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
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