Yes, you're exactly right - this system has 2 Phi cards per node. I
believe the "PCI 8086" device in the lstopo output is them. Possibly
related, we've observed a weird bug with Torque and the allocation it
provides when you request the Phis. When requesting them you get a
nodefile with only 1 entry per node (instead of 16). This doesn't seem
to be a problem when you ignore the phis in the request, which I did
in these tests. Not sure if that's related.
This system is down for maintenance for a few days so it'll be a bit
before I can get more out of it.
On the slot issue - OK, which machinefile should I use? If I use my
modified one (2 lines per node) I still get the same error when using
"socket" or "slot".
When using the Torque provided one I seem to get some weird behavior.
With 2 processes, I end up with 1 on each of my allocated nodes and
then I get this:
$ mpirun --display-allocation -np 2 -map-by socket:pe=8 ./hello
====================== ALLOCATED NODES ======================
carter-a247: slots=8 max_slots=0 slots_inuse=0
carter-a521: slots=8 max_slots=0 slots_inuse=0
=================================================================
...
OMP: Info #204: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #202: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info
OMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: {0,4,6,7}
OMP: Info #156: KMP_AFFINITY: 4 available OS procs
OMP: Info #157: KMP_AFFINITY: Uniform topology
OMP: Info #179: KMP_AFFINITY: 1 packages x 4 cores/pkg x 1
threads/core (4 total cores)
OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set {0,4,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set {0,4,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set {0,4,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 4 bound to OS proc set {0,4,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set {0,4,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 5 bound to OS proc set {0,4,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 6 bound to OS proc set {0,4,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 7 bound to OS proc set {0,4,6,7}
...
OMP: Info #204: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #202: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info
OMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: {0,1,2,3,4,5,6,7}
OMP: Info #156: KMP_AFFINITY: 8 available OS procs
OMP: Info #157: KMP_AFFINITY: Uniform topology
OMP: Info #179: KMP_AFFINITY: 1 packages x 8 cores/pkg x 1
threads/core (8 total cores)
OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set
{0,1,2,3,4,5,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set
{0,1,2,3,4,5,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set
{0,1,2,3,4,5,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set
{0,1,2,3,4,5,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 4 bound to OS proc set
{0,1,2,3,4,5,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 5 bound to OS proc set
{0,1,2,3,4,5,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 6 bound to OS proc set
{0,1,2,3,4,5,6,7}
OMP: Info #147: KMP_AFFINITY: Internal thread 7 bound to OS proc set
{0,1,2,3,4,5,6,7}
Any ideas?
Thanks!
Dan
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
