Kernel dies when trying to execute first line of notebook Tutorial 1: Bases and Domains

[Claudio Pierard]

Hi,

When I try to run the first line of code in the Tutorial1 notebook:

    from dedalus import public as de

the kernel dies immediately, and it doesn't print and error message. I already updated my ipython version, but the kernel continues dying.

I'm using Jupyter version 1.0.0, and my ipython version is 5.3.0.

I'm in a mac os 10.11.6.

Dedalus works fine when I run the examples in the repository.

Any ideas of what might be the cause?

Thank you,

Claudio

[Keaton Burns]

Hi Claudio,

Can you create and run your own jupyter notebooks?  If so, does importing dedalus fail there, too, or only when you try the example notebooks?

-Keaton

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[Claudio Pierard]

Hi Keaton,

It also fails when I create a new notebook and try to import dedalus. It is strange...

Best,

c

[Keaton Burns]

Can you run things besides dedalus in a notebook?  Matplotlib, numpy, scipy, and “from mpi4py import MPI”?

To view this discussion on the web visit https://groups.google.com/d/msgid/dedalus-users/ef32163a-5efa-4091-8621-f72124face3e%40googlegroups.com.

[Claudio Pierard]

Yes, I can run Matplotlib, numpy and scipy, but when I run ""from mpi4py import MPI"" the kernel dies.

[Keaton Burns]

Does it work from the ipython terminal? If not, but does work from the regular python terminal, perhaps jupyter might be using a different python version than the one you manually used to run the other example scripts?

On Mar 2, 2017, at 12:48 PM, Claudio Pierard <c.pi...@ciencias.unam.mx> wrote:

Yes, I can run Matplotlib, numpy and scipy, but when I run ""from mpi4py import MPI"" the kernel dies.

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[Claudio Pierard]

When I run it from ipython notebook, it appears the error message from openmpi trying to connect to the local network

In [1]: from dedalus import public as de
[MacBook-Pro-de-Claudio.local:03998] [[10693,0],0] ORTE_ERROR_LOG: Bad parameter in file orted/pmix/pmix_server.c at line 262
[MacBook-Pro-de-Claudio.local:03998] [[10693,0],0] ORTE_ERROR_LOG: Bad parameter in file ess_hnp_module.c at line 666
--------------------------------------------------------------------------
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):

  pmix server init failed
  --> Returned value Bad parameter (-5) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
[MacBook-Pro-de-Claudio.local:03997] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 575
[MacBook-Pro-de-Claudio.local:03997] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ess_singleton_module.c at line 165
--------------------------------------------------------------------------
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_init failed
  --> Returned value Unable to start a daemon on the local node (-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: ompi_rte_init failed
  --> Returned "Unable to start a daemon on the local node" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init_thread
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[MacBook-Pro-de-Claudio.local:3997] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!


So I did "export TMPDIR=/tmp" before executing the ipython terminal, and it worked!  So I did the same before launching jupyter notebook and everything worked fine.

[Keaton Burns]

Hi Claudio,

Perhaps it’s related to the errors we saw here: https://groups.google.com/forum/#!searchin/dedalus-users/wifi%7Csort:relevance/dedalus-users/kU9AaTRqVAs/4eZn3d7gBgAJ.

I’d try the fixes suggested in that thread (setting TMPDIR, etc.), and also checking how things differ between the notebook and terminals, etc.

Best,

-Keaton

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[Keaton Burns]

Hi Claudio,

Whoops, your previous e-mail only partially loaded on my laptop, so I hadn’t seen that you tried the TMPDIR fix and it worked.  So please ignore my last message!

Best,

-Keaton