Thanks Alberto; the "Deferred-length character" error vanishes with a modern gcc.
On Fri, 7 Jun 2024 at 22:00, Alberto Garcia <alber...@icmab.es> wrote: > You compiler (gnu 4.8.5) is *very* old. Please upgrade to a modern version. > > Best regards, > > Alberto > > > ----- El 6 de Junio de 2024, a las 19:09, Boubacar Traore < > bt.bouba...@gmail.com> escribió: > > I finally sorted out the issue of scalapack linking by adding its path to > LIBRARY_PATH instead of LD_LIBRARY_PATH (more info here: > https://urldefense.com/v3/__https://stackoverflow.com/questions/47105835/ld-library-path-is-ignored-by-gcc__;!!D9dNQwwGXtA!V3AkKMLCSGZOKkh_zfS8r1kcYcyK6WFVYg9o6fg3LQbmBE9vrhj8bkJqVK30r8O-MI2SQbO6_pxVcf_zSf4$ > > <https://urldefense.com/v3/__https://stackoverflow.com/questions/47105835/ld-library-path-is-ignored-by-gcc__;!!D9dNQwwGXtA!UKXFsN93oU7fdjctS5itiA2CMH4YTUW-VUxSJl8f5ejE_wN2ffrRXxBautffKqwBfEnjMj-Kg2AAYGfMdi0$> > ). > > I used this for cmake build stage: > $ cmake -S. -B_build > -DCMAKE_INSTALL_PREFIX=/home/boubacart/SIESTA/siesta/bin > -DSIESTA_WITH_MPI=ON -DSIESTA_WITH_ELPA=ON > -DSCALAPACK_LIBRARY_DIR=/usr/lib64/openmpi/lib > -DSCALAPACK_LIBRARY="-lscalapack" > > The config steps then succeeds. > > However, I encounter other issues during the compilation stage and I am > not sure what is the problem and from the start it issues errors regarding > some deferred-length character : > =============== > [ 0%] Building Fortran object > _deps/libfdf-build/CMakeFiles/libfdf-lib.dir/src/prec.F90.o > [ 0%] Building Fortran object > _deps/mctc-lib-build/CMakeFiles/mctc-lib-lib.dir/src/mctc/env/accuracy.f90.o > [ 0%] Building Fortran object > _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/wxml/m_wxml_array_str.f90.o > [ 0%] Building Fortran object > _deps/libfdf-build/CMakeFiles/libfdf-lib.dir/src/utils.F90.o > [ 0%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/alloc.F90.o > [ 0%] Building Fortran object > _deps/mctc-lib-build/CMakeFiles/mctc-lib-lib.dir/src/mctc/env/error.f90.o > > /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/mctc-lib-src/src/mctc/env/error.f90:46.46: > > character(len=:), allocatable :: message > 1 > Error: Deferred-length character component 'message' at (1) is not yet > supported > > /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/mctc-lib-src/src/mctc/env/error.f90:46.46: > > character(len=:), allocatable :: message > 1 > Error: Deferred-length character component 'message' at (1) is not yet > supported > gmake[2]: *** > [_deps/mctc-lib-build/CMakeFiles/mctc-lib-lib.dir/src/mctc/env/error.f90.o] > Error 1 > gmake[1]: *** [_deps/mctc-lib-build/CMakeFiles/mctc-lib-lib.dir/all] Error > 2 > gmake[1]: *** Waiting for unfinished jobs.... > [ 0%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/precision.F90.o > [ 0%] Building Fortran object > _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/wxml/m_wxml_error.f90.o > [ 0%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/sys.F90.o > [ 0%] Building Fortran object > _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/wxml/m_wxml_escape.f90.o > > .. > .. > .. > [ 2%] Building Fortran object > _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/dom/m_dom_parse.f90.o > [ 2%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/debugxc.F90.o > [ 3%] Building Fortran object > _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/xpath/xmlf90_xpath.f90.o > [ 3%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/vv_vdwxc.F90.o > [ 3%] Building Fortran object > _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/dom/xmlf90_dom.f90.o > [ 3%] Linking Fortran static library libxmlf90.a > [ 3%] Built target xmlf90-lib > [ 3%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/fft3d.F90.o > > /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:234.25: > > call c_f_pointer(c_loc(aDat(:,:,:,1)),aux1,[aMesh(1)*aMesh(2)*aMesh(3)]) > 1 > Warning: Array section in 'c_loc' call at (1) > > /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:235.25: > > call c_f_pointer(c_loc(aDat(:,:,:,2)),aux2,[aMesh(1)*aMesh(2)*aMesh(3)]) > 1 > Warning: Array section in 'c_loc' call at (1) > > /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:249.28: > > call c_f_pointer(c_loc(aDat(:,:,i3,1)),aux1,[aMesh(1)*aMesh(2)]) > 1 > Warning: Array section in 'c_loc' call