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
