Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos
Hi Bruno and Luca, I finally made it. Here is what I did: spack install gmsh@4.8.4%gcc@7.4.0~med+tetgen+oce less ~/.spack/linux/packages.yaml packages: all: compiler: [gcc@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: flex@2.6.4%gcc@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: gmsh@4.8.4%gcc@7.4.0~med+tetgen+oce spack install dealii%gcc@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.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Fri, Jul 30, 2021 at 5:14 PM Bruno Turcksin wrote: > 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 > > On Friday, July 30, 2021 at 11:09:28 AM UTC-4 Alberto Salvadori wrote: > >> 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 >> >> >> On Fri, Jul 30, 2021 at 5:01 PM Bruno Turcksin >> wrote: >> >>> 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 >>> >>> On Friday, July 30, 2021 at 10:39:13 AM UTC-4 Alberto Salvadori wrote: >>> 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 On Fri, Jul 30, 2021 at 4:12 PM Bruno Turcksin wrote: > 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 > > On Friday, July 30, 2021 at 8:48:04 AM UTC-4 Alberto Salvadori wrote: > >> 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' >>
Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos
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 On Friday, July 30, 2021 at 11:09:28 AM UTC-4 Alberto Salvadori wrote: > 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 > > > On Fri, Jul 30, 2021 at 5:01 PM Bruno Turcksin > wrote: > >> 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 >> >> On Friday, July 30, 2021 at 10:39:13 AM UTC-4 Alberto Salvadori wrote: >> >>> 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 >>> >>> >>> >>> On Fri, Jul 30, 2021 at 4:12 PM Bruno Turcksin >>> wrote: >>> 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 On Friday, July 30, 2021 at 8:48:04 AM UTC-4 Alberto Salvadori wrote: > 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' >
Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos
[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%gcc@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%gcc@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%gcc@7.4.0~cuda~ipo+mpi~openmp~rocm+serial+trilinos build_type=RelWithDebInfo arch=linux-centos7-broadwell ^cmake@3.20.5%gcc@7.4.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-centos7-broadwell ^ncurses@6.2%gcc@7.4.0~symlinks+termlib abi=none arch=linux-centos7-broadwell ^pkgconf@1.7.4%gcc@7.4.0 arch=linux-centos7-broadwell ^openssl@1.1.1k%gcc@7.4.0~docs+systemcerts arch=linux-centos7-broadwell ^perl@5.34.0%gcc@7.4.0+cpanm+shared+threads arch=linux-centos7-broadwell ^berkeley-db@18.1.40%gcc@7.4.0+cxx~docs+stl arch=linux-centos7-broadwell ^bzip2@1.0.8%gcc@7.4.0~debug~pic+shared arch=linux-centos7-broadwell ^diffutils@3.7%gcc@7.4.0 arch=linux-centos7-broadwell ^libiconv@1.16%gcc@7.4.0 arch=linux-centos7-broadwell ^gdbm@1.19%gcc@7.4.0 arch=linux-centos7-broadwell ^readline@8.1%gcc@7.4.0 arch=linux-centos7-broadwell ^zlib@1.2.11%gcc@7.4.0+optimize+pic+shared arch=linux-centos7-broadwell ^openmpi@4.1.1%gcc@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%gcc@7.4.0 arch=linux-centos7-broadwell ^autoconf@2.69%gcc@7.4.0 arch=linux-centos7-broadwell ^m4@1.4.19%gcc@7.4.0+sigsegv arch=linux-centos7-broadwell ^libsigsegv ^automake@1.16.3%gcc@7.4.0 arch=linux-centos7-broadwell ^libtool@2.4.6%gcc@7.4.0 arch=linux-centos7-broadwell ^openssh ^libedit ^trilinos@13.0.1%gcc@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%gcc@7.4.0~bignuma~consistent_fpcsr~ilp64+locking+pic+shared threads=none arch=linux-centos7-broadwell ^arpack-ng@3.8.0%gcc@7.4.0+mpi+shared arch=linux-centos7-broadwell ^metis@5.1.0%gcc@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.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Fri, Jul 30, 2021 at 5:01 PM Bruno Turcksin wrote: > 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 > > On Friday, July 30, 2021 at 10:39:13 AM UTC-4 Alberto Salvadori wrote: > >> Thank you, Bruno. >> It looks like gmsh is the package which requires med: >> >> >>
Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos
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.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Fri, Jul 30, 2021 at 5:01 PM Bruno Turcksin wrote: > 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 > > On Friday, July 30, 2021 at 10:39:13 AM UTC-4 Alberto Salvadori wrote: > >> 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 >> >> >> >> On Fri, Jul 30, 2021 at 4:12 PM Bruno Turcksin >> wrote: >> >>> 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 >>> >>> On Friday, July 30, 2021 at 8:48:04 AM UTC-4 Alberto Salvadori wrote: >>> 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'
Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos
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 > ha scritto: > > > Thank you, Bruno. > It looks like gmsh is the package which requires med: > > > ^gmsh@4.8.4%gcc@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.salvad...@unibs.it > web-page: > http://m4lab.unibs.it/faculty.html > > > >> On Fri, Jul 30, 2021 at 4:12 PM Bruno Turcksin >> wrote: >> 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 >> >>> On Friday, July 30, 2021 at 8:48:04 AM UTC-4 Alberto Salvadori wrote: >>> 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' >>> >>>
Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos
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 On Friday, July 30, 2021 at 10:39:13 AM UTC-4 Alberto Salvadori wrote: > 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 > > > > On Fri, Jul 30, 2021 at 4:12 PM Bruno Turcksin > wrote: > >> 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 >> >> On Friday, July 30, 2021 at 8:48:04 AM UTC-4 Alberto Salvadori wrote: >> >>> 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' >>> >>>
Re: [deal.II] Re: issue in installing dealii 9.2 and .3 on centos
Thank you, Bruno. It looks like gmsh is the package which requires med: ^gmsh@4.8.4%gcc@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.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Fri, Jul 30, 2021 at 4:12 PM Bruno Turcksin wrote: > 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 > > On Friday, July 30, 2021 at 8:48:04 AM UTC-4 Alberto Salvadori wrote: > >> 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' >>
