Docker MPI

[Doug Shi-Dong]

Hello everyone,

I would like to use Travis CI to test pull requests, and I am currently following the steps described in https://github.com/dealii/dealii/wiki/Docker-Images

Except I am using the following Docker image: dealii/dealii:v9.1.1-gcc-mpi-fulldepsspack-debugrelease

It seems that this Docker imagine does not contain an MPI package in its installation. Here is a log of my Travis CI build

https://travis-ci.org/dougshidong/PHiLiP/builds/600536273

The command apt search mpi shows that no packages such as openmpi or mpich is available. However, oddly enough, DEAL_II_WITH_MPI is ON, when my CMake checks for it.

If no MPI is available, how do I compile the code within this Docker container?

Best regards,

Doug

[Bruno Turcksin]

Doug,

You are using an image build using spack so everything is installed using spack instead of the package manager. If you type `spack find` inside a container, you will see that mpich is installed.

Best,

Bruno

[Doug Shi-Dong]

Dr. Turcksin,

Thank you for the answer. Makes sense why I couldn't find it use apt search. CMake's FindMPI was unable to find it though. Might just need to give it some hints on the spack MPI location.

Either way, I realised that I'm using some features with bugs that were fixed in the current development version.

Are you aware of anyone hosting a "development" Docker build for their own continuous integration. I know this can be very expensive to keep up with the commits. Otherwise, I guess I should just build my own Docker with my current deal.II fork.

Best regards,

Doug

[Bruno Turcksin]

Doug,

Le mer. 23 oct. 2019 à 18:15, Doug Shi-Dong <doug.s...@gmail.com> a écrit :
> Are you aware of anyone hosting a "development" Docker build for their own continuous integration. I know this can be very expensive to keep up with the commits. Otherwise, I guess I should just build my own Docker with my current deal.II fork.

No, I don't know of anyone building a Docker image for each commit in
the master but I guess we could do it. If there is a bug fix or a new
feature in master that I need, I usually just create a new image from
master. Since the library is very stable, I don't need to create a new
image very often.

Best,

Bruno

[Reza Rastak]

Hi,

I have a related issue regarding the docker image. I can see `mpich` when I type `spack find`. However, I don't have access to executable programs `mpirun` or `mpiexec`.

>> mpirun
bash: mpirun: command not found

when I try to load the module I see the following error messages.

>> spack load mpich

==> This command requires spack's shell integration.

  

  To initialize spack's shell commands:

  

      # for bash and zsh

      . /usr/local/share/spack/setup-env.sh

  

      # for csh and tcsh

      setenv SPACK_ROOT /usr/local

      source /usr/local/share/spack/setup-env.csh

  

  This exposes a 'spack' shell function, which you can use like

      $ spack load package-foo

  

  Running the Spack executable directly (for example, invoking

  ./bin/spack) will bypass the shell function and print this

  placeholder message, even if you have sourced one of the above

  shell integration scripts.

>> . /usr/local/share/spack/setup-env.sh

>> spack load mpich

bash: module: command not found

Does anyone know how I can access `mpirun`?

Thank you,

Reza

[luca.heltai]

You can do

export PATH=$(spack location -i mpich)/bin:$PATH

to prepend the path of mpich to your PATH. This is not done automatically. Alternatively, you could also run, as root:

cd /usr/local
spack view add . mpich

which aliases all mpi commands to /usr/local/bin

I usually do this in a custom docker image, derived from the official deal.II image, which I then upload to my personal docker hub, and use for my CI needs.

Best,
Luca.

---
FROM dealii/dealii:v9.1.1-gcc-mpi-fulldepsspack-debugrelease

MAINTAINER luca....@gmail.com

USER root
RUN spack install googletest ninja \
&& spack clean -a \
&& cd /usr/local && spack view add . googletest ninja mpich

RUN chmod 777 /home/$USER

USER $USER

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