I've poked and prodded, and the 1.8.2 tarball seems to be handling this situation just fine. I don't have access to a Torque machine, but I did set everything to follow the same code path, added faux coprocessors, etc. - and it ran just fine.
Can you try the 1.8.2 tarball and see if it solves the problem? On Jun 11, 2014, at 2:15 PM, Ralph Castain <r...@open-mpi.org> wrote: > Okay, let me poke around some more. It is clearly tied to the coprocessors, > but I'm not yet sure just why. > > One thing you might do is try the nightly 1.8.2 tarball - there have been a > number of fixes, and this may well have been caught there. Worth taking a > look. > > > On Jun 11, 2014, at 6:44 AM, Dan Dietz <ddi...@purdue.edu> wrote: > >> Sorry - it crashes with both torque and rsh launchers. The output from >> a gdb backtrace on the core files looks identical. >> >> Dan >> >> On Wed, Jun 11, 2014 at 9:37 AM, Ralph Castain <r...@open-mpi.org> wrote: >>> Afraid I'm a little confused now - are you saying it works fine under >>> Torque, but segfaults under rsh? Could you please clarify your current >>> situation? >>> >>> >>> On Jun 11, 2014, at 6:27 AM, Dan Dietz <ddi...@purdue.edu> wrote: >>> >>>> It looks like it is still segfaulting with the rsh launcher: >>>> >>>> ddietz@conte-a084:/scratch/conte/d/ddietz/hello$ mpirun -mca plm rsh >>>> -np 4 -machinefile ./nodes ./hello >>>> [conte-a084:51113] *** Process received signal *** >>>> [conte-a084:51113] Signal: Segmentation fault (11) >>>> [conte-a084:51113] Signal code: Address not mapped (1) >>>> [conte-a084:51113] Failing at address: 0x2c >>>> [conte-a084:51113] [ 0] /lib64/libpthread.so.0[0x36ddc0f710] >>>> [conte-a084:51113] [ 1] >>>> /apps/rhel6/openmpi/1.8.1/intel-14.0.2.144/lib/libopen-rte.so.7(orte_plm_base_complete_setup+0x615)[0x2b857e203015] >>>> [conte-a084:51113] [ 2] >>>> /apps/rhel6/openmpi/1.8.1/intel-14.0.2.144/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0xa05)[0x2b857ee10715] >>>> [conte-a084:51113] [ 3] mpirun(orterun+0x1b45)[0x40684f] >>>> [conte-a084:51113] [ 4] mpirun(main+0x20)[0x4047f4] >>>> [conte-a084:51113] [ 5] >>>> /lib64/libc.so.6(__libc_start_main+0xfd)[0x36dd41ed1d] >>>> [conte-a084:51113] [ 6] mpirun[0x404719] >>>> [conte-a084:51113] *** End of error message *** >>>> Segmentation fault (core dumped) >>>> >>>> On Sun, Jun 8, 2014 at 4:54 PM, Ralph Castain <r...@open-mpi.org> wrote: >>>>> I'm having no luck poking at this segfault issue. For some strange >>>>> reason, we seem to think there are coprocessors on those remote nodes - >>>>> e.g., a Phi card. Yet your lstopo output doesn't seem to show it. >>>>> >>>>> Out of curiosity, can you try running this with "-mca plm rsh"? This will >>>>> substitute the rsh/ssh launcher in place of Torque - assuming your system >>>>> will allow it, this will let me see if the problem is somewhere in the >>>>> Torque launcher or elsewhere in OMPI. >>>>> >>>>> Thanks >>>>> Ralph >>>>> >>>>> On Jun 6, 2014, at 12:48 PM, Dan Dietz <ddi...@purdue.edu> wrote: >>>>> >>>>>> No problem - >>>>>> >>>>>> These are model name : Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz chips. >>>>>> 2 per node, 8 cores each. No threading enabled. >>>>>> >>>>>> $ lstopo >>>>>> Machine (64GB) >>>>>> NUMANode L#0 (P#0 32GB) >>>>>> Socket L#0 + L3 L#0 (20MB) >>>>>> L2 L#0 (256KB) + L1d L#0 (32KB) + L1i L#0 (32KB) + Core L#0 + PU L#0 >>>>>> (P#0) >>>>>> L2 L#1 (256KB) + L1d L#1 (32KB) + L1i L#1 (32KB) + Core L#1 + PU L#1 >>>>>> (P#1) >>>>>> L2 L#2 (256KB) + L1d L#2 (32KB) + L1i L#2 (32KB) + Core L#2 + PU L#2 >>>>>> (P#2) >>>>>> L2 L#3 (256KB) + L1d L#3 (32KB) + L1i L#3 (32KB) + Core L#3 + PU L#3 >>>>>> (P#3) >>>>>> L2 L#4 (256KB) + L1d L#4 (32KB) + L1i L#4 (32KB) + Core L#4 + PU L#4 >>>>>> (P#4) >>>>>> L2 L#5 (256KB) + L1d L#5 (32KB) + L1i