Error in installing deal.ii with spack on CentOs7

[Alberto Salvadori]

Dear community

I am installing deal.ii (latest release) on a CentOS7 equipped machine. After typing

spack install --test=root dealii

I see this error:

==> Error: An unsatisfiable version constraint has been detected for spec:

    suite-...@5.3.0%g...@4.8.5~cuda~openmp+pic~tbb arch=linux-centos7-x86_64 


while trying to concretize the partial spec:

    dea...@9.0.1%g...@4.8.5+adol-c+arpack+assimp build_type=DebugRelease ~cuda cuda_arch= ~doc+gmsh+gsl+hdf5~int64+metis+mpi+nanoflann+netcdf+oce~optflags+p4est+petsc~python+scalapack+slepc+sundials+trilinos arch=linux-centos7-x86_64 
        ^ado...@2.6.4:
        ^arpack-ng+mpi
            ^mpi
            ^open...@0.3.3%g...@4.8.5 cpu_target= ~ilp64+pic+shared threads=none ~virtual_machine arch=linux-centos7-x86_64 
        ^assimp
            ^bo...@1.59.0:1.63,1.65.1,1.67.0:+iostreams+serialization+system+thread
                ^bzip2
                    ^diffutils
                ^zl...@1.2.11%g...@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64 
            ^cm...@3.12.2%g...@4.8.5~doc+ncurses+openssl+ownlibs~qt arch=linux-centos7-x86_64 
                ^ncurses
                    ^pkgconfig
                ^openssl
                    ^pe...@5.14.0:
                        ^gdbm
                            ^readline
        ^gmsh+netgen+oce+tetgen
            ^gmp
                ^autoconf
                    ^m...@1.4.6:
                ^automake
                ^lib...@2.4.2:
            ^netgen
            ^oce
            ^tetgen
        ^hd...@1.8.9:+hl+mpi
        ^intel-tbb@2019%g...@4.8.5 cxxstd=default +shared+tm arch=linux-centos7-x86_64 
        ^metis@5:~int64+real64
        ^mupa...@2.2.5%g...@4.8.5 arch=linux-centos7-x86_64 
        ^nanoflann
        ^netcdf+mpi
        ^p4est
        ^sundials~pthread
        ^trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos
            ^glm
            ^matio


dealii requires suite-sparse version :5.1.0, but spec asked for 5.3.0

I wonder which is the source of the error and which files ( ~/.spack/linux/packages.yaml perhaps?)
shall I edit to sort out the issue.

Many thanks in advance

Alberto

[Praveen C]

When I check spec on my opensuse machine, dea...@9.0.1 wants to use suite-...@5.3.0

Have you perhaps already set some versions in your “.spack/linux/packages.yaml” file ?

What does your file look like ?

Also, you may want to update your spack to see it that fixes it.

Thanks

praveen

Informativa sulla Privacy: http://www.unibs.it/node/8155

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[Alberto Salvadori]

Thank you, Praveen.

While installing deal.ii all detailed instructions on the spack wiki page have been followed. I cloned spack from git (I thus assume it is the latest version) and made no modifications (yet :-) ) to the  “.spack/linux/packages.yaml” file. By the way, I did install deal.ii on opensuse a couple of weeks ago without this issue.

Shall I attach my  “.spack/linux/packages.yaml”  here?

Alberto 

Alberto Salvadori
 Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

[Jean-Paul Pelteret]

Hi Alberto,

As best I recall, their is a problem with a hidden clash in the dependencies between the latest PETSc and Trilinos versions. (I thought that there was an issue/PR on github/spack, but I couldn’t find it right now.) The former wants a new version of SuiteSparse while the latter does not yet support it. I think that the solution is to specify an older version of PETSc when building with both PETSc and Trilinos.

Best,

J-P

[Alberto Salvadori]

Thank you J-P.

Can you please remind me how to do what you suggest? Shall I edit “.spack/linux/packages.yaml” file ?

Alberto Salvadori
 Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

[Jean-Paul Pelteret]

Shall I edit “.spack/linux/packages.yaml” file ?

Yes, since you’re already using this file to constrain other packages I would suggest adding

  petsc:

    version: [3.9.4]

  suite-sparse:

    version: [5.1.0]

to that list. You should check to see if the version of PETSc can be safely incremented upwards - I’ve taken a conservative guess as to which version is safe to use.

[Alberto Salvadori]

J-P  and Praveen,

Thanks for your help. Spack installation for deal.ii  worked out well. Petsc 3.10 or later is required, I used 3.10. 

Alberto

Alberto Salvadori

Associate Professor 

DIMI, University of Brescia, Italy

[Denis Davydov]

Yes, JP is correct that it has to do with incompatible requirements on suitesparse from Trilinos and latest release of PETSc.
To overcome this I recently disabled suitesparse by default in Trilinos, but it could be that the commit hash we recommend currently on wiki does not have this. I will check it later today and update wiki if needed.

Regards,
Denis

[Denis Davydov]

Alberto,

Did you reset Spack to the current recommended version, namely e38f39e4eafeaa6daed580cece935141e5d8f04b  (I edited the wiki 7 days ago)?

I double checked that 9.0.1 has no issues with concretization there with empty packages.yaml settings.

My guess would be that

(i) either you used older version where the conflict between PETSc and Trilinos is not resolved or

(ii) you have extra preferences in your packages.yaml that cause this conflict

Regards,

Denis.

[Alberto Salvadori]

Hi Denis,

thanks! Here is my history file.

   90  cd Pubblici/
   91  mkdir spack
   94  cd spack/
   95  git clone https://github.com/spack/spack.git .
   96  git checkout develop
   97  git reset --hard e38f39e4eafeaa6daed580cece935141e5d8f04b
   98  spack install dealii
   99  cd ..
  100  nano .spack/linux/packages.yaml
  101  cd Pubblici/spack/
  102  spack install dealii
  103  ls -lta
  104  cd share/
  105  ls
  106  cd spack/
  107  ls
  108  cd /home/alberto.salvadori/Pubblici/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/dealii-9.0.1-jdludrcm25brf6vxyb5l6dqnmjigzvyq
  109  ls -lta
  110  ls share/

You see that there are two calls "spack install dealii" since I had to edit the file ".spack/linux/packages.yam" in order to install petsc 3.10

Hope this helps

Alberto

Alberto Salvadori
 Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

[Denis Davydov]

Hi Alberto,

Unfortunately I can reproduce you error in a clean environment on my Ubuntu machine. But I am glad that you solved the issue.

Regards,

Denis

23 окт. 2018 г., в 18:06, Alberto Salvadori <alberto....@unibs.it> написал(а):

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[Denis Davydov]

On Tuesday, October 23, 2018 at 6:39:46 PM UTC+2, Denis Davydov wrote:
>
> Unfortunately I can reproduce you error in a clean environment on my Ubuntu machine. But I am glad that you solved the issue.

I meant “can NOT reproduce”, sorry for the typo.

Regards,
Denis
.

[Denis Davydov]

Hi Alberto,

I figured out what's happening. The issue you see is NOT related to what me and JP suggested.

It is a separate issues related to constraints on compilers from suite-sparse. I created a PR in spack to clarify this:

https://github.com/spack/spack/pull/9622/ 

Once it's merged, you would not see the "conretization" error, but you should see that you can't build the most recent suite-sparse with older GCC.

The end solution would be the same: 

(i) you need to choose suite-...@5.1.0 which can be built with GCC 4.8.5

(ii) you need to choose older version of PETSc which support older versions of suite-sparse.

Regards,

Denis.

[Alberto Salvadori]

Very good, thanks!

Sent from my iPad

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