issue in installing dealii 9.2 and .3 on centos

Alberto Salvadori

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Jul 30, 2021, 8:48:04 AM7/30/21

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Dear community

while installing deal.ii on a centos cluster, I am facing the following issue related to med :

==> Installing med-4.0.0-d65qwjrfigoxirhf5xy6lsumdwpcvluf

==> Warning: Spack will not check SSL certificates. You need to update your Python to enable certificate verification.

==> No binary for med-4.0.0-d65qwjrfigoxirhf5xy6lsumdwpcvluf found: installing from source

==> Using cached archive: /marconi_work/uBS21_CivSal_0/spack/var/spack/cache/_source-cache/archive/a4/a474e90b5882ce69c5e9f66f6359c53b8b73eb448c5f631fa96e8cd2c14df004.tar.gz

==> No patches needed for med

==> med: Executing phase: 'cmake'

==> Error: ProcessError: Command exited with status 1:

'cmake' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:STRING=/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/med-4.0.0-d65qwjrfigoxirhf5xy6lsumdwpcvluf' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF' '-DCMAKE_INSTALL_RPATH:STRING=/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/med-4.0.0-d65qwjrfigoxirhf5xy6lsumdwpcvluf/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/med-4.0.0-d65qwjrfigoxirhf5xy6lsumdwpcvluf/lib64;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/hdf5-1.10.7-nrpa5xndtz4a2yo6xjulubsoqufllvpo/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/numactl-2.0.14-qtf6zwk7cppy35evzpg5bvngl4uioe7v/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/openmpi-4.1.1-ctp6zbck3skxoohx24qake6oljk6ufzr/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/hwloc-2.5.0-g27bmqmr42ruvvwvhvxuqoyk22xokrah/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/libpciaccess-0.16-3lmrc4ak3cqlrwdmu3rwgmdzj6256j6q/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/libxml2-2.9.10-r7ofye65rymwgmbdqgka3tnwbzw3kcvx/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/libiconv-1.16-meyg2avc5ldglxqayvrmzltjirkpgplv/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/xz-5.2.5-wczw77mhc2n2anwdvurydxw45nifh5ik/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/zlib-1.2.11-w4v4ex6wf3qcmkuxdnmga7snctdxiz6h/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/ncurses-6.2-73efdut6ehthgyksblf3qjpmgm7rtced/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/libevent-2.1.12-2y4ktlntxfx32bacu2rrpvmummy7zslt/lib;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/openssl-1.1.1k-p5o7iymffnfrwrakncqzibjwoxoutlsj/lib' '-DCMAKE_PREFIX_PATH:STRING=/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/hdf5-1.10.7-nrpa5xndtz4a2yo6xjulubsoqufllvpo;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/openmpi-4.1.1-ctp6zbck3skxoohx24qake6oljk6ufzr;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/libevent-2.1.12-2y4ktlntxfx32bacu2rrpvmummy7zslt;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/hwloc-2.5.0-g27bmqmr42ruvvwvhvxuqoyk22xokrah;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/libxml2-2.9.10-r7ofye65rymwgmbdqgka3tnwbzw3kcvx;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/xz-5.2.5-wczw77mhc2n2anwdvurydxw45nifh5ik;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/libpciaccess-0.16-3lmrc4ak3cqlrwdmu3rwgmdzj6256j6q;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/numactl-2.0.14-qtf6zwk7cppy35evzpg5bvngl4uioe7v;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/cmake-3.20.5-gnzlzwmoxs5uf2q2sxke33gf2f7atp7h;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/openssl-1.1.1k-p5o7iymffnfrwrakncqzibjwoxoutlsj;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/zlib-1.2.11-w4v4ex6wf3qcmkuxdnmga7snctdxiz6h;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/libiconv-1.16-meyg2avc5ldglxqayvrmzltjirkpgplv;/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/ncurses-6.2-73efdut6ehthgyksblf3qjpmgm7rtced' '-DHDF5_ROOT_DIR:STRING=/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/hdf5-1.10.7-nrpa5xndtz4a2yo6xjulubsoqufllvpo' '-DMEDFILE_BUILD_TESTS:BOOL=OFF' '-DMEDFILE_BUILD_PYTHON:BOOL=OFF' '-DMEDFILE_INSTALL_DOC:BOOL=OFF' '-DCMAKE_Fortran_COMPILER=' '-DCMAKE_CXX_FLAGS:STRING=-DMED_API_23=1' '-DCMAKE_C_FLAGS:STRING=-DMED_API_23=1' '-DMED_API_23=1' '-DMEDFILE_BUILD_SHARED_LIBS=OFF' '-DMEDFILE_BUILD_STATIC_LIBS=ON' '-DMEDFILE_USE_MPI=YES' '-DMPI_ROOT_DIR=/marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/openmpi-4.1.1-ctp6zbck3skxoohx24qake6oljk6ufzr' '/marconi_scratch/userexternal/asalvado/tmp/spack-stage/spack-stage-med-4.0.0-d65qwjrfigoxirhf5xy6lsumdwpcvluf/spack-src'