L#5 (32KB) + Core L#5 + PU L#5 >>>>>> (P#5) >>>>>> L2 L#6 (256KB) + L1d L#6 (32KB) + L1i L#6 (32KB) + Core L#6 + PU L#6 >>>>>> (P#6) >>>>>> L2 L#7 (256KB) + L1d L#7 (32KB) + L1i L#7 (32KB) + Core L#7 + PU L#7 >>>>>> (P#7) >>>>>> HostBridge L#0 >>>>>> PCIBridge >>>>>> PCI 1000:0087 >>>>>> Block L#0 "sda" >>>>>> PCIBridge >>>>>> PCI 8086:2250 >>>>>> PCIBridge >>>>>> PCI 8086:1521 >>>>>> Net L#1 "eth0" >>>>>> PCI 8086:1521 >>>>>> Net L#2 "eth1" >>>>>> PCIBridge >>>>>> PCI 102b:0533 >>>>>> PCI 8086:1d02 >>>>>> NUMANode L#1 (P#1 32GB) >>>>>> Socket L#1 + L3 L#1 (20MB) >>>>>> L2 L#8 (256KB) + L1d L#8 (32KB) + L1i L#8 (32KB) + Core L#8 + PU L#8 >>>>>> (P#8) >>>>>> L2 L#9 (256KB) + L1d L#9 (32KB) + L1i L#9 (32KB) + Core L#9 + PU L#9 >>>>>> (P#9) >>>>>> L2 L#10 (256KB) + L1d L#10 (32KB) + L1i L#10 (32KB) + Core L#10 >>>>>> + PU L#10 (P#10) >>>>>> L2 L#11 (256KB) + L1d L#11 (32KB) + L1i L#11 (32KB) + Core L#11 >>>>>> + PU L#11 (P#11) >>>>>> L2 L#12 (256KB) + L1d L#12 (32KB) + L1i L#12 (32KB) + Core L#12 >>>>>> + PU L#12 (P#12) >>>>>> L2 L#13 (256KB) + L1d L#13 (32KB) + L1i L#13 (32KB) + Core L#13 >>>>>> + PU L#13 (P#13) >>>>>> L2 L#14 (256KB) + L1d L#14 (32KB) + L1i L#14 (32KB) + Core L#14 >>>>>> + PU L#14 (P#14) >>>>>> L2 L#15 (256KB) + L1d L#15 (32KB) + L1i L#15 (32KB) + Core L#15 >>>>>> + PU L#15 (P#15) >>>>>> HostBridge L#5 >>>>>> PCIBridge >>>>>> PCI 15b3:1011 >>>>>> Net L#3 "ib0" >>>>>> OpenFabrics L#4 "mlx5_0" >>>>>> PCIBridge >>>>>> PCI 8086:2250 >>>>>> >>>>>> From the segfault below. I tried reproducing the crash on less than an >>>>>> 4 node allocation but wasn't able to. >>>>>> >>>>>> ddietz@conte-a009:/scratch/conte/d/ddietz/hello$ mpirun -np 2 >>>>>> -machinefile ./nodes -mca plm_base_verbose 10 ./hello >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> registering plm components >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> found loaded component isolated >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> component isolated has no register or open function >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> found loaded component slurm >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> component slurm register function successful >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> found loaded component rsh >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> component rsh register function successful >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> found loaded component tm >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_register: >>>>>> component tm register function successful >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: opening >>>>>> plm components >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: found >>>>>> loaded component isolated >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: >>>>>> component isolated open function successful >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: found >>>>>> loaded component slurm >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: >>>>>> component slurm open function successful >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: found >>>>>> loaded component rsh >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: >>>>>> component rsh open function successful >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: found >>>>>> loaded component tm >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: components_open: >>>>>> component tm open function successful >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select: Auto-selecting plm >>>>>> components >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Querying >>>>>> component [isolated] >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Query of >>>>>> component [isolated] set priority to 0 >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Querying >>>>>> component [slurm] >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Skipping >>>>>> component [slurm]. Query failed to return a module >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Querying >>>>>> component [rsh] >>>>>> [conte-a009.rcac.purdue.edu:55685] [[INVALID],INVALID] plm:rsh_lookup >>>>>> on agent ssh : rsh path NULL >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Query of >>>>>> component [rsh] set priority to 10 >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Querying >>>>>> component [tm] >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Query of >>>>>> component [tm] set priority to 75 >>>>>> [conte-a009.rcac.purdue.edu:55685] mca:base:select:( plm) Selected >>>>>> component [tm] >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: close: component isolated >>>>>> closed >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: close: unloading >>>>>> component isolated >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: close: component slurm >>>>>> closed >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: close: unloading component >>>>>> slurm >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: close: component rsh closed >>>>>> [conte-a009.rcac.purdue.edu:55685] mca: base: close: unloading component >>>>>> rsh >>>>>> [conte-a009.rcac.purdue.edu:55685] plm:base:set_hnp_name: initial bias >>>>>> 55685 nodename hash 3965217721 >>>>>> [conte-a009.rcac.purdue.edu:55685] plm:base:set_hnp_name: final jobfam >>>>>> 24164 >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:base:receive start >>>>>> comm >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:base:setup_job >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:base:setup_vm >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:base:setup_vm >>>>>> creating map >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:base:setup_vm add >>>>>> new daemon [[24164,0],1] >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:base:setup_vm >>>>>> assigning new daemon [[24164,0],1] to node conte-a055 >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:tm: launching vm >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:tm: final top-level >>>>>> argv: >>>>>> orted -mca ess tm -mca orte_ess_jobid 1583611904 -mca orte_ess_vpid >>>>>> <template> -mca orte_ess_num_procs 2 -mca orte_hnp_uri >>>>>> "1583611904.0;tcp://172.18.96.49,172.31.1.254,172.31.2.254,172.18.112.49:37380" >>>>>> -mca plm_base_verbose 10 >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:tm: resetting >>>>>> LD_LIBRARY_PATH: >>>>>> /scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/lib:/scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/lib:/scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/lib:/usr/pbs/lib:/apps/rhel6/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/apps/rhel6/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64:/apps/rhel6/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/apps/rhel6/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/apps/rhel6/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/apps/rhel6/intel/opencl-1.2-3.2.1.16712/lib64 >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:tm: resetting >>>>>> PATH: >>>>>> /scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/bin:/scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/bin:/scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/bin:/apps/rhel6/intel/composer_xe_2013_sp1.2.144/bin/intel64:/opt/intel/mic/bin:/apps/rhel6/intel/inspector_xe_2013/bin64:/apps/rhel6/intel/advisor_xe_2013/bin64:/apps/rhel6/intel/vtune_amplifier_xe_2013/bin64:/apps/rhel6/intel/opencl-1.2-3.2.1.16712/bin:/usr/lib64/qt-3.3/bin:/opt/moab/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/hpss/bin:/opt/hsi/bin:/opt/ibutils/bin:/usr/pbs/bin:/opt/moab/bin:/usr/site/rcac/scripts:/usr/site/rcac/support_scripts:/usr/site/rcac/bin:/usr/site/rcac/sbin:/usr/sbin >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:tm: launching on >>>>>> node conte-a055 >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:tm: executing: >>>>>> orted -mca ess tm -mca orte_ess_jobid 1583611904 -mca orte_ess_vpid 1 >>>>>> -mca orte_ess_num_procs 2 -mca orte_hnp_uri >>>>>> "1583611904.0;tcp://172.18.96.49,172.31.1.254,172.31.2.254,172.18.112.49:37380" >>>>>> -mca plm_base_verbose 10 >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] plm:tm:launch: >>>>>> finished spawning orteds >>>>>> [conte-a055.rcac.purdue.edu:32094] mca: base: components_register: >>>>>> registering plm components >>>>>> [conte-a055.rcac.purdue.edu:32094] mca: base: components_register: >>>>>> found loaded component rsh >>>>>> [conte-a055.rcac.purdue.edu:32094] mca: base: components_register: >>>>>> component rsh register function successful >>>>>> [conte-a055.rcac.purdue.edu:32094] mca: base: components_open: opening >>>>>> plm components >>>>>> [conte-a055.rcac.purdue.edu:32094] mca: base: components_open: found >>>>>> loaded component rsh >>>>>> [conte-a055.rcac.purdue.edu:32094] mca: base: components_open: >>>>>> component rsh open function successful >>>>>> [conte-a055.rcac.purdue.edu:32094] mca:base:select: Auto-selecting plm >>>>>> components >>>>>> [conte-a055.rcac.purdue.edu:32094] mca:base:select:( plm) Querying >>>>>> component [rsh] >>>>>> [conte-a055.rcac.purdue.edu:32094] [[24164,0],1] plm:rsh_lookup on >>>>>> agent ssh : rsh path NULL >>>>>> [conte-a055.rcac.purdue.edu:32094] mca:base:select:( plm) Query of >>>>>> component [rsh] set priority to 10 >>>>>> [conte-a055.rcac.purdue.edu:32094] mca:base:select:( plm) Selected >>>>>> component [rsh] >>>>>> [conte-a055.rcac.purdue.edu:32094] [[24164,0],1] plm:rsh_setup on >>>>>> agent ssh : rsh path NULL >>>>>> [conte-a055.rcac.purdue.edu:32094] [[24164,0],1] plm:base:receive start >>>>>> comm >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] >>>>>> plm:base:orted_report_launch from daemon [[24164,0],1] >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] >>>>>> plm:base:orted_report_launch from daemon [[24164,0],1] on node >>>>>> conte-a055 >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] RECEIVED TOPOLOGY >>>>>> FROM NODE conte-a055 >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] NEW TOPOLOGY - ADDING >>>>>> [conte-a009.rcac.purdue.edu:55685] [[24164,0],0] >>>>>> plm:base:orted_report_launch completed for daemon [[24164,0],1] at >>>>>> contact >>>>>> 1583611904.1;tcp://172.18.96.95,172.31.1.254,172.31.2.254,172.18.112.95:58312 >>>>>> [conte-a009:55685] *** Process received signal *** >>>>>> [conte-a009:55685] Signal: Segmentation fault (11) >>>>>> [conte-a009:55685] Signal code: Address not mapped (1) >>>>>> [conte-a009:55685] Failing at address: 0x4c >>>>>> [conte-a009:55685] [ 0] /lib64/libpthread.so.0[0x327f80f500] >>>>>> [conte-a009:55685] [ 1] >>>>>> /scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/lib/libopen-rte.so.7(orte_plm_base_complete_setup+0x951)[0x2b5b069a50e1] >>>>>> [conte-a009:55685] [ 2] >>>>>> /scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0xa05)[0x2b5b075ff145] >>>>>> [conte-a009:55685] [ 3] mpirun(orterun+0x1ffd)[0x4073b5] >>>>>> [conte-a009:55685] [ 4] mpirun(main+0x20)[0x4048f4] >>>>>> [conte-a009:55685] [ 5] >>>>>> /lib64/libc.so.6(__libc_start_main+0xfd)[0x327f41ecdd] >>>>>> [conte-a009:55685] [ 6] mpirun[0x404819] >>>>>> [conte-a009:55685] *** End of error message *** >>>>>> Segmentation fault (core dumped) >>>>>> ddietz@conte-a009:/scratch/conte/d/ddietz/hello$ >>>>>> [conte-a055.rcac.purdue.edu:32094] [[24164,0],1] plm:base:receive stop >>>>>> comm >>>>>> >>>>>> On Fri, Jun 6, 2014 at 3:00 PM, Ralph Castain <r...