at (1) > > /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:250.28: > > call c_f_pointer(c_loc(aDat(:,:,i3,2)),aux2,[aMesh(1)*aMesh(2)]) > 1 > Warning: Array section in 'c_loc' call at (1) > > /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:263.25: > > call c_f_pointer(c_loc(aDat(:,:,:,1)),aux1,[aMesh(1)*aMesh(2)*aMesh(3)]) > 1 > Warning: Array section in 'c_loc' call at (1) > > /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:264.25: > > call c_f_pointer(c_loc(aDat(:,:,:,2)),aux2,[aMesh(1)*aMesh(2)*aMesh(3)]) > 1 > Warning: Array section in 'c_loc' call at (1) > [ 3%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/vdwxc.F90.o > [ 4%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/fftr.F90.o > [ 4%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/xcmod.F90.o > [ 4%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/cellxc.F90.o > [ 4%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/atomxc.F90.o > [ 4%] Building Fortran object > _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/gridxc.F90.o > [ 4%] Linking Fortran static library libgridxc.a > [ 4%] Built target libgridxc-lib > gmake: *** [all] Error 2 > > Time spent in user mode (CPU seconds) : 16.861s > Time spent in kernel mode (CPU seconds) : 1.792s > Total time : 0:07.27s > CPU utilisation (percentage) : 256.5% > Times the process was swapped : 0 > Times of major page faults : 1 > Times of minor page faults : 863847 > =========================================== > > > Anyone have an idea about solutions to this ? > > Thanks, > Boubacar > > On Thu, 6 Jun 2024 at 09:25, Boubacar Traore <bt.bouba...@gmail.com> > wrote: > >> More specifically it stops at scalapack stage when : >> "-- Performing Test scalapack_has_blacs_gridinit - Failed" >> >> The config routine finds scalapack but it fails in >> "SiestaCheckLinalg.cmake" routine. >> All the dependencies were installed according to the doc. So, I am not >> sure if I still missed something or if it is a bug ? >> >> Thanks, >> Boubacar >> >> On Wed, 5 Jun 2024 at 21:54, Boubacar Traore <bt.bouba...@gmail.com> >> wrote: >> >>> Hi, >>> I am trying to compile siesta with cmake but I encounter issues with >>> scalapack linking. I notice that the compilation process has changed >>> compared to what I was used to. >>> >>> Here is my cmake build command: >>> >>> $ cmake -S. -B_build >>> -DCMAKE_INSTALL_PREFIX=/home/boubacart/SIESTA/siesta/bin >>> -DSIESTA_WITH_MPI=ON -DSIESTA_WITH_ELPA=ON -DSIESTA_WITH_LIBXC=ON >>> -DSCALAPACK_LIBRARY="-lscalapack-openmpi-devel" >>> >>> It fails at with a linking error as shown below: >>> =================================== >>> -- The Fortran compiler identification is GNU 4.8.5 >>> -- The C compiler identification is GNU 4.8.5 >>> -- Detecting Fortran compiler ABI info >>> -- Detecting Fortran compiler ABI info - done >>> -- Check for working Fortran compiler: /bin/f95 - skipped >>> -- Detecting C compiler ABI info >>> -- Detecting C compiler ABI info - done >>> -- Check for working C compiler: /bin/cc - skipped >>> -- Detecting C compile features >>> -- Detecting C compile features - done >>> -- Check use of deprecated variables >>> -- All Siesta variables/options are prefixed with SIESTA_, e.g. >>> SIESTA_WITH_MPI >>> -- Check use of deprecated variables - success >>> -- Using GNU compiler >>> -- Using toolchain: Config/cmake/toolchains/gnu.cmake >>> -- >>> No build type selected. SIESTA will default to 'Release'. >>> To override pass -DCMAKE_BUILD_TYPE=<type> in order to configure SIESTA. >>> Available options are: >>> * -DCMAKE_BUILD_TYPE=Release - For an optimized build with no >>> assertions or debug info. >>> * -DCMAKE_BUILD_TYPE=Debug - For an unoptimized build with assertions >>> and debug info. >>> * -DCMAKE_BUILD_TYPE=Check - For an unoptimized build with assertions >>> and debug info + code checks. >>> * -DCMAKE_BUILD_TYPE=RelWithDebInfo - For an optimized build with no >>> assertions but with debug info. >>> * -DCMAKE_BUILD_TYPE=MinSizeRel - For a build optimized for size >>> instead of speed. >>> >>> -- Flags for C-compiler (build type: Release): -O3 -march=native >>> -- Flags for Fortran-compiler (build type: Release): -O3 -march=native >>> -- Found PkgConfig: /bin/pkg-config (found version "0.27.1") >>> -- Checking Siesta version >>> -- SIESTA_VERSION: 