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Subject: Re: [OMPI users] Open-MPI 1.4.2 : mpirun core-dumps when "-npernode N" is used at command line
From: Michael E. Thomadakis (miket7777_at_[hidden])
Date: 2010-08-24 15:25:19


  On 08/24/10 14:22, Michael E. Thomadakis wrote:
> Hi,
>
> I used a 'tee' command to capture the output but I forgot to also redirect
> stderr to the file.
>
> This is what a fresh make gave (gcc 4.1.2 again) :
>
> ------------------------------------------------------------------
> ompi_debuggers.c:81: error: missing terminating " character
> ompi_debuggers.c:81: error: expected expression before \u2018;\u2019 token
> ompi_debuggers.c: In function \u2018ompi_wait_for_debugger\u2019:
> ompi_debuggers.c:212: error: \u2018mpidbg_dll_locations\u2019 undeclared
> (first use in this function)
> ompi_debuggers.c:212: error: (Each undeclared identifier is reported only once
> ompi_debuggers.c:212: error: for each function it appears in.)
> ompi_debuggers.c:212: warning: passing argument 3 of \u2018check\u2019 from
> incompatible pointer type
> make[2]: *** [libdebuggers_la-ompi_debuggers.lo] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
> ------------------------------------------------------------------
>
> Is this critical to run OMPI code?
>
> Thanks for the quick reply Ralph,
>
> Michael
>
> On Tue, 24 Aug 2010, Ralph Castain wrote:
>
> | Date: Tue, 24 Aug 2010 13:16:10 -0600
> | From: Ralph Castain<rhc_at_[hidden]>
> | To: Michael E.Thomadakis<miket7777_at_[hidden]>
> | Cc: Open MPI Users<users_at_[hidden]>, miket_at_[hidden]
> | Subject: Re: [OMPI users] Open-MPI 1.4.2 : mpirun core-dumps when
> | "-npernode N" is used at command line
> |
> | Ummm....the configure log terminates normally, indicating it configured fine. The make log ends, but with no error shown - everything was building just fine.
> |
> | Did you maybe stop it before it was complete? Run out of disk quota? Or...?
> |
> |
> | On Aug 24, 2010, at 1:06 PM, Michael E. Thomadakis wrote:
> |
> |> Hi Ralph,
> |>
> |> I tried to build 1.4.3.a1r23542 (08/02/2010) with
> |>
> |> ./configure --prefix="/g/software/openmpi-1.4.3a1r23542/gcc-4.1.2 2" --enable-cxx-exceptions CFLAGS="-O2" CXXFLAGS="-O2" FFLAGS="-O2" FCFLAGS="-O2"
> |> with the GCC 4.1.2
> |>
> |> miket_at_login002[pts/26]openmpi-1.4.3a1r23542 $ gcc -v
> |> Using built-in specs.
> |> Target: x86_64-redhat-linux
> |> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
> |> Thread model: posix
> |> gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
> |>
> |>
> |> but it failed. I am attaching the configure and make logs.
> |>
> |> regards
> |>
> |> Michael
> |>
> |>
> |> On 08/23/10 20:53, Ralph Castain wrote:
> |>>
> |>> Nope - none of them will work with 1.4.2. Sorry - bug not discovered until after release
> |>>
> |>> On Aug 23, 2010, at 7:45 PM, Michael E. Thomadakis wrote:
> |>>
> |>>> Hi Jeff,
> |>>> thanks for the quick reply.
> |>>>
> |>>> Would using '--cpus-per-proc N' in place of '-npernode N' or just '-bynode' do the trick?
> |>>>
> |>>> It seems that using '--loadbalance' also crashes mpirun.
> |>>>
> |>>> best ...
> |>>>
> |>>> Michael
> |>>>
> |>>>
> |>>> On 08/23/10 19:30, Jeff Squyres wrote:
> |>>>>
> |>>>> Yes, the -npernode segv is a known issue.
> |>>>>
> |>>>> We have it fixed in the 1.4.x nightly tarballs; can you give it a whirl and see if that fixes your problem?
> |>>>>
> |>>>> http://www.open-mpi.org/nightly/v1.4/
> |>>>>
> |>>>>
> |>>>>
> |>>>> On Aug 23, 2010, at 8:20 PM, Michael E. Thomadakis wrote:
> |>>>>
> |>>>>> Hello OMPI:
> |>>>>>
> |>>>>> We have installed OMPI V1.4.2 on a Nehalem cluster running CentOS5.4. OMPI was built uisng Intel compilers 11.1.072. I am attaching the configuration log and output from ompi_info -a.