@open-mpi.org> wrote: >>>>>>> Sorry to pester with questions, but I'm trying to narrow down the issue. >>>>>>> >>>>>>> * What kind of chips are on these machines? >>>>>>> >>>>>>> * If they have h/w threads, are they enabled? >>>>>>> >>>>>>> * you might have lstopo on one of those machines - could you pass along >>>>>>> its output? Otherwise, you can run a simple "mpirun -n 1 -mca >>>>>>> ess_base_verbose 20 hostname" and it will print out. Only need one node >>>>>>> in your allocation as we don't need a fountain of output. >>>>>>> >>>>>>> I'll look into the segfault - hard to understand offhand, but could be >>>>>>> an uninitialized variable. If you have a chance, could you rerun that >>>>>>> test with "-mca plm_base_verbose 10" on the cmd line? >>>>>>> >>>>>>> Thanks again >>>>>>> Ralph >>>>>>> >>>>>>> On Jun 6, 2014, at 10:31 AM, Dan Dietz <ddi...@purdue.edu> wrote: >>>>>>> >>>>>>>> Thanks for the reply. I tried out the --display-allocation option with >>>>>>>> several different combinations and have attached the output. I see >>>>>>>> this behavior on both RHEL6.4, RHEL6.5, and RHEL5.10 clusters. >>>>>>>> >>>>>>>> >>>>>>>> Here's debugging info on the segfault. Does that help? FWIW this does >>>>>>>> not seem to crash on the RHEL5 cluster or RHEL6.5 cluster. Just >>>>>>>> crashes on RHEL6.4. >>>>>>>> >>>>>>>> ddietz@conte-a009:/scratch/conte/d/ddietz/hello$ gdb -c core.22623 >>>>>>>> `which mpirun` >>>>>>>> No symbol table is loaded. Use the "file" command. >>>>>>>> GNU gdb (GDB) 7.5-1.3.187 >>>>>>>> Copyright (C) 2012 Free Software Foundation, Inc. >>>>>>>> License GPLv3+: GNU GPL version 3 or later >>>>>>>> <http://gnu.org/licenses/gpl.html> >>>>>>>> This is free software: you are free to change and redistribute it. >>>>>>>> There is NO WARRANTY, to the extent permitted by law. Type "show >>>>>>>> copying" >>>>>>>> and "show warranty" for details. >>>>>>>> This GDB was configured as "x86_64-unknown-linux-gnu". >>>>>>>> For bug reporting instructions, please see: >>>>>>>> <http://www.gnu.org/software/gdb/bugs/>... >>>>>>>> Reading symbols from >>>>>>>> /scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/bin/mpirun...done. >>>>>>>> [New LWP 22623] >>>>>>>> [New LWP 22624] >>>>>>>> >>>>>>>> warning: Can't read pathname for load map: Input/output error. >>>>>>>> [Thread debugging using libthread_db enabled] >>>>>>>> Using host libthread_db library "/lib64/libthread_db.so.1". >>>>>>>> Core was generated by `mpirun -np 2 -machinefile ./nodes ./hello'. >>>>>>>> Program terminated with signal 11, Segmentation fault. >>>>>>>> #0 0x00002acc602920e1 in orte_plm_base_complete_setup (fd=-1, >>>>>>>> args=-1, cbdata=0x20c0840) at base/plm_base_launch_support.c:422 >>>>>>>> 422 node->hostid = node->daemon->name.vpid; >>>>>>>> (gdb) bt >>>>>>>> #0 0x00002acc602920e1 in orte_plm_base_complete_setup (fd=-1, >>>>>>>> args=-1, cbdata=0x20c0840) at base/plm_base_launch_support.c:422 >>>>>>>> #1 0x00002acc60eec145 in opal_libevent2021_event_base_loop () from >>>>>>>> /scratch/conte/d/ddietz/openmpi-1.8.1-debug/intel-14.0.2.144/lib/libopen-pal.so.6 >>>>>>>> #2 0x00000000004073b5 in orterun (argc=6, argv=0x7fff5bb2a3a8) at >>>>>>>> orterun.c:1077 >>>>>>>> #3 0x00000000004048f4 in main (argc=6, argv=0x7fff5bb2a3a8) at >>>>>>>> main.c:13 >>>>>>>> >>>>>>>> ddietz@conte-a009:/scratch/conte/d/ddietz/hello$ cat nodes >>>>>>>> conte-a009 >>>>>>>> conte-a009 >>>>>>>> conte-a055 >>>>>>>> conte-a055 >>>>>>>> ddietz@conte-a009:/scratch/conte/d/ddietz/hello$ uname -r >>>>>>>> 2.6.32-358.14.1.el6.x86_64 >>>>>>>> >>>>>>>> On Thu, Jun 5, 2014 at 7:54 PM, Ralph Castain <r...@open-mpi.org> >>>>>>>> wrote: >>>>>>>>> >>>>>>>>> On Jun 5, 2014, at 2:13 PM, Dan Dietz <ddi...