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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/a3cf5c27-281e-42fc-9d49-dd6789afbbb5n%40googlegroups.com.
