Arggh - is there any way I can get access to this beast so I can debug this? I can't figure out what in the world is going on, but it seems to be something triggered by your specific setup.
On Jun 12, 2014, at 8:48 AM, Dan Dietz <ddi...@purdue.edu> wrote: > Unfortunately, the nightly tarball appears to be crashing in a similar > fashion. :-( I used the latest snapshot 1.8.2a1r31981. > > Dan > > On Thu, Jun 12, 2014 at 10:56 AM, Ralph Castain <r...@open-mpi.org> wrote: >> 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 >>> >> >> _______________________________________________ >> 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/2014/06/24642.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/2014/06/24645.php
