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.salvad...@unibs.it> 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 <bruno.turck...@gmail.com> >> 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' >>> >>> '-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 >>> >> >> -- >> The deal.II project is located at http://www.dealii.org/ >> For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> --- >> You received this message because you are subscribed to the Google Groups >> "deal.II User Group" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to dealii+unsubscr...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/a3cf5c27-281e-42fc-9d49-dd6789afbbb5n%40googlegroups.com. > > > Informativa sulla Privacy: http://www.unibs.it/node/8155 > -- > The deal.II project is located at http://www.dealii.org/ > For mailing list/forum options, see > https://groups.google.com/d/forum/dealii?hl=en > --- > You received this message because you are subscribed to the Google Groups > "deal.II User Group" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/CABcATpcWV7LroeEMiN2WGW%3D%2Bjrf%3DeaR3MZoRX0NjvN6Ufde43A%40mail.gmail.com. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/6523682E-1871-45E2-A45F-7CFE8AE3145A%40gmail.com.
