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Subject: Re: [OMPI users] [EXTERNAL] Re: open-mpi on Mac OS 10.9 (Mavericks)
From: Meredith, Karl (karl.meredith_at_[hidden])
Date: 2013-11-25 11:53:09


Digging a little deeper by running the code in the lldb debugger, I found that the stall occurs in a call to init_orte from ompi_mpi_init.c:
   356 /* Setup ORTE - note that we are an MPI process */
   357 if (ORTE_SUCCESS != (ret = orte_init(NULL, NULL, ORTE_PROC_MPI))) {
   358 error = "ompi_mpi_init: orte_init failed";
   359 goto error;
   360 }

The code never returns from orte_init.

It gets stuck in orte_ess.init() called from orte_init.c:
   126 /* initialize the RTE for this environment */
   127 if (ORTE_SUCCESS != (ret = orte_ess.init())) {

When I step through this orte_ess_init in the lldb debugger, I actually get some output from the code (no output if not using the debugger and stepping through):
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  ompi_mpi_init: orte_init failed
  --> Returned "Unable to start a daemon on the local node" (-128) instead of "Success" (0)

Karl

On Nov 25, 2013, at 9:20 AM, Meredith, Karl <karl.meredith_at_[hidden]> wrote:

> Here’s the back trace from lldb:
> $ )ps -elf | grep hello
> 1042653210 45231 45230 4006 0 31 0 2448976 2148 - S+ 0 ttys002 0:00.01 hello_cxx 9:07AM
> 1042653210 45232 45230 4006 0 31 0 2457168 2156 - S+ 0 ttys002 0:00.04 hello_cxx 9:07AM
>
> (meredithk_at_meredithk-mac)-(09:15 AM Mon Nov 25)-(~/tools/openmpi-1.6.5/examples)
> $ )lldb -p 45231
> Attaching to process with:
> process attach -p 45231
> Process 45231 stopped
> Executable module set to "/Users/meredithk/tools/openmpi-1.6.5/examples/hello_cxx".
> Architecture set to: x86_64-apple-macosx.
> (lldb) bt
> * thread #1: tid = 0x168535, 0x00007fff8c1859aa libsystem_kernel.dylib`select$DARWIN_EXTSN + 10, queue = 'com.apple.main-thread, stop reason = signal SIGSTOP
> frame #0: 0x00007fff8c1859aa libsystem_kernel.dylib`select$DARWIN_EXTSN + 10
> frame #1: 0x0000000106b73ea0 libmpi.1.dylib`select_dispatch(base=0x00007f84c3c0b430, arg=0x00007f84c3c0b3e0, tv=0x00007fff5924ca70) + 80 at select.c:174
> frame #2: 0x0000000106b3eb0f libmpi.1.dylib`opal_event_base_loop(base=0x00007f84c3c0b430, flags=5) + 415 at event.c:838
>
> Both processors are at this state.
>
> Here’s the output from otool -L ./hello_cxx:
>
> $ )otool -L ./hello_cxx
> ./hello_cxx:
> /Users/meredithk/tools/openmpi/lib/libmpi_cxx.1.dylib (compatibility version 2.0.0, current version 2.2.0)
> /Users/meredithk/tools/openmpi/lib/libmpi.1.dylib (compatibility version 2.0.0, current version 2.8.0)
> /opt/local/lib/libgcc/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.18.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
> /opt/local/lib/libgcc/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
>
>
> On Nov 25, 2013, at 9:14 AM, George Bosilca <bosilca_at_[hidden]> wrote:
>
>> Mac OS X 1.9 dropped support for gdb. Please report the output of lldb instead.
>>
>> Also, can you run “otool -L ./hello_cxx” and report the output.
>>
>> Thanks,
>> George.
>>
>>
>> On Nov 25, 2013, at 15:09 , Meredith, Karl <karl.meredith_at_[hidden]> wrote:
>>
>>> I do have DYLD_LIBRARY_PATH set to the same paths as LD_LIBRARY_PATH. This does not resolve the problem. The code still hangs on MPI::Init().
>>>
>>> Another thing I tried is I recompiled openmpi with the debug flags activated:
>>> ./configure --prefix=$HOME/tools/openmpi --enable-debug
>>> make
>>> make install
>>>
>>> Then, I attached to the running process using gdb. I tried to do a back trace and see where it was hanging up at, but all I got was this:
>>> Attaching to process 45231
