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A friend of mine wanted the libboost libraries installed on our shared computer so after installing libboost-all-dev 1.49.0.1 (a Debian wheezy machine), I get this error when using the "pydoc modules" command on the commandline. It spits out the following error --

root@debian:/usr/include/c++/4.7# pydoc modules

Please wait a moment while I gather a list of all available modules...

**[debian:49065] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357
[debian:49065] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230
[debian:49065] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during orte_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):
  orte_ess_set_name failed
  --> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
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 "A system-required executable either could not be found or was not executable by this user" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** The MPI_Init() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[debian:49065] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!**
root@debian:/usr/include/c++/4.7# 

I tried looking into the problem and ended up uninstalling the following to get it to work again.

openmpi common all 1.4.5-1
libibverbs-dev amd64 1.1.6-1                                   
libopenmpi-dev amd64 1.4.5-1                                   
mpi-default-dev amd64 1.0.1
libboost-mpi-python1.49.0

Although pydoc works again, I'm assuming the packages I removed are going to hurt something else down the track? As you guessed I'm not a C/C++ programmer. So I guess my question is, will this hurt something later? Is there a way to install those packages without hurting Python?

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How did you install pydoc? from repo? or pip? or compile it?pydoc doesn't any hurt to your system. –  Mohsen Pahlevanzadeh Oct 26 '13 at 1:52
    
It does look like the bug reported below by @Alexander. If I understood the report correctly, you should install mpi-default-bin to fix the issue. –  Faheem Mitha Oct 26 '13 at 15:15
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migrated from serverfault.com Oct 26 '13 at 1:42

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1 Answer

There is a debian bug for your issue http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=691635 - mpirun binary not avaliable and thats why pydoc cannot start.

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I wasn't trying to imply that pydoc was the problem. I was leaning more towards openmpi being the problem as after it was installed from the libboost-all-dev 1.49.0.1 package, pydoc stopped working. Pydoc itself was also installed by a deb package ( previous to installing the boost package ). Admittedly I might be completely wrong though plus I don't know C or C++. –  Cameron Metzke Oct 26 '13 at 7:20
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