Re: update woes on ubuntu 18.04

[Jeffrey S. Oishi]

Hi Christopher,

I've just installed dedalus using the install script on 18.04, and I can't reproduce this problem. Did you do a fresh update of 18.04 or did you upgrade an earlier ubuntu version? If the latter, could you do

$ which mpirun

and let me know what it says? Can you run any mpi programs? That is, does a simple hello_world.c mpi program work?

j

On Thu, May 3, 2018 at 11:52 AM Christopher Marcotte <christophe...@gmail.com> wrote:

I upgraded ubuntu to 18.04 and dedalus has broken. I tried to in-place update, and it all goes through without any errors, but trying to run any examples leads to an error about a missing mpi.h:

from mpi4py import MPI
ImportError: libmpi.so.12: cannot open shared object file: No such file or directory

Then I tried re-installing dedalus, and the error remains.

I've attached the install log.

CM

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[Christopher Marcotte]

Hi Jeff, I upgraded from 16.04. 

which mpirun points at /usr/bin/mpirun, both with and without dedalus activated. 

I was eventually able to reinstall the system with the script by first removing the dedalus directory that was already there -- something I probably should have tried after updating in place before posting on the forum, but thank you for taking a look at things.

CM

[Jeffrey S. Oishi]

Hi Chris,

Ah, yeah. Probably what was happening was that mpi4py was not rebuilt when you tried to reinstall in place. Ubuntu moved the location of the MPI libraries between 16 and 17; you can see the effect of that here:

https://bitbucket.org/dedalus-project/dedalus/src/8692db00847363af9b518765f9e098cde62abc18/docs/install.sh#lines-349

This meant that although everything seemed ok, mpi4py couldn't find the MPI libraries because they moved.

A clean install in a new directory is often the fix for things like this...Sorry for the headache!

Jeff

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[louisalexan...@gmail.com]

Hi Jeff,

Just to follow-up, so it's fine to have a dedalus install on ubuntu 18.04 as long as we first have ubuntu 18.04, then install dedalus?

Thanks
Louis