what a pain trying to install deal.II

[Henri Girard]

Hi,
I decided to join the mailing list because I can't get dealii working. I tried linuxbrew but it can't get two deps hdf5 and petsc.
With hdf5 he wants "15" but now is 16 then it can't find the patch (apparently)
I compiled it from git, no problem but it didn't work (no examples compiled)
I really would it working on ubuntu 15.10 because I would like it working with visit (i am translating it in french)
Any help :)
Best regards
Henri

[Jean-Paul Pelteret]

Hi Henri,

I see that you've read the discussion on the mailing list regarding installers for deal.II. Firstly, you should note that none of those, including Linuxbrew, are "officially" supported as of yet. This is still a work in progress.

If you are set on using Linuxbrew to install deal.II then there is a repository that has an install script that has been tested with Ubuntu 14.04 (last done about 3 weeks ago). That said, it should work with 15.10 as well. If you are still running into problems, then you can easily adjust the formulae and submit a patch / pull request to help update them.

J-P

[Henri Girard]

Thanks for the answer.
That's the bash file I used. I first tried from there (sorry for not mentioning it).
I didn't find yet the way of changing it. I am not an expert on patch.
I just comment the two lines to see if the install would go to the end.
Henri

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[Uwe Köcher]

Dear Henri,

candi should work out of the box on ubuntu 15.10.

I've tested it a lot of times in the recent past on virtual machines and

I know from Timo Heister and Bruno Turcksin that they are using candi on ubuntu.

git clone https://github.com/koecher/candi
cd  candi
./candi.sh

Please install the system packages from the first output and re-run candi again.

More user documentation can be found online: https://github.com/koecher/candi

Best

  Uwe

[Henri Girard]

Thanks, I am doing candi.sh. Apparently deal.II is a long compilation.
I will try it after on fedora and I am testing ubuntu 16.04 but it seems i change to change the platform because it doesn't find it ?
Thank you for your help :)
Henri

[Uwe Köcher]

Sigh. I did not know that there is a new ubuntu 16. You can try to force the ubuntu 15 platform by

./candi.sh -pf=./deal.II-toolchain/platforms/supported/ubuntu15.platform

You can additionally speed up the compilation by using more than one build process

./candi.sh -j4

if you have 4 processors.

Fedora (21)/22/23 are supported and working out of the box (I'm using fedora on my workstations / notebooks).

[Henri Girard]

Build finished in 11175 seconds.

Summary of timings:

dealii-prepare: 0 s
parmetis: 61 s
superlu_dist: 10 s
hdf5: 325 s
p4est: 150 s
trilinos: 3742 s
petsc: 150 s
slepc: 14 s
dealii: 6704 s
riri@pc:~/candi$
riri@pc:~/candi$

[Henri Girard]

Wonderbar !
step-1 compiled perfectly
I will try to copy this version to my partition 16.04 and see if it works with setting path

Le 26/11/2015 16:15, Uwe Köcher a écrit :

[Uwe Köcher]

I will try to copy this version to my partition 16.04 and see if it works with setting path

Some of the libraries are picking up system pathes during configuration. I don't think that this will work.

If copying does not work, you need to run candi on the other system again. 

[Henri Girard]

You are right ... It doesn't work, but that's a good exercise ! lol

[Henri Girard]

-pf worked I add too -j9 and  prefix

Le 26/11/2015 16:15, Uwe Köcher a écrit :

[Uwe Köcher]

good to know, so there are good indicators that we do not have to change much for the upcoming ubuntu 16.

May you be so kind and send me the outputs for ubuntu 16 from the following commands:

lsb_release -i -s
lsb_release -c -s
lsb_release -d -s

Then I can add the platformfile for ubuntu16

Kind regards

  Uwe

[Henri Girard]

ok
wih -j9 it's nearly finished
lsb_release -i -s
Ubuntu
lsb_release -c -s
xenial
lsb_release -d -s
Ubuntu Xenial Xerus (development branch)

[Henri Girard]

Look the difference of time :
Build finished in 3609 seconds.

Summary of timings:

dealii-prepare: 0 s

parmetis: 57 s
superlu_dist: 9 s
hdf5: 158 s
p4est: 75 s
trilinos: 1263 s
petsc: 168 s
slepc: 15 s
dealii: 1859 s

[Uwe Köcher]

Thanks a lot,

after a fresh git clone or git pull of/within your current candi ubuntu 16 (xenial) should be automatically detected.

[Henri Girard]

Works fine I set export deal_ii and source .bashrc. Perfect detection of lib, as you told me I hadn't to change dealii dir... Because it the same happy end.Well next time I don't change anything in your candi install just add -j xx

[Henri Girard]

I am compiling the new version 16.04

[Henri Girard]

I got this problem while compiling new git candi :
/usr/lib/openmpi/include/mpi_portable_platform.h:374:63: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
              _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEVEL__)
                                                               ^
[ 30%] Built target obj_grid.debug
Makefile:116: recipe for target 'all' failed
make: *** [all] Error 2
Failure with exit status: 2
Exit message: There was a problem building dealii v8.3.0.
Any help welcome
Kind regards
Henri

--

[Uwe Köcher]

Just for notice: this issue is resolved. The problem was the copying of an old build directory to another machine.

Thx Henri for testing this on the upcoming ubuntu version so far with candi.

@Henri: may you please set your issue as "answered" and if you like mark the "best answer" for further reference?

Kind regards

  Uwe

[Henri Girard]

Thank you again for the rapid and efficient help you bring to me to solve this issue, otherwise I think i couldn't use deal.II. What a pity !
Kind regards
Henri

[Henri Girard]

So coming back to deal.ii after a long time... But surprise to see candi.sh is not mentioned anywhere to compile it ?

As I am on 16.04 I can't get a newer version so I am trying to compile it with candy. Fortunatly I didn't remenber the way to compile it but I remenber candy.sh was very easy, and my mails were still here.

Thanks for this nice software

Henri

[Uwe Köcher]

Dear Henri,

candi is now hosted additionally as a official deal.II github repository:

  https://github.com/dealii/candi

Indeed, the documentation on the website for candi is still not there. (I did not find the time to contribute in this).

On Friday, January 27, 2017 at 6:51:14 PM UTC+1, Henri Girard wrote:

So coming back to deal.ii after a long time... But surprise to see candi.sh is not mentioned anywhere to compile it ?

As I am on 16.04 I can't get a newer version so I am trying to compile it with candy. Fortunatly I didn't remenber the way to compile it but I remenber candy.sh was very easy, and my mails were still here.

Thanks for this nice software

Henri

Thanks for the credit. That's the reason why candi is still there and get updates.

If you have checked out the current version, you may have noticed that we have worked hard on it to make it as easy to use and flexible as possible.

Kind regards

  Uwe

[Henri Girard]

Excellent ! I run candi.sh and I got after a "certain" times deal.ii, compiled and working (examples too), which is not always the case with a lot of software. I don't remenber if it's possible but I noticed one can run candi.sh --prefix=/usr (for me on ubuntu) I like to put everythink there so there are less problems with path.

What I was suggesting is just having a link to remenber this wonderfull, perfect way of installing it, before reading all installation doc and being frighten with all deps and application lying under it.

Thanks you :)

Best

Henri