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
