That shouldn't be a problem. Let me figure out the process and I'll get back to you.
Dan On Thu, Jun 12, 2014 at 11:50 AM, Ralph Castain <r...@open-mpi.org> wrote: > 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 > > _______________________________________________ > 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/2014/06/24646.php -- Dan Dietz Scientific Applications Analyst ITaP Research Computing, Purdue University