5.1-MaX-28-gf3224d62e (err=3) >>> -- >>> WARNING: This is *not* an official SIESTA release. >>> WARNING: >>> WARNING: Unless you are trying a feature or fix that has not >>> WARNING: been released yet, we strongly recommend the use of >>> WARNING: official releases of SIESTA, which can be downloaded from >>> WARNING: >>> https://urldefense.com/v3/__https://gitlab.com/siesta-project/siesta/-/releases__;!!D9dNQwwGXtA!V3AkKMLCSGZOKkh_zfS8r1kcYcyK6WFVYg9o6fg3LQbmBE9vrhj8bkJqVK30r8O-MI2SQbO6_pxVtGQMjJg$ >>> >>> <https://urldefense.com/v3/__https://gitlab.com/siesta-project/siesta/-/releases__;!!D9dNQwwGXtA!UKXFsN93oU7fdjctS5itiA2CMH4YTUW-VUxSJl8f5ejE_wN2ffrRXxBautffKqwBfEnjMj-Kg2AAMxgnUgg$> >>> >>> >>> -- Checking Siesta version - found development version >>> -- Parsing BLAS options >>> -- Locating BLAS library >>> -- Looking for Fortran sgemm >>> -- Looking for Fortran sgemm - not found >>> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD >>> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed >>> -- Looking for pthread_create in pthreads >>> -- Looking for pthread_create in pthreads - not found >>> -- Looking for pthread_create in pthread >>> -- Looking for pthread_create in pthread - found >>> -- Found Threads: TRUE >>> -- Looking for Fortran sgemm >>> -- Looking for Fortran sgemm - found >>> -- Found BLAS: /usr/lib64/libblas.so >>> -- Found CustomBlas: /usr/lib64/libblas.so >>> -- Locating BLAS library - found >>> -- BLAS library: /usr/lib64/libblas.so >>> -- BLAS link flags: >>> -- Parsing LAPACK options >>> -- Locating LAPACK library >>> -- Looking for Fortran cheev >>> -- Looking for Fortran cheev - not found >>> -- Looking for Fortran cheev >>> -- Looking for Fortran cheev - found >>> -- Found LAPACK: /usr/lib64/liblapack.so;/usr/lib64/libblas.so >>> -- Found CustomLapack: /usr/lib64/liblapack.so;/usr/lib64/libblas.so >>> -- Locating LAPACK library - found >>> -- LAPACK library: /usr/lib64/liblapack.so;/usr/lib64/libblas.so >>> -- LAPACK link flags: >>> -- Found MPI_C: /usr/lib64/openmpi/lib/libmpi.so (found version "3.0") >>> -- Found MPI_Fortran: /usr/lib64/openmpi/lib/libmpi_usempi.so (found >>> version "3.0") >>> -- Found MPI: TRUE (found version "3.0") found components: Fortran C >>> -- Parsing ScaLAPACK options >>> -- Locating ScaLAPACK library >>> -- Using user-defined variables >>> -- Found CustomScalapack: -lscalapack-openmpi-devel >>> -- Locating ScaLAPACK library - found >>> -- ScaLAPACK library: -lscalapack-openmpi-devel >>> -- ScaLAPACK link flags: >>> -- Checking that BLAS library works... >>> -- Performing Test blas_has_sgemm >>> -- Performing Test blas_has_sgemm - Success >>> -- Performing Test blas_cdotu_return_convention >>> -- Performing Test blas_cdotu_return_convention - Success >>> -- Checking that LAPACK library works... >>> -- Performing Test lapack_has_dsysv >>> -- Performing Test lapack_has_dsysv - Success >>> -- Checking that ScaLAPACK library works... >>> -- Performing Test scalapack_has_blacs_gridinit >>> -- Performing Test scalapack_has_blacs_gridinit - Failed >>> CMake Warning at Config/cmake/SiestaCheckLinalg.cmake:125 (message): >>> --------------------------------------------- >>> >>> ScaLAPACK library cannot link properly Please check the library >>> linking string found or used by >>> CMake--------------------------------------------- >>> Call Stack (most recent call first): >>> CMakeLists.txt:189 (include) >>> >>> >>> CMake Error at Config/cmake/SiestaCheckLinalg.cmake:130 (message): >>> *** ScaLAPACK library does not link properly >>> Call Stack (most recent call first): >>> CMakeLists.txt:189 (include) >>> >>> >>> -- Configuring incomplete, errors occurred! >>> =================================== >>> >>> Can anyone help me solve this issue? I tried but I so far did not find a >>> solution. >>> >>> Thanks, >>> Boubacar >>> >> > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence ( > https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!Ur3mYMzmBYqYxB8SxtLvkDxXwBqLomhmZmzAYOZO1h3dx_Uxi6JP0997AuAsq7Y_eDKB5HWJjDkFyKgai97G$ > ) > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence > (https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!V3AkKMLCSGZOKkh_zfS8r1kcYcyK6WFVYg9o6fg3LQbmBE9vrhj8bkJqVK30r8O-MI2SQbO6_pxVVBwqshI$ > ) >
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