@purdue.edu> wrote: >>>>>>>>> >>>>>>>>>> Hello all, >>>>>>>>>> >>>>>>>>>> I'd like to bind 8 cores to a single MPI rank for hybrid MPI/OpenMP >>>>>>>>>> codes. In OMPI 1.6.3, I can do: >>>>>>>>>> >>>>>>>>>> $ mpirun -np 2 -cpus-per-rank 8 -machinefile ./nodes ./hello >>>>>>>>>> >>>>>>>>>> I get one rank bound to procs 0-7 and the other bound to 8-15. Great! >>>>>>>>>> >>>>>>>>>> But I'm having some difficulties doing this with openmpi 1.8.1: >>>>>>>>>> >>>>>>>>>> $ mpirun -np 2 -cpus-per-rank 8 -machinefile ./nodes ./hello >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> The following command line options and corresponding MCA parameter >>>>>>>>>> have >>>>>>>>>> been deprecated and replaced as follows: >>>>>>>>>> >>>>>>>>>> Command line options: >>>>>>>>>> Deprecated: --cpus-per-proc, -cpus-per-proc, --cpus-per-rank, >>>>>>>>>> -cpus-per-rank >>>>>>>>>> Replacement: --map-by <obj>:PE=N >>>>>>>>>> >>>>>>>>>> Equivalent MCA parameter: >>>>>>>>>> Deprecated: rmaps_base_cpus_per_proc >>>>>>>>>> Replacement: rmaps_base_mapping_policy=<obj>:PE=N >>>>>>>>>> >>>>>>>>>> The deprecated forms *will* disappear in a future version of Open >>>>>>>>>> MPI. >>>>>>>>>> Please update to the new syntax. >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> There are not enough slots available in the system to satisfy the 2 >>>>>>>>>> slots >>>>>>>>>> that were requested by the application: >>>>>>>>>> ./hello >>>>>>>>>> >>>>>>>>>> Either request fewer slots for your application, or make more slots >>>>>>>>>> available >>>>>>>>>> for use. >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> OK, let me try the new syntax... >>>>>>>>>> >>>>>>>>>> $ mpirun -np 2 --map-by core:pe=8 -machinefile ./nodes ./hello >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> There are not enough slots available in the system to satisfy the 2 >>>>>>>>>> slots >>>>>>>>>> that were requested by the application: >>>>>>>>>> ./hello >>>>>>>>>> >>>>>>>>>> Either request fewer slots for your application, or make more slots >>>>>>>>>> available >>>>>>>>>> for use. >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> What am I doing wrong? The documentation on these new options is >>>>>>>>>> somewhat poor and confusing so I'm probably doing something wrong. If >>>>>>>>>> anyone could provide some pointers here it'd be much appreciated! If >>>>>>>>>> it's not something simple and you need config logs and such please >>>>>>>>>> let >>>>>>>>>> me know. >>>>>>>>> >>>>>>>>> Looks like we think there are less than 16 slots allocated on that >>>>>>>>> node. What is in this "nodes" file? Without it, OMPI should read the >>>>>>>>> Torque allocation directly. You might check what we think the >>>>>>>>> allocation is by adding --display-allocation to the cmd line >>>>>>>>> >>>>>>>>>> >>>>>>>>>> As a side note - >>>>>>>>>> >>>>>>>>>> If I try this using the PBS nodefile with the above, I get a >>>>>>>>>> confusing message: >>>>>>>>>> >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> A request for multiple cpus-per-proc was given, but a directive >>>>>>>>>> was also give to map to an object level that has less cpus than >>>>>>>>>> requested ones: >>>>>>>>>> >>>>>>>>>> #cpus-per-proc: 8 >>>>>>>>>> number of cpus: 1 >>>>>>>>>> map-by: BYCORE:NOOVERSUBSCRIBE >>>>>>>>>> >>>>>>>>>> Please specify a mapping level that has more cpus, or else let us >>>>>>>>>> define a default mapping that will allow multiple cpus-per-proc. >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> From what I've gathered this is because I have a node listed 16 times >>>>>>>>>> in my PBS nodefile so it's assuming then I have 1 core per node? >>>>>>>>> >>>>>>>>> >>>>>>>>> No - if listed 16 times, it should compute 16 slots. Try adding >>>>>>>>> --display-allocation