1 error found in build log:

21 -- Detecting CXX compile features

22 -- Detecting CXX compile features - done

23 -- No Fortran support

24 -- Check for HDF5 ...

25 -- Found HDF5 in CONFIG mode!

26 -- Found HDF5 version 1.10.7 -- parallel flag is set to ON

>> 27 CMake Error at config/cmake_files/FindMedfileHDF5.cmake:118 (GET_PRO

PERTY):

28 GET_PROPERTY could not find TARGET hdf5. Perhaps it has not yet b

een

29 created.

30 Call Stack (most recent call first):

31 config/cmake_files/medMacros.cmake:396 (FIND_PACKAGE)

32 CMakeLists.txt:101 (MED_FIND_HDF5)

33

The build log

/marconi_scratch/userexternal/asalvado/tmp/spack-stage/spack-stage-med-4.0.0-d65qwjrfigoxirhf5xy6lsumdwpcvluf/spack-build-out.txt

clarifies that the error is

-- Check for HDF5 ...

-- Found HDF5 in CONFIG mode!

-- Found HDF5 version 1.10.7 -- parallel flag is set to ON

CMake Error at config/cmake_files/FindMedfileHDF5.cmake:118 (GET_PROPERTY):

GET_PROPERTY could not find TARGET hdf5. Perhaps it has not yet been

created.

Call Stack (most recent call first):

config/cmake_files/medMacros.cmake:396 (FIND_PACKAGE)

CMakeLists.txt:101 (MED_FIND_HDF5)

This looks like a SPACK issue, isn't it? Is there anyway a way to advice spack not to install med or is it a basic ingredient for deal.ii?

Thank you,

Alberto

Bruno Turcksin

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Jul 30, 2021, 10:12:36 AM7/30/21

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Alberto,

I have no clue what med is, so it's not a basic dependency of deal.II. Which version of spack are you using? I don't see a dependency on med when I do `spack speck dealii` You can tell spack not to install med but you need to know which package pulled it.

Best,

Bruno

Alberto Salvadori

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Jul 30, 2021, 10:39:13 AM7/30/21

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Thank you, Bruno.

It looks like gmsh is the package which requires med:

^gm...@4.8.4%g...@7.4.0+alglib~cairo+cgns+compression~eigen~external+fltk+gmp~hdf5~ipo+med+metis+mmg~mpi+netgen+oce~opencascade~openmp~petsc~privateapi+shared~slepc+tetgen+voropp build_type=RelWithDebInfo arch=linux-centos7-broadwell

I am using

[asalvado@r000u07l02 uBS21_CivSal_0]$ spack --version

0.16.2-3715-a904418

Your help is appreciated.

