FAQ:
Troubleshooting building and running MPI jobs

Table of contents:

1. Open MPI tells me that it fails to load components with a "file not found" error — but the file is there! Why does it say this?
2. I see strange messages about missing symbols in my application; what do these mean?
3. What is mca_pml_teg.so? Why am I getting warnings about not finding the mca_ptl_base_modules_initialized symbol from it?
4. Can I build shared libraries on AIX with the IBM XL compilers?
5. Why am I getting a seg fault in libopen-pal (or libopal)?
6. Why am I getting seg faults / MPI parameter errors when compiling C++ applications with the Intel 9.1 C++ compiler?
7. All my MPI applications segv! Why? (Intel Linux 12.1 compiler)
8. Why can't I attach my parallel debugger (TotalView, DDT, fx2, etc.) to parallel jobs?
9. When launching large MPI jobs, I see messages like: mca_oob_tcp_peer_complete_connect: connection failed: Connection timed out (110) - retrying
10. How do I find out what MCA parameters are being seen/used by my job?

Open MPI loads a lot of plugins at run time. It opens its plugins via the excellent GNU Libtool libltdl portability library. If a plugin fails to load, Open MPI queries libltdl to get a printable string indicating why the plugin failed to load.

Unfortunately, there is a well-known bug in libltdl that may cause a "file not found" error message to be displayed, even when the file is found. The "file not found" error usually masks the real, underlying cause of the problem. For example:

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mca: base: component_find: unable to open /opt/openmpi/mca_ras_dash_host: file not found (ignored)

Note that Open MPI put in a libltdl workaround starting with version 1.5. This workaround should print the real reason the plugin failed to load instead of the erroneous "file not found" message.

There are two common underlying causes why a plugin fails to load:

1. The plugin is for a different version of Open MPI. This FAQ entry has more information about this case.
2. The plugin cannot find shared libraries that it requires. For example, if the openib plugin fails to load, ensure that libibverbs.so can be found by the linker at run time (e.g., check the value of your LD_LIBRARY_PATH environment variable). The same is true for any other plugins that have shared library dependencies (e.g., the mx BTL and MTL plugins need to be able to find the libmyriexpress.so shared library at run time).

Open MPI loads a lot of plugins at run time. It opens its plugins via the excellent GNU Libtool libltdl portability library. Sometimes a plugin can fail to load because it can't resolve all the symbols that it needs. There are a few reasons why this can happen.

• The plugin is for a different version of Open MPI. See this FAQ entry for an explanation of how Open MPI might try to open the "wrong" plugins.
• An application is trying to manually dynamically open libmpi in a private symbol space. For example, if an application is not linked against libmpi, but rather calls something like this:

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  /* This is a Linux example — the issue is similar/the same on other    operating systems */ handle = dlopen("libmpi.so", RTLD_NOW | RTLD_LOCAL);

  This is due to some deep run time linker voodoo — it is discussed towards the end of this post to the Open MPI developer's list. Briefly, the issue is this:

  1. The dynamic library libmpi is opened in a "local" symbol space.
  2. MPI_INIT is invoked, which tries to open Open MPI's plugins.
  3. Open MPI's plugins rely on symbols in libmpi (and other Open MPI support libraries); these symbols must be resolved when the plugin is loaded.
  4. However, since libmpi was opened in a "local" symbol space, its symbols are not available to the plugins that it opens.
  5. Hence, the plugin fails to load because it can't resolve all of its symbols, and displays a warning message to that effect.

  The ultimate fix for this issue is a bit bigger than Open MPI, unfortunately — it's a POSIX issue (as briefly described in the devel posting, above).

  However, there are several common workarounds:

  • Dynamically open libmpi in a public / global symbol scope — not a private / local scope. This will enable libmpi's symbols to be available for resolution when Open MPI dynamically opens its plugins.
  • If libmpi is opened as part of some underlying framework where it is not possible to change the private / local scope to a public / global scope, then dynamically open libmpi in a public / global scope before invoking the underlying framework. This sounds a little gross (and it is), but at least the run-time linker is smart enough to not load libmpi twice — but it does keeps libmpi in a public scope.
  • Use the --disable-dlopen or --disable-mca-dso options to Open MPI's configure script (see this FAQ entry for more details on these options). These options slurp all of Open MPI's plugins up in to libmpi — meaning that the plugins physically reside in libmpi and will not be dynamically opened at run time.
  • Build Open MPI as a static library by configuring Open MPI with --disable-shared and --enable-static. This has the same effect as --disable-dlopen, but it also makes libmpi.a (as opposed to a shared library).