to your cmd line and it should tell you how many >>>>>>>>> slots are present. >>>>>>>>> >>>>>>>>> However, it doesn't assume there is a core for each slot. Instead, it >>>>>>>>> detects the cores directly on the node. It sounds like it isn't >>>>>>>>> seeing them for some reason. What OS are you running on that node? >>>>>>>>> >>>>>>>>> FWIW: the 1.6 series has a different detection system for cores. >>>>>>>>> Could be something is causing problems for the new one. >>>>>>>>> >>>>>>>>>> Some >>>>>>>>>> better documentation here would be helpful. I haven't been able to >>>>>>>>>> figure out how to use the "oversubscribe" option listed in the docs. >>>>>>>>>> Not that I really want to oversubscribe, of course, I need to modify >>>>>>>>>> the nodefile, but this just stumped me for a while as 1.6.3 didn't >>>>>>>>>> have this behavior. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> As a extra bonus, I get a segfault in this situation: >>>>>>>>>> >>>>>>>>>> $ mpirun -np 2 -machinefile ./nodes ./hello >>>>>>>>>> [conte-a497:13255] *** Process received signal *** >>>>>>>>>> [conte-a497:13255] Signal: Segmentation fault (11) >>>>>>>>>> [conte-a497:13255] Signal code: Address not mapped (1) >>>>>>>>>> [conte-a497:13255] Failing at address: 0x2c >>>>>>>>>> [conte-a497:13255] [ 0] /lib64/libpthread.so.0[0x3c9460f500] >>>>>>>>>> [conte-a497:13255] [ 1] >>>>>>>>>> /apps/rhel6/openmpi/1.8.1/intel-14.0.2.144/lib/libopen-rte.so.7(orte_plm_base_complete_setup+0x615)[0x2ba960a59015] >>>>>>>>>> [conte-a497:13255] [ 2] >>>>>>>>>> /apps/rhel6/openmpi/1.8.1/intel-14.0.2.144/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0xa05)[0x2ba961666715] >>>>>>>>>> [conte-a497:13255] [ 3] mpirun(orterun+0x1b45)[0x40684f] >>>>>>>>>> [conte-a497:13255] [ 4] mpirun(main+0x20)[0x4047f4] >>>>>>>>>> [conte-a497:13255] [ 5] >>>>>>>>>> /lib64/libc.so.6(__libc_start_main+0xfd)[0x3a1bc1ecdd] >>>>>>>>>> [conte-a497:13255] [ 6] mpirun[0x404719] >>>>>>>>>> [conte-a497:13255] *** End of error message *** >>>>>>>>>> Segmentation fault (core dumped) >>>>>>>>>> >>>>>>>>> >>>>>>>>> Huh - that's odd. Could you perhaps configure OMPI with >>>>>>>>> --enable-debug and gdb the core file to tell us the line numbers >>>>>>>>> involved? >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Ralph >>>>>>>>> >>>>>>>>>> >>>>>>>>>> My "nodes" file simply contains the first two lines of my original >>>>>>>>>> $PBS_NODEFILE provided by Torque. See above why I modified. Works >>>>>>>>>> fine >>>>>>>>>> if use the full file. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks in advance for any pointers you all may have! >>>>>>>>>> >>>>>>>>>> Dan >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Dan Dietz >>>>>>>>>> Scientific Applications Analyst >>>>>>>>>> ITaP Research Computing, Purdue University >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Dan Dietz >>>>>>>> Scientific Applications Analyst >>>>>>>> ITaP Research Computing, Purdue University >>>>>>>> <slots>_______________________________________________ >>>>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Dan Dietz >>>>>> Scientific Applications Analyst >>>>>> ITaP Research Computing, Purdue University >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>>> >>>> -- >>>> Dan Dietz >>>> Scientific Applications Analyst >>>> ITaP Research Computing, Purdue University >>>> _______________________________________________ >>>> 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/2014/06/24629.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/2014/06/24630.php >> >> >> >> -- >> Dan Dietz >> Scientific Applications Analyst >> ITaP Research Computing, Purdue University >> _______________________________________________ >> 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/2014/06/24631.php >