Alberto

Alberto Salvadori
Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
Universita` di Brescia, via Branze 43, 25123 Brescia
Italy
tel 030 3715426

e-mail:
alberto....@unibs.it
web-page:
http://m4lab.unibs.it/faculty.html

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Bruno Turcksin

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Jul 30, 2021, 11:01:49 AM7/30/21

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Alberto,

My experience with spack is to use a release version instead of the development version. They are too many moving parts in spack to expect the development version to be stable. My first question is do you need gmsh support in deal.II? If not you can just do spack install dealii~gmsh. If you need gmsh, can you try spack spec dealii^gmsh~med to check that spack can concretize the package.

Best,

Bruno

Luca Heltai

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Jul 30, 2021, 11:06:09 AM7/30/21

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Can you try

spack edit gmsh

And Comment out the line “depends_on(‘gl2ps’)”?

That line brings in too many deps, and it’s not really necessary.

Luca

Il giorno 30 lug 2021, alle ore 16:39, Alberto Salvadori <alberto....@unibs.it> ha scritto:

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Alberto Salvadori

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Jul 30, 2021, 11:09:28 AM7/30/21

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Bruno,

I do import gmsh triangulations in dealii simulations. Would this be possible without including gmsh ?

Alberto

Alberto Salvadori
Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
Universita` di Brescia, via Branze 43, 25123 Brescia
Italy
tel 030 3715426

e-mail:
alberto....@unibs.it
web-page:
http://m4lab.unibs.it/faculty.html

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Alberto Salvadori

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Jul 30, 2021, 11:10:22 AM7/30/21

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[asalvado@r000u07l02 uBS21_CivSal_0]$ spack spec dealii^gmsh~med

Input spec

--------------------------------

dealii

^gmsh~med

Concretized

--------------------------------

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

gmsh@4.8.4%g...@7.4.0+alglib~cairo+cgns+compression~eigen~external+fltk+gmp~hdf5~ipo+med+metis+mmg~mpi+netgen~oce~opencascade~openmp~petsc~privateapi+shared~slepc~tetgen+voropp build_type=RelWithDebInfo arch=linux-centos7-broadwell

while trying to concretize the partial spec:

dealii@9.3.0%g...@7.4.0+adol-c+arborx+arpack+assimp~cuda~doc+examples+ginkgo+gmsh+gsl+hdf5~int64~ipo+metis+mpi+muparser~nanoflann~netcdf+oce~optflags+p4est+petsc~python+scalapack+simplex+slepc+sundials+symengine+threads+trilinos build_type=DebugRelease cuda_arch=none cxxstd=default arch=linux-centos7-broadwell

^arborx@1.0%g...@7.4.0~cuda~ipo+mpi~openmp~rocm+serial+trilinos build_type=RelWithDebInfo arch=linux-centos7-broadwell

^cmake@3.20.5%g...@7.4.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-centos7-broadwell

^ncurses@6.2%g...@7.4.0~symlinks+termlib abi=none arch=linux-centos7-broadwell

^pkgconf@1.7.4%g...@7.4.0 arch=linux-centos7-broadwell

^openssl@1.1.1k%g...@7.4.0~docs+systemcerts arch=linux-centos7-broadwell

^perl@5.34.0%g...@7.4.0+cpanm+shared+threads arch=linux-centos7-broadwell

^berkeley-db@18.1.40%g...@7.4.0+cxx~docs+stl arch=linux-centos7-broadwell

^bzip2@1.0.8%g...@7.4.0~debug~pic+shared arch=linux-centos7-broadwell

^diffutils@3.7%g...@7.4.0 arch=linux-centos7-broadwell

^libiconv@1.16%g...@7.4.0 arch=linux-centos7-broadwell

^gdbm@1.19%g...@7.4.0 arch=linux-centos7-broadwell

^readline@8.1%g...@7.4.0 arch=linux-centos7-broadwell

^zlib@1.2.11%g...@7.4.0+optimize+pic+shared arch=linux-centos7-broadwell

^openmpi@4.1.1%g...@7.4.0~atomics~cuda~cxx~cxx_exceptions+gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker~pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=none schedulers=none arch=linux-centos7-broadwell

^hwloc@2:

^libevent@2.0:

^numactl@2.0.14%g...@7.4.0 arch=linux-centos7-broadwell

^autoconf@2.69%g...@7.4.0 arch=linux-centos7-broadwell

^m4@1.4.19%g...@7.4.0+sigsegv arch=linux-centos7-broadwell

^libsigsegv

^automake@1.16.3%g...@7.4.0 arch=linux-centos7-broadwell

^libtool@2.4.6%g...@7.4.0 arch=linux-centos7-broadwell

^openssh

^libedit

^trilinos@13.0.1%g...@7.4.0~adios2+amesos+amesos2+anasazi+aztec~basker+belos~boost~cgns~chaco~complex~cuda~cuda_rdc~debug~dtk+epetra+epetraext~epetraextbtf~epetraextexperimental~epetraextgraphreorderings~exodus+explicit_template_instantiation~float+fortran~hdf5~hypre+ifpack+ifpack2~intrepid~intrepid2~ipo~isorropia+kokkos~matio~mesquite~minitensor+ml+mpi+muelu~mumps~netcdf~nox~openmp~phalanx~piro~pnetcdf~python~rol~rythmos+sacado~scorec~shards+shared~shylu~stk~stokhos~stratimikos~strumpack~suite-sparse~superlu~superlu-dist~teko~tempus+tpetra~trilinoscouplings~wrapper~zlib~zoltan~zoltan2 build_type=RelWithDebInfo cuda_arch=none cxxstd=11 gotype=long arch=linux-centos7-broadwell

^openblas@0.3.17%g...@7.4.0~bignuma~consistent_fpcsr~ilp64+locking+pic+shared threads=none arch=linux-centos7-broadwell

^arpack-ng@3.8.0%g...@7.4.0+mpi+shared arch=linux-centos7-broadwell

^metis@5.1.0%g...@7.4.0~gdb~int64~real64+shared build_type=Release arch=linux-centos7-broadwell

dealii requires gmsh variant +tetgen, but spec asked for ~tetgen

[asalvado@r000u07l02 uBS21_CivSal_0]$

Alberto Salvadori
Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
Universita` di Brescia, via Branze 43, 25123 Brescia
Italy
tel 030 3715426

e-mail:
alberto....@unibs.it
web-page:
http://m4lab.unibs.it/faculty.html

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/ee97462e-8364-41a8-80e7-88467925d876n%40googlegroups.com.

Bruno Turcksin

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Jul 30, 2021, 11:14:22 AM7/30/21

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Alberto,

If the question is "can dealii read a gmsh file without gmsh support ?" the answer is yes. The gmsh support is for deal.II to use gmsh internally not to read a gmsh file.

Best,

Bruno

Alberto Salvadori

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Jul 30, 2021, 12:10:29 PM7/30/21

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Hi Bruno and Luca,

I finally made it. Here is what I did:

spack install gm...@4.8.4%g...@7.4.0~med+tetgen+oce

less ~/.spack/linux/packages.yaml

packages:

all:

compiler: [g...@7.4.0]

flex:

version: [2.6.4]

buildable: false

gmsh:

version: [4.8.4]

buildable: false

externals:

- prefix: /marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/flex-2.6.4-qqacz2f6twfpyotvlzqgtktpmcdn5cni

spec: fl...@2.6.4%g...@7.4.0

- prefix: /marconi_work/uBS21_CivSal_0/spack/opt/spack/linux-centos7-broadwell/gcc-7.4.0/gmsh-4.8.4-476qnx2qlzhfboru3b6cn5sw4auxjtkp

spec: gm...@4.8.4%g...@7.4.0~med+tetgen+oce

spack install dealii%g...@7.4.0

Thank you for your help.

Alberto

Alberto Salvadori
Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
Universita` di Brescia, via Branze 43, 25123 Brescia
Italy
tel 030 3715426

e-mail:
alberto....@unibs.it
web-page:
http://m4lab.unibs.it/faculty.html

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/b7ba5659-17be-4f3d-90ed-3de67ee1805dn%40googlegroups.com.

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