> |>>>>>
> |>>>>> The problem we are encountering is that whenever we use option '-npernode N' in the mpirun command line we get a segmentation fault as in below:
> |>>>>>
> |>>>>>
> |>>>>> miket_at_login002[pts/7]PS $ mpirun -npernode 1 --display-devel-map --tag-output -np 6 -cpus-per-proc 2 -H 'login001,login002,login003' hostname
> |>>>>>
> |>>>>> Map generated by mapping policy: 0402
> |>>>>> Npernode: 1 Oversubscribe allowed: TRUE CPU Lists: FALSE
> |>>>>> Num new daemons: 2 New daemon starting vpid 1
> |>>>>> Num nodes: 3
> |>>>>>
> |>>>>> Data for node: Name: login001 Launch id: -1 Arch: 0 State: 2
> |>>>>> Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
> |>>>>> Daemon: [[44812,0],1] Daemon launched: False
> |>>>>> Num slots: 1 Slots in use: 2
> |>>>>> Num slots allocated: 1 Max slots: 0
> |>>>>> Username on node: NULL
> |>>>>> Num procs: 1 Next node_rank: 1
> |>>>>> Data for proc: [[44812,1],0]
> |>>>>> Pid: 0 Local rank: 0 Node rank: 0
> |>>>>> State: 0 App_context: 0 Slot list: NULL
> |>>>>>
> |>>>>> Data for node: Name: login002 Launch id: -1 Arch: ffc91200 State: 2
> |>>>>> Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
> |>>>>> Daemon: [[44812,0],0] Daemon launched: True
> |>>>>> Num slots: 1 Slots in use: 2
> |>>>>> Num slots allocated: 1 Max slots: 0
> |>>>>> Username on node: NULL
> |>>>>> Num procs: 1 Next node_rank: 1
> |>>>>> Data for proc: [[44812,1],0]
> |>>>>> Pid: 0 Local rank: 0 Node rank: 0
> |>>>>> State: 0 App_context: 0 Slot list: NULL
> |>>>>>
> |>>>>> Data for node: Name: login003 Launch id: -1 Arch: 0 State: 2
> |>>>>> Num boards: 1 Num sockets/board: 2 Num cores/socket: 4
> |>>>>> Daemon: [[44812,0],2] Daemon launched: False
> |>>>>> Num slots: 1 Slots in use: 2
> |>>>>> Num slots allocated: 1 Max slots: 0
> |>>>>> Username on node: NULL
> |>>>>> Num procs: 1 Next node_rank: 1
> |>>>>> Data for proc: [[44812,1],0]
> |>>>>> Pid: 0 Local rank: 0 Node rank: 0
> |>>>>> State: 0 App_context: 0 Slot list: NULL
> |>>>>> [login002:02079] *** Process received signal ***
> |>>>>> [login002:02079] Signal: Segmentation fault (11)
> |>>>>> [login002:02079] Signal code: Address not mapped (1)
> |>>>>> [login002:02079] Failing at address: 0x50
> |>>>>> [login002:02079] [ 0] /lib64/libpthread.so.0 [0x3569a0e7c0]
> |>>>>> [login002:02079] [ 1] /g/software/openmpi-1.4.2/intel/lib/libopen-rte.so.0(orte_util_encode_pidmap+0xa7) [0x2afa70d25de7]
> |>>>>> [login002:02079] [ 2] /g/software/openmpi-1.4.2/intel/lib/libopen-rte.so.0(orte_odls_base_default_get_add_procs_data+0x3b8) [0x2afa70d36088]
> |>>>>> [login002:02079] [ 3] /g/software/openmpi-1.4.2/intel/lib/libopen-rte.so.0(orte_plm_base_launch_apps+0xd7) [0x2afa70d37fc7]
> |>>>>> [login002:02079] [ 4] /g/software/openmpi-1.4.2/intel/lib/openmpi/mca_plm_rsh.so [0x2afa721085a1]
> |>>>>> [login002:02079] [ 5] mpirun [0x404c27]
> |>>>>> [login002:02079] [ 6] mpirun [0x403e38]
> |>>>>> [login002:02079] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3568e1d994]
> |>>>>> [login002:02079] [ 8] mpirun [0x403d69]
> |>>>>> [login002:02079] *** End of error message ***
> |>>>>> Segmentation fault
> |>>>>>
> |>>>>> We tried version 1.4.1 and this problem did not emerge.
> |>>>>>
> |>>>>> This option is necessary for when our users launch hybrid MPI-OMP code were they can request M nodes and n ppn in a PBS/Torque setup so they can only get the right amount of MPI taks. Unfortunately, as soon as we use the 'npernode N' option mprun crashes.
> |>>>>>
> |>>>>> Is this a known issue? I found related problem (of around May, 2010) when people were using the same option but in a SLURM environment.
> |>>>>>
> |>>>>> regards
> |>>>>>
> |>>>>> Michael
> |>>>>>
> |>>>>> <config.log.gz><ompi_info-a.out.gz>_______________________________________________
> |>>>>> users mailing list
> |>>>>> users_at_[hidden]
> |>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> |>>>
> |>>> _______________________________________________
> |>>> users mailing list
> |>>> users_at_[hidden]
> |>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> |>>
> |>>
> |>> _______________________________________________
> |>> users mailing list
> |>> users_at_[hidden]
> |>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> |>
> |> <config_1.4.3.log.gz><make_1.4.3.out.gz>
> |
> |
>