dealii 8.5.1 installation issue (spack, docker, debian)

[Marquito Forrest]

Hallo dear reader of my question,

I am trying to help my girlfriend (who studies mechanical engineering) to make dealii available on her Macbook, since she wants to work with this library (project / thesis work).

Originally I tried to install dealii via spack but I failed various times. Hence I decided to use a linux system as the basis, since this seems to be much better supported (according to spack documentation, and github issues of both dealii and spackpm).

Unfortunately there is no up-to-date docker image. In case I shall succeed I am very willing to share my success in the form of such an image. But I am still running into problems with compiling dealii, having had success with the dependencies.

I am incapable of detecting any potential issue / cause of the problem from the spack-build.out. This file is attached to this question as the third file.

The first and second file are two Dockerfiles and hence define exactly on what system I tried to install dealii.

In summary the situation is:

- Debian testing image (to get recent gcc)

- Miniconda Python 3.6 (my own Dockerfile, cf. file 1)

- Latest spack from github (another Dockerfile derived from file 1, cf. file 2)

- Then in a bash I ran "spack install dealii -trilinos -oce ^cm...@3.9.4"

     Since PETSc failed to build some FORTRAN specific stuff (f90-mod) and I assumed we don't need any FORTRAN bindings

     I ran "spack edit petsc" and set "--with-fc=0", which led to a successful compilation of PETSc.

     At last the dealii compilation failed but I was not able to deduce any logical steps to take from the error messages.

If anyone can help me and my girlfriend, I will try my best to make this available to other potential users who are not able to get dealii running. I think a working docker-image of a recent version will be very helpful for many users.

Best regards,

Marquito

[Bruno Turcksin]

Marquito,

On Sunday, March 11, 2018 at 9:27:40 AM UTC-4, Marquito Forrest wrote:

In summary the situation is:

- Debian testing image (to get recent gcc)

- Miniconda Python 3.6 (my own Dockerfile, cf. file 1)

- Latest spack from github (another Dockerfile derived from file 1, cf. file 2)

- Then in a bash I ran "spack install dealii -trilinos -oce ^cm...@3.9.4"

     Since PETSc failed to build some FORTRAN specific stuff (f90-mod) and I assumed we don't need any FORTRAN bindings

     I ran "spack edit petsc" and set "--with-fc=0", which led to a successful compilation of PETSc.

     At last the dealii compilation failed but I was not able to deduce any logical steps to take from the error messages.

A few things:
1) there is a binary available for Mac see here http://dealii.org/download.html
2) there are people installing deal.II with spack on mac so you may want to post your problem here so we can help you
3) we have several docker images on dockerhub see https://hub.docker.com/u/dealii/ deal.ii/full-depends was updated two days ago so you may want to give it a try. If you want to have your own Dockerfile, I suggest that you take a look at ours here https://github.com/dealii/docker-files
4) your installation fails with this error:
       g++: internal compiler error
    this happens when you don't have enough ram. Try using less processors. You are using 4 right now, try with one.

Best,

Bruno

[Denis Davydov]

Marquito,

A few things to add to what Bruno says:

On Monday, March 12, 2018 at 2:40:37 AM UTC+1, Bruno Turcksin wrote:

Marquito,

On Sunday, March 11, 2018 at 9:27:40 AM UTC-4, Marquito Forrest wrote:

In summary the situation is:

- Debian testing image (to get recent gcc)

- Miniconda Python 3.6 (my own Dockerfile, cf. file 1)

- Latest spack from github (another Dockerfile derived from file 1, cf. file 2)

- Then in a bash I ran "spack install dealii -trilinos -oce ^cm...@3.9.4"

     Since PETSc failed to build some FORTRAN specific stuff (f90-mod) and I assumed we don't need any FORTRAN bindings

     I ran "spack edit petsc" and set "--with-fc=0", which led to a successful compilation of PETSc.

     At last the dealii compilation failed but I was not able to deduce any logical steps to take from the error messages.

A few things:
1) there is a binary available for Mac see here http://dealii.org/download.html 

2) there are people installing deal.II with spack on mac so you may want to post your problem here so we can help you

yes. My best guess is that you miss fortran compiler, which is required in a few places for dependencies.

This is mention here  https://github.com/dealii/dealii/wiki/deal.II-in-Spack

You would need to install `spack install gcc` and then add `gfortran` to the `clang` compiler family in 

~./spack/compilers.yaml

 

3) we have several docker images on dockerhub see https://hub.docker.com/u/dealii/ deal.ii/full-depends was updated two days ago so you may want to give it a try. If you want to have your own Dockerfile, I suggest that you take a look at ours here https://github.com/dealii/docker-files
4) your installation fails with this error:
       g++: internal compiler error
    this happens when you don't have enough ram. Try using less processors. You are using 4 right now, try with one.

you can do that with `spack install -j 1 dealii

 

Best,

Bruno

[Marquito Forrest]

Thanks so much both Bruno and Denis!

I upped the RAM in the Docker settings a bit and added “-j 2” as a parameter to the install command and everything went fine :)
Great!

Best,
Marquito

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[Timo Heister]

> g++: internal compiler error: Killed

are you running out of memory by any chance? Use a smaller number for "-j".

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Timo Heister
http://www.math.clemson.edu/~heister/