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
