, mpirun fails to >> >> >>allocate >> >> >> > process by cores. For example, I allocated 32 cores (on 2 >> >>nodes) >> >> >>by "qsub >> >> >> > -lmppwidth=32 -lmppnppn=16", mpirun recognizes it as 2 slots. >> >> >>Is it >> >> >> > possible to mpirun to handle mluticore nodes of XE6 properly >>or >> >>is >> >> >>there >> >> >> > any options to handle MCA parameters for aprun? >> >> >> > Regards, >> >> >> > >> >> >> >>>>>>--------------------------------------------------------------------- >>>>>>-- >> >>>>-- >> >> >>---- >> >> >> > Keita Teranishi >> >> >> > Principal Member of Technical Staff >> >> >> > Scalable Modeling and Analysis Systems >> >> >> > Sandia National Laboratories >> >> >> > Livermore, CA 94551 >> >> >> > +1 (925) 294-3738 >> >> >> >> >> >> > _______________________________________________ >> >> >> > 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