>>> Reading symbols from /Users/meredithk/tools/openmpi-1.6.5/examples/hello_cxx...Reading symbols from /Users/meredithk/tools/openmpi-1.6.5/examples/hello_cxx.dSYM/Contents/Resources/DWARF/hello_cxx...done.
>>> done.
>>> 0x00007fff8c1859aa in ?? ()
>>> (gdb) bt
>>> #0 0x00007fff8c1859aa in ?? ()
>>> #1 0x0000000106b73ea0 in ?? ()
>>> #2 0x706d6e65706f2f2f in ?? ()
>>> #3 0x0000000000000001 in ?? ()
>>> #4 0x0000000000000000 in ?? ()
>>>
>>> This output from gdb was not terribly helpful to me.
>>>
>>> Karl
>>>
>>>
>>> On Nov 25, 2013, at 8:30 AM, Hammond, Simon David (-EXP) <sdhammo_at_[hidden]<mailto:sdhammo_at_[hidden]>> wrote:
>>>
>>> We have occasionally had a problem like this when we set LD_LIBRARY_PATH only. On OSX you may need to set DYLD_LIBRARY_PATH instead ( set it to the same lib directory )
>>>
>>> Can you try that and see if it resolves the problem?
>>>
>>>
>>>
>>> Si Hammond
>>> Sandia National Laboratories
>>> Remote Connection
>>>
>>>
>>> -----Original Message-----
>>> From: Meredith, Karl [karl.meredith_at_[hidden]<mailto:karl.meredith_at_[hidden]>]
>>> Sent: Monday, November 25, 2013 06:25 AM Mountain Standard Time
>>> To: Open MPI Users
>>> Subject: [EXTERNAL] Re: [OMPI users] open-mpi on Mac OS 10.9 (Mavericks)
>>>
>>>
>>> I do have these two environment variables set:
>>>
>>> LD_LIBRARY_PATH=/Users/meredithk/tools/openmpi/lib
>>> PATH=/Users/meredithk/tools/openmpi/bin
>>>
>>> Running mpirun seems to work fine with a simple command, like hostname:
>>>
>>> $ )mpirun -n 2 hostname
>>> meredithk-mac.corp.fmglobal.com<http://meredithk-mac.corp.fmglobal.com>
>>> meredithk-mac.corp.fmglobal.com<http://meredithk-mac.corp.fmglobal.com>
>>>
>>> I am trying to run the simple hello_cxx example from the openmpi distribution, compiled as such:
>>> mpic++ -g hello_cxx.cc -o hello_cxx
>>>
>>> It compiles fine, without warning or error. However, when I go to run the example, it stalls on the MPI::Init() command:
>>> mpirun -np 1 hello_cxx
>>> It never errors out or crashes. It simply hangs.
>>>
>>> I am using the same mpic++ and mpirun version:
>>> $ )which mpirun
>>> /Users/meredithk/tools/openmpi/bin/mpirun
>>>
>>> $ )which mpic++
>>> /Users/meredithk/tools/openmpi/bin/mpic++
>>>
>>> Not quite sure what else to check.
>>>
>>> Karl
>>>
>>>
>>> On Nov 23, 2013, at 5:29 PM, Ralph Castain <rhc_at_[hidden]<mailto:rhc_at_[hidden]>> wrote:
>>>
>>>> Strange - I run on Mavericks now without problem. Can you run "mpirun -n 1 hostname"?
>>>>
>>>> You also might want to check your PATH and LD_LIBRARY_PATH to ensure you have the prefix where you installed OMPI 1.6.5 at the front. Mac distributes a very old version of OMPI with its software and you don't want to pick it up by mistake.
>>>>
>>>>
>>>> On Nov 22, 2013, at 1:45 PM, Meredith, Karl <karl.meredith_at_[hidden]<mailto:karl.meredith_at_[hidden]>> wrote:
>>>>
>>>>> I recently upgraded my 2013 Macbook Pro (Retina display) from 10.8 to 10.9. I downloaded and installed openmpi-1.6.5 and compiled it with gcc 4.8 (gcc installed from macports).
>>>>> openmpi compiled and installed without error.
>>>>>
>>>>> However, when I try to run any of the example test cases, the code gets stuck inside the first MPI::Init() call and never returns.
>>>>>
>>>>> Any thoughts on what might be going wrong?
>>>>>
>>>>> The same install on OS 10.8 works fine and the example test cases run without error.
>>>>>
>>>>> Karl
>>>>>
>>>>> _______________________________________________
>>>>> users mailing list
>>>>> users_at_[hidden]<mailto:users_at_[hidden]>
>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>
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