You may wonder why you see this warning message (put here verbatim so that it becomes web-searchable):

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mca_pml_teg.so:undefined symbol:mca_ptl_base_modules_initialized

This happens when you upgrade to Open MPI v1.1 (or later) over an old installation of Open MPI v1.0.x without previously uninstalling v1.0.x. There are fairly uninteresting reasons why this problem occurs; the simplest, safest solution is to uninstall version 1.0.x and then re-install your newer version. For example:

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shell# cd /path/to/openmpi-1.0
shell# make uninstall
[... lots of output ...]
shell# cd /path/to/openmpi-1.1
shell# make install

The above example shows changing into the Open MPI 1.1 directory to re-install, but the same concept applies to any version after Open MPI version 1.0.x.

Note that this problem is fairly specific to installing / upgrading Open MPI from the source tarball. Pre-packaged installers (e.g., RPM) typically do not incur this problem.

Short answer: in older versions of Open MPI, maybe.

Add "LDFLAGS=-Wl,-brtl" to your configure command line:

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shell$ ./configure LDFLAGS=-Wl,-brtl ...

This enables "runtimelinking", which will make GNU Libtool name the libraries properly (i.e., *.so). More importantly, runtimelinking will cause the runtime linker to behave more or less like an ELF linker would (with respect to symbol resolution).

Future versions of OMPI may not require this flag (and "runtimelinking" on AIX).

NOTE: As of OMPI v1.2, AIX is no longer supported.

It is likely that you did not get a segv in libopen-pal (or "libopal", in older versions of Open MPI); it is likely that you are seeing a message like this:

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[0] func:/opt/ompi/lib/libopen-pal.so.0(opal_backtrace_print+0x2b) [0x2a958de8a7]

Or something like this in older versions of Open MPI:

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[0] func:/opt/ompi/lib/libopal.so.0 [0x2a958de8a7]

This is actually the function that is printing out the stack trace message; it is not the function that caused the segv itself. The function that caused the problem will be a few below this. Future versions of OMPI will simply not display this libopen-pal function in the segv reporting to avoid confusion.

Let's provide a concrete example. Take the following trivial MPI program that is guaranteed to cause a seg fault in MPI_COMM_WORLD rank 1:

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#include <mpi.h>
 
int main(int argc, char **argv)
{
    int rank;
    MPI_Init(&argc, &argv);
    MPI_Comm_rank(MPI_COMM_WORLD, &rank);
    if (rank == 1) {
        char *d = 0;
        /* This will cause a seg fault */
        *d = 3;
    }
 
    MPI_Finalize();
    return 0;
}

Running this code, you'll see something similar to the following:

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shell$ mpicc segv.c -o segv -g
shell$ mpirun -np 2 --mca btl tcp,self segv
Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Failing at addr:(nil)
[0] func:/opt/ompi/lib/libopen-pal.so.0(opal_backtrace_print+0x2b) [0x2a958de8a7]
[1] func:/opt/ompi/lib/libopen-pal.so.0 [0x2a958dd2b7]
[2] func:/lib64/tls/libpthread.so.0 [0x3be410c320]
[3] func:segv(main+0x3c) [0x400894]
[4] func:/lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3be361c4bb]
[5] func:segv [0x4007ca]
*** End of error message ***

The real error was back up in main, which is #3 on the stack trace. But Open MPI's stack-tracing function (opal_backtrace_print, in this case) is what is displayed as #0, so it's an easy mistake to assume that libopen-pal is the culprit.

Users have reported on the Open MPI users mailing list multiple times that when they compile Open MPI with the Intel 12.1 compiler suite, Open MPI tools (such as the wrapper compilers, including mpicc) and MPI applications will seg fault immediately.

As far as we know, this affects both Open MPI v1.4.4 (and later) and v1.5.4 (and later).

Here's one example of a user reporting this to the Open MPI User's list.

The cause of the problem has turned out to be a bug in early versions of the Intel Linux 12.1 compiler series itself. *If you upgrade your Intel compiler to the latest version of the Intel 12.1 compiler suite and rebuild Open MPI, the problem will go away.*

As noted in this FAQ entry, Open MPI supports parallel debuggers that utilize the TotalView API for parallel process attaching. However, it can sometimes fail if Open MPI is not installed correctly. Symptoms of this failure typically involve having the debugger hang (or crash) when attempting to attach to a parallel MPI application.

Parallel debuggers may rely on having Open MPI's mpirun program being compiled without optimization. Open MPI's configure and build process therefore attempts to identify optimization flags and remove them when compiling mpirun, but it does not have knowledge of all optimization flags for all compilers. Hence, if you specify some esoteric optimization flags to Open MPI's configure script, some optimization flags may slip through the process and create an mpirun that cannot be read by TotalView and other parallel debuggers.

If you run into this problem, you can manully build mpirun without optimization flags. Go into the tree where you built Open MPI:

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shell$ cd /path/to/openmpi/build/tree
shell$ cd orte/tools/orterun
shell$ make clean
[...output not shown...]
shell$ make all CFLAGS=-g
[...output not shown...]
shell$

This will build mpirun (also known as orterun) with just the "-g" flag. Once this completes, run make install, also from within the orte/tools/orterun directory, and possibly as root depending on where you installed Open MPI. Using this new orterun (mpirun), your parallel debugger should be able to attach to MPI jobs.

Additionally, a user reported to us that setting some TotalView flags may be helpful with attaching. The user specifically cited the Open MPI v1.3 series compiled with the Intel 11 compilers and TotalView 8.6, but it may also be helpful for other versions, too:

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shell$ export with_tv_debug_flags="-O0 -g -fno-inline-functions"

This is a known issue in the Open MPI v1.2 series. Try the following:

1. If you are using Linux-based systems, increase some of the limits on the node where mpirun is invoked (you must have administrator/root privlidges to increase these limits):

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   # The default is 128; increase it to 10,000 shell# echo 10000 > /proc/sys/net/core/somaxconn   # The default is 1,000; increase it to 100,000 shell# echo 100000 > /proc/sys/net/core/netdev_max_backlog

2. Set the oob_tcp_listen_mode MCA parameter to the string value listen_thread. This enables Open MPI's mpirun to respond much more quickly to incoming TCP connections during job launch, for example:

   1	shell$ mpirun --mca oob_tcp_listen_mode listen_thread -np 1024 my_mpi_program

   See this FAQ entry for more details on how to set MCA parameters.

As described elsewhere, MCA parameters are the "life's blood" of Open MPI. MCA parameters are used to control both detailed and large-scale behavior of Open MPI and are present throughout the code base.

This raises an important question: since MCA parameters can be set from a file, the environment, the command line, and even internally within Open MPI, how do I actually know what MCA params my job is seeing, and their value?

One way, of course, is to use the ompi_info command, which is documented elsewhere (you can use "man ompi_info", or "ompi_info --help" to get more info on this command). However, this still doesn't fully answer the question since ompi_info isn't an MPI process.

To help relieve this problem, Open MPI (starting with the 1.3 release) provides the MCA parameter mpi_show_mca_params that directs the rank=0 MPI process to report the name of MCA parameters, their current value as seen by that process, and the source that set that value. The parameter can take several values that define which MCA parameters to report:

• all: report all MCA params. Note that this typically generates a rather long list of parameters since it includes all of the default parameters defined inside Open MPI
• default: MCA params that are at their default settings - i.e., all MCA params that are at the values set as default within Open MPI
• file: MCA params that had their value set by a file
• api: MCA params set using Open MPI's internal APIs, perhaps to override an incompatible set of conditions specified by the user
• enviro: MCA params that obtained their value either from the local environment or the command line. Open MPI treats environmental and command line parameters as equivalent, so there currently is no way to separate these two sources

These options can be combined in any order by separating them with commas.

Here is an example of the output generated by this parameter:

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$ mpirun -mca grpcomm basic -mca mpi_show_mca_params enviro ./hello
ess=env (environment or cmdline)
orte_ess_jobid=1016725505 (environment or cmdline)
orte_ess_vpid=0 (environment or cmdline)
grpcomm=basic (environment or cmdline)
mpi_yield_when_idle=0 (environment or cmdline)
mpi_show_mca_params=enviro (environment or cmdline)
Hello, World, I am 0 of 1

Note that several MCA parameters set by Open MPI itself for internal uses are displayed in addition to the ones actually set by the user.

Since the output from this option can be long, and since it can be helpful to have a more permanent record of the MCA parameters used for a job, a companion MCA parameter mpi_show_mca_params_file is provided. If mpi_show_mca_params is also set, the output listing of MCA parameters will be directed into the specified file instead of being printed to